DOI: 10.1038/nrg3662. Coupling mRNA processing with transcription in time and space

Coupling mRNA processing with transcription in time and space

10.1038/nrg3662

Crossref journal-article

Springer Science and Business Media LLC

Nature Reviews Genetics (297)

Bibliography

Bentley, D. L. (2014). Coupling mRNA processing with transcription in time and space. Nature Reviews Genetics, 15(3), 163â175.

Authors 1

David L. Bentley (first)

References 188 Referenced 710

Beyer, A. L. & Osheim, Y. N. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts. Genes Dev. 2, 754–765 (1988). This is an early graphic demonstration of co-transcriptional splicing. (10.1101/gad.2.6.754) / Genes Dev. by AL Beyer (1988)
Bird, G., Zorio, D. A. & Bentley, D. L. RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3′-end formation. Mol. Cell. Biol. 24, 8963–8969 (2004). (10.1128/MCB.24.20.8963-8969.2004) / Mol. Cell. Biol. by G Bird (2004)
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genet. 41, 376–381 (2009). This paper is the first to show that histone modifications correlate with splicing activity. (10.1038/ng.322) / Nature Genet. by P Kolasinska-Zwierz (2009)
Bieberstein, N. I., Carrillo Oesterreich, F., Straube, K. & Neugebauer, K. M. First exon length controls active chromatin signatures and transcription. Cell Rep. 2, 62–68 (2012). (10.1016/j.celrep.2012.05.019) / Cell Rep. by NI Bieberstein (2012)
Gomez Acuna, L. I., Fiszbein, A., Allo, M., Schor, I. E. & Kornblihtt, A. R. Connections between chromatin signatures and splicing. Wiley Interdiscip. Rev. RNA 4, 77–91 (2013). (10.1002/wrna.1142) / Wiley Interdiscip. Rev. RNA by LI Gomez Acuna (2013)
Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012). This study shows a powerful effect of the U1 snRNA, which is a subunit of the spliceosome, in repressing premature polyadenylation and potentially regulating alternative poly(A) site choice. (10.1016/j.cell.2012.05.029) / Cell by MG Berg (2012)
Cramer, P., Pesce, C., Baralle, F. & Kornblihtt, A. Functional association between promoter structure and transcripts alternative splicing. Proc. Natl Acad. Sci. USA 94, 11456–11460 (1997). This paper provides early key evidence that transcription and splicing are mechanistically coupled. (10.1073/pnas.94.21.11456) / Proc. Natl Acad. Sci. USA by P Cramer (1997)
Chiu, Y. L. et al. Tat stimulates cotranscriptional capping of HIV mRNA. Mol. Cell 10, 585–597 (2002). (10.1016/S1097-2765(02)00630-5) / Mol. Cell by YL Chiu (2002)
Monsalve, M. et al. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6, 307–316 (2000). (10.1016/S1097-2765(00)00031-9) / Mol. Cell by M Monsalve (2000)
Huang, Y. et al. Mediator complex regulates alternative mRNA processing via the MED23 subunit. Mol. Cell 45, 459–469 (2012). (10.1016/j.molcel.2011.12.022) / Mol. Cell by Y Huang (2012)
Benson, M. J. et al. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc. Natl Acad. Sci. USA 109, 16252–16257 (2012). (10.1073/pnas.1214414109) / Proc. Natl Acad. Sci. USA by MJ Benson (2012)
Rosonina, E., Bakowski, M. A., McCracken, S. & Blencowe, B. J. Transcriptional activators control splicing and 3′-end cleavage levels. J. Biol. Chem. 278, 43034–43040 (2003). (10.1074/jbc.M307289200) / J. Biol. Chem. by E Rosonina (2003)
Nagaike, T. et al. Transcriptional activators enhance polyadenylation of mRNA precursors. Mol. Cell 41, 409–418 (2011). (10.1016/j.molcel.2011.01.022) / Mol. Cell by T Nagaike (2011)
Schroeder, S. C., Zorio, D. A., Schwer, B., Shuman, S. & Bentley, D. A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II. Mol. Cell 13, 377–387 (2004). (10.1016/S1097-2765(04)00007-3) / Mol. Cell by SC Schroeder (2004)
Lenasi, T., Peterlin, B. M. & Barboric, M. Cap-binding protein complex links pre-mRNA capping to transcription elongation and alternative splicing through positive transcription elongation factor b (P-TEFb). J. Biol. Chem. 286, 22758–22768 (2011). (10.1074/jbc.M111.235077) / J. Biol. Chem. by T Lenasi (2011)
Martins, S. B. et al. Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3′ end of human genes. Nature Struct. Mol. Biol. 18, 1115–1123 (2011). (10.1038/nsmb.2124) / Nature Struct. Mol. Biol. by SB Martins (2011)
Andersen, P. K., Lykke-Andersen, S. & Jensen, T. H. Promoter-proximal polyadenylation sites reduce transcription activity. Genes Dev. 26, 2169–2179 (2012). (10.1101/gad.189126.112) / Genes Dev. by PK Andersen (2012)
Ji, X. et al. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153, 855–868 (2013). (10.1016/j.cell.2013.04.028) / Cell by X Ji (2013)
Sisodia, S. S., Sollner, W. B. & Cleveland, D. W. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol. Cell. Biol. 7, 3602–3612 (1987). (10.1128/MCB.7.10.3602) / Mol. Cell. Biol. by SS Sisodia (1987)
Smale, S. T. & Tjian, R. Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters. Mol. Cell. Biol. 5, 352–362 (1985). (10.1128/MCB.5.2.352) / Mol. Cell. Biol. by ST Smale (1985)
Corden, J. L., Cadena, D. L., Ahearn, J. M. Jr & Dahmus, M. E. A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc. Natl Acad. Sci. USA 82, 7934–7938 (1985). (10.1073/pnas.82.23.7934) / Proc. Natl Acad. Sci. USA by JL Corden (1985)
Greenleaf, A. L. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18, 117–119 (1993). This paper presents a prescient speculation that the CTD functions in pre-mRNA processing. (10.1016/0968-0004(93)90016-G) / Trends Biochem. Sci. by AL Greenleaf (1993)
Perales, R. & Bentley, D. “Cotranscriptionality”: the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 36, 178–191 (2009). (10.1016/j.molcel.2009.09.018) / Mol. Cell by R Perales (2009)
Egloff, S., Dienstbier, M. & Murphy, S. Updating the RNA polymerase CTD code: adding gene-specific layers. Trends Genet. 28, 333–341 (2012). (10.1016/j.tig.2012.03.007) / Trends Genet. by S Egloff (2012)
Hsin, J. P. & Manley, J. L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 26, 2119–2137 (2012). (10.1101/gad.200303.112) / Genes Dev. by JP Hsin (2012)
Ho, C. & Shuman, S. Distinct effector roles for Ser2 and Ser5 phosphorylation of the RNA polymerase II CTD in the recruitment and allosteric activation of mammalian capping enzyme. Mol. Cell 3, 405–411 (1999). (10.1016/S1097-2765(00)80468-2) / Mol. Cell by C Ho (1999)
Johnson, S. A., Kim, H., Erickson, B. & Bentley, D. L. The export factor Yra1 modulates mRNA 3′ end processing. Nature Struct. Mol. Biol. 18, 1164–1171 (2011). (10.1038/nsmb.2126) / Nature Struct. Mol. Biol. by SA Johnson (2011)
Lunde, B. M. et al. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol. 17, 1195–1201 (2010). (10.1038/nsmb.1893) / Nature Struct. Mol. Biol. by BM Lunde (2010)
Hirose, Y. & Manley, J. L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature 395, 93–96 (1998). (10.1038/25786) / Nature by Y Hirose (1998)
Hirose, Y., Tacke, R. & Manley, J. L. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234–1239 (1999). (10.1101/gad.13.10.1234) / Genes Dev. by Y Hirose (1999)
McCracken, S. et al. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357–361 (1997). References 29–31 show the importance of the Pol II CTD for mRNA processing both in vitro and in vivo. (10.1038/385357a0) / Nature by S McCracken (1997)
Rigo, F., Kazerouninia, A., Nag, A. & Martinson, H. G. The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation. Mol. Cell 20, 733–745 (2005). (10.1016/j.molcel.2005.09.026) / Mol. Cell by F Rigo (2005)
Bird, G., Fong, N., Gatlin, J. C., Farabaugh, S. & Bentley, D. L. Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing. Mol. Cell 20, 747–758 (2005). (10.1016/j.molcel.2005.11.009) / Mol. Cell by G Bird (2005)
Buratowski, S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 36, 541–546 (2009). (10.1016/j.molcel.2009.10.019) / Mol. Cell by S Buratowski (2009)
Dujardin, G. et al. Transcriptional elongation and alternative splicing. Biochim. Biophys. Acta 1829, 134–140 (2013). (10.1016/j.bbagrm.2012.08.005) / Biochim. Biophys. Acta by G Dujardin (2013)
Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457–463 (2010). (10.1038/nature08909) / Nature by TW Nilsen (2010)
Aebi, M., Hornig, H., Padgett, R. A., Reiser, J. & Weissmann, C. Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell 47, 555–565 (1986). (10.1016/0092-8674(86)90620-3) / Cell by M Aebi (1986)
de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525–532 (2003). This study proposes the influential window of opportunity model to explain how transcription elongation rate could affect the outcome of alternative splicing decisions. (10.1016/j.molcel.2003.08.001) / Mol. Cell by M de la Mata (2003)
Rasmussen, E. B. & Lis, J. T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl Acad. Sci. USA 90, 7923–7927 (1993). (10.1073/pnas.90.17.7923) / Proc. Natl Acad. Sci. USA by EB Rasmussen (1993)
Jiao, X. et al. Identification of a quality-control mechanism for mRNA 5′-end capping. Nature 467, 608–611 (2010). (10.1038/nature09338) / Nature by X Jiao (2010)
Chang, J. H. et al. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′-3′ exoribonuclease activity. Nature Struct. Mol. Biol. 19, 1011–1017 (2012). (10.1038/nsmb.2381) / Nature Struct. Mol. Biol. by JH Chang (2012)
Jiao, X., Chang, J. H., Kilic, T., Tong, L. & Kiledjian, M. A mammalian pre-mRNA 5′ end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Mol. Cell 50, 104–115 (2013). References 40–42 show a conserved function that monitors the quality of mRNA 5′ cap structures and that destroys transcripts that do not meet quality control standards. (10.1016/j.molcel.2013.02.017) / Mol. Cell by X Jiao (2013)
Otsuka, Y., Kedersha, N. L. & Schoenberg, D. R. Identification of a cytoplasmic complex that adds a cap onto 5′-monophosphate RNA. Mol. Cell. Biol. 29, 2155–2167 (2009). (10.1128/MCB.01325-08) / Mol. Cell. Biol. by Y Otsuka (2009)
Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457, 1028–1032 (2009). (10.1038/nature07759) / Nature by K Fejes-Toth (2009)
Fernandez-Sanchez, M. E., Gonatopoulos-Pournatzis, T., Preston, G., Lawlor, M. A. & Cowling, V. H. S-adenosyl homocysteine hydrolase is required for Myc-induced mRNA cap methylation, protein synthesis, and cell proliferation. Mol. Cell. Biol. 29, 6182–6191 (2009). (10.1128/MCB.00973-09) / Mol. Cell. Biol. by ME Fernandez-Sanchez (2009)
Brannan, K. et al. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol. Cell 46, 311–324 (2012). (10.1016/j.molcel.2012.03.006) / Mol. Cell by K Brannan (2012)
Davidson, L., Kerr, A. & West, S. Co-transcriptional degradation of aberrant pre-mRNA by Xrn2. EMBO J. 31, 2566–2578 (2012). References 46 and 47 suggest that capping, which is a co-transcriptional mRNA processing step, can be reversed by decapping, which leads to premature transcriptional termination. (10.1038/emboj.2012.101) / EMBO J. by L Davidson (2012)
McCracken, S. et al. 5′-capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11, 3306–3318 (1997). (10.1101/gad.11.24.3306) / Genes Dev. by S McCracken (1997)
Cho, E. J., Takagi, T. & Moore, C. R. and Buratowski, S. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 11, 3319–3326 (1997). References 26, 48 and 49 show recruitment of mRNA-capping enzyme to the Pol II CTD and consequent allosteric activation of the guanylyltransferase. (10.1101/gad.11.24.3319) / Genes Dev. by EJ Cho (1997)
Glover-Cutter, K., Kim, S., Espinosa, J. & Bentley, D. L. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Struct. Mol. Biol. 15, 71–78 (2008). (10.1038/nsmb1352) / Nature Struct. Mol. Biol. by K Glover-Cutter (2008)
Listerman, I., Sapra, A. K. & Neugebauer, K. M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nature Struct. Mol. Biol. 13, 815–822 (2006). (10.1038/nsmb1135) / Nature Struct. Mol. Biol. by I Listerman (2006)
Wen, Y. & Shatkin, A. J. Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev. 13, 1774–1779 (1999). (10.1101/gad.13.14.1774) / Genes Dev. by Y Wen (1999)
Mandal, S. S. et al. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl Acad. Sci. USA 101, 7572–7577 (2004). (10.1073/pnas.0401493101) / Proc. Natl Acad. Sci. USA by SS Mandal (2004)
Pei, Y. & Shuman, S. Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5. J. Biol. Chem. 277, 19639–19648 (2002). (10.1074/jbc.M200015200) / J. Biol. Chem. by Y Pei (2002)
Schmidt, U. et al. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J. Cell Biol. 193, 819–829 (2011). (10.1083/jcb.201009012) / J. Cell Biol. by U Schmidt (2011)
Audibert, A., Weil, D. & Dautry, F. In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell. Biol. 22, 6706–6718 (2002). (10.1128/MCB.22.19.6706-6718.2002) / Mol. Cell. Biol. by A Audibert (2002)
Singh, J. & Padgett, R. A. Rates of in situ transcription and splicing in large human genes. Nature Struct. Mol. Biol. 16, 1128–1133 (2009). (10.1038/nsmb.1666) / Nature Struct. Mol. Biol. by J Singh (2009)
Danko, C. G. et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 50, 212–222 (2013). This study uses powerful global run-on sequencing analysis to measure transcription elongation rates on many gene in vivo and shows remarkable variation in Pol II speed between genes and between 5′ and 3′ regions within genes. (10.1016/j.molcel.2013.02.015) / Mol. Cell by CG Danko (2013)
Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nature Struct. Mol. Biol. 14, 796–806 (2007). (10.1038/nsmb1280) / Nature Struct. Mol. Biol. by X Darzacq (2007)
Boireau, S. et al. The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 179, 291–304 (2007). (10.1083/jcb.200706018) / J. Cell Biol. by S Boireau (2007)
Bauren, G. & Wieslander, L. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76, 183–192 (1994). (10.1016/0092-8674(94)90182-1) / Cell by G Bauren (1994)
Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nature Struct. Mol. Biol. 15, 902–909 (2008). (10.1038/nsmb.1475) / Nature Struct. Mol. Biol. by M Morlando (2008)
Darnell, J. E. Jr. Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA 19, 443–460 (2013). (10.1261/rna.038596.113) / RNA by JE Darnell Jr. (2013)
Brugiolo, M., Herzel, L. & Neugebauer, K. M. Counting on co-transcriptional splicing. F1000Prime Rep. 5, 9 (2013). / Rep. by M Brugiolo (2013)
Wuarin, J. & Schibler, U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell. Biol. 14, 7219–7225 (1994). (10.1128/MCB.14.11.7219) / Mol. Cell. Biol. by J Wuarin (1994)
Bhatt, D. M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279–290 (2012). (10.1016/j.cell.2012.05.043) / Cell by DM Bhatt (2012)
Pandya-Jones, A. et al. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA 19, 811–827 (2013). (10.1261/rna.039081.113) / RNA by A Pandya-Jones (2013)
Mili, S. & Steitz, J. A. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692–1694 (2004). (10.1261/rna.7151404) / RNA by S Mili (2004)
Khodor, Y. L., Menet, J. S., Tolan, M. & Rosbash, M. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA 18, 2174–2186 (2012). (10.1261/rna.034090.112) / RNA by YL Khodor (2012)
Khodor, Y. L. et al. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev. 25, 2502–2512 (2011). (10.1101/gad.178962.111) / Genes Dev. by YL Khodor (2011)
Tilgner, H. et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 22, 1616–1625 (2012). (10.1101/gr.134445.111) / Genome Res. by H Tilgner (2012)
Churchman, L. S. & Weissman, J. S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469, 368–373 (2011). (10.1038/nature09652) / Nature by LS Churchman (2011)
Carrillo Oesterreich, F., Preibisch, S. & Neugebauer, K. M. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol. Cell 40, 571–581 (2010). (10.1016/j.molcel.2010.11.004) / Mol. Cell by F Carrillo Oesterreich (2010)
Ameur, A. et al. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nature Struct. Mol. Biol. 18, 1435–1440 (2011). (10.1038/nsmb.2143) / Nature Struct. Mol. Biol. by A Ameur (2011)
Windhager, L. et al. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res. 22, 2031–2042 (2012). References 69–75 show that co-transcriptional splicing is widespread in vivo using genome-wide sequencing of nascent RNA populations. (10.1101/gr.131847.111) / Genome Res. by L Windhager (2012)
Girard, C. et al. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nature Commun. 3, 994 (2012). (10.1038/ncomms1998) / Nature Commun. by C Girard (2012)
Hao, S. & Baltimore, D. RNA splicing regulates the temporal order of TNF-induced gene expression. Proc. Natl Acad. Sci. USA 110, 11934–11939 (2013). (10.1073/pnas.1309990110) / Proc. Natl Acad. Sci. USA by S Hao (2013)
Takashima, Y., Ohtsuka, T., Gonzalez, A., Miyachi, H. & Kageyama, R. Intronic delay is essential for oscillatory expression in the segmentation clock. Proc. Natl Acad. Sci. USA 108, 3300–3305 (2011). (10.1073/pnas.1014418108) / Proc. Natl Acad. Sci. USA by Y Takashima (2011)
Pandya-Jones, A. & Black, D. L. Co-transcriptional splicing of constitutive and alternative exons. RNA 15, 1896–1908 (2009). (10.1261/rna.1714509) / RNA by A Pandya-Jones (2009)
Vargas, D. Y. et al. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147, 1054–1065 (2011). (10.1016/j.cell.2011.10.024) / Cell by DY Vargas (2011)
Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C. B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA 102, 2850–2855 (2005). (10.1073/pnas.0409742102) / Proc. Natl Acad. Sci. USA by GW Yeo (2005)
Licatalosi, D. D. & Darnell, R. B. RNA processing and its regulation: global insights into biological networks. Nature Rev. Genet. 11, 75–87 (2010). (10.1038/nrg2673) / Nature Rev. Genet. by DD Licatalosi (2010)
de la Mata, M., Lafaille, C. & Kornblihtt, A. R. First come, first served revisited: factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. RNA 16, 904–912 (2010). (10.1261/rna.1993510) / RNA by M de la Mata (2010)
Abovich, N. & Rosbash, M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89, 403–412 (1997). (10.1016/S0092-8674(00)80221-4) / Cell by N Abovich (1997)
Huranova, M. et al. The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. J. Cell Biol. 191, 75–86 (2010). (10.1083/jcb.201004030) / J. Cell Biol. by M Huranova (2010)
Hoskins, A. A. et al. Ordered and dynamic assembly of single spliceosomes. Science 331, 1289–1295 (2011). (10.1126/science.1198830) / Science by AA Hoskins (2011)
Abelson, J. et al. Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nature Struct. Mol. Biol. 17, 504–512 (2010). (10.1038/nsmb.1767) / Nature Struct. Mol. Biol. by J Abelson (2010)
Braberg, H. et al. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell 154, 775–788 (2013). (10.1016/j.cell.2013.07.033) / Cell by H Braberg (2013)
Aguilera, A. & Garcia-Muse, T. R loops: from transcription byproducts to threats to genome stability. Mol. Cell 46, 115–124 (2012). (10.1016/j.molcel.2012.04.009) / Mol. Cell by A Aguilera (2012)
Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S. & Fu, X. D. The splicing factor SC35 has an active role in transcriptional elongation. Nature Struct. Mol. Biol. 15, 819–826 (2008). (10.1038/nsmb.1461) / Nature Struct. Mol. Biol. by S Lin (2008)
Close, P. et al. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484, 386–389 (2012). (10.1038/nature10925) / Nature by P Close (2012)
Batsche, E., Yaniv, M. & Muchardt, C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nature Struct. Mol. Biol. 13, 22–29 (2006). (10.1038/nsmb1030) / Nature Struct. Mol. Biol. by E Batsche (2006)
Alexander, R. D., Innocente, S. A., Barrass, J. D. & Beggs, J. D. Splicing-dependent RNA polymerase pausing in yeast. Mol. Cell 40, 582–593 (2010). (10.1016/j.molcel.2010.11.005) / Mol. Cell by RD Alexander (2010)
Zhou, H. L. et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc. Natl Acad. Sci. USA 108, E627–E635 (2011). (10.1073/pnas.1103344108) / Proc. Natl Acad. Sci. USA by HL Zhou (2011)
Schor, I. E., Rascovan, N., Pelisch, F., Allo, M. & Kornblihtt, A. R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl Acad. Sci. USA 106, 4325–4330 (2009). (10.1073/pnas.0810666106) / Proc. Natl Acad. Sci. USA by IE Schor (2009)
Saint-Andre, V., Batsche, E., Rachez, C. & Muchardt, C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nature Struct. Mol. Biol. 18, 337–344 (2011). (10.1038/nsmb.1995) / Nature Struct. Mol. Biol. by V Saint-Andre (2011)
Brody, Y. et al. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol. 9, e1000573 (2011). (10.1371/journal.pbio.1000573) / PLoS Biol. by Y Brody (2011)
Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74–79 (2011). (10.1038/nature10442) / Nature by S Shukla (2011)
Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950–953 (2013). (10.1126/science.1229386) / Science by H Kwak (2013)
Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nature Struct. Mol. Biol. 16, 990–995 (2009). (10.1038/nsmb.1659) / Nature Struct. Mol. Biol. by S Schwartz (2009)
Bintu, L. et al. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151, 738–749 (2012). (10.1016/j.cell.2012.10.009) / Cell by L Bintu (2012)
Gunderson, F. Q., Merkhofer, E. C. & Johnson, T. L. Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc. Natl Acad. Sci. USA 108, 2004–2009 (2011). (10.1073/pnas.1011982108) / Proc. Natl Acad. Sci. USA by FQ Gunderson (2011)
Hilleren, P., McCarthy, T., Rosbash, M., Parker, R. & Jensen, T. H. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 413, 538–542 (2001). (10.1038/35097110) / Nature by P Hilleren (2001)
de Almeida, S. F., Garcia-Sacristan, A., Custodio, N. & Carmo-Fonseca, M. A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Res. 38, 8015–8026 (2010). (10.1093/nar/gkq703) / Nucleic Acids Res. by SF de Almeida (2010)
Eberle, A. B. et al. Splice-site mutations cause Rrp6-mediated nuclear retention of the unspliced RNAs and transcriptional down-regulation of the splicing-defective genes. PLoS ONE 5, e11540 (2010). (10.1371/journal.pone.0011540) / PLoS ONE by AB Eberle (2010)
Rodriguez, J., Menet, J. S. & Rosbash, M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol. Cell 47, 27–37 (2012). (10.1016/j.molcel.2012.05.002) / Mol. Cell by J Rodriguez (2012)
Schwartz, J. C. et al. FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev. 26, 2690–2695 (2012). (10.1101/gad.204602.112) / Genes Dev. by JC Schwartz (2012)
Dichmann, D. S. & Harland, R. M. fus/TLS orchestrates splicing of developmental regulators during gastrulation. Genes Dev. 26, 1351–1363 (2012). (10.1101/gad.187278.112) / Genes Dev. by DS Dichmann (2012)
Ryman, K., Fong, N., Bratt, E., Bentley, D. L. & Ohman, M. The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA 13, 1071–1078 (2007). (10.1261/rna.404407) / RNA by K Ryman (2007)
Kim, H. et al. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nature Struct. Mol. Biol. 17, 1279–1286 (2010). (10.1038/nsmb.1913) / Nature Struct. Mol. Biol. by H Kim (2010)
Mayer, A. et al. Uniform transitions of the general RNA polymerase II transcription complex. Nature Struct. Mol. Biol. 17, 1272–1278 (2010). (10.1038/nsmb.1903) / Nature Struct. Mol. Biol. by A Mayer (2010)
Zaret, K. S. & Sherman, F. DNA sequence required for efficient transcription termination in yeast. Cell 28, 563–573 (1982). (10.1016/0092-8674(82)90211-2) / Cell by KS Zaret (1982)
Logan, J., Falck, P. E., Darnell, J. E. J. & Shenk, T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse β maj-globin gene. Proc. Natl Acad. Sci. USA 84, 8306–8310 (1987). (10.1073/pnas.84.23.8306) / Proc. Natl Acad. Sci. USA by J Logan (1987)
Whitelaw, E. & Proudfoot, N. α-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3′ end processing in the human α2 globin gene. EMBO J. 5, 2915–2922 (1986). (10.1002/j.1460-2075.1986.tb04587.x) / EMBO J. by E Whitelaw (1986)
Nojima, T., Dienstbier, M., Murphy, S., Proudfoot, N. J. & Dye, M. J. Definition of RNA polymerase II CoTC terminator elements in the human genome. Cell Rep. 3, 1080–1092 (2013). (10.1016/j.celrep.2013.03.012) / Cell Rep. by T Nojima (2013)
Connelly, S. & Manley, J. L. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 2, 440–452 (1988). (10.1101/gad.2.4.440) / Genes Dev. by S Connelly (1988)
Niwa, M. & Berget, S. M. Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns. Genes Dev. 5, 2086–2095 (1991). (10.1101/gad.5.11.2086) / Genes Dev. by M Niwa (1991)
Niwa, M., Rose, S. D. & Berget, S. M. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev. 4, 1552–1559 (1990). (10.1101/gad.4.9.1552) / Genes Dev. by M Niwa (1990)
Lu, S. & Cullen, B. R. Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9, 618–630 (2003). (10.1261/rna.5260303) / RNA by S Lu (2003)
Martinson, H. G. An active role for splicing in 3′-end formation. Wiley Interdiscip. Rev. RNA 2, 459–470 (2011). (10.1002/wrna.68) / Wiley Interdiscip. Rev. RNA by HG Martinson (2011)
David, C. J., Boyne, A. R., Millhouse, S. R. & Manley, J. L. The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65–Prp19 complex. Genes Dev. 25, 972–983 (2011). (10.1101/gad.2038011) / Genes Dev. by CJ David (2011)
Venkataraman, K., Brown, K. M. & Gilmartin, G. M. Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev. 19, 1315–1327 (2005). (10.1101/gad.1298605) / Genes Dev. by K Venkataraman (2005)
Bauren, G., Belikov, S. & Wieslander, L. Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intron. Genes Dev. 12, 2759–2769 (1998). (10.1101/gad.12.17.2759) / Genes Dev. by G Bauren (1998)
Di Giammartino, D. C., Nishida, K. & Manley, J. L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853–866 (2011). (10.1016/j.molcel.2011.08.017) / Mol. Cell by DC Di Giammartino (2011)
Lianoglou, S., Garg, V., Yang, J. L., Leslie, C. S. & Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380–2396 (2013). (10.1101/gad.229328.113) / Genes Dev. by S Lianoglou (2013)
Mayr, C. & Bartel, D. P. Widespread shortening of 3′ UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673–684 (2009). (10.1016/j.cell.2009.06.016) / Cell by C Mayr (2009)
Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26, 867–881 (2007). (10.1016/j.molcel.2007.05.036) / Mol. Cell by R Das (2007)
Enriquez, H. P., Levitt, N., Briggs, D. & Proudfoot, N. J. A pause site for RNA polymerase II is associated with termination of transcription. EMBO J. 10, 1833–1842 (1991). (10.1002/j.1460-2075.1991.tb07709.x) / EMBO J. by HP Enriquez (1991)
Peterson, M. L., Bertolino, S. & Davis, F. An RNA polymerase pause site is associated with the immunoglobulin mus poly(A) site. Mol. Cell. Biol. 22, 5606–5615 (2002). (10.1128/MCB.22.15.5606-5615.2002) / Mol. Cell. Biol. by ML Peterson (2002)
Pinto, P. A. et al. RNA polymerase II kinetics in polo polyadenylation signal selection. EMBO J. 30, 2431–2444 (2011). (10.1038/emboj.2011.156) / EMBO J. by PA Pinto (2011)
Hazelbaker, D. Z., Marquardt, S., Wlotzka, W. & Buratowski, S. Kinetic competition between RNA polymerase II and Sen1-dependent transcription termination. Mol. Cell 49, 55–66 (2013). (10.1016/j.molcel.2012.10.014) / Mol. Cell by DZ Hazelbaker (2013)
Eperon, L. P., Graham, I. R., Griffiths, A. D. & Eperon, I. C. Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase? Cell 54, 393–401 (1988). (10.1016/0092-8674(88)90202-4) / Cell by LP Eperon (1988)
Zhao, P., Zhang, W. & Chen, S. J. Cotranscriptional folding kinetics of ribonucleic acid secondary structures. J. Chem. Phys. 135, 245101 (2011). (10.1063/1.3671644) / J. Chem. Phys. by P Zhao (2011)
Pan, T. & Sosnick, T. RNA folding during transcription. Annu. Rev. Biophys. Biomol. Struct. 35, 161–175 (2006). (10.1146/annurev.biophys.35.040405.102053) / Annu. Rev. Biophys. Biomol. Struct. by T Pan (2006)
Meyer, M., Plass, M., Perez-Valle, J., Eyras, E. & Vilardell, J. Deciphering 3′ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. Mol. Cell 43, 1033–1039 (2011). (10.1016/j.molcel.2011.07.030) / Mol. Cell by M Meyer (2011)
Zamft, B., Bintu, L., Ishibashi, T. & Bustamante, C. Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. Proc. Natl Acad. Sci. USA 109, 8948–8953 (2012). (10.1073/pnas.1205063109) / Proc. Natl Acad. Sci. USA by B Zamft (2012)
Egloff, S. & Murphy, S. Cracking the RNA polymerase II CTD code. Trends Genet. 24, 280–288 (2008). (10.1016/j.tig.2008.03.008) / Trends Genet. by S Egloff (2008)
Jasnovidova, O. & Stefl, R. The CTD code of RNA polymerase II: a structural view. Wiley Interdiscip. Rev. RNA 4, 1–16 (2013). (10.1002/wrna.1138) / Wiley Interdiscip. Rev. RNA by O Jasnovidova (2013)
Tardiff, D. F., Lacadie, S. A. & Rosbash, M. A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol. Cell 24, 917–929 (2006). (10.1016/j.molcel.2006.12.002) / Mol. Cell by DF Tardiff (2006)
Spiluttini, B. et al. Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells. J. Cell Sci. 123, 2085–2093 (2010). (10.1242/jcs.061358) / J. Cell Sci. by B Spiluttini (2010)
Ujvari, A. & Luse, D. S. Newly initiated RNA encounters a factor involved in splicing immediately upon emerging from within RNA polymerase II. J. Biol. Chem. 279, 49773–49779 (2004). (10.1074/jbc.M409087200) / J. Biol. Chem. by A Ujvari (2004)
Schroeder, S. C., Schwer, B., Shuman, S. & Bentley, D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435–2440 (2000). (10.1101/gad.836300) / Genes Dev. by SC Schroeder (2000)
Komarnitsky, P., Cho, E. J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452–2460 (2000). This study shows that dynamic changes in Pol II CTD phosphorylation are coordinated with transcription initiation, elongation and termination. (10.1101/gad.824700) / Genes Dev. by P Komarnitsky (2000)
Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S. & Meinhart, A. The Nrd1–Nab3–Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol. 15, 795–804 (2008). (10.1038/nsmb.1468) / Nature Struct. Mol. Biol. by L Vasiljeva (2008)
Licatalosi, D. D. et al. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell 9, 1101–1111 (2002). (10.1016/S1097-2765(02)00518-X) / Mol. Cell by DD Licatalosi (2002)
Buratowski, S. The CTD code. Nature Struct. Biol. 10, 679–680 (2003). (10.1038/nsb0903-679) / Nature Struct. Biol. by S Buratowski (2003)
Gu, B., Eick, D. & Bensaude, O. CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res. 41, 1591–1603 (2013). (10.1093/nar/gks1327) / Nucleic Acids Res. by B Gu (2013)
Munoz, M. J. et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 137, 708–720 (2009). (10.1016/j.cell.2009.03.010) / Cell by MJ Munoz (2009)
Schwer, B. & Shuman, S. Deciphering the RNA polymerase II CTD code in fission yeast. Mol. Cell 43, 311–318 (2011). This paper uses an elegant genetic test of the CTD code hypothesis to show that the essential function of Ser5 phosphorylation is to recruit the mRNA-capping enzyme. (10.1016/j.molcel.2011.05.024) / Mol. Cell by B Schwer (2011)
Schwer, B., Sanchez, A. M. & Shuman, S. Punctuation and syntax of the RNA polymerase II CTD code in fission yeast. Proc. Natl Acad. Sci. USA 109, 18024–18029 (2012). (10.1073/pnas.1208995109) / Proc. Natl Acad. Sci. USA by B Schwer (2012)
Lee, J. M. & Greenleaf, A. L. CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expr. 1, 149–167 (1991). / Gene Expr. by JM Lee (1991)
Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13, 67–76 (2004). (10.1016/S1097-2765(03)00492-1) / Mol. Cell by SH Ahn (2004)
Shen, Z., St-Denis, A. & Chartrand, P. Cotranscriptional recruitment of She2p by RNA Pol II elongation factor Spt4–Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev. 24, 1914–1926 (2010). (10.1101/gad.1937510) / Genes Dev. by Z Shen (2010)
Suh, M. H. et al. A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme. J. Biol. Chem. 285, 34027–34038 (2010). (10.1074/jbc.M110.145110) / J. Biol. Chem. by MH Suh (2010)
Luco, R. F. et al. Regulation of alternative splicing by histone modifications. Science 327, 996–1000 (2010). (10.1126/science.1184208) / Science by RF Luco (2010)
Pradeepa, M. M., Sutherland, H. G., Ule, J., Grimes, G. R. & Bickmore, W. A. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet. 8, e1002717 (2012). (10.1371/journal.pgen.1002717) / PLoS Genet. by MM Pradeepa (2012)
Sims, R. J. 3rd et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell 28, 665–676 (2007). (10.1016/j.molcel.2007.11.010) / Mol. Cell by RJ Sims (2007)
Govind, C. K. et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol. Cell 39, 234–246 (2010). (10.1016/j.molcel.2010.07.003) / Mol. Cell by CK Govind (2010)
Kizer, K. O. et al. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell. Biol. 25, 3305–3316 (2005). (10.1128/MCB.25.8.3305-3316.2005) / Mol. Cell. Biol. by KO Kizer (2005)
de Almeida, S. F. et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nature Struct. Mol. Biol. 18, 977–983 (2011). (10.1038/nsmb.2123) / Nature Struct. Mol. Biol. by SF de Almeida (2011)
Kim, S., Kim, H., Fong, N., Erickson, B. & Bentley, D. L. Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc. Natl Acad. Sci. USA 108, 13564–13569 (2011). (10.1073/pnas.1109475108) / Proc. Natl Acad. Sci. USA by S Kim (2011)
Lionnet, T. & Singer, R. H. Transcription goes digital. EMBO Rep. 13, 313–321 (2012). (10.1038/embor.2012.31) / EMBO Rep. by T Lionnet (2012)
Batada, N. N., Westover, K. D., Bushnell, D. A., Levitt, M. & Kornberg, R. D. Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. Proc. Natl Acad. Sci. USA 101, 17361–17364 (2004). (10.1073/pnas.0408168101) / Proc. Natl Acad. Sci. USA by NN Batada (2004)
Ehrensberger, A. H., Kelly, G. P. & Svejstrup, J. Q. Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps. Cell 154, 713–715 (2013). (10.1016/j.cell.2013.07.032) / Cell by AH Ehrensberger (2013)
Zhou, Q., Li, T. & Price, D. H. RNA polymerase II elongation control. Annu. Rev. Biochem. 81, 119–143 (2012). (10.1146/annurev-biochem-052610-095910) / Annu. Rev. Biochem. by Q Zhou (2012)
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008). (10.1126/science.1162228) / Science by LJ Core (2008)
Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A. & Singer, R. H. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332, 475–478 (2011). (10.1126/science.1202142) / Science by DR Larson (2011)
Payne, J. M., Laybourn, P. J. & Dahmus, M. E. The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIA. J. Biol. Chem. 264, 19621–19629 (1989). (10.1016/S0021-9258(19)47159-7) / J. Biol. Chem. by JM Payne (1989)
Heidemann, M., Hintermair, C., Voss, K. & Eick, D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim. Biophys. Acta 1829, 55–62 (2013). (10.1016/j.bbagrm.2012.08.013) / Biochim. Biophys. Acta by M Heidemann (2013)
Ranuncolo, S. M., Ghosh, S., Hanover, J. A., Hart, G. W. & Lewis, B. A. Evidence of the involvement of O-GlcNAc-modified human RNA polymerase II CTD in transcription in vitro and in vivo. J. Biol. Chem. 287, 23549–23561 (2012). (10.1074/jbc.M111.330910) / J. Biol. Chem. by SM Ranuncolo (2012)
Mayer, A. et al. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 336, 1723–1725 (2012). (10.1126/science.1219651) / Science by A Mayer (2012)
Garrido-Lecca, A. & Blumenthal, T. RNA polymerase II C-terminal domain phosphorylation patterns in Caenorhabditis elegans operons, polycistronic gene clusters with only one promoter. Mol. Cell. Biol. 30, 3887–3893 (2010). (10.1128/MCB.00325-10) / Mol. Cell. Biol. by A Garrido-Lecca (2010)
Bartkowiak, B. et al. CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev. 24, 2303–2316 (2010). (10.1101/gad.1968210) / Genes Dev. by B Bartkowiak (2010)
Bitoun, E., Oliver, P. L. & Davies, K. E. The mixed-lineage leukemia fusion partner AF4 stimulates RNA polymerase II transcriptional elongation and mediates coordinated chromatin remodeling. Hum. Mol. Genet. 16, 92–106 (2007). (10.1093/hmg/ddl444) / Hum. Mol. Genet. by E Bitoun (2007)
Lin, C. et al. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol. Cell 37, 429–437 (2010). (10.1016/j.molcel.2010.01.026) / Mol. Cell by C Lin (2010)
Roy, R. et al. The MO15 cell-cycle kinase is associated with the TFIIH transcription DNA-repair factor. Cell 79, 1093–1101 (1994). (10.1016/0092-8674(94)90039-6) / Cell by R Roy (1994)
Akhtar, M. S. et al. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol. Cell 34, 387–393 (2009). (10.1016/j.molcel.2009.04.016) / Mol. Cell by MS Akhtar (2009)
Czudnochowski, N., Bosken, C. A. & Geyer, M. Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition. Nature Commun. 3, 842 (2012). (10.1038/ncomms1846) / Nature Commun. by N Czudnochowski (2012)
He, X. et al. Functional interactions between the transcription and mRNA 3′ end processing machineries mediated by Ssu72 and Sub1. Genes Dev. 17, 1030–1042 (2003). (10.1101/gad.1075203) / Genes Dev. by X He (2003)
Xiang, K. et al. Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex. Nature 467, 729–733 (2010). (10.1038/nature09391) / Nature by K Xiang (2010)
Phatnani, H. P., Jones, J. C. & Greenleaf, A. L. Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 43, 15702–15719 (2004). (10.1021/bi048364h) / Biochemistry by HP Phatnani (2004)
Ghosh, A., Shuman, S. & Lima, C. D. Structural insights to how mammalian capping enzyme reads the CTD code. Mol. Cell 43, 299–310 (2011). (10.1016/j.molcel.2011.06.001) / Mol. Cell by A Ghosh (2011)
Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004). (10.1038/nature02679) / Nature by A Meinhart (2004)
Kubicek, K. et al. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes Dev. 26, 1891–1896 (2012). (10.1101/gad.192781.112) / Genes Dev. by K Kubicek (2012)
Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004). (10.1038/nature03041) / Nature by M Kim (2004)
Egloff, S. et al. Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 318, 1777–1779 (2007). (10.1126/science.1145989) / Science by S Egloff (2007)
Chen, H.-C. & Cheng, S.-C. Functional roles of protein splicing factors. Biosci. Rep. 32, 345–359 (2012). (10.1042/BSR20120007) / Biosci. Rep. by H-C Chen (2012)
Cramer, P., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 292, 1863–1876 (2001). (10.1126/science.1059493) / Science by P Cramer (2001)

Dates

Type	When
Created	11 years, 6 months ago (Feb. 11, 2014, 4:53 a.m.)
Deposited	2 years, 3 months ago (May 18, 2023, 11:31 p.m.)
Indexed	5 days, 16 hours ago (Aug. 31, 2025, 6:34 a.m.)
Issued	11 years, 6 months ago (Feb. 11, 2014)
Published	11 years, 6 months ago (Feb. 11, 2014)
Published Online	11 years, 6 months ago (Feb. 11, 2014)
Published Print	11 years, 6 months ago (March 1, 2014)

Funders 0

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BibTeX

@article{Bentley_2014, title={Coupling mRNA processing with transcription in time and space}, volume={15}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/nrg3662}, DOI={10.1038/nrg3662}, number={3}, journal={Nature Reviews Genetics}, publisher={Springer Science and Business Media LLC}, author={Bentley, David L.}, year={2014}, month=feb, pages={163–175} }

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      "unstructured": "Bird, G., Zorio, D. A. & Bentley, D. L. RNA polymerase II carboxy-terminal domain phosphorylation is required for cotranscriptional pre-mRNA splicing and 3\u2032-end formation. Mol. Cell. Biol. 24, 8963\u20138969 (2004).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR3",
      "doi-asserted-by": "crossref",
      "first-page": "376",
      "DOI": "10.1038/ng.322",
      "volume": "41",
      "author": "P Kolasinska-Zwierz",
      "year": "2009",
      "unstructured": "Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genet. 41, 376\u2013381 (2009). This paper is the first to show that histone modifications correlate with splicing activity.",
      "journal-title": "Nature Genet."
    },
    {
      "key": "BFnrg3662_CR4",
      "doi-asserted-by": "crossref",
      "first-page": "62",
      "DOI": "10.1016/j.celrep.2012.05.019",
      "volume": "2",
      "author": "NI Bieberstein",
      "year": "2012",
      "unstructured": "Bieberstein, N. I., Carrillo Oesterreich, F., Straube, K. & Neugebauer, K. M. First exon length controls active chromatin signatures and transcription. Cell Rep. 2, 62\u201368 (2012).",
      "journal-title": "Cell Rep."
    },
    {
      "key": "BFnrg3662_CR5",
      "doi-asserted-by": "crossref",
      "first-page": "77",
      "DOI": "10.1002/wrna.1142",
      "volume": "4",
      "author": "LI Gomez Acuna",
      "year": "2013",
      "unstructured": "Gomez Acuna, L. I., Fiszbein, A., Allo, M., Schor, I. E. & Kornblihtt, A. R. Connections between chromatin signatures and splicing. Wiley Interdiscip. Rev. RNA 4, 77\u201391 (2013).",
      "journal-title": "Wiley Interdiscip. Rev. RNA"
    },
    {
      "key": "BFnrg3662_CR6",
      "doi-asserted-by": "crossref",
      "first-page": "53",
      "DOI": "10.1016/j.cell.2012.05.029",
      "volume": "150",
      "author": "MG Berg",
      "year": "2012",
      "unstructured": "Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53\u201364 (2012). This study shows a powerful effect of the U1 snRNA, which is a subunit of the spliceosome, in repressing premature polyadenylation and potentially regulating alternative poly(A) site choice.",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR7",
      "doi-asserted-by": "crossref",
      "first-page": "11456",
      "DOI": "10.1073/pnas.94.21.11456",
      "volume": "94",
      "author": "P Cramer",
      "year": "1997",
      "unstructured": "Cramer, P., Pesce, C., Baralle, F. & Kornblihtt, A. Functional association between promoter structure and transcripts alternative splicing. Proc. Natl Acad. Sci. USA 94, 11456\u201311460 (1997). This paper provides early key evidence that transcription and splicing are mechanistically coupled.",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR8",
      "doi-asserted-by": "crossref",
      "first-page": "585",
      "DOI": "10.1016/S1097-2765(02)00630-5",
      "volume": "10",
      "author": "YL Chiu",
      "year": "2002",
      "unstructured": "Chiu, Y. L. et al. Tat stimulates cotranscriptional capping of HIV mRNA. Mol. Cell 10, 585\u2013597 (2002).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR9",
      "doi-asserted-by": "crossref",
      "first-page": "307",
      "DOI": "10.1016/S1097-2765(00)00031-9",
      "volume": "6",
      "author": "M Monsalve",
      "year": "2000",
      "unstructured": "Monsalve, M. et al. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6, 307\u2013316 (2000).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR10",
      "doi-asserted-by": "crossref",
      "first-page": "459",
      "DOI": "10.1016/j.molcel.2011.12.022",
      "volume": "45",
      "author": "Y Huang",
      "year": "2012",
      "unstructured": "Huang, Y. et al. Mediator complex regulates alternative mRNA processing via the MED23 subunit. Mol. Cell 45, 459\u2013469 (2012).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR11",
      "doi-asserted-by": "crossref",
      "first-page": "16252",
      "DOI": "10.1073/pnas.1214414109",
      "volume": "109",
      "author": "MJ Benson",
      "year": "2012",
      "unstructured": "Benson, M. J. et al. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc. Natl Acad. Sci. USA 109, 16252\u201316257 (2012).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR12",
      "doi-asserted-by": "crossref",
      "first-page": "43034",
      "DOI": "10.1074/jbc.M307289200",
      "volume": "278",
      "author": "E Rosonina",
      "year": "2003",
      "unstructured": "Rosonina, E., Bakowski, M. A., McCracken, S. & Blencowe, B. J. Transcriptional activators control splicing and 3\u2032-end cleavage levels. J. Biol. Chem. 278, 43034\u201343040 (2003).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR13",
      "doi-asserted-by": "crossref",
      "first-page": "409",
      "DOI": "10.1016/j.molcel.2011.01.022",
      "volume": "41",
      "author": "T Nagaike",
      "year": "2011",
      "unstructured": "Nagaike, T. et al. Transcriptional activators enhance polyadenylation of mRNA precursors. Mol. Cell 41, 409\u2013418 (2011).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR14",
      "doi-asserted-by": "crossref",
      "first-page": "377",
      "DOI": "10.1016/S1097-2765(04)00007-3",
      "volume": "13",
      "author": "SC Schroeder",
      "year": "2004",
      "unstructured": "Schroeder, S. C., Zorio, D. A., Schwer, B., Shuman, S. & Bentley, D. A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II. Mol. Cell 13, 377\u2013387 (2004).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR15",
      "doi-asserted-by": "crossref",
      "first-page": "22758",
      "DOI": "10.1074/jbc.M111.235077",
      "volume": "286",
      "author": "T Lenasi",
      "year": "2011",
      "unstructured": "Lenasi, T., Peterlin, B. M. & Barboric, M. Cap-binding protein complex links pre-mRNA capping to transcription elongation and alternative splicing through positive transcription elongation factor b (P-TEFb). J. Biol. Chem. 286, 22758\u201322768 (2011).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR16",
      "doi-asserted-by": "crossref",
      "first-page": "1115",
      "DOI": "10.1038/nsmb.2124",
      "volume": "18",
      "author": "SB Martins",
      "year": "2011",
      "unstructured": "Martins, S. B. et al. Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3\u2032 end of human genes. Nature Struct. Mol. Biol. 18, 1115\u20131123 (2011).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR17",
      "doi-asserted-by": "crossref",
      "first-page": "2169",
      "DOI": "10.1101/gad.189126.112",
      "volume": "26",
      "author": "PK Andersen",
      "year": "2012",
      "unstructured": "Andersen, P. K., Lykke-Andersen, S. & Jensen, T. H. Promoter-proximal polyadenylation sites reduce transcription activity. Genes Dev. 26, 2169\u20132179 (2012).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR18",
      "doi-asserted-by": "crossref",
      "first-page": "855",
      "DOI": "10.1016/j.cell.2013.04.028",
      "volume": "153",
      "author": "X Ji",
      "year": "2013",
      "unstructured": "Ji, X. et al. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153, 855\u2013868 (2013).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR19",
      "doi-asserted-by": "crossref",
      "first-page": "3602",
      "DOI": "10.1128/MCB.7.10.3602",
      "volume": "7",
      "author": "SS Sisodia",
      "year": "1987",
      "unstructured": "Sisodia, S. S., Sollner, W. B. & Cleveland, D. W. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol. Cell. Biol. 7, 3602\u20133612 (1987).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR20",
      "doi-asserted-by": "crossref",
      "first-page": "352",
      "DOI": "10.1128/MCB.5.2.352",
      "volume": "5",
      "author": "ST Smale",
      "year": "1985",
      "unstructured": "Smale, S. T. & Tjian, R. Transcription of herpes simplex virus tk sequences under the control of wild-type and mutant human RNA polymerase I promoters. Mol. Cell. Biol. 5, 352\u2013362 (1985).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR21",
      "doi-asserted-by": "crossref",
      "first-page": "7934",
      "DOI": "10.1073/pnas.82.23.7934",
      "volume": "82",
      "author": "JL Corden",
      "year": "1985",
      "unstructured": "Corden, J. L., Cadena, D. L., Ahearn, J. M. Jr & Dahmus, M. E. A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc. Natl Acad. Sci. USA 82, 7934\u20137938 (1985).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR22",
      "doi-asserted-by": "crossref",
      "first-page": "117",
      "DOI": "10.1016/0968-0004(93)90016-G",
      "volume": "18",
      "author": "AL Greenleaf",
      "year": "1993",
      "unstructured": "Greenleaf, A. L. Positive patches and negative noodles: linking RNA processing to transcription? Trends Biochem. Sci. 18, 117\u2013119 (1993). This paper presents a prescient speculation that the CTD functions in pre-mRNA processing.",
      "journal-title": "Trends Biochem. Sci."
    },
    {
      "key": "BFnrg3662_CR23",
      "doi-asserted-by": "crossref",
      "first-page": "178",
      "DOI": "10.1016/j.molcel.2009.09.018",
      "volume": "36",
      "author": "R Perales",
      "year": "2009",
      "unstructured": "Perales, R. & Bentley, D. \u201cCotranscriptionality\u201d: the transcription elongation complex as a nexus for nuclear transactions. Mol. Cell 36, 178\u2013191 (2009).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR24",
      "doi-asserted-by": "crossref",
      "first-page": "333",
      "DOI": "10.1016/j.tig.2012.03.007",
      "volume": "28",
      "author": "S Egloff",
      "year": "2012",
      "unstructured": "Egloff, S., Dienstbier, M. & Murphy, S. Updating the RNA polymerase CTD code: adding gene-specific layers. Trends Genet. 28, 333\u2013341 (2012).",
      "journal-title": "Trends Genet."
    },
    {
      "key": "BFnrg3662_CR25",
      "doi-asserted-by": "crossref",
      "first-page": "2119",
      "DOI": "10.1101/gad.200303.112",
      "volume": "26",
      "author": "JP Hsin",
      "year": "2012",
      "unstructured": "Hsin, J. P. & Manley, J. L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 26, 2119\u20132137 (2012).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR26",
      "doi-asserted-by": "crossref",
      "first-page": "405",
      "DOI": "10.1016/S1097-2765(00)80468-2",
      "volume": "3",
      "author": "C Ho",
      "year": "1999",
      "unstructured": "Ho, C. & Shuman, S. Distinct effector roles for Ser2 and Ser5 phosphorylation of the RNA polymerase II CTD in the recruitment and allosteric activation of mammalian capping enzyme. Mol. Cell 3, 405\u2013411 (1999).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR27",
      "doi-asserted-by": "crossref",
      "first-page": "1164",
      "DOI": "10.1038/nsmb.2126",
      "volume": "18",
      "author": "SA Johnson",
      "year": "2011",
      "unstructured": "Johnson, S. A., Kim, H., Erickson, B. & Bentley, D. L. The export factor Yra1 modulates mRNA 3\u2032 end processing. Nature Struct. Mol. Biol. 18, 1164\u20131171 (2011).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR28",
      "doi-asserted-by": "crossref",
      "first-page": "1195",
      "DOI": "10.1038/nsmb.1893",
      "volume": "17",
      "author": "BM Lunde",
      "year": "2010",
      "unstructured": "Lunde, B. M. et al. Cooperative interaction of transcription termination factors with the RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol. 17, 1195\u20131201 (2010).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR29",
      "doi-asserted-by": "crossref",
      "first-page": "93",
      "DOI": "10.1038/25786",
      "volume": "395",
      "author": "Y Hirose",
      "year": "1998",
      "unstructured": "Hirose, Y. & Manley, J. L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature 395, 93\u201396 (1998).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR30",
      "doi-asserted-by": "crossref",
      "first-page": "1234",
      "DOI": "10.1101/gad.13.10.1234",
      "volume": "13",
      "author": "Y Hirose",
      "year": "1999",
      "unstructured": "Hirose, Y., Tacke, R. & Manley, J. L. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234\u20131239 (1999).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR31",
      "doi-asserted-by": "crossref",
      "first-page": "357",
      "DOI": "10.1038/385357a0",
      "volume": "385",
      "author": "S McCracken",
      "year": "1997",
      "unstructured": "McCracken, S. et al. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357\u2013361 (1997). References 29\u201331 show the importance of the Pol II CTD for mRNA processing both in vitro and in vivo.",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR32",
      "doi-asserted-by": "crossref",
      "first-page": "733",
      "DOI": "10.1016/j.molcel.2005.09.026",
      "volume": "20",
      "author": "F Rigo",
      "year": "2005",
      "unstructured": "Rigo, F., Kazerouninia, A., Nag, A. & Martinson, H. G. The RNA tether from the poly(A) signal to the polymerase mediates coupling of transcription to cleavage and polyadenylation. Mol. Cell 20, 733\u2013745 (2005).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR33",
      "doi-asserted-by": "crossref",
      "first-page": "747",
      "DOI": "10.1016/j.molcel.2005.11.009",
      "volume": "20",
      "author": "G Bird",
      "year": "2005",
      "unstructured": "Bird, G., Fong, N., Gatlin, J. C., Farabaugh, S. & Bentley, D. L. Ribozyme cleavage reveals connections between mRNA release from the site of transcription and pre-mRNA processing. Mol. Cell 20, 747\u2013758 (2005).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR34",
      "doi-asserted-by": "crossref",
      "first-page": "541",
      "DOI": "10.1016/j.molcel.2009.10.019",
      "volume": "36",
      "author": "S Buratowski",
      "year": "2009",
      "unstructured": "Buratowski, S. Progression through the RNA polymerase II CTD cycle. Mol. Cell 36, 541\u2013546 (2009).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR35",
      "doi-asserted-by": "crossref",
      "first-page": "134",
      "DOI": "10.1016/j.bbagrm.2012.08.005",
      "volume": "1829",
      "author": "G Dujardin",
      "year": "2013",
      "unstructured": "Dujardin, G. et al. Transcriptional elongation and alternative splicing. Biochim. Biophys. Acta 1829, 134\u2013140 (2013).",
      "journal-title": "Biochim. Biophys. Acta"
    },
    {
      "key": "BFnrg3662_CR36",
      "doi-asserted-by": "crossref",
      "first-page": "457",
      "DOI": "10.1038/nature08909",
      "volume": "463",
      "author": "TW Nilsen",
      "year": "2010",
      "unstructured": "Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457\u2013463 (2010).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR37",
      "doi-asserted-by": "crossref",
      "first-page": "555",
      "DOI": "10.1016/0092-8674(86)90620-3",
      "volume": "47",
      "author": "M Aebi",
      "year": "1986",
      "unstructured": "Aebi, M., Hornig, H., Padgett, R. A., Reiser, J. & Weissmann, C. Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell 47, 555\u2013565 (1986).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR38",
      "doi-asserted-by": "crossref",
      "first-page": "525",
      "DOI": "10.1016/j.molcel.2003.08.001",
      "volume": "12",
      "author": "M de la Mata",
      "year": "2003",
      "unstructured": "de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525\u2013532 (2003). This study proposes the influential window of opportunity model to explain how transcription elongation rate could affect the outcome of alternative splicing decisions.",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR39",
      "doi-asserted-by": "crossref",
      "first-page": "7923",
      "DOI": "10.1073/pnas.90.17.7923",
      "volume": "90",
      "author": "EB Rasmussen",
      "year": "1993",
      "unstructured": "Rasmussen, E. B. & Lis, J. T. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proc. Natl Acad. Sci. USA 90, 7923\u20137927 (1993).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR40",
      "doi-asserted-by": "crossref",
      "first-page": "608",
      "DOI": "10.1038/nature09338",
      "volume": "467",
      "author": "X Jiao",
      "year": "2010",
      "unstructured": "Jiao, X. et al. Identification of a quality-control mechanism for mRNA 5\u2032-end capping. Nature 467, 608\u2013611 (2010).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR41",
      "doi-asserted-by": "crossref",
      "first-page": "1011",
      "DOI": "10.1038/nsmb.2381",
      "volume": "19",
      "author": "JH Chang",
      "year": "2012",
      "unstructured": "Chang, J. H. et al. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5\u2032-3\u2032 exoribonuclease activity. Nature Struct. Mol. Biol. 19, 1011\u20131017 (2012).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR42",
      "doi-asserted-by": "crossref",
      "first-page": "104",
      "DOI": "10.1016/j.molcel.2013.02.017",
      "volume": "50",
      "author": "X Jiao",
      "year": "2013",
      "unstructured": "Jiao, X., Chang, J. H., Kilic, T., Tong, L. & Kiledjian, M. A mammalian pre-mRNA 5\u2032 end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Mol. Cell 50, 104\u2013115 (2013). References 40\u201342 show a conserved function that monitors the quality of mRNA 5\u2032 cap structures and that destroys transcripts that do not meet quality control standards.",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR43",
      "doi-asserted-by": "crossref",
      "first-page": "2155",
      "DOI": "10.1128/MCB.01325-08",
      "volume": "29",
      "author": "Y Otsuka",
      "year": "2009",
      "unstructured": "Otsuka, Y., Kedersha, N. L. & Schoenberg, D. R. Identification of a cytoplasmic complex that adds a cap onto 5\u2032-monophosphate RNA. Mol. Cell. Biol. 29, 2155\u20132167 (2009).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR44",
      "doi-asserted-by": "crossref",
      "first-page": "1028",
      "DOI": "10.1038/nature07759",
      "volume": "457",
      "author": "K Fejes-Toth",
      "year": "2009",
      "unstructured": "Fejes-Toth, K. et al. Post-transcriptional processing generates a diversity of 5\u2032-modified long and short RNAs. Nature 457, 1028\u20131032 (2009).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR45",
      "doi-asserted-by": "crossref",
      "first-page": "6182",
      "DOI": "10.1128/MCB.00973-09",
      "volume": "29",
      "author": "ME Fernandez-Sanchez",
      "year": "2009",
      "unstructured": "Fernandez-Sanchez, M. E., Gonatopoulos-Pournatzis, T., Preston, G., Lawlor, M. A. & Cowling, V. H. S-adenosyl homocysteine hydrolase is required for Myc-induced mRNA cap methylation, protein synthesis, and cell proliferation. Mol. Cell. Biol. 29, 6182\u20136191 (2009).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR46",
      "doi-asserted-by": "crossref",
      "first-page": "311",
      "DOI": "10.1016/j.molcel.2012.03.006",
      "volume": "46",
      "author": "K Brannan",
      "year": "2012",
      "unstructured": "Brannan, K. et al. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol. Cell 46, 311\u2013324 (2012).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR47",
      "doi-asserted-by": "crossref",
      "first-page": "2566",
      "DOI": "10.1038/emboj.2012.101",
      "volume": "31",
      "author": "L Davidson",
      "year": "2012",
      "unstructured": "Davidson, L., Kerr, A. & West, S. Co-transcriptional degradation of aberrant pre-mRNA by Xrn2. EMBO J. 31, 2566\u20132578 (2012). References 46 and 47 suggest that capping, which is a co-transcriptional mRNA processing step, can be reversed by decapping, which leads to premature transcriptional termination.",
      "journal-title": "EMBO J."
    },
    {
      "key": "BFnrg3662_CR48",
      "doi-asserted-by": "crossref",
      "first-page": "3306",
      "DOI": "10.1101/gad.11.24.3306",
      "volume": "11",
      "author": "S McCracken",
      "year": "1997",
      "unstructured": "McCracken, S. et al. 5\u2032-capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II. Genes Dev. 11, 3306\u20133318 (1997).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR49",
      "doi-asserted-by": "crossref",
      "first-page": "3319",
      "DOI": "10.1101/gad.11.24.3319",
      "volume": "11",
      "author": "EJ Cho",
      "year": "1997",
      "unstructured": "Cho, E. J., Takagi, T. & Moore, C. R. and Buratowski, S. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 11, 3319\u20133326 (1997). References 26, 48 and 49 show recruitment of mRNA-capping enzyme to the Pol II CTD and consequent allosteric activation of the guanylyltransferase.",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR50",
      "doi-asserted-by": "crossref",
      "first-page": "71",
      "DOI": "10.1038/nsmb1352",
      "volume": "15",
      "author": "K Glover-Cutter",
      "year": "2008",
      "unstructured": "Glover-Cutter, K., Kim, S., Espinosa, J. & Bentley, D. L. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Struct. Mol. Biol. 15, 71\u201378 (2008).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR51",
      "doi-asserted-by": "crossref",
      "first-page": "815",
      "DOI": "10.1038/nsmb1135",
      "volume": "13",
      "author": "I Listerman",
      "year": "2006",
      "unstructured": "Listerman, I., Sapra, A. K. & Neugebauer, K. M. Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells. Nature Struct. Mol. Biol. 13, 815\u2013822 (2006).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR52",
      "doi-asserted-by": "crossref",
      "first-page": "1774",
      "DOI": "10.1101/gad.13.14.1774",
      "volume": "13",
      "author": "Y Wen",
      "year": "1999",
      "unstructured": "Wen, Y. & Shatkin, A. J. Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev. 13, 1774\u20131779 (1999).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR53",
      "doi-asserted-by": "crossref",
      "first-page": "7572",
      "DOI": "10.1073/pnas.0401493101",
      "volume": "101",
      "author": "SS Mandal",
      "year": "2004",
      "unstructured": "Mandal, S. S. et al. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl Acad. Sci. USA 101, 7572\u20137577 (2004).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR54",
      "doi-asserted-by": "crossref",
      "first-page": "19639",
      "DOI": "10.1074/jbc.M200015200",
      "volume": "277",
      "author": "Y Pei",
      "year": "2002",
      "unstructured": "Pei, Y. & Shuman, S. Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5. J. Biol. Chem. 277, 19639\u201319648 (2002).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR55",
      "doi-asserted-by": "crossref",
      "first-page": "819",
      "DOI": "10.1083/jcb.201009012",
      "volume": "193",
      "author": "U Schmidt",
      "year": "2011",
      "unstructured": "Schmidt, U. et al. Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation. J. Cell Biol. 193, 819\u2013829 (2011).",
      "journal-title": "J. Cell Biol."
    },
    {
      "key": "BFnrg3662_CR56",
      "doi-asserted-by": "crossref",
      "first-page": "6706",
      "DOI": "10.1128/MCB.22.19.6706-6718.2002",
      "volume": "22",
      "author": "A Audibert",
      "year": "2002",
      "unstructured": "Audibert, A., Weil, D. & Dautry, F. In vivo kinetics of mRNA splicing and transport in mammalian cells. Mol. Cell. Biol. 22, 6706\u20136718 (2002).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR57",
      "doi-asserted-by": "crossref",
      "first-page": "1128",
      "DOI": "10.1038/nsmb.1666",
      "volume": "16",
      "author": "J Singh",
      "year": "2009",
      "unstructured": "Singh, J. & Padgett, R. A. Rates of in situ transcription and splicing in large human genes. Nature Struct. Mol. Biol. 16, 1128\u20131133 (2009).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR58",
      "doi-asserted-by": "crossref",
      "first-page": "212",
      "DOI": "10.1016/j.molcel.2013.02.015",
      "volume": "50",
      "author": "CG Danko",
      "year": "2013",
      "unstructured": "Danko, C. G. et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 50, 212\u2013222 (2013). This study uses powerful global run-on sequencing analysis to measure transcription elongation rates on many gene in vivo and shows remarkable variation in Pol II speed between genes and between 5\u2032 and 3\u2032 regions within genes.",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR59",
      "doi-asserted-by": "crossref",
      "first-page": "796",
      "DOI": "10.1038/nsmb1280",
      "volume": "14",
      "author": "X Darzacq",
      "year": "2007",
      "unstructured": "Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nature Struct. Mol. Biol. 14, 796\u2013806 (2007).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR60",
      "doi-asserted-by": "crossref",
      "first-page": "291",
      "DOI": "10.1083/jcb.200706018",
      "volume": "179",
      "author": "S Boireau",
      "year": "2007",
      "unstructured": "Boireau, S. et al. The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 179, 291\u2013304 (2007).",
      "journal-title": "J. Cell Biol."
    },
    {
      "key": "BFnrg3662_CR61",
      "doi-asserted-by": "crossref",
      "first-page": "183",
      "DOI": "10.1016/0092-8674(94)90182-1",
      "volume": "76",
      "author": "G Bauren",
      "year": "1994",
      "unstructured": "Bauren, G. & Wieslander, L. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription. Cell 76, 183\u2013192 (1994).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR62",
      "doi-asserted-by": "crossref",
      "first-page": "902",
      "DOI": "10.1038/nsmb.1475",
      "volume": "15",
      "author": "M Morlando",
      "year": "2008",
      "unstructured": "Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nature Struct. Mol. Biol. 15, 902\u2013909 (2008).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR63",
      "doi-asserted-by": "crossref",
      "first-page": "443",
      "DOI": "10.1261/rna.038596.113",
      "volume": "19",
      "author": "JE Darnell Jr.",
      "year": "2013",
      "unstructured": "Darnell, J. E. Jr. Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA 19, 443\u2013460 (2013).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR64",
      "first-page": "9",
      "volume": "5",
      "author": "M Brugiolo",
      "year": "2013",
      "unstructured": "Brugiolo, M., Herzel, L. & Neugebauer, K. M. Counting on co-transcriptional splicing. F1000Prime Rep. 5, 9 (2013).",
      "journal-title": "Rep."
    },
    {
      "key": "BFnrg3662_CR65",
      "doi-asserted-by": "crossref",
      "first-page": "7219",
      "DOI": "10.1128/MCB.14.11.7219",
      "volume": "14",
      "author": "J Wuarin",
      "year": "1994",
      "unstructured": "Wuarin, J. & Schibler, U. Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing. Mol. Cell. Biol. 14, 7219\u20137225 (1994).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR66",
      "doi-asserted-by": "crossref",
      "first-page": "279",
      "DOI": "10.1016/j.cell.2012.05.043",
      "volume": "150",
      "author": "DM Bhatt",
      "year": "2012",
      "unstructured": "Bhatt, D. M. et al. Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell 150, 279\u2013290 (2012).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR67",
      "doi-asserted-by": "crossref",
      "first-page": "811",
      "DOI": "10.1261/rna.039081.113",
      "volume": "19",
      "author": "A Pandya-Jones",
      "year": "2013",
      "unstructured": "Pandya-Jones, A. et al. Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression. RNA 19, 811\u2013827 (2013).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR68",
      "doi-asserted-by": "crossref",
      "first-page": "1692",
      "DOI": "10.1261/rna.7151404",
      "volume": "10",
      "author": "S Mili",
      "year": "2004",
      "unstructured": "Mili, S. & Steitz, J. A. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA 10, 1692\u20131694 (2004).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR69",
      "doi-asserted-by": "crossref",
      "first-page": "2174",
      "DOI": "10.1261/rna.034090.112",
      "volume": "18",
      "author": "YL Khodor",
      "year": "2012",
      "unstructured": "Khodor, Y. L., Menet, J. S., Tolan, M. & Rosbash, M. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA 18, 2174\u20132186 (2012).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR70",
      "doi-asserted-by": "crossref",
      "first-page": "2502",
      "DOI": "10.1101/gad.178962.111",
      "volume": "25",
      "author": "YL Khodor",
      "year": "2011",
      "unstructured": "Khodor, Y. L. et al. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev. 25, 2502\u20132512 (2011).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR71",
      "doi-asserted-by": "crossref",
      "first-page": "1616",
      "DOI": "10.1101/gr.134445.111",
      "volume": "22",
      "author": "H Tilgner",
      "year": "2012",
      "unstructured": "Tilgner, H. et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 22, 1616\u20131625 (2012).",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnrg3662_CR72",
      "doi-asserted-by": "crossref",
      "first-page": "368",
      "DOI": "10.1038/nature09652",
      "volume": "469",
      "author": "LS Churchman",
      "year": "2011",
      "unstructured": "Churchman, L. S. & Weissman, J. S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469, 368\u2013373 (2011).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR73",
      "doi-asserted-by": "crossref",
      "first-page": "571",
      "DOI": "10.1016/j.molcel.2010.11.004",
      "volume": "40",
      "author": "F Carrillo Oesterreich",
      "year": "2010",
      "unstructured": "Carrillo Oesterreich, F., Preibisch, S. & Neugebauer, K. M. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. Mol. Cell 40, 571\u2013581 (2010).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR74",
      "doi-asserted-by": "crossref",
      "first-page": "1435",
      "DOI": "10.1038/nsmb.2143",
      "volume": "18",
      "author": "A Ameur",
      "year": "2011",
      "unstructured": "Ameur, A. et al. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nature Struct. Mol. Biol. 18, 1435\u20131440 (2011).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR75",
      "doi-asserted-by": "crossref",
      "first-page": "2031",
      "DOI": "10.1101/gr.131847.111",
      "volume": "22",
      "author": "L Windhager",
      "year": "2012",
      "unstructured": "Windhager, L. et al. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res. 22, 2031\u20132042 (2012). References 69\u201375 show that co-transcriptional splicing is widespread in vivo using genome-wide sequencing of nascent RNA populations.",
      "journal-title": "Genome Res."
    },
    {
      "key": "BFnrg3662_CR76",
      "doi-asserted-by": "crossref",
      "first-page": "994",
      "DOI": "10.1038/ncomms1998",
      "volume": "3",
      "author": "C Girard",
      "year": "2012",
      "unstructured": "Girard, C. et al. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nature Commun. 3, 994 (2012).",
      "journal-title": "Nature Commun."
    },
    {
      "key": "BFnrg3662_CR77",
      "doi-asserted-by": "crossref",
      "first-page": "11934",
      "DOI": "10.1073/pnas.1309990110",
      "volume": "110",
      "author": "S Hao",
      "year": "2013",
      "unstructured": "Hao, S. & Baltimore, D. RNA splicing regulates the temporal order of TNF-induced gene expression. Proc. Natl Acad. Sci. USA 110, 11934\u201311939 (2013).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR78",
      "doi-asserted-by": "crossref",
      "first-page": "3300",
      "DOI": "10.1073/pnas.1014418108",
      "volume": "108",
      "author": "Y Takashima",
      "year": "2011",
      "unstructured": "Takashima, Y., Ohtsuka, T., Gonzalez, A., Miyachi, H. & Kageyama, R. Intronic delay is essential for oscillatory expression in the segmentation clock. Proc. Natl Acad. Sci. USA 108, 3300\u20133305 (2011).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR79",
      "doi-asserted-by": "crossref",
      "first-page": "1896",
      "DOI": "10.1261/rna.1714509",
      "volume": "15",
      "author": "A Pandya-Jones",
      "year": "2009",
      "unstructured": "Pandya-Jones, A. & Black, D. L. Co-transcriptional splicing of constitutive and alternative exons. RNA 15, 1896\u20131908 (2009).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR80",
      "doi-asserted-by": "crossref",
      "first-page": "1054",
      "DOI": "10.1016/j.cell.2011.10.024",
      "volume": "147",
      "author": "DY Vargas",
      "year": "2011",
      "unstructured": "Vargas, D. Y. et al. Single-molecule imaging of transcriptionally coupled and uncoupled splicing. Cell 147, 1054\u20131065 (2011).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR81",
      "doi-asserted-by": "crossref",
      "first-page": "2850",
      "DOI": "10.1073/pnas.0409742102",
      "volume": "102",
      "author": "GW Yeo",
      "year": "2005",
      "unstructured": "Yeo, G. W., Van Nostrand, E., Holste, D., Poggio, T. & Burge, C. B. Identification and analysis of alternative splicing events conserved in human and mouse. Proc. Natl Acad. Sci. USA 102, 2850\u20132855 (2005).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR82",
      "doi-asserted-by": "crossref",
      "first-page": "75",
      "DOI": "10.1038/nrg2673",
      "volume": "11",
      "author": "DD Licatalosi",
      "year": "2010",
      "unstructured": "Licatalosi, D. D. & Darnell, R. B. RNA processing and its regulation: global insights into biological networks. Nature Rev. Genet. 11, 75\u201387 (2010).",
      "journal-title": "Nature Rev. Genet."
    },
    {
      "key": "BFnrg3662_CR83",
      "doi-asserted-by": "crossref",
      "first-page": "904",
      "DOI": "10.1261/rna.1993510",
      "volume": "16",
      "author": "M de la Mata",
      "year": "2010",
      "unstructured": "de la Mata, M., Lafaille, C. & Kornblihtt, A. R. First come, first served revisited: factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. RNA 16, 904\u2013912 (2010).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR84",
      "doi-asserted-by": "crossref",
      "first-page": "403",
      "DOI": "10.1016/S0092-8674(00)80221-4",
      "volume": "89",
      "author": "N Abovich",
      "year": "1997",
      "unstructured": "Abovich, N. & Rosbash, M. Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals. Cell 89, 403\u2013412 (1997).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR85",
      "doi-asserted-by": "crossref",
      "first-page": "75",
      "DOI": "10.1083/jcb.201004030",
      "volume": "191",
      "author": "M Huranova",
      "year": "2010",
      "unstructured": "Huranova, M. et al. The differential interaction of snRNPs with pre-mRNA reveals splicing kinetics in living cells. J. Cell Biol. 191, 75\u201386 (2010).",
      "journal-title": "J. Cell Biol."
    },
    {
      "key": "BFnrg3662_CR86",
      "doi-asserted-by": "crossref",
      "first-page": "1289",
      "DOI": "10.1126/science.1198830",
      "volume": "331",
      "author": "AA Hoskins",
      "year": "2011",
      "unstructured": "Hoskins, A. A. et al. Ordered and dynamic assembly of single spliceosomes. Science 331, 1289\u20131295 (2011).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR87",
      "doi-asserted-by": "crossref",
      "first-page": "504",
      "DOI": "10.1038/nsmb.1767",
      "volume": "17",
      "author": "J Abelson",
      "year": "2010",
      "unstructured": "Abelson, J. et al. Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nature Struct. Mol. Biol. 17, 504\u2013512 (2010).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR88",
      "doi-asserted-by": "crossref",
      "first-page": "775",
      "DOI": "10.1016/j.cell.2013.07.033",
      "volume": "154",
      "author": "H Braberg",
      "year": "2013",
      "unstructured": "Braberg, H. et al. From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II. Cell 154, 775\u2013788 (2013).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR89",
      "doi-asserted-by": "crossref",
      "first-page": "115",
      "DOI": "10.1016/j.molcel.2012.04.009",
      "volume": "46",
      "author": "A Aguilera",
      "year": "2012",
      "unstructured": "Aguilera, A. & Garcia-Muse, T. R loops: from transcription byproducts to threats to genome stability. Mol. Cell 46, 115\u2013124 (2012).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR90",
      "doi-asserted-by": "crossref",
      "first-page": "819",
      "DOI": "10.1038/nsmb.1461",
      "volume": "15",
      "author": "S Lin",
      "year": "2008",
      "unstructured": "Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S. & Fu, X. D. The splicing factor SC35 has an active role in transcriptional elongation. Nature Struct. Mol. Biol. 15, 819\u2013826 (2008).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR91",
      "doi-asserted-by": "crossref",
      "first-page": "386",
      "DOI": "10.1038/nature10925",
      "volume": "484",
      "author": "P Close",
      "year": "2012",
      "unstructured": "Close, P. et al. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484, 386\u2013389 (2012).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR92",
      "doi-asserted-by": "crossref",
      "first-page": "22",
      "DOI": "10.1038/nsmb1030",
      "volume": "13",
      "author": "E Batsche",
      "year": "2006",
      "unstructured": "Batsche, E., Yaniv, M. & Muchardt, C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nature Struct. Mol. Biol. 13, 22\u201329 (2006).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR93",
      "doi-asserted-by": "crossref",
      "first-page": "582",
      "DOI": "10.1016/j.molcel.2010.11.005",
      "volume": "40",
      "author": "RD Alexander",
      "year": "2010",
      "unstructured": "Alexander, R. D., Innocente, S. A., Barrass, J. D. & Beggs, J. D. Splicing-dependent RNA polymerase pausing in yeast. Mol. Cell 40, 582\u2013593 (2010).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR94",
      "doi-asserted-by": "crossref",
      "first-page": "E627",
      "DOI": "10.1073/pnas.1103344108",
      "volume": "108",
      "author": "HL Zhou",
      "year": "2011",
      "unstructured": "Zhou, H. L. et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc. Natl Acad. Sci. USA 108, E627\u2013E635 (2011).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR95",
      "doi-asserted-by": "crossref",
      "first-page": "4325",
      "DOI": "10.1073/pnas.0810666106",
      "volume": "106",
      "author": "IE Schor",
      "year": "2009",
      "unstructured": "Schor, I. E., Rascovan, N., Pelisch, F., Allo, M. & Kornblihtt, A. R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl Acad. Sci. USA 106, 4325\u20134330 (2009).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR96",
      "doi-asserted-by": "crossref",
      "first-page": "337",
      "DOI": "10.1038/nsmb.1995",
      "volume": "18",
      "author": "V Saint-Andre",
      "year": "2011",
      "unstructured": "Saint-Andre, V., Batsche, E., Rachez, C. & Muchardt, C. Histone H3 lysine 9 trimethylation and HP1\u03b3 favor inclusion of alternative exons. Nature Struct. Mol. Biol. 18, 337\u2013344 (2011).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR97",
      "doi-asserted-by": "crossref",
      "first-page": "e1000573",
      "DOI": "10.1371/journal.pbio.1000573",
      "volume": "9",
      "author": "Y Brody",
      "year": "2011",
      "unstructured": "Brody, Y. et al. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol. 9, e1000573 (2011).",
      "journal-title": "PLoS Biol."
    },
    {
      "key": "BFnrg3662_CR98",
      "doi-asserted-by": "crossref",
      "first-page": "74",
      "DOI": "10.1038/nature10442",
      "volume": "479",
      "author": "S Shukla",
      "year": "2011",
      "unstructured": "Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74\u201379 (2011).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR99",
      "doi-asserted-by": "crossref",
      "first-page": "950",
      "DOI": "10.1126/science.1229386",
      "volume": "339",
      "author": "H Kwak",
      "year": "2013",
      "unstructured": "Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950\u2013953 (2013).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR100",
      "doi-asserted-by": "crossref",
      "first-page": "990",
      "DOI": "10.1038/nsmb.1659",
      "volume": "16",
      "author": "S Schwartz",
      "year": "2009",
      "unstructured": "Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nature Struct. Mol. Biol. 16, 990\u2013995 (2009).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR101",
      "doi-asserted-by": "crossref",
      "first-page": "738",
      "DOI": "10.1016/j.cell.2012.10.009",
      "volume": "151",
      "author": "L Bintu",
      "year": "2012",
      "unstructured": "Bintu, L. et al. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151, 738\u2013749 (2012).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR102",
      "doi-asserted-by": "crossref",
      "first-page": "2004",
      "DOI": "10.1073/pnas.1011982108",
      "volume": "108",
      "author": "FQ Gunderson",
      "year": "2011",
      "unstructured": "Gunderson, F. Q., Merkhofer, E. C. & Johnson, T. L. Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc. Natl Acad. Sci. USA 108, 2004\u20132009 (2011).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR103",
      "doi-asserted-by": "crossref",
      "first-page": "538",
      "DOI": "10.1038/35097110",
      "volume": "413",
      "author": "P Hilleren",
      "year": "2001",
      "unstructured": "Hilleren, P., McCarthy, T., Rosbash, M., Parker, R. & Jensen, T. H. Quality control of mRNA 3\u2032-end processing is linked to the nuclear exosome. Nature 413, 538\u2013542 (2001).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR104",
      "doi-asserted-by": "crossref",
      "first-page": "8015",
      "DOI": "10.1093/nar/gkq703",
      "volume": "38",
      "author": "SF de Almeida",
      "year": "2010",
      "unstructured": "de Almeida, S. F., Garcia-Sacristan, A., Custodio, N. & Carmo-Fonseca, M. A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Res. 38, 8015\u20138026 (2010).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "BFnrg3662_CR105",
      "doi-asserted-by": "crossref",
      "first-page": "e11540",
      "DOI": "10.1371/journal.pone.0011540",
      "volume": "5",
      "author": "AB Eberle",
      "year": "2010",
      "unstructured": "Eberle, A. B. et al. Splice-site mutations cause Rrp6-mediated nuclear retention of the unspliced RNAs and transcriptional down-regulation of the splicing-defective genes. PLoS ONE 5, e11540 (2010).",
      "journal-title": "PLoS ONE"
    },
    {
      "key": "BFnrg3662_CR106",
      "doi-asserted-by": "crossref",
      "first-page": "27",
      "DOI": "10.1016/j.molcel.2012.05.002",
      "volume": "47",
      "author": "J Rodriguez",
      "year": "2012",
      "unstructured": "Rodriguez, J., Menet, J. S. & Rosbash, M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol. Cell 47, 27\u201337 (2012).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR107",
      "doi-asserted-by": "crossref",
      "first-page": "2690",
      "DOI": "10.1101/gad.204602.112",
      "volume": "26",
      "author": "JC Schwartz",
      "year": "2012",
      "unstructured": "Schwartz, J. C. et al. FUS binds the CTD of RNA polymerase II and regulates its phosphorylation at Ser2. Genes Dev. 26, 2690\u20132695 (2012).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR108",
      "doi-asserted-by": "crossref",
      "first-page": "1351",
      "DOI": "10.1101/gad.187278.112",
      "volume": "26",
      "author": "DS Dichmann",
      "year": "2012",
      "unstructured": "Dichmann, D. S. & Harland, R. M. fus/TLS orchestrates splicing of developmental regulators during gastrulation. Genes Dev. 26, 1351\u20131363 (2012).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR109",
      "doi-asserted-by": "crossref",
      "first-page": "1071",
      "DOI": "10.1261/rna.404407",
      "volume": "13",
      "author": "K Ryman",
      "year": "2007",
      "unstructured": "Ryman, K., Fong, N., Bratt, E., Bentley, D. L. & Ohman, M. The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript. RNA 13, 1071\u20131078 (2007).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR110",
      "doi-asserted-by": "crossref",
      "first-page": "1279",
      "DOI": "10.1038/nsmb.1913",
      "volume": "17",
      "author": "H Kim",
      "year": "2010",
      "unstructured": "Kim, H. et al. Gene-specific RNA polymerase II phosphorylation and the CTD code. Nature Struct. Mol. Biol. 17, 1279\u20131286 (2010).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR111",
      "doi-asserted-by": "crossref",
      "first-page": "1272",
      "DOI": "10.1038/nsmb.1903",
      "volume": "17",
      "author": "A Mayer",
      "year": "2010",
      "unstructured": "Mayer, A. et al. Uniform transitions of the general RNA polymerase II transcription complex. Nature Struct. Mol. Biol. 17, 1272\u20131278 (2010).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR112",
      "doi-asserted-by": "crossref",
      "first-page": "563",
      "DOI": "10.1016/0092-8674(82)90211-2",
      "volume": "28",
      "author": "KS Zaret",
      "year": "1982",
      "unstructured": "Zaret, K. S. & Sherman, F. DNA sequence required for efficient transcription termination in yeast. Cell 28, 563\u2013573 (1982).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR113",
      "doi-asserted-by": "crossref",
      "first-page": "8306",
      "DOI": "10.1073/pnas.84.23.8306",
      "volume": "84",
      "author": "J Logan",
      "year": "1987",
      "unstructured": "Logan, J., Falck, P. E., Darnell, J. E. J. & Shenk, T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse \u03b2 maj-globin gene. Proc. Natl Acad. Sci. USA 84, 8306\u20138310 (1987).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR114",
      "doi-asserted-by": "crossref",
      "first-page": "2915",
      "DOI": "10.1002/j.1460-2075.1986.tb04587.x",
      "volume": "5",
      "author": "E Whitelaw",
      "year": "1986",
      "unstructured": "Whitelaw, E. & Proudfoot, N. \u03b1-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3\u2032 end processing in the human \u03b12 globin gene. EMBO J. 5, 2915\u20132922 (1986).",
      "journal-title": "EMBO J."
    },
    {
      "key": "BFnrg3662_CR115",
      "doi-asserted-by": "crossref",
      "first-page": "1080",
      "DOI": "10.1016/j.celrep.2013.03.012",
      "volume": "3",
      "author": "T Nojima",
      "year": "2013",
      "unstructured": "Nojima, T., Dienstbier, M., Murphy, S., Proudfoot, N. J. & Dye, M. J. Definition of RNA polymerase II CoTC terminator elements in the human genome. Cell Rep. 3, 1080\u20131092 (2013).",
      "journal-title": "Cell Rep."
    },
    {
      "key": "BFnrg3662_CR116",
      "doi-asserted-by": "crossref",
      "first-page": "440",
      "DOI": "10.1101/gad.2.4.440",
      "volume": "2",
      "author": "S Connelly",
      "year": "1988",
      "unstructured": "Connelly, S. & Manley, J. L. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 2, 440\u2013452 (1988).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR117",
      "doi-asserted-by": "crossref",
      "first-page": "2086",
      "DOI": "10.1101/gad.5.11.2086",
      "volume": "5",
      "author": "M Niwa",
      "year": "1991",
      "unstructured": "Niwa, M. & Berget, S. M. Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns. Genes Dev. 5, 2086\u20132095 (1991).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR118",
      "doi-asserted-by": "crossref",
      "first-page": "1552",
      "DOI": "10.1101/gad.4.9.1552",
      "volume": "4",
      "author": "M Niwa",
      "year": "1990",
      "unstructured": "Niwa, M., Rose, S. D. & Berget, S. M. In vitro polyadenylation is stimulated by the presence of an upstream intron. Genes Dev. 4, 1552\u20131559 (1990).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR119",
      "doi-asserted-by": "crossref",
      "first-page": "618",
      "DOI": "10.1261/rna.5260303",
      "volume": "9",
      "author": "S Lu",
      "year": "2003",
      "unstructured": "Lu, S. & Cullen, B. R. Analysis of the stimulatory effect of splicing on mRNA production and utilization in mammalian cells. RNA 9, 618\u2013630 (2003).",
      "journal-title": "RNA"
    },
    {
      "key": "BFnrg3662_CR120",
      "doi-asserted-by": "crossref",
      "first-page": "459",
      "DOI": "10.1002/wrna.68",
      "volume": "2",
      "author": "HG Martinson",
      "year": "2011",
      "unstructured": "Martinson, H. G. An active role for splicing in 3\u2032-end formation. Wiley Interdiscip. Rev. RNA 2, 459\u2013470 (2011).",
      "journal-title": "Wiley Interdiscip. Rev. RNA"
    },
    {
      "key": "BFnrg3662_CR121",
      "doi-asserted-by": "crossref",
      "first-page": "972",
      "DOI": "10.1101/gad.2038011",
      "volume": "25",
      "author": "CJ David",
      "year": "2011",
      "unstructured": "David, C. J., Boyne, A. R., Millhouse, S. R. & Manley, J. L. The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65\u2013Prp19 complex. Genes Dev. 25, 972\u2013983 (2011).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR122",
      "doi-asserted-by": "crossref",
      "first-page": "1315",
      "DOI": "10.1101/gad.1298605",
      "volume": "19",
      "author": "K Venkataraman",
      "year": "2005",
      "unstructured": "Venkataraman, K., Brown, K. M. & Gilmartin, G. M. Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev. 19, 1315\u20131327 (2005).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR123",
      "doi-asserted-by": "crossref",
      "first-page": "2759",
      "DOI": "10.1101/gad.12.17.2759",
      "volume": "12",
      "author": "G Bauren",
      "year": "1998",
      "unstructured": "Bauren, G., Belikov, S. & Wieslander, L. Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3\u2032-end formation and excision of the 3\u2032-terminal intron. Genes Dev. 12, 2759\u20132769 (1998).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR124",
      "doi-asserted-by": "crossref",
      "first-page": "853",
      "DOI": "10.1016/j.molcel.2011.08.017",
      "volume": "43",
      "author": "DC Di Giammartino",
      "year": "2011",
      "unstructured": "Di Giammartino, D. C., Nishida, K. & Manley, J. L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 43, 853\u2013866 (2011).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR125",
      "doi-asserted-by": "crossref",
      "first-page": "2380",
      "DOI": "10.1101/gad.229328.113",
      "volume": "27",
      "author": "S Lianoglou",
      "year": "2013",
      "unstructured": "Lianoglou, S., Garg, V., Yang, J. L., Leslie, C. S. & Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380\u20132396 (2013).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR126",
      "doi-asserted-by": "crossref",
      "first-page": "673",
      "DOI": "10.1016/j.cell.2009.06.016",
      "volume": "138",
      "author": "C Mayr",
      "year": "2009",
      "unstructured": "Mayr, C. & Bartel, D. P. Widespread shortening of 3\u2032 UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673\u2013684 (2009).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR127",
      "doi-asserted-by": "crossref",
      "first-page": "867",
      "DOI": "10.1016/j.molcel.2007.05.036",
      "volume": "26",
      "author": "R Das",
      "year": "2007",
      "unstructured": "Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26, 867\u2013881 (2007).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR128",
      "doi-asserted-by": "crossref",
      "first-page": "1833",
      "DOI": "10.1002/j.1460-2075.1991.tb07709.x",
      "volume": "10",
      "author": "HP Enriquez",
      "year": "1991",
      "unstructured": "Enriquez, H. P., Levitt, N., Briggs, D. & Proudfoot, N. J. A pause site for RNA polymerase II is associated with termination of transcription. EMBO J. 10, 1833\u20131842 (1991).",
      "journal-title": "EMBO J."
    },
    {
      "key": "BFnrg3662_CR129",
      "doi-asserted-by": "crossref",
      "first-page": "5606",
      "DOI": "10.1128/MCB.22.15.5606-5615.2002",
      "volume": "22",
      "author": "ML Peterson",
      "year": "2002",
      "unstructured": "Peterson, M. L., Bertolino, S. & Davis, F. An RNA polymerase pause site is associated with the immunoglobulin mus poly(A) site. Mol. Cell. Biol. 22, 5606\u20135615 (2002).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR130",
      "doi-asserted-by": "crossref",
      "first-page": "2431",
      "DOI": "10.1038/emboj.2011.156",
      "volume": "30",
      "author": "PA Pinto",
      "year": "2011",
      "unstructured": "Pinto, P. A. et al. RNA polymerase II kinetics in polo polyadenylation signal selection. EMBO J. 30, 2431\u20132444 (2011).",
      "journal-title": "EMBO J."
    },
    {
      "key": "BFnrg3662_CR131",
      "doi-asserted-by": "crossref",
      "first-page": "55",
      "DOI": "10.1016/j.molcel.2012.10.014",
      "volume": "49",
      "author": "DZ Hazelbaker",
      "year": "2013",
      "unstructured": "Hazelbaker, D. Z., Marquardt, S., Wlotzka, W. & Buratowski, S. Kinetic competition between RNA polymerase II and Sen1-dependent transcription termination. Mol. Cell 49, 55\u201366 (2013).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR132",
      "doi-asserted-by": "crossref",
      "first-page": "393",
      "DOI": "10.1016/0092-8674(88)90202-4",
      "volume": "54",
      "author": "LP Eperon",
      "year": "1988",
      "unstructured": "Eperon, L. P., Graham, I. R., Griffiths, A. D. & Eperon, I. C. Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase? Cell 54, 393\u2013401 (1988).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR133",
      "doi-asserted-by": "crossref",
      "first-page": "245101",
      "DOI": "10.1063/1.3671644",
      "volume": "135",
      "author": "P Zhao",
      "year": "2011",
      "unstructured": "Zhao, P., Zhang, W. & Chen, S. J. Cotranscriptional folding kinetics of ribonucleic acid secondary structures. J. Chem. Phys. 135, 245101 (2011).",
      "journal-title": "J. Chem. Phys."
    },
    {
      "key": "BFnrg3662_CR134",
      "doi-asserted-by": "crossref",
      "first-page": "161",
      "DOI": "10.1146/annurev.biophys.35.040405.102053",
      "volume": "35",
      "author": "T Pan",
      "year": "2006",
      "unstructured": "Pan, T. & Sosnick, T. RNA folding during transcription. Annu. Rev. Biophys. Biomol. Struct. 35, 161\u2013175 (2006).",
      "journal-title": "Annu. Rev. Biophys. Biomol. Struct."
    },
    {
      "key": "BFnrg3662_CR135",
      "doi-asserted-by": "crossref",
      "first-page": "1033",
      "DOI": "10.1016/j.molcel.2011.07.030",
      "volume": "43",
      "author": "M Meyer",
      "year": "2011",
      "unstructured": "Meyer, M., Plass, M., Perez-Valle, J., Eyras, E. & Vilardell, J. Deciphering 3\u2032ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. Mol. Cell 43, 1033\u20131039 (2011).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR136",
      "doi-asserted-by": "crossref",
      "first-page": "8948",
      "DOI": "10.1073/pnas.1205063109",
      "volume": "109",
      "author": "B Zamft",
      "year": "2012",
      "unstructured": "Zamft, B., Bintu, L., Ishibashi, T. & Bustamante, C. Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. Proc. Natl Acad. Sci. USA 109, 8948\u20138953 (2012).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR137",
      "doi-asserted-by": "crossref",
      "first-page": "280",
      "DOI": "10.1016/j.tig.2008.03.008",
      "volume": "24",
      "author": "S Egloff",
      "year": "2008",
      "unstructured": "Egloff, S. & Murphy, S. Cracking the RNA polymerase II CTD code. Trends Genet. 24, 280\u2013288 (2008).",
      "journal-title": "Trends Genet."
    },
    {
      "key": "BFnrg3662_CR138",
      "doi-asserted-by": "crossref",
      "first-page": "1",
      "DOI": "10.1002/wrna.1138",
      "volume": "4",
      "author": "O Jasnovidova",
      "year": "2013",
      "unstructured": "Jasnovidova, O. & Stefl, R. The CTD code of RNA polymerase II: a structural view. Wiley Interdiscip. Rev. RNA 4, 1\u201316 (2013).",
      "journal-title": "Wiley Interdiscip. Rev. RNA"
    },
    {
      "key": "BFnrg3662_CR139",
      "doi-asserted-by": "crossref",
      "first-page": "917",
      "DOI": "10.1016/j.molcel.2006.12.002",
      "volume": "24",
      "author": "DF Tardiff",
      "year": "2006",
      "unstructured": "Tardiff, D. F., Lacadie, S. A. & Rosbash, M. A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol. Cell 24, 917\u2013929 (2006).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR140",
      "doi-asserted-by": "crossref",
      "first-page": "2085",
      "DOI": "10.1242/jcs.061358",
      "volume": "123",
      "author": "B Spiluttini",
      "year": "2010",
      "unstructured": "Spiluttini, B. et al. Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells. J. Cell Sci. 123, 2085\u20132093 (2010).",
      "journal-title": "J. Cell Sci."
    },
    {
      "key": "BFnrg3662_CR141",
      "doi-asserted-by": "crossref",
      "first-page": "49773",
      "DOI": "10.1074/jbc.M409087200",
      "volume": "279",
      "author": "A Ujvari",
      "year": "2004",
      "unstructured": "Ujvari, A. & Luse, D. S. Newly initiated RNA encounters a factor involved in splicing immediately upon emerging from within RNA polymerase II. J. Biol. Chem. 279, 49773\u201349779 (2004).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR142",
      "doi-asserted-by": "crossref",
      "first-page": "2435",
      "DOI": "10.1101/gad.836300",
      "volume": "14",
      "author": "SC Schroeder",
      "year": "2000",
      "unstructured": "Schroeder, S. C., Schwer, B., Shuman, S. & Bentley, D. Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev. 14, 2435\u20132440 (2000).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR143",
      "doi-asserted-by": "crossref",
      "first-page": "2452",
      "DOI": "10.1101/gad.824700",
      "volume": "14",
      "author": "P Komarnitsky",
      "year": "2000",
      "unstructured": "Komarnitsky, P., Cho, E. J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452\u20132460 (2000). This study shows that dynamic changes in Pol II CTD phosphorylation are coordinated with transcription initiation, elongation and termination.",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR144",
      "doi-asserted-by": "crossref",
      "first-page": "795",
      "DOI": "10.1038/nsmb.1468",
      "volume": "15",
      "author": "L Vasiljeva",
      "year": "2008",
      "unstructured": "Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S. & Meinhart, A. The Nrd1\u2013Nab3\u2013Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nature Struct. Mol. Biol. 15, 795\u2013804 (2008).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR145",
      "doi-asserted-by": "crossref",
      "first-page": "1101",
      "DOI": "10.1016/S1097-2765(02)00518-X",
      "volume": "9",
      "author": "DD Licatalosi",
      "year": "2002",
      "unstructured": "Licatalosi, D. D. et al. Functional interaction of yeast pre-mRNA 3\u2032 end processing factors with RNA polymerase II. Mol. Cell 9, 1101\u20131111 (2002).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR146",
      "doi-asserted-by": "crossref",
      "first-page": "679",
      "DOI": "10.1038/nsb0903-679",
      "volume": "10",
      "author": "S Buratowski",
      "year": "2003",
      "unstructured": "Buratowski, S. The CTD code. Nature Struct. Biol. 10, 679\u2013680 (2003).",
      "journal-title": "Nature Struct. Biol."
    },
    {
      "key": "BFnrg3662_CR147",
      "doi-asserted-by": "crossref",
      "first-page": "1591",
      "DOI": "10.1093/nar/gks1327",
      "volume": "41",
      "author": "B Gu",
      "year": "2013",
      "unstructured": "Gu, B., Eick, D. & Bensaude, O. CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res. 41, 1591\u20131603 (2013).",
      "journal-title": "Nucleic Acids Res."
    },
    {
      "key": "BFnrg3662_CR148",
      "doi-asserted-by": "crossref",
      "first-page": "708",
      "DOI": "10.1016/j.cell.2009.03.010",
      "volume": "137",
      "author": "MJ Munoz",
      "year": "2009",
      "unstructured": "Munoz, M. J. et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 137, 708\u2013720 (2009).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR149",
      "doi-asserted-by": "crossref",
      "first-page": "311",
      "DOI": "10.1016/j.molcel.2011.05.024",
      "volume": "43",
      "author": "B Schwer",
      "year": "2011",
      "unstructured": "Schwer, B. & Shuman, S. Deciphering the RNA polymerase II CTD code in fission yeast. Mol. Cell 43, 311\u2013318 (2011). This paper uses an elegant genetic test of the CTD code hypothesis to show that the essential function of Ser5 phosphorylation is to recruit the mRNA-capping enzyme.",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR150",
      "doi-asserted-by": "crossref",
      "first-page": "18024",
      "DOI": "10.1073/pnas.1208995109",
      "volume": "109",
      "author": "B Schwer",
      "year": "2012",
      "unstructured": "Schwer, B., Sanchez, A. M. & Shuman, S. Punctuation and syntax of the RNA polymerase II CTD code in fission yeast. Proc. Natl Acad. Sci. USA 109, 18024\u201318029 (2012).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR151",
      "first-page": "149",
      "volume": "1",
      "author": "JM Lee",
      "year": "1991",
      "unstructured": "Lee, J. M. & Greenleaf, A. L. CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expr. 1, 149\u2013167 (1991).",
      "journal-title": "Gene Expr."
    },
    {
      "key": "BFnrg3662_CR152",
      "doi-asserted-by": "crossref",
      "first-page": "67",
      "DOI": "10.1016/S1097-2765(03)00492-1",
      "volume": "13",
      "author": "SH Ahn",
      "year": "2004",
      "unstructured": "Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3\u2032 end processing. Mol. Cell 13, 67\u201376 (2004).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR153",
      "doi-asserted-by": "crossref",
      "first-page": "1914",
      "DOI": "10.1101/gad.1937510",
      "volume": "24",
      "author": "Z Shen",
      "year": "2010",
      "unstructured": "Shen, Z., St-Denis, A. & Chartrand, P. Cotranscriptional recruitment of She2p by RNA Pol II elongation factor Spt4\u2013Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev. 24, 1914\u20131926 (2010).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR154",
      "doi-asserted-by": "crossref",
      "first-page": "34027",
      "DOI": "10.1074/jbc.M110.145110",
      "volume": "285",
      "author": "MH Suh",
      "year": "2010",
      "unstructured": "Suh, M. H. et al. A dual interface determines the recognition of RNA polymerase II by RNA capping enzyme. J. Biol. Chem. 285, 34027\u201334038 (2010).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR155",
      "doi-asserted-by": "crossref",
      "first-page": "996",
      "DOI": "10.1126/science.1184208",
      "volume": "327",
      "author": "RF Luco",
      "year": "2010",
      "unstructured": "Luco, R. F. et al. Regulation of alternative splicing by histone modifications. Science 327, 996\u20131000 (2010).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR156",
      "doi-asserted-by": "crossref",
      "first-page": "e1002717",
      "DOI": "10.1371/journal.pgen.1002717",
      "volume": "8",
      "author": "MM Pradeepa",
      "year": "2012",
      "unstructured": "Pradeepa, M. M., Sutherland, H. G., Ule, J., Grimes, G. R. & Bickmore, W. A. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet. 8, e1002717 (2012).",
      "journal-title": "PLoS Genet."
    },
    {
      "key": "BFnrg3662_CR157",
      "doi-asserted-by": "crossref",
      "first-page": "665",
      "DOI": "10.1016/j.molcel.2007.11.010",
      "volume": "28",
      "author": "RJ Sims",
      "year": "2007",
      "unstructured": "Sims, R. J. 3rd et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell 28, 665\u2013676 (2007).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR158",
      "doi-asserted-by": "crossref",
      "first-page": "234",
      "DOI": "10.1016/j.molcel.2010.07.003",
      "volume": "39",
      "author": "CK Govind",
      "year": "2010",
      "unstructured": "Govind, C. K. et al. Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Mol. Cell 39, 234\u2013246 (2010).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR159",
      "doi-asserted-by": "crossref",
      "first-page": "3305",
      "DOI": "10.1128/MCB.25.8.3305-3316.2005",
      "volume": "25",
      "author": "KO Kizer",
      "year": "2005",
      "unstructured": "Kizer, K. O. et al. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell. Biol. 25, 3305\u20133316 (2005).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR160",
      "doi-asserted-by": "crossref",
      "first-page": "977",
      "DOI": "10.1038/nsmb.2123",
      "volume": "18",
      "author": "SF de Almeida",
      "year": "2011",
      "unstructured": "de Almeida, S. F. et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nature Struct. Mol. Biol. 18, 977\u2013983 (2011).",
      "journal-title": "Nature Struct. Mol. Biol."
    },
    {
      "key": "BFnrg3662_CR161",
      "doi-asserted-by": "crossref",
      "first-page": "13564",
      "DOI": "10.1073/pnas.1109475108",
      "volume": "108",
      "author": "S Kim",
      "year": "2011",
      "unstructured": "Kim, S., Kim, H., Fong, N., Erickson, B. & Bentley, D. L. Pre-mRNA splicing is a determinant of histone H3K36 methylation. Proc. Natl Acad. Sci. USA 108, 13564\u201313569 (2011).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR162",
      "doi-asserted-by": "crossref",
      "first-page": "313",
      "DOI": "10.1038/embor.2012.31",
      "volume": "13",
      "author": "T Lionnet",
      "year": "2012",
      "unstructured": "Lionnet, T. & Singer, R. H. Transcription goes digital. EMBO Rep. 13, 313\u2013321 (2012).",
      "journal-title": "EMBO Rep."
    },
    {
      "key": "BFnrg3662_CR163",
      "doi-asserted-by": "crossref",
      "first-page": "17361",
      "DOI": "10.1073/pnas.0408168101",
      "volume": "101",
      "author": "NN Batada",
      "year": "2004",
      "unstructured": "Batada, N. N., Westover, K. D., Bushnell, D. A., Levitt, M. & Kornberg, R. D. Diffusion of nucleoside triphosphates and role of the entry site to the RNA polymerase II active center. Proc. Natl Acad. Sci. USA 101, 17361\u201317364 (2004).",
      "journal-title": "Proc. Natl Acad. Sci. USA"
    },
    {
      "key": "BFnrg3662_CR164",
      "doi-asserted-by": "crossref",
      "first-page": "713",
      "DOI": "10.1016/j.cell.2013.07.032",
      "volume": "154",
      "author": "AH Ehrensberger",
      "year": "2013",
      "unstructured": "Ehrensberger, A. H., Kelly, G. P. & Svejstrup, J. Q. Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps. Cell 154, 713\u2013715 (2013).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR165",
      "doi-asserted-by": "crossref",
      "first-page": "119",
      "DOI": "10.1146/annurev-biochem-052610-095910",
      "volume": "81",
      "author": "Q Zhou",
      "year": "2012",
      "unstructured": "Zhou, Q., Li, T. & Price, D. H. RNA polymerase II elongation control. Annu. Rev. Biochem. 81, 119\u2013143 (2012).",
      "journal-title": "Annu. Rev. Biochem."
    },
    {
      "key": "BFnrg3662_CR166",
      "doi-asserted-by": "crossref",
      "first-page": "1845",
      "DOI": "10.1126/science.1162228",
      "volume": "322",
      "author": "LJ Core",
      "year": "2008",
      "unstructured": "Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845\u20131848 (2008).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR167",
      "doi-asserted-by": "crossref",
      "first-page": "475",
      "DOI": "10.1126/science.1202142",
      "volume": "332",
      "author": "DR Larson",
      "year": "2011",
      "unstructured": "Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A. & Singer, R. H. Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science 332, 475\u2013478 (2011).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR168",
      "doi-asserted-by": "crossref",
      "first-page": "19621",
      "DOI": "10.1016/S0021-9258(19)47159-7",
      "volume": "264",
      "author": "JM Payne",
      "year": "1989",
      "unstructured": "Payne, J. M., Laybourn, P. J. & Dahmus, M. E. The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIA. J. Biol. Chem. 264, 19621\u201319629 (1989).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR169",
      "doi-asserted-by": "crossref",
      "first-page": "55",
      "DOI": "10.1016/j.bbagrm.2012.08.013",
      "volume": "1829",
      "author": "M Heidemann",
      "year": "2013",
      "unstructured": "Heidemann, M., Hintermair, C., Voss, K. & Eick, D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim. Biophys. Acta 1829, 55\u201362 (2013).",
      "journal-title": "Biochim. Biophys. Acta"
    },
    {
      "key": "BFnrg3662_CR170",
      "doi-asserted-by": "crossref",
      "first-page": "23549",
      "DOI": "10.1074/jbc.M111.330910",
      "volume": "287",
      "author": "SM Ranuncolo",
      "year": "2012",
      "unstructured": "Ranuncolo, S. M., Ghosh, S., Hanover, J. A., Hart, G. W. & Lewis, B. A. Evidence of the involvement of O-GlcNAc-modified human RNA polymerase II CTD in transcription in vitro and in vivo. J. Biol. Chem. 287, 23549\u201323561 (2012).",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "BFnrg3662_CR171",
      "doi-asserted-by": "crossref",
      "first-page": "1723",
      "DOI": "10.1126/science.1219651",
      "volume": "336",
      "author": "A Mayer",
      "year": "2012",
      "unstructured": "Mayer, A. et al. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science 336, 1723\u20131725 (2012).",
      "journal-title": "Science"
    },
    {
      "key": "BFnrg3662_CR172",
      "doi-asserted-by": "crossref",
      "first-page": "3887",
      "DOI": "10.1128/MCB.00325-10",
      "volume": "30",
      "author": "A Garrido-Lecca",
      "year": "2010",
      "unstructured": "Garrido-Lecca, A. & Blumenthal, T. RNA polymerase II C-terminal domain phosphorylation patterns in Caenorhabditis elegans operons, polycistronic gene clusters with only one promoter. Mol. Cell. Biol. 30, 3887\u20133893 (2010).",
      "journal-title": "Mol. Cell. Biol."
    },
    {
      "key": "BFnrg3662_CR173",
      "doi-asserted-by": "crossref",
      "first-page": "2303",
      "DOI": "10.1101/gad.1968210",
      "volume": "24",
      "author": "B Bartkowiak",
      "year": "2010",
      "unstructured": "Bartkowiak, B. et al. CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev. 24, 2303\u20132316 (2010).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR174",
      "doi-asserted-by": "crossref",
      "first-page": "92",
      "DOI": "10.1093/hmg/ddl444",
      "volume": "16",
      "author": "E Bitoun",
      "year": "2007",
      "unstructured": "Bitoun, E., Oliver, P. L. & Davies, K. E. The mixed-lineage leukemia fusion partner AF4 stimulates RNA polymerase II transcriptional elongation and mediates coordinated chromatin remodeling. Hum. Mol. Genet. 16, 92\u2013106 (2007).",
      "journal-title": "Hum. Mol. Genet."
    },
    {
      "key": "BFnrg3662_CR175",
      "doi-asserted-by": "crossref",
      "first-page": "429",
      "DOI": "10.1016/j.molcel.2010.01.026",
      "volume": "37",
      "author": "C Lin",
      "year": "2010",
      "unstructured": "Lin, C. et al. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol. Cell 37, 429\u2013437 (2010).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR176",
      "doi-asserted-by": "crossref",
      "first-page": "1093",
      "DOI": "10.1016/0092-8674(94)90039-6",
      "volume": "79",
      "author": "R Roy",
      "year": "1994",
      "unstructured": "Roy, R. et al. The MO15 cell-cycle kinase is associated with the TFIIH transcription DNA-repair factor. Cell 79, 1093\u20131101 (1994).",
      "journal-title": "Cell"
    },
    {
      "key": "BFnrg3662_CR177",
      "doi-asserted-by": "crossref",
      "first-page": "387",
      "DOI": "10.1016/j.molcel.2009.04.016",
      "volume": "34",
      "author": "MS Akhtar",
      "year": "2009",
      "unstructured": "Akhtar, M. S. et al. TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II. Mol. Cell 34, 387\u2013393 (2009).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR178",
      "doi-asserted-by": "crossref",
      "first-page": "842",
      "DOI": "10.1038/ncomms1846",
      "volume": "3",
      "author": "N Czudnochowski",
      "year": "2012",
      "unstructured": "Czudnochowski, N., Bosken, C. A. & Geyer, M. Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition. Nature Commun. 3, 842 (2012).",
      "journal-title": "Nature Commun."
    },
    {
      "key": "BFnrg3662_CR179",
      "doi-asserted-by": "crossref",
      "first-page": "1030",
      "DOI": "10.1101/gad.1075203",
      "volume": "17",
      "author": "X He",
      "year": "2003",
      "unstructured": "He, X. et al. Functional interactions between the transcription and mRNA 3\u2032 end processing machineries mediated by Ssu72 and Sub1. Genes Dev. 17, 1030\u20131042 (2003).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR180",
      "doi-asserted-by": "crossref",
      "first-page": "729",
      "DOI": "10.1038/nature09391",
      "volume": "467",
      "author": "K Xiang",
      "year": "2010",
      "unstructured": "Xiang, K. et al. Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex. Nature 467, 729\u2013733 (2010).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR181",
      "doi-asserted-by": "crossref",
      "first-page": "15702",
      "DOI": "10.1021/bi048364h",
      "volume": "43",
      "author": "HP Phatnani",
      "year": "2004",
      "unstructured": "Phatnani, H. P., Jones, J. C. & Greenleaf, A. L. Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 43, 15702\u201315719 (2004).",
      "journal-title": "Biochemistry"
    },
    {
      "key": "BFnrg3662_CR182",
      "doi-asserted-by": "crossref",
      "first-page": "299",
      "DOI": "10.1016/j.molcel.2011.06.001",
      "volume": "43",
      "author": "A Ghosh",
      "year": "2011",
      "unstructured": "Ghosh, A., Shuman, S. & Lima, C. D. Structural insights to how mammalian capping enzyme reads the CTD code. Mol. Cell 43, 299\u2013310 (2011).",
      "journal-title": "Mol. Cell"
    },
    {
      "key": "BFnrg3662_CR183",
      "doi-asserted-by": "crossref",
      "first-page": "223",
      "DOI": "10.1038/nature02679",
      "volume": "430",
      "author": "A Meinhart",
      "year": "2004",
      "unstructured": "Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3\u2032-RNA-processing factors. Nature 430, 223\u2013226 (2004).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR184",
      "doi-asserted-by": "crossref",
      "first-page": "1891",
      "DOI": "10.1101/gad.192781.112",
      "volume": "26",
      "author": "K Kubicek",
      "year": "2012",
      "unstructured": "Kubicek, K. et al. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes Dev. 26, 1891\u20131896 (2012).",
      "journal-title": "Genes Dev."
    },
    {
      "key": "BFnrg3662_CR185",
      "doi-asserted-by": "crossref",
      "first-page": "517",
      "DOI": "10.1038/nature03041",
      "volume": "432",
      "author": "M Kim",
      "year": "2004",
      "unstructured": "Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517\u2013522 (2004).",
      "journal-title": "Nature"
    },
    {
      "key": "BFnrg3662_CR186",
      "doi-asserted-by": "crossref",
      "first-page": "1777",
      "DOI": "10.1126/science.1145989",
      "volume": "318",
      "author": "S Egloff",
      "year": "2007",
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