Uniform transitions of the general RNA polymerase II transcription complex
10.1038/nsmb.1903
Crossref journal-article
Springer Science and Business Media LLC
Nature Structural & Molecular Biology (297)
Bibliography

Mayer, A., Lidschreiber, M., Siebert, M., Leike, K., Söding, J., & Cramer, P. (2010). Uniform transitions of the general RNA polymerase II transcription complex. Nature Structural & Molecular Biology, 17(10), 1272–1278.

Authors 6
  1. Andreas Mayer (first)
  2. Michael Lidschreiber (additional)
  3. Matthias Siebert (additional)
  4. Kristin Leike (additional)
  5. Johannes Söding (additional)
  6. Patrick Cramer (additional)
References 55 Referenced 418
  1. Pokholok, D.K., Hannett, N.M. & Young, R.A. Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol. Cell 9, 799–809 (2002). (10.1016/S1097-2765(02)00502-6) / Mol. Cell by DK Pokholok (2002)
  2. Orphanides, G. & Reinberg, D. RNA polymerase II elongation through chromatin. Nature 407, 471–475 (2000). (10.1038/35035000) / Nature by G Orphanides (2000)
  3. Orphanides, G. & Reinberg, D. A unified theory of gene expression. Cell 108, 439–451 (2002). (10.1016/S0092-8674(02)00655-4) / Cell by G Orphanides (2002)
  4. 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). (10.1101/gad.824700) / Genes Dev. by P Komarnitsky (2000)
  5. 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)
  6. 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)
  7. 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)
  8. Meinhart, A., Kamenski, T., Hoeppner, S., Baumli, S. & Cramer, P. A structural perspective of CTD function. Genes Dev. 19, 1401–1415 (2005). (10.1101/gad.1318105) / Genes Dev. by A Meinhart (2005)
  9. Hirose, Y. & Manley, J.L. RNA polymerase II and the integration of nuclear events. Genes Dev. 14, 1415–1429 (2000). (10.1101/gad.14.12.1415) / Genes Dev. by Y Hirose (2000)
  10. Venters, B.J. & Pugh, B.F. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 19, 360–371 (2009). (10.1101/gr.084970.108) / Genome Res. by BJ Venters (2009)
  11. Aparicio, O. et al. Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. in Current Protocols in Molecular Biology (eds. Ausubel, F.A. et al.) Ch. 21, Unit 21.3 (Wiley, 2005). (10.1002/0471142727.mb2103s65)
  12. David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA 103, 5320–5325 (2006). (10.1073/pnas.0601091103) / Proc. Natl. Acad. Sci. USA by L David (2006)
  13. Jasiak, A.J. et al. Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. J. Biol. Chem. 283, 26423–26427 (2008). (10.1074/jbc.M803237200) / J. Biol. Chem. by AJ Jasiak (2008)
  14. Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033–1037 (2009). (10.1038/nature07728) / Nature by Z Xu (2009)
  15. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008). (10.1126/science.1158441) / Science by U Nagalakshmi (2008)
  16. Dengl, S., Mayer, A., Sun, M. & Cramer, P. Structure and in vivo requirement of the yeast Spt6 SH2 domain. J. Mol. Biol. 389, 211–225 (2009). (10.1016/j.jmb.2009.04.016) / J. Mol. Biol. by S Dengl (2009)
  17. Kuehner, J.N. & Brow, D.A. Quantitative analysis of in vivo initiator selection by yeast RNA polymerase II supports a scanning model. J. Biol. Chem. 281, 14119–14128 (2006). (10.1074/jbc.M601937200) / J. Biol. Chem. by JN Kuehner (2006)
  18. Kostrewa, D. et al. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462, 323–330 (2009). (10.1038/nature08548) / Nature by D Kostrewa (2009)
  19. Renner, D.B., Yamaguchi, Y., Wada, T., Handa, H. & Price, D.H. A highly purified RNA polymerase II elongation control system. J. Biol. Chem. 276, 42601–42609 (2001). (10.1074/jbc.M104967200) / J. Biol. Chem. by DB Renner (2001)
  20. Chapman, R.D. et al. Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science 318, 1780–1782 (2007). (10.1126/science.1145977) / Science by RD Chapman (2007)
  21. Kim, M., Suh, H., Cho, E.-J. & Buratowski, S. Phosphorylation of the yeast Rpb1 C-terminal domain at serines 2, 5, and 7. J. Biol. Chem. 284, 26421–26426 (2009). (10.1074/jbc.M109.028993) / J. Biol. Chem. by M Kim (2009)
  22. 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)
  23. Boeing, S., Rigault, C., Heidemann, M., Eick, D. & Meisterernst, M. RNA polymerase II C-terminal heptarepeat domain Ser-7 phosphorylation is established in a Mediator-dependent fashion. J. Biol. Chem. 285, 188–196 (2010). (10.1074/jbc.M109.046565) / J. Biol. Chem. by S Boeing (2010)
  24. Murray, S., Udupa, R., Yao, S., Hartzog, G. & Prelich, G. Phosphorylation of the RNA polymerase II carboxy-terminal domain by the Bur1 cyclin-dependent kinase. Mol. Cell. Biol. 21, 4089–4096 (2001). (10.1128/MCB.21.13.4089-4096.2001) / Mol. Cell. Biol. by S Murray (2001)
  25. Liu, Y. et al. Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol. Cell. Biol. 29, 4852–4863 (2009). (10.1128/MCB.00609-09) / Mol. Cell. Biol. by Y Liu (2009)
  26. Rodriguez, C.R. et al. Kin28, the TFIIH-Associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol. Cell. Biol. 20, 104–112 (2000). (10.1128/MCB.20.1.104-112.2000) / Mol. Cell. Biol. by CR Rodriguez (2000)
  27. Yoh, S.M., Cho, H., Pickle, L., Evans, R.M. & Jones, K.A. The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export. Genes Dev. 21, 160–174 (2007). (10.1101/gad.1503107) / Genes Dev. by SM Yoh (2007)
  28. Barillà, D., Lee, B.A. & Proudfoot, N.J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 98, 445–450 (2001). / Proc. Natl. Acad. Sci. USA by D Barillà (2001)
  29. Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335–338 (2010). (10.1126/science.1181421) / Science by S Nechaev (2010)
  30. Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 39, 1512–1516 (2007). (10.1038/ng.2007.26) / Nat. Genet. by J Zeitlinger (2007)
  31. 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)
  32. Rahl, P.B. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010). (10.1016/j.cell.2010.03.030) / Cell by PB Rahl (2010)
  33. Jiang, C. & Pugh, B.F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161–172 (2009). (10.1038/nrg2522) / Nat. Rev. Genet. by C Jiang (2009)
  34. Radonjic, M. et al. Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit. Mol. Cell 18, 171–183 (2005). (10.1016/j.molcel.2005.03.010) / Mol. Cell by M Radonjic (2005)
  35. Chen, H.-T., Warfield, L. & Hahn, S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat. Struct. Mol. Biol. 14, 696–703 (2007). (10.1038/nsmb1272) / Nat. Struct. Mol. Biol. by H-T Chen (2007)
  36. Hirtreiter, A. et al. Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif. Nucleic Acids Res. 38, 4040–4051 (2010). (10.1093/nar/gkq135) / Nucleic Acids Res. by A Hirtreiter (2010)
  37. Guo, M. et al. Core structure of the yeast Spt4-Spt5 complex: a conserved module for regulation of transcription elongation. Structure 16, 1649–1658 (2008). (10.1016/j.str.2008.08.013) / Structure by M Guo (2008)
  38. Lindstrom, D.L. et al. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23, 1368–1378 (2003). (10.1128/MCB.23.4.1368-1378.2003) / Mol. Cell. Biol. by DL Lindstrom (2003)
  39. Krogan, N.J. et al. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22, 6979–6992 (2002). (10.1128/MCB.22.20.6979-6992.2002) / Mol. Cell. Biol. by NJ Krogan (2002)
  40. Prather, D., Krogan, N.J., Emili, A., Greenblatt, J.F. & Winston, F. Identification and characterization of Elf1, a conserved transcription elongation factor in Saccharomyces cerevisiae. Mol. Cell. Biol. 25, 10122–10135 (2005). (10.1128/MCB.25.22.10122-10135.2005) / Mol. Cell. Biol. by D Prather (2005)
  41. Qiu, H., Hu, C. & Hinnebusch, A.G. Phosphorylation of the Pol II CTD by KIN28 enhances BUR1/BUR2 recruitment and Ser2 CTD phosphorylation near promoters. Mol. Cell 33, 752–762 (2009). (10.1016/j.molcel.2009.02.018) / Mol. Cell by H Qiu (2009)
  42. Zhou, K., Kuo, W.H.W., Fillingham, J. & Greenblatt, J.F. Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5. Proc. Natl. Acad. Sci. USA 106, 6956–6961 (2009). (10.1073/pnas.0806302106) / Proc. Natl. Acad. Sci. USA by K Zhou (2009)
  43. Laribee, R.N. et al. BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr. Biol. 15, 1487–1493 (2005). (10.1016/j.cub.2005.07.028) / Curr. Biol. by RN Laribee (2005)
  44. Stuwe, T. et al. The FACT Spt16 “peptidase” domain is a histone H3–H4 binding module. Proc. Natl. Acad. Sci. USA 105, 8884–8889 (2008). (10.1073/pnas.0712293105) / Proc. Natl. Acad. Sci. USA by T Stuwe (2008)
  45. Belotserkovskaya, R. et al. FACT facilitates transcription-dependent nucleosome alteration. Science 301, 1090–1093 (2003). (10.1126/science.1085703) / Science by R Belotserkovskaya (2003)
  46. Ahn, S.H., Keogh, M.-C. & Buratowski, S. Ctk1 promotes dissociation of basal transcription factors from elongating RNA polymerase II. EMBO J. 28, 205–212 (2009). (10.1038/emboj.2008.280) / EMBO J. by SH Ahn (2009)
  47. Kim, M., Ahn, S.-H., Krogan, N.J., Greenblatt, J.F. & Buratowski, S. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J. 23, 354–364 (2004). (10.1038/sj.emboj.7600053) / EMBO J. by M Kim (2004)
  48. Keogh, M.-C., Podolny, V. & Buratowski, S. Bur1 kinase is required for efficient transcription elongation by RNA polymerase II. Mol. Cell. Biol. 23, 7005–7018 (2003). (10.1128/MCB.23.19.7005-7018.2003) / Mol. Cell. Biol. by M-C Keogh (2003)
  49. 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. Nat. Struct. Mol. Biol. 15, 71–78 (2008). (10.1038/nsmb1352) / Nat. Struct. Mol. Biol. by K Glover-Cutter (2008)
  50. Kaplan, C.D., Holland, M.J. & Winston, F. Interaction between transcription elongation factors and mRNA 3′-end formation at the Saccharomyces cerevisiae GAL10–GAL7 locus. J. Biol. Chem. 280, 913–922 (2005). (10.1074/jbc.M411108200) / J. Biol. Chem. by CD Kaplan (2005)
  51. Kaplan, C.D., Laprade, L. & Winston, F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301, 1096–1099 (2003). (10.1126/science.1087374) / Science by CD Kaplan (2003)
  52. 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)
  53. Hesselberth, J.R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods 6, 283–289 (2009). (10.1038/nmeth.1313) / Nat. Methods by JR Hesselberth (2009)
  54. Yuan, G.C. et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626–630 (2005). (10.1126/science.1112178) / Science by GC Yuan (2005)
  55. Fan, X., Lamarre-Vincent, N., Wang, Q. & Struhl, K. Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucleic Acids Res. 36, e125 (2008). (10.1093/nar/gkn535) / Nucleic Acids Res. by X Fan (2008)
Dates
Type When
Created 14 years, 11 months ago (Sept. 5, 2010, 3:36 p.m.)
Deposited 1 year, 4 months ago (March 30, 2024, 12:53 a.m.)
Indexed 2 days, 3 hours ago (Aug. 21, 2025, 12:41 p.m.)
Issued 14 years, 11 months ago (Sept. 5, 2010)
Published 14 years, 11 months ago (Sept. 5, 2010)
Published Online 14 years, 11 months ago (Sept. 5, 2010)
Published Print 14 years, 10 months ago (Oct. 1, 2010)
Funders 0

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@article{Mayer_2010, title={Uniform transitions of the general RNA polymerase II transcription complex}, volume={17}, ISSN={1545-9985}, url={http://dx.doi.org/10.1038/nsmb.1903}, DOI={10.1038/nsmb.1903}, number={10}, journal={Nature Structural & Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Mayer, Andreas and Lidschreiber, Michael and Siebert, Matthias and Leike, Kristin and Söding, Johannes and Cramer, Patrick}, year={2010}, month=sep, pages={1272–1278} }