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References
63
Referenced
241
-
Matsui, T., Segall, J., Weil, P. A. & Roeder, R. G. Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. Biol. Chem. 255, 11992–11996 (1980)
(
10.1016/S0021-9258(19)70232-4
) / J. Biol. Chem. by T Matsui (1980) -
Roeder, R. G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21, 327–335 (1996)
(
10.1016/0968-0004(96)10050-5
) / Trends Biochem. Sci. by RG Roeder (1996) -
Goodrich, J. A., Cutler, G. & Tjian, R. Contacts in context: promoter specificity and macromolecular interactions in transcription. Cell 84, 825–830 (1996)
(
10.1016/S0092-8674(00)81061-2
) / Cell by JA Goodrich (1996) -
Kornberg, R. D. The molecular basis of eukaryotic transcription. Proc. Natl Acad. Sci. USA 104, 12955–12961 (2007)
(
10.1073/pnas.0704138104
) / Proc. Natl Acad. Sci. USA by RD Kornberg (2007) -
Cramer, P. et al. Structure of eukaryotic RNA polymerases. Annu. Rev. Biophys. 37, 337–352 (2008)
(
10.1146/annurev.biophys.37.032807.130008
) / Annu. Rev. Biophys. by P Cramer (2008) -
Grünberg, S., Warfield, L. & Hahn, S. Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening. Nature Struct. Mol. Biol. 19, 788–796 (2012)
(
10.1038/nsmb.2334
) / Nature Struct. Mol. Biol. by S Grünberg (2012) -
Thomas, M. C. & Chiang, C. M. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol. 41, 105–178 (2006)
(
10.1080/10409230600648736
) / Crit. Rev. Biochem. Mol. Biol. by MC Thomas (2006) -
Andel, F., III, Ladurner, A. G., Inouye, C., Tjian, R. & Nogales, E. Three-dimensional structure of the human TFIID-IIA-IIB complex. Science 286, 2153–2156 (1999)
(
10.1126/science.286.5447.2153
) / Science by F Andel III (1999) -
Chung, W. H. et al. RNA polymerase II/TFIIF structure and conserved organization of the initiation complex. Mol. Cell 12, 1003–1013 (2003)
(
10.1016/S1097-2765(03)00387-3
) / Mol. Cell by WH Chung (2003) -
Bernecky, C., Grob, P., Ebmeier, C. C., Nogales, E. & Taatjes, D. J. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol. 9, e1000603 (2011)
(
10.1371/journal.pbio.1000603
) / PLoS Biol. by C Bernecky (2011) -
Liu, X., Bushnell, D. A., Wang, D., Calero, G. & Kornberg, R. D. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 327, 206–209 (2010)
(
10.1126/science.1182015
) / Science by X Liu (2010) -
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) -
Bleichenbacher, M., Tan, S. & Richmond, T. J. Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. J. Mol. Biol. 332, 783–793 (2003)
(
10.1016/S0022-2836(03)00887-8
) / J. Mol. Biol. by M Bleichenbacher (2003) -
Tsai, F. T. & Sigler, P. B. Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 19, 25–36 (2000)
(
10.1093/emboj/19.1.25
) / EMBO J. by FT Tsai (2000) -
Sainsbury, S., Niesser, J. & Cramer, P. Structure and function of the initially transcribing RNA polymerase II–TFIIB complex. Nature 493, 437–440 (2013)
(
10.1038/nature11715
) / Nature by S Sainsbury (2013) -
Gaiser, F., Tan, S. & Richmond, T. J. Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 Å resolution. J. Mol. Biol. 302, 1119–1127 (2000)
(
10.1006/jmbi.2000.4110
) / J. Mol. Biol. by F Gaiser (2000) -
Chen, Z. A. et al. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 29, 717–726 (2010)
(
10.1038/emboj.2009.401
) / EMBO J. by ZA Chen (2010) -
Eichner, J., Chen, H. T., Warfield, L. & Hahn, S. Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. EMBO J. 29, 706–716 (2010)
(
10.1038/emboj.2009.386
) / EMBO J. by J Eichner (2010) -
Robert, F., Forget, D., Li, J., Greenblatt, J. & Coulombe, B. Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter. J. Biol. Chem. 271, 8517–8520 (1996)
(
10.1074/jbc.271.15.8517
) / J. Biol. Chem. by F Robert (1996) -
Tyree, C. M. et al. Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 7, 1254–1265 (1993)
(
10.1101/gad.7.7a.1254
) / Genes Dev. by CM Tyree (1993) -
Tan, S., Garrett, K. P., Conaway, R. C. & Conaway, J. W. Cryptic DNA-binding domain in the C terminus of RNA polymerase II general transcription factor RAP30. Proc. Natl Acad. Sci. USA 91, 9808–9812 (1994)
(
10.1073/pnas.91.21.9808
) / Proc. Natl Acad. Sci. USA by S Tan (1994) -
Ghazy, M. A., Brodie, S. A., Ammerman, M. L., Ziegler, L. M. & Ponticelli, A. S. Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II. Mol. Cell. Biol. 24, 10975–10985 (2004)
(
10.1128/MCB.24.24.10975-10985.2004
) / Mol. Cell. Biol. by MA Ghazy (2004) -
Yan, Q., Moreland, R. J., Conaway, J. W. & Conaway, R. C. Dual roles for transcription factor IIF in promoter escape by RNA polymerase II. J. Biol. Chem. 274, 35668–35675 (1999)
(
10.1074/jbc.274.50.35668
) / J. Biol. Chem. by Q Yan (1999) -
Forget, D. et al. RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc. Natl Acad. Sci. USA 94, 7150–7155 (1997)
(
10.1073/pnas.94.14.7150
) / Proc. Natl Acad. Sci. USA by D Forget (1997) -
Orlicky, S. M., Tran, P. T., Sayre, M. H. & Edwards, A. M. Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J. Biol. Chem. 276, 10097–10102 (2001)
(
10.1074/jbc.M003165200
) / J. Biol. Chem. by SM Orlicky (2001) -
Grohmann, D. et al. The initiation factor TFE and the elongation factor Spt4/5 compete for the RNAP clamp during transcription initiation and elongation. Mol. Cell 43, 263–274 (2011)
(
10.1016/j.molcel.2011.05.030
) / Mol. Cell by D Grohmann (2011) -
Buratowski, S., Sopta, M., Greenblatt, J. & Sharp, P. A. RNA polymerase II-associated proteins are required for a DNA conformation change in the transcription initiation complex. Proc. Natl Acad. Sci. USA 88, 7509–7513 (1991)
(
10.1073/pnas.88.17.7509
) / Proc. Natl Acad. Sci. USA by S Buratowski (1991) -
Giardina, C. & Lis, J. T. DNA melting on yeast RNA polymerase II promoters. Science 261, 759–762 (1993)
(
10.1126/science.8342041
) / Science by C Giardina (1993) -
Chen, H. T. & Hahn, S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell 119, 169–180 (2004)
(
10.1016/j.cell.2004.09.028
) / Cell by HT Chen (2004) -
Freire-Picos, M. A., Krishnamurthy, S., Sun, Z. W. & Hampsey, M. Evidence that the Tfg1/Tfg2 dimer interface of TFIIF lies near the active center of the RNA polymerase II initiation complex. Nucleic Acids Res. 33, 5045–5052 (2005)
(
10.1093/nar/gki825
) / Nucleic Acids Res. by MA Freire-Picos (2005) -
Sun, Z. W. & Hampsey, M. Identification of the gene (SSU71/TFG1) encoding the largest subunit of transcription factor TFIIF as a suppressor of a TFIIB mutation in Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 92, 3127–3131 (1995)
(
10.1073/pnas.92.8.3127
) / Proc. Natl Acad. Sci. USA by ZW Sun (1995) -
Fernández-Tornero, C. et al. Conformational flexibility of RNA polymerase III during transcriptional elongation. EMBO J. 29, 3762–3772 (2010)
(
10.1038/emboj.2010.266
) / EMBO J. by C Fernández-Tornero (2010) -
Cheung, A. C. & Cramer, P. Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 471, 249–253 (2011)
(
10.1038/nature09785
) / Nature by AC Cheung (2011) -
Goodrich, J. A. & Tjian, R. Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II. Cell 77, 145–156 (1994)
(
10.1016/0092-8674(94)90242-9
) / Cell by JA Goodrich (1994) -
Conaway, R. C. & Conaway, J. W. General initiation factors for RNA polymerase II. Annu. Rev. Biochem. 62, 161–190 (1993)
(
10.1146/annurev.bi.62.070193.001113
) / Annu. Rev. Biochem. by RC Conaway (1993) -
Andrecka, J. et al. Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res. 37, 5803–5809 (2009)
(
10.1093/nar/gkp601
) / Nucleic Acids Res. by J Andrecka (2009) -
Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution. Science 292, 1876–1882 (2001)
(
10.1126/science.1059495
) / Science by AL Gnatt (2001) -
Chakraborty, A. et al. Opening and closing of the bacterial RNA polymerase clamp. Science 337, 591–595 (2012)
(
10.1126/science.1218716
) / Science by A Chakraborty (2012) -
Gibbons, B. J. et al. Subunit architecture of general transcription factor TFIIH. Proc. Natl Acad. Sci. USA 109, 1949–1954 (2012)
(
10.1073/pnas.1105266109
) / Proc. Natl Acad. Sci. USA by BJ Gibbons (2012) -
Fan, L. et al. XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell 133, 789–800 (2008)
(
10.1016/j.cell.2008.04.030
) / Cell by L Fan (2008) -
Kim, T. K., Ebright, R. H. & Reinberg, D. Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288, 1418–1421 (2000)
(
10.1126/science.288.5470.1418
) / Science by TK Kim (2000) -
Revyakin, A. et al. Transcription initiation by human RNA polymerase II visualized at single-molecule resolution. Genes Dev. 26, 1691–1702 (2012)
(
10.1101/gad.194936.112
) / Genes Dev. by A Revyakin (2012) -
Juven-Gershon, T., Cheng, S. & Kadonaga, J. T. Rational design of a super core promoter that enhances gene expression. Nature Methods 3, 917–922 (2006)
(
10.1038/nmeth937
) / Nature Methods by T Juven-Gershon (2006) -
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005)
(
10.1016/j.jsb.2005.03.010
) / J. Struct. Biol. by C Suloway (2005) -
Lander, G. C. et al. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J. Struct. Biol. 166, 95–102 (2009)
(
10.1016/j.jsb.2009.01.002
) / J. Struct. Biol. by GC Lander (2009) -
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007)
(
10.1016/j.jsb.2006.05.009
) / J. Struct. Biol. by G Tang (2007) -
Hohn, M. et al. SPARX, a new environment for Cryo-EM image processing. J. Struct. Biol. 157, 47–55 (2007)
(
10.1016/j.jsb.2006.07.003
) / J. Struct. Biol. by M Hohn (2007) -
Goddard, T. D., Huang, C. C. & Ferrin, T. E. Visualizing density maps with UCSF Chimera. J. Struct. Biol. 157, 281–287 (2007)
(
10.1016/j.jsb.2006.06.010
) / J. Struct. Biol. by TD Goddard (2007) -
Groft, C. M., Uljon, S. N., Wang, R. & Werner, M. H. Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly. Proc. Natl Acad. Sci. USA 95, 9117–9122 (1998)
(
10.1073/pnas.95.16.9117
) / Proc. Natl Acad. Sci. USA by CM Groft (1998) -
Chen, H. T., Warfield, L. & Hahn, S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nature Struct. Mol. Biol. 14, 696–703 (2007)
(
10.1038/nsmb1272
) / Nature Struct. Mol. Biol. by HT Chen (2007) -
Knuesel, M. T., Meyer, K. D., Bernecky, C. & Taatjes, D. J. The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function. Genes Dev. 23, 439–451 (2009)
(
10.1101/gad.1767009
) / Genes Dev. by MT Knuesel (2009) -
Pal, M., Ponticelli, A. S. & Luse, D. S. The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Mol. Cell 19, 101–110 (2005)
(
10.1016/j.molcel.2005.05.024
) / Mol. Cell by M Pal (2005) -
Voss, N. R., Yoshioka, C. K., Radermacher, M., Potter, C. S. & Carragher, B. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. J. Struct. Biol. 166, 205–213 (2009)
(
10.1016/j.jsb.2009.01.004
) / J. Struct. Biol. by NR Voss (2009) -
Mallick, S. P., Carragher, B., Potter, C. S. & Kriegman, D. J. ACE: automated CTF estimation. Ultramicroscopy 104, 8–29 (2005)
(
10.1016/j.ultramic.2005.02.004
) / Ultramicroscopy by SP Mallick (2005) -
Mindell, J. A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334–347 (2003)
(
10.1016/S1047-8477(03)00069-8
) / J. Struct. Biol. by JA Mindell (2003) -
Sorzano, C. O. et al. XMIPP: a new generation of an open-source image processing package for electron microscopy. J. Struct. Biol. 148, 194–204 (2004)
(
10.1016/j.jsb.2004.06.006
) / J. Struct. Biol. by CO Sorzano (2004) -
van Heel, M., Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol. 116, 17–24 (1996)
(
10.1006/jsbi.1996.0004
) / J. Struct. Biol. by M van Heel (1996) -
Kostek, S. A. et al. Molecular architecture and conformational flexibility of human RNA polymerase II. Structure 14, 1691–1700 (2006)
(
10.1016/j.str.2006.09.011
) / Structure by SA Kostek (2006) -
Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190–199 (1996)
(
10.1006/jsbi.1996.0030
) / J. Struct. Biol. by J Frank (1996) -
Heymann, J. B. & Belnap, D. M. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157, 3–18 (2007)
(
10.1016/j.jsb.2006.06.006
) / J. Struct. Biol. by JB Heymann (2007) -
Lander, G. C. et al. Complete subunit architecture of the proteasome regulatory particle. Nature 482, 186–191 (2012)
(
10.1038/nature10774
) / Nature by GC Lander (2012) -
van Dijk, M. & Bonvin, A. M. 3D-DART: a DNA structure modelling server. Nucleic Acids Res. 37, W235–W239 (2009)
(
10.1093/nar/gkp287
) / Nucleic Acids Res. by M van Dijk (2009) -
Lu, X. J. & Olson, W. K. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature Protocols 3, 1213–1227 (2008)
(
10.1038/nprot.2008.104
) / Nature Protocols by XJ Lu (2008)
Dates
Type | When |
---|---|
Created | 12 years, 5 months ago (Feb. 26, 2013, 12:27 p.m.) |
Deposited | 2 years, 3 months ago (May 18, 2023, 2:09 p.m.) |
Indexed | 3 weeks ago (July 30, 2025, 9:59 a.m.) |
Issued | 12 years, 5 months ago (Feb. 27, 2013) |
Published | 12 years, 5 months ago (Feb. 27, 2013) |
Published Online | 12 years, 5 months ago (Feb. 27, 2013) |
Published Print | 12 years, 5 months ago (March 1, 2013) |
@article{He_2013, title={Structural visualization of key steps in human transcription initiation}, volume={495}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature11991}, DOI={10.1038/nature11991}, number={7442}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={He, Yuan and Fang, Jie and Taatjes, Dylan J. and Nogales, Eva}, year={2013}, month=feb, pages={481–486} }