The transition from transcriptional initiation to elongation
Open accessAbstract
Transcription is the first step in gene expression, and its regulation underlies multicellular development and the response to environmental changes. Most studies of transcriptional regulation have focused on the recruitment of RNA polymerase to promoters. However, recent work has shown that, for many promoters, post-recruitment steps in transcriptional initiation are likely to be rate limiting. The rate at which RNA polymerase transitions from transcriptional initiation to elongation varies dramatically between promoters and between organisms and is the target of multiple regulatory proteins that can function to both repress and activate transcription.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In various cell types, including ES cells, Pol II often occupies promoter regions and not the gene body.
“In various cell types, including ES cells, Pol II often occupies promoter regions and not the gene body.”
From Molecular regulation of stem cell quiescence (2013) · cites this paper as [145]
Evidence of promoter-proximal pausing indicates some form of post-initiation regulation.
“This is consistent with evidence of promoter-proximal pausing which indicates some form of post-initiation regulation144–146.”
From Molecular regulation of stem cell quiescence (2013) · cites this paper as [145]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390 · see citing works
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 1,946 · see citing works
Genome-wide analysis of estrogen receptor binding sites
Carroll, J. S., Meyer, C. A., Song, J. S., Li, W., Geistlinger, T., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G., et al. (2006) · Nature Genetics · doi:10.1038/ng1901 · Cited by 1,368 · see citing works
Transcriptional activation by recruitment
Ptashne, M., & Gann, A. (1997) · Nature · doi:10.1038/386569a0 · Cited by 1,158 · see citing works
Controlling the elongation phase of transcription with P-TEFb
Peterlin, B. M., & Price, D. H. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.014 · Cited by 1,144 · see citing works
The RNA Polymerase II Core Promoter
Smale, S. T., & Kadonaga, J. T. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161520 · Cited by 1,138 · see citing works
Komarnitsky, P. B., Cho, E., & Buratowski, S. (2000) · Genes & Development · doi:10.1101/gad.824700 · Cited by 1,098 · see citing works
MECHANISM AND CONTROL OF TRANSCRIPTION INITIATION IN PROKARYOTES
McClure, W. R. (1985) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.54.070185.001131 · Cited by 1,023 · see citing works
A high-resolution map of active promoters in the human genome
Kim, T. H., Barrera, L., Zheng, M., Qu, C.-X., Singer, M. A., Richmond, T., Wu, Y. N., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 1,019 · see citing works
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
Zeitlinger, J., Stark, A., Kellis, M., Hong, J., Nechaev, S., Adelman, K., Levine, M., & Young, R. A. (2007) · Nature Genetics · doi:10.1038/ng.2007.26 · Cited by 766 · see citing works
RNA polymerase is poised for activation across the genome
Muse, G. W., Gilchrist, D. A., Nechaev, S., Shah, R., Parker, J. S., Grissom, S. F., Zeitlinger, J., & Adelman, K. (2007) · Nature Genetics · doi:10.1038/ng.2007.21 · Cited by 762 · see citing works
Elongation by RNA polymerase II: the short and long of itPreprint
Sims, R. J., Belotserkovskaya, R., & Reinberg, D. (2004) · Genes & Development · doi:10.1101/gad.1235904 · Cited by 709 · see citing works
Rougvie, A. E., & Lis, J. T. (1988) · Cell · doi:10.1016/s0092-8674(88)91087-2 · Cited by 680 · see citing works
ppGpp: a global regulator in Escherichia coli
Magnusson, L. U., Farewell, A., & Nyström, T. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.03.008 · Cited by 644 · see citing works
Breaking barriers to transcription elongation
Saunders, A., Core, L. J., & Lis, J. T. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1981 · Cited by 506 · see citing works
Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
Liu, C. L., Kaplan, T., Kim, M., Buratowski, S., Schreiber, S. L., Friedman, N., & Rando, O. J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030328 · Cited by 491 · see citing works
Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes
Struhl, K. (1999) · Cell · doi:10.1016/s0092-8674(00)80599-1 · Cited by 486 · see citing works
Self-citationInitial Transcription by RNA Polymerase Proceeds Through a DNA-Scrunching Mechanism
Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., & Ebright, R. H. (2006) · Science · doi:10.1126/science.1131399 · Cited by 453 · see citing works
Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme
Kuras, L., & Struhl, K. (1999) · Nature · doi:10.1038/21239 · Cited by 450 · see citing works
Self-citationThe Bacterial Enhancer-Dependent ς54(ςN) Transcription Factor
Buck, M., Gallegos, M., Studholme, D. J., et al. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.15.4129-4136.2000 · Cited by 418 · see citing works
Nuclear actin and myosin I are required for RNA polymerase I transcription
Philimonenko, V. V., Zhao, J., Iben, S., Dingová, H., Gaplovská-Kyselá, K., Kahle, M., Zentgraf, H., Hofmann, W. A., de Lanerolle, P., Hozák, P., et al. (2004) · Nature Cell Biology · doi:10.1038/ncb1190 · Cited by 398 · see citing works
Abortive Initiation and Productive Initiation by RNA Polymerase Involve DNA Scrunching
Revyakin, A. G., Liu, C., Ebright, R. H., & Strick, T. R. (2006) · Science · doi:10.1126/science.1131398 · Cited by 397 · see citing works
The Functional and Regulatory Roles of Sigma Factors in TranscriptionPreprint
Gross, C. A., Chan, C. L., Dombroski, A. J., GRUBER, T., Sharp, M. M., Tupy, J. L., & Young, B. A. (1998) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1998.63.141 · Cited by 367 · see citing works
Genome-Wide Distribution of Yeast RNA Polymerase II and Its Control by Sen1 Helicase
Steinmetz, E. J., Warren, C. L., Kuehner, J. N., Panbehi, B., Ansari, A. Z., & Brow, D. A. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.10.023 · Cited by 323 · see citing works
P-TEFb kinase recruitment and function at heat shock lociPreprint
Lis, J. T., Mason, P., Peng, J., Price, D. H., & Werner, J. K. (2000) · Genes & Development · doi:10.1101/gad.14.7.792 · Cited by 314 · see citing works
Exchange of RNA Polymerase II Initiation and Elongation Factors during Gene Expression In Vivo
Pokholok, D., Hannett, N. M., & Young, R. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00502-6 · Cited by 311 · see citing works
Enhancement of TBP binding by activators and general transcription factors
Li, X., Virbasius, A., Zhu, X., & Green, M. R. (1999) · Nature · doi:10.1038/21232 · Cited by 237 · see citing works
Krumm, A., Hickey, L. B., & Groudine, M. T. (1995) · Genes & Development · doi:10.1101/gad.9.5.559 · Cited by 229 · see citing works
Radonjić, M., Andrau, J., Lijnzaad, P., Kemmeren, P., Kockelkorn, T. T. J. P., van Leenen, D., van Berkum, N. L., & Holstege, F. C. P. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.03.010 · Cited by 223 · see citing works
Mediator Requirement for Both Recruitment and Postrecruitment Steps in Transcription Initiation
Wang, G., Balamotis, M. A., Stevens, J. L., Yamaguchi, Y., Handa, H., & Berk, A. J. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.010 · Cited by 211 · see citing works
Reppas, N. B., Wade, J. T., Church, G. M., & Struhl, K. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.10.030 · Cited by 203 · see citing works
Self-citationYEAST TRANSCRIPTIONAL REGULATORY MECHANISMS
Struhl, K. (1995) · Annual Review of Genetics · doi:10.1146/annurev.ge.29.120195.003251 · Cited by 198 · see citing works
Self-citationWade, J. T., Reppas, N. B., Church, G. M., & Struhl, K. (2005) · Genes & Development · doi:10.1101/gad.1355605 · Cited by 166 · see citing works
Self-citationSigma and RNA Polymerase: An On-Again, Off-Again Relationship?
Mooney, R. A., Darst, S. A., & Landick, R. C. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.10.015 · Cited by 161 · see citing works
P-TEFb Is Critical for the Maturation of RNA Polymerase II into Productive Elongation In Vivo
Ni, Z., Saunders, A., Fuda, N. J., Yao, J., Suárez, J.-R., Webb, W. W., & Lis, J. T. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.01859-07 · Cited by 157 · see citing works
RNA Polymerase II Initiation Factor Interactions and Transcription Start Site Selection
Li, Y., Flanagan, P. M., Tschochner, H., et al. (1994) · Science · doi:10.1126/science.8303296 · Cited by 156 · see citing works
Shin, M., Song, M., Rhee, J. H., et al. (2005) · Genes & Development · doi:10.1101/gad.1316305 · Cited by 156 · see citing works
UBF activates RNA polymerase I transcription by stimulating promoter escape
Panov, K. I., Friedrich, J. K., Russell, J., & Zomerdijk, J. C. B. M. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601221 · Cited by 121 · see citing works
A model of repression: CTD analogs and PIE-1 inhibit transcriptional elongation by P-TEFbPreprint
Zhang, F., Barborič, M., Blackwell, T. K., & Peterlin, B. M. (2003) · Genes & Development · doi:10.1101/gad.1068203 · Cited by 117 · see citing works
Ivaldi, M. S., Karam, C. S., & Corces, V. G. (2007) · Genes & Development · doi:10.1101/gad.1604007 · Cited by 114 · see citing works
Dynamic Protein-DNA Architecture of a Yeast Heat Shock Promoter
Giardina, C. A., & Lis, J. T. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.5.2737 · Cited by 110 · see citing works
Activator-specific recruitment of Mediator in vivo
Fan, X., Chou, D. M., & Struhl, K. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1049 · Cited by 107 · see citing works
Self-citationControl of rRNA expression in Escherichia coli
Schneider, D. A., Ross, W., & Gourse, R. L. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00038-9 · Cited by 100 · see citing works
Osmo-Regulation of Bacterial Transcription via Poised RNA Polymerase
Lee, S. J., & Gralla, J. D. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00202-3 · Cited by 95 · see citing works
The σ70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter
Nickels, B. E., Mukhopadhyay, J., Garrity, S. J., Ebright, R. H., & Hochschild, A. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb757 · Cited by 85 · see citing works
Cheng, C., & Sharp, P. A. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.6.1961-1967.2003 · Cited by 81 · see citing works
The σ70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription
Brodolin, K. L., Zenkin, N., MUSTAEV, A. A., et al. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb768 · Cited by 79 · see citing works
Vo, N. V., Hsu, L. M., Kane, C. M., et al. (2003) · Biochemistry · doi:10.1021/bi026962v · Cited by 70 · see citing works
Stepanova, E. N., Lee, J., Ozerova, M., et al. (2007) · Journal of Bacteriology · doi:10.1128/jb.00911-07 · Cited by 65 · see citing works
Hsu, L. M., Vo, N. V., Kane, C. M., et al. (2003) · Biochemistry · doi:10.1021/bi026954e · Cited by 60 · see citing works
Mechanism for a transcriptional activator that works at the isomerization step
Dove, S. L., Huang, F. W., & Hochschild, A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.24.13215 · Cited by 60 · see citing works
A pathway branching in transcription initiation in Escherichia coli
Susa, M., Kubori, T., & Shimamoto, N. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05058.x · Cited by 58 · see citing works
Dorris, D. R., & Struhl, K. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.12.4350-4358.2000 · Cited by 41 · see citing works
Self-citationTranscriptional activation by artificial recruitment in mammalian cells
Nevado, J. B., Gaudreau, L. R., Adam, M., & Ptashne, M. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2674 · Cited by 40 · see citing works
Repression and activation of promoter-bound RNA polymerase activity by gal repressor
Choy, H. E., Hanger, R. R., Aki, T., et al. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1221 · Cited by 40 · see citing works
Eichenberger, P., Déthiollaz, S., BUC, H. C., et al. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.17.9022 · Cited by 39 · see citing works
Generality of the Branched Pathway in Transcription Initiation byEscherichia coli RNA Polymerase
Susa, M., Sen, R., & Shimamoto, N. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m112481200 · Cited by 38 · see citing works
Environmental regulation operating at the promoter clearance step of bacterial transcriptionPreprint
Laishram, R. S., & Gowrishankar, J. (2007) · Genes & Development · doi:10.1101/gad.1520507 · Cited by 38 · see citing works
RNA polymerase II and TBP occupy the repressed CYC1 promoter
Martens, C., Krett, B., & Laybourn, P. J. (2001) · Molecular Microbiology · doi:10.1046/j.1365-2958.2001.02445.x · Cited by 32 · see citing works
Vo, N. V., Hsu, L. M., Kane, C. M., et al. (2003) · Biochemistry · doi:10.1021/bi0269613 · Cited by 31 · see citing works
Kinetics of Transcription Initiation at lacP1
Liu, M., Gupte, G., Roy, S., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m305995200 · Cited by 24 · see citing works
Asynchronous basepair openings in transcription initiation: CRP enhances the rate‐limiting step
Roy, S., Lim, H. M., Liu, M., & Adhya, S. L. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600098 · Cited by 22 · see citing works
Xu, J. W., McCabe, B. C., & Koudelka, G. B. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.9.2866-2873.2001 · Cited by 14 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
c-Myc Regulates Transcriptional Pause Release
Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279 · see citing works
Molecular regulation of stem cell quiescence
Cheung, T. H., & Rando, T. A. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3591 · Cited by 1,148 · see citing works
Pharmacological perturbation of CDK9 using selective CDK9 inhibition or degradation
Olson, C. M., Jiang, B., Erb, M. A., Liang, Y., Doctor, Z. M., Zhang, Z., Zhang, T., Kwiatkowski, N., Boukhali, M., Green, J. L., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2538 · Cited by 552 · see citing works
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure
Anand, P., Brown, J. D., Lin, C. Y., Qi, J., Zhang, R., Artero, P. C., Alaiti, M. A., Bullard, J., Alazem, K., Margulies, K. B., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.013 · Cited by 406 · see citing works
YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers
Galli, G. G., Carrara, M., Yuan, W.-C., Valdes-Quezada, C., Gurung, B., Pepe-Mooney, B., Zhang, T., Geeven, G., Gray, N. S., de Laat, W., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.001 · Cited by 290 · see citing works
Cdc48/p97 mediates UV-dependent turnover of RNA Pol II
Verma, R., Oania, R., Fang, R., Smith, G. T., & Deshaies, R. J. (2011) · Molecular Cell · doi:10.1016/j.molcel.2010.12.017 · Cited by 196 · see citing works
Ali, S. Y., Prasad, A., & Das, D. (2025) · Physical Review E · doi:10.1103/physreve.111.014405 · Cited by 2 · see citing works
- Authors
- Wade, J. T., & Struhl, K.
- Affiliations
- New York State Department of Health (US)
- Harvard University (US)
- Corresponding author
- Wade, Joseph T
- Struhl, Kevin
- Venue
- Current Opinion in Genetics & Development
- Publisher
- Elsevier BV
- Published
- 2008-04
- Volume
- 18
- Issue
- 2
- Pages
- 130-136
- ISSN
- 0959-437X (ISSN-L)
- PMC
- PMC2563432
- OpenAlex
- W2000137398
- Cited by
- 117
- References
- 64
- Citations by year
- 2026: 4 · 2025: 5 · 2024: 1 · 2023: 2 · 2022: 5 · 2021: 3 · 2020: 7 · 2019: 2 · 2018: 4 · 2017: 3 · 2016: 3 · 2015: 7 · 2014: 7 · 2013: 6 · 2012: 7
- FWCI
- 1.31
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Current Opinion in Genetics & Development (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (GM30186)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- transcription initiation, transcription elongation, RNA polymerase, promoter recruitment, rate-determining step, transcriptional regulation, transcriptional repression, transcriptional activation, gene expression regulation
- MeSH terms
- Animals, Base Sequence, Humans, RNA Polymerase II, Transcription, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
