c-Myc Regulates Transcriptional Pause Release
Open accessAbstract
Recruitment of the RNA polymerase II (Pol II) transcription initiation apparatus to promoters by specific DNA-binding transcription factors is well recognized as a key regulatory step in gene expression. We report here that promoter-proximal pausing is a general feature of transcription by Pol II in mammalian cells and thus an additional step where regulation of gene expression occurs. This suggests that some transcription factors recruit the transcription apparatus to promoters, whereas others effect promoter-proximal pause release. Indeed, we find that the transcription factor c-Myc, a key regulator of cellular proliferation, plays a major role in Pol II pause release rather than Pol II recruitment at its target genes. We discuss the implications of these results for the role of c-Myc amplification in human cancer.
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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 [144]
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 [144]
MYC controls Pol II-mediated elongation and pause release.
“MYC controls Pol II-mediated elongation and pause release, and it can activate a large number of genes that promote rapid proliferation144.”
From Molecular regulation of stem cell quiescence (2013) · cites this paper as [144]
MYC can activate a large number of genes that promote rapid proliferation.
“MYC controls Pol II-mediated elongation and pause release, and it can activate a large number of genes that promote rapid proliferation144.”
From Molecular regulation of stem cell quiescence (2013) · cites this paper as [144]
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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143 · see citing works
Self-citationSelective inhibition of BET bromodomains
Filippakopoulos, P., Qi, J., Picaud, S., Shen, Y., Smith, W. B., Fedorov, O., Morse, E. M., Keates, T., Hickman, T. T., Felletar, I., et al. (2010) · Nature · doi:10.1038/nature09504 · Cited by 4,262 · see citing works
Dang, C. V. (2012) · Cell · doi:10.1016/j.cell.2012.03.003 · Cited by 3,390 · see citing works
CpG islands and the regulation of transcription
Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187 · see citing works
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works
Self-citationTranscriptional architecture and chromatin landscape of the core circadian clock in mammals
Koike, N., Yoo, S.-H., Huang, H.-C., Kumar, V., Lee, C., Kim, T.-K., & Takahashi, J. S. (2012) · Science · doi:10.1126/science.1226339 · Cited by 1,464 · 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
Charting histone modifications and the functional organization of mammalian genomes
Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147 · see citing works
Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials
Cheng, Y., He, C., Wang, M., Ma, X., Mo, F., Yang, S., Han, J., & Wei, X. (2019) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0095-0 · Cited by 1,097 · see citing works
TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity
Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021 · see citing works
Getting up to speed with transcription elongation by RNA polymerase II
Jonkers, I., & Lis, J. T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3953 · Cited by 876 · see citing works
The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism
Sebastián, C., Zwaans, B. M. M., Silberman, D. M., Gymrek, M., Goren, A., Zhong, L., Ram, O., Truelove, J., Guimaraes, A. R., Toiber, D., et al. (2012) · Cell · doi:10.1016/j.cell.2012.10.047 · Cited by 660 · see citing works
Jonkers, I., Kwak, H., & Lis, J. T. (2014) · eLife · doi:10.7554/elife.02407 · Cited by 581 · see citing works
Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing
Nojima, T., Gomes, T., Grosso, A. R. F., Kimura, H., Dye, M. J., Dhir, S., Carmo-Fonseca, M., & Proudfoot, N. J. (2015) · Cell · doi:10.1016/j.cell.2015.03.027 · Cited by 562 · 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
Self-citationBlazek, D., Kohoutek, J., Bartholomeeusen, K., Johansen, E., Hulinkova, P., Luo, Z., Cimermancic, P., Ule, J., & Peterlin, B. M. (2011) · Genes & Development · doi:10.1101/gad.16962311 · Cited by 522 · see citing works
MYC: Connecting selective transcriptional control to global RNA production
Kress, T. R., Sabò, A., & Amati, B. (2015) · Nature reviews. Cancer · doi:10.1038/nrc3984 · Cited by 521 · see citing works
Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497 · see citing works
Genome-Informed Targeted Therapy for Osteosarcoma
Sayles, L. C., Breese, M. R., Koehne, A. L., Leung, S. G., Lee, A. G., Liu, H.-Y., Spillinger, A., Shah, A. T., Tanasa, B., Straessler, K., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-1152 · Cited by 452 · see citing works
Farrell, A. S., & Sears, R. C. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a014365 · Cited by 468 · see citing works
Winter, G. E., Mayer, A., Buckley, D. L., Erb, M. A., Roderick, J. E., Vittori, S., Reyes, J. M., di Iulio, J., Souza, A., Ott, C. J., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.004 · Cited by 465 · see citing works
Self-citationBorn to run: control of transcription elongation by RNA polymerase II
Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447 · 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
Self-citationAn Overview of MYC and Its Interactome
Conacci-Sorrell, M., McFerrin, L., & Eisenman, R. N. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a014357 · Cited by 408 · see citing works
Chen, K., Chen, Z., Wu, D., Zhang, L., Lin, X., Su, J., Rodriguez, B., Xi, Y., Xia, Z., Chen, X., et al. (2015) · Nature Genetics · doi:10.1038/ng.3385 · Cited by 373 · see citing works
Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.010 · Cited by 367 · see citing works
Parsing the interferon transcriptional network and its disease associations
Mostafavi, S., Yoshida, H., Moodley, D., LeBoité, H., Rothamel, K., Raj, T., Ye, C. J., Chevrier, N., Zhang, S.-Y., Feng, T., et al. (2016) · Cell · doi:10.1016/j.cell.2015.12.032 · Cited by 337 · see citing works
Target gene-independent functions of MYC oncoproteins
Baluapuri, A., Wolf, E., & Eilers, M. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0215-2 · Cited by 310 · see citing works
The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis
Carroll, P. A., Freie, B. W., Mathsyaraja, H., & Eisenman, R. N. (2018) · Frontiers of Medicine · doi:10.1007/s11684-018-0650-z · Cited by 289 · see citing works
Paused RNA Polymerase II as a Developmental Checkpoint
Levine, M. (2011) · Cell · doi:10.1016/j.cell.2011.04.021 · Cited by 288 · see citing works
Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate
Fong, N., Kim, H., Zhou, Y., Ji, X., Qiu, J., Saldi, T., Diener, K., Jones, K., Fu, X.-D., & Bentley, D. L. (2014) · Genes & Development · doi:10.1101/gad.252106.114 · Cited by 287 · see citing works
Li, M., He, Y., Dubois, W., Wu, X., Shi, J., & Huang, J. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.01.020 · Cited by 264 · see citing works
Henriques, T., Gilchrist, D. A., Nechaev, S., Bern, M., Muse, G. W., Burkholder, A., Fargo, D. C., & Adelman, K. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.10.001 · Cited by 240 · see citing works
Cortazar, M. A., Sheridan, R. M., Erickson, B., Fong, N., Glover-Cutter, K., Brannan, K., & Bentley, D. L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.031 · Cited by 227 · see citing works
Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands
Gechijian, L. N., Buckley, D. L., Lawlor, M. A., Reyes, J. M., Paulk, J., Ott, C. J., Winter, G. E., Erb, M. A., Scott, T. G., Xu, M., et al. (2018) · Nature Chemical Biology · doi:10.1038/s41589-018-0010-y · Cited by 222 · see citing works
Saponaro, M., Kantidakis, T., Mitter, R., Kelly, G. P., Heron, M., Williams, H., Söding, J., Stewart, A., & Svejstrup, J. Q. (2014) · Cell · doi:10.1016/j.cell.2014.03.048 · Cited by 207 · see citing works
Global Regulation of Promoter Melting in Naive Lymphocytes
Kouzine, F., Wojtowicz, D., Yamane, A., Resch, W., Kieffer-Kwon, K.-R., Bandle, R., Nelson, S., Nakahashi, H., Awasthi, P., Feigenbaum, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.033 · Cited by 154 · see citing works
Bonhoure, N., Bounova, G., Bernasconi, D., Praz, V., Lammers, F., Canella, D., Willis, I. M., Herr, W., Hernandez, N., Delorenzi, M., et al. (2014) · Genome Research · doi:10.1101/gr.168260.113 · Cited by 155 · see citing works
“…Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. ences at specific loci even in samples displaying relatively uniform global differences at all enriched loci (for examples, see Rahl et al. 2010; Le Martelot et al. 2012).”
BackgroundInfluentialPlacing the HIRA Histone Chaperone Complex in the Chromatin Landscape
Pchelintsev, N. A., McBryan, T., Rai, T. S., van Tuyn, J., Ray-Gallet, D., Almouzni, G., & Adams, P. D. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.03.026 · Cited by 143 · see citing works
Zhong, H.-J., Lu, L., Leung, K.-H., Wong, C. C. L., Peng, C., Yan, S.-C., Ma, D.-L., Cai, Z., David Wang, H.-M., & Leung, C.-H. (2015) · Chemical Science · doi:10.1039/c5sc02321a · Cited by 138 · see citing works
MYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation
Baluapuri, A., Hofstetter, J., Dudvarski Stankovic, N., Endres, T., Bhandare, P., Vos, S. M., Adhikari, B., Schwarz, J. D., Narain, A., Vogt, M., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.031 · Cited by 138 · see citing works
Paf1C regulates RNA polymerase II progression by modulating elongation rate
Hou, L., Wang, Y., Liu, Y., Zhang, N., Shamovsky, I., Nudler, E., Tian, B., & Dynlacht, B. D. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1904324116 · Cited by 129 · see citing works
Pause & go: from the discovery of RNA polymerase pausing to its functional implications
Mayer, A., Landry, H. M., & Churchman, L. S. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2017.03.002 · Cited by 125 · see citing works
Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy
Liang, K., Smith, E. R., Aoi, Y., Stoltz, K. L., Katagi, H., Woodfin, A. R., Rendleman, E. J., Marshall, S. A., Murray, D. C., Wang, L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.027 · Cited by 124 · see citing works
Sleutels, F., Soochit, W., Bartkuhn, M., Heath, H., Dienstbach, S., Bergmaier, P., Franke, V., Rosa-Garrido, M., van de Nobelen, S., Caesar, L., et al. (2012) · Epigenetics & Chromatin · doi:10.1186/1756-8935-5-8 · Cited by 96 · see citing works
Fine-tuning of the intracellular canonical Notch signaling pathway
Borggrefe, T., & Liefke, R. (2012) · Cell Cycle · doi:10.4161/cc.11.2.18995 · Cited by 102 · see citing works
Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors
Richters, A., Doyle, S. K., Freeman, D. B., Lee, C., Leifer, B. S., Jagannathan, S., Kabinger, F., Koren, J. V., Struntz, N. B., Urgiles, J., et al. (2021) · Cell Chemical Biology · doi:10.1016/j.chembiol.2020.10.001 · Cited by 86 · see citing works
Self-citationCook, K. D., Shpargel, K. B., Starmer, J., Whitfield-Larry, F., Conley, B., Allard, D. E., Rager, J. E., Fry, R. C., Davenport, M. L., Magnuson, T., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.09.002 · Cited by 83 · see citing works
Fitz, J., Neumann, T., & Pavri, R. (2018) · The EMBO Journal · doi:10.15252/embj.201797965 · Cited by 74 · see citing works
Feng, L., Wang, G., Chen, Y., He, G., Liu, B., Liu, J., Chiang, C., & Ouyang, L. (2022) · Medicinal Research Reviews · doi:10.1002/med.21859 · Cited by 65 · see citing works
Epigenetic Mechanisms Governing Innate Inflammatory Responses
Perkins, D. J., Patel, M. C., Blanco, J. C. G., & Vogel, S. N. (2016) · Journal of Interferon & Cytokine Research · doi:10.1089/jir.2016.0003 · Cited by 51 · see citing works
Muniz, L., Deb, M. K., Aguirrebengoa, M., Lazorthes, S., Trouche, D., & Nicolas, E. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.006 · Cited by 56 · see citing works
Caggiano, C., Pieraccioli, M., Panzeri, V., Sette, C., & Bielli, P. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz344 · Cited by 44 · see citing works
- Authors
- Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Massachusetts Institute of Technology (US)
- Corresponding author
- Young, Richard A.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2010-04
- Volume
- 141
- Issue
- 3
- Pages
- 432-445
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2864022
- OpenAlex
- W2135229538
- Cited by
- 1,279
- References
- 94
- Citations by year
- 2026: 38 · 2025: 42 · 2024: 68 · 2023: 58 · 2022: 41 · 2021: 71 · 2020: 72 · 2019: 68 · 2018: 70 · 2017: 86 · 2016: 94 · 2015: 101 · 2014: 116 · 2013: 100 · 2012: 119
- FWCI
- 45.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- National Institutes of Health
- National Human Genome Research Institute (R01HG002668)
- National Cancer Institute (R01CA133404, P01CA042063, R01CA146445, P30CA014051)
- National Institute of General Medical Sciences (R01GM034277, R37GM034277)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (F32HD051190)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- c-Myc, promoter-proximal pausing, RNA polymerase II, transcription initiation, gene expression regulation, transcription factors, cell proliferation, cancer
- MeSH terms
- Animals, Humans, Nuclear Proteins, Promoter Regions, Genetic, RNA Polymerase II, Transcription Factors, Transcription, Genetic, Proto-Oncogene Proteins c-myc, Transcriptional Elongation Factors, Chromatin Immunoprecipitation, Cell Proliferation, Octamer Transcription Factor-3, Mice, Embryonic Stem Cells
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.
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