Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II
Leighton J. Core, and
John T. Lis*
Abstract:
Recent work has shown that the RNA polymerase II enzyme pausesat a promoter-proximal site of many genes in Drosophila andmammals. This rate-limiting step occurs after recruitment andinitiation of RNA polymerase II at a gene promoter. This stagein early elongation appears to be an important and broadly usedtarget of gene regulation.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
* To whom correspondence should be addressed. E-mail: jtl10{at}cornell.edu
The editors suggest the following Related Resources on Science sites:
In Science Magazine
INTRODUCTION TO SPECIAL ISSUE
Guy Riddihough, Beverly A. Purnell, and John Travis (28 March 2008) Science319 (5871), 1781.
[DOI: 10.1126/science.319.5871.1781] |Summary »|PDF »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation.
P. Y. Bertucci, A. S. Nacht, M. Allo, L. Rocha-Viegas, C. Ballare, D. Soronellas, G. Castellano, R. Zaurin, A. R. Kornblihtt, M. Beato, et al. (2013)
Nucleic Acids Res.
|Abstract »|Full Text »|PDF »
Heterochromatin protein 1 promotes self-renewal and triggers regenerative proliferation in adult stem cells.
A. Zeng, Y.-Q. Li, C. Wang, X.-S. Han, G. Li, J.-Y. Wang, D.-S. Li, Y.-W. Qin, Y. Shi, G. Brewer, et al. (2013)
J. Cell Biol.
201, 409-425
|Abstract »|Full Text »|PDF »
Reflections on the history of pre-mRNA processing and highlights of current knowledge: A unified picture.
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing.
H. Kwak, N. J. Fuda, L. J. Core, and J. T. Lis (2013)
Science
339, 950-953
|Abstract »|Full Text »|PDF »
CTCF Regulates Kaposi's Sarcoma-Associated Herpesvirus Latency Transcription by Nucleosome Displacement and RNA Polymerase Programming.
H. Kang, H. Cho, G.-H. Sung, and P. M. Lieberman (2013)
J. Virol.
87, 1789-1799
|Abstract »|Full Text »|PDF »
Transcriptional Regulation Patterns Revealed by High Resolution Chromatin Immunoprecipitation during Cardiac Hypertrophy.
D. Sayed, M. He, Z. Yang, L. Lin, and M. Abdellatif (2013)
J. Biol. Chem.
288, 2546-2558
|Abstract »|Full Text »|PDF »
HIV-1 Tat recruits transcription elongation factors dispersed along a flexible AFF4 scaffold.
S. Chou, H. Upton, K. Bao, U. Schulze-Gahmen, A. J. Samelson, N. He, A. Nowak, H. Lu, N. J. Krogan, Q. Zhou, et al. (2013)
PNAS
110, E123-E131
|Abstract »|Full Text »|PDF »
Transition Step during Assembly of HIV Tat:P-TEFb Transcription Complexes and Transfer to TAR RNA.
I. D'Orso, G. M. Jang, A. W. Pastuszak, T. B. Faust, E. Quezada, D. S. Booth, and A. D. Frankel (2012)
Mol. Cell. Biol.
32, 4780-4793
|Abstract »|Full Text »|PDF »
Identification of Core DNA Elements That Target Somatic Hypermutation.
K. M. Kohler, J. J. McDonald, J. L. Duke, H. Arakawa, S. Tan, S. H. Kleinstein, J.-M. Buerstedde, and D. G. Schatz (2012)
J. Immunol.
189, 5314-5326
|Abstract »|Full Text »|PDF »
S. M. Tan-Wong, J. B. Zaugg, J. Camblong, Z. Xu, D. W. Zhang, H. E. Mischo, A. Z. Ansari, N. M. Luscombe, L. M. Steinmetz, and N. J. Proudfoot (2012)
Science
338, 671-675
|Abstract »|Full Text »|PDF »
Target DNA Sequence Directly Regulates the Frequency of Activation-Induced Deaminase-Dependent Mutations.
Z. Chen, S. S. Viboolsittiseri, B. P. O'Connor, and J. H. Wang (2012)
J. Immunol.
189, 3970-3982
|Abstract »|Full Text »|PDF »
Fcp1 Dephosphorylation of the RNA Polymerase II C-Terminal Domain Is Required for Efficient Transcription of Heat Shock Genes.
N. J. Fuda, M. S. Buckley, W. Wei, L. J. Core, C. T. Waters, D. Reinberg, and J. T. Lis (2012)
Mol. Cell. Biol.
32, 3428-3437
|Abstract »|Full Text »|PDF »
Drug Experience Epigenetically Primes Fosb Gene Inducibility in Rat Nucleus Accumbens.
D. Damez-Werno, Q. LaPlant, H. Sun, K. N. Scobie, D. M. Dietz, I. M. Walker, J. W. Koo, V. F. Vialou, E. Mouzon, S. J. Russo, et al. (2012)
J. Neurosci.
32, 10267-10272
|Abstract »|Full Text »|PDF »
The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output.
Z. Luo, C. Lin, E. Guest, A. S. Garrett, N. Mohaghegh, S. Swanson, S. Marshall, L. Florens, M. P. Washburn, and A. Shilatifard (2012)
Mol. Cell. Biol.
32, 2608-2617
|Abstract »|Full Text »|PDF »
The Drosophila 7SK snRNP and the essential role of dHEXIM in development.
D. Nguyen, B. J. Krueger, S. C. Sedore, J. E. Brogie, J. T. Rogers, T. K. Rajendra, A. Saunders, A. G. Matera, J. T. Lis, P. Uguen, et al. (2012)
Nucleic Acids Res.
40, 5283-5297
|Abstract »|Full Text »|PDF »
Vezf1 protein binding sites genome-wide are associated with pausing of elongating RNA polymerase II.
H. Gowher, K. Brick, R. D. Camerini-Otero, and G. Felsenfeld (2012)
PNAS
109, 2370-2375
|Abstract »|Full Text »|PDF »
Transcription factor TFIIF is not required for initiation by RNA polymerase II, but it is essential to stabilize transcription factor TFIIB in early elongation complexes.
Human Polymerase-Associated Factor complex (PAFc) connects the Super Elongation Complex (SEC) to RNA polymerase II on chromatin.
N. He, C. K. Chan, B. Sobhian, S. Chou, Y. Xue, M. Liu, T. Alber, M. Benkirane, and Q. Zhou (2011)
PNAS
108, E636-E645
|Abstract »|Full Text »|PDF »
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing.
S. Perez-Lluch, E. Blanco, A. Carbonell, D. Raha, M. Snyder, F. Serras, and M. Corominas (2011)
Nucleic Acids Res.
39, 4628-4639
|Abstract »|Full Text »|PDF »
PTGS2 (Prostaglandin Endoperoxide Synthase-2) Expression in Term Human Amnion in Vivo Involves Rapid mRNA Turnover, Polymerase-II 5'-Pausing, and Glucocorticoid Transrepression.
C. Mitchell, R. Johnson, A. Bisits, J. Hirst, and T. Zakar (2011)
Endocrinology
152, 2113-2122
|Abstract »|Full Text »|PDF »
Long Noncoding RNAs as Enhancers of Gene Expression.
U. A. Orom, T. Derrien, R. Guigo, and R. Shiekhattar (2011)
Cold Spring Harb Symp Quant Biol
|Abstract »|PDF »
Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription.
Y.-N. Anno, E. Myslinski, R. P. Ngondo-Mbongo, A. Krol, O. Poch, O. Lecompte, and P. Carbon (2011)
Nucleic Acids Res.
39, 3116-3127
|Abstract »|Full Text »|PDF »
TDP-43 Is a Transcriptional Repressor: THE TESTIS-SPECIFIC MOUSE acrv1 GENE IS A TDP-43 TARGET IN VIVO.
A. S. Lalmansingh, C. J. Urekar, and P. P. Reddi (2011)
J. Biol. Chem.
286, 10970-10982
|Abstract »|Full Text »|PDF »
Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation.
J. Y. Ip, D. Schmidt, Q. Pan, A. K. Ramani, A. G. Fraser, D. T. Odom, and B. J. Blencowe (2011)
Genome Res.
21, 390-401
|Abstract »|Full Text »|PDF »
Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors.
D. S. Luse, L. C. Spangler, and A. Ujvari (2011)
J. Biol. Chem.
286, 6040-6048
|Abstract »|Full Text »|PDF »
S. Hocine, R. H. Singer, and D. Grunwald (2010)
Cold Spring Harb Perspect Biol
2, a000752
|Abstract »|Full Text »|PDF »
Multiple functions of Ldb1 required for {beta}-globin activation during erythroid differentiation.
S.-H. Song, A. Kim, T. Ragoczy, M. A. Bender, M. Groudine, and A. Dean (2010)
Blood
116, 2356-2364
|Abstract »|Full Text »|PDF »
Chromatin interaction of TATA-binding protein is dynamically regulated in human cells.
P. de Graaf, F. Mousson, B. Geverts, E. Scheer, L. Tora, A. B. Houtsmuller, and H. T. M. Timmers (2010)
J. Cell Sci.
123, 2663-2671
|Abstract »|Full Text »|PDF »
Spt4/5 stimulates transcription elongation through the RNA polymerase clamp coiled-coil motif.
A. Hirtreiter, G. E. Damsma, A. C. M. Cheung, D. Klose, D. Grohmann, E. Vojnic, A. C. R. Martin, P. Cramer, and F. Werner (2010)
Nucleic Acids Res.
38, 4040-4051
|Abstract »|Full Text »|PDF »
Exon Array Analyses across the NCI-60 Reveal Potential Regulation of TOP1 by Transcription Pausing at Guanosine Quartets in the First Intron.
W. C. Reinhold, J.-L. Mergny, H. Liu, M. Ryan, T. D. Pfister, R. Kinders, R. Parchment, J. Doroshow, J. N. Weinstein, and Y. Pommier (2010)
Cancer Res.
70, 2191-2203
|Abstract »|Full Text »|PDF »
Activation of a Poised RNAPII-Dependent Promoter Requires Both SAGA and Mediator.
S. K. Lee, A. G. L. Fletcher, L. Zhang, X. Chen, J. A. Fischbeck, and L. A. Stargell (2010)
Genetics
184, 659-672
|Abstract »|Full Text »|PDF »
Arabidopsis IWS1 interacts with transcription factor BES1 and is involved in plant steroid hormone brassinosteroid regulated gene expression.
DNA topoisomerase I inhibition by camptothecin induces escape of RNA polymerase II from promoter-proximal pause site, antisense transcription and histone acetylation at the human HIF-1{alpha} gene locus.
L. Baranello, D. Bertozzi, M. V. Fogli, Y. Pommier, and G. Capranico (2010)
Nucleic Acids Res.
38, 159-171
|Abstract »|Full Text »|PDF »
A capping-independent function of MePCE in stabilizing 7SK snRNA and facilitating the assembly of 7SK snRNP.
Y. Xue, Z. Yang, R. Chen, and Q. Zhou (2010)
Nucleic Acids Res.
38, 360-369
|Abstract »|Full Text »|PDF »
Molecular mechanisms of RNA polymerase--the F/E (RPB4/7) complex is required for high processivity in vitro.
A. Hirtreiter, D. Grohmann, and F. Werner (2010)
Nucleic Acids Res.
38, 585-596
|Abstract »|Full Text »|PDF »
Archaeal Intrinsic Transcription Termination In Vivo.
T. J. Santangelo, L. Cubonova, K. M. Skinner, and J. N. Reeve (2009)
J. Bacteriol.
191, 7102-7108
|Abstract »|Full Text »|PDF »
Establishing legitimacy and function in the new transcriptome.
H. van Bakel and T. R. Hughes (2009)
Briefings in Functional Genomics
8, 424-436
|Abstract »|Full Text »|PDF »
Male-Specific Hepatic Bcl6: Growth Hormone-Induced Block of Transcription Elongation in Females and Binding to Target Genes Inversely Coordinated with STAT5.
R. D. Meyer, E. V. Laz, T. Su, and D. J. Waxman (2009)
Mol. Endocrinol.
23, 1914-1926
|Abstract »|Full Text »|PDF »
A wave of nascent transcription on activated human genes.
Y. Wada, Y. Ohta, M. Xu, S. Tsutsumi, T. Minami, K. Inoue, D. Komura, J. Kitakami, N. Oshida, A. Papantonis, et al. (2009)
PNAS
106, 18357-18361
|Abstract »|Full Text »|PDF »
TFIIH-Associated Cdk7 Kinase Functions in Phosphorylation of C-Terminal Domain Ser7 Residues, Promoter-Proximal Pausing, and Termination by RNA Polymerase II.
K. Glover-Cutter, S. Larochelle, B. Erickson, C. Zhang, K. Shokat, R. P. Fisher, and D. L. Bentley (2009)
Mol. Cell. Biol.
29, 5455-5464
|Abstract »|Full Text »|PDF »
Chromatin poises miRNA- and protein-coding genes for expression.
A. Barski, R. Jothi, S. Cuddapah, K. Cui, T.-Y. Roh, D. E. Schones, and K. Zhao (2009)
Genome Res.
19, 1742-1751
|Abstract »|Full Text »|PDF »
Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome.
S. W. Hong, S. M. Hong, J. W. Yoo, Y. C. Lee, S. Kim, J. T. Lis, and D.-k. Lee (2009)
PNAS
106, 14276-14280
|Abstract »|Full Text »|PDF »
Induction of HoxB Transcription by Retinoic Acid Requires Actin Polymerization.
C. Ferrai, G. Naum-Ongania, E. Longobardi, M. Palazzolo, A. Disanza, V. M. Diaz, M. P. Crippa, G. Scita, and F. Blasi (2009)
Mol. Biol. Cell
20, 3543-3551
|Abstract »|Full Text »|PDF »
Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II.
C. Hodges, L. Bintu, L. Lubkowska, M. Kashlev, and C. Bustamante (2009)
Science
325, 626-628
|Abstract »|Full Text »|PDF »
Paused Pol II captures enhancer activity and acts as a potent insulator.
7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development.
M. Barboric, T. Lenasi, H. Chen, E. B. Johansen, S. Guo, and B. M. Peterlin (2009)
PNAS
106, 7798-7803
|Abstract »|Full Text »|PDF »
Complexity in Transcription Control at the Activation Domain-Mediator Interface.
M. A. Balamotis, M. A. Pennella, J. L. Stevens, B. Wasylyk, A. S. Belmont, and A. J. Berk (2009)
Science Signaling
2, ra20
|Abstract »|Full Text »|PDF »
Postrecruitment Regulation of RNA Polymerase II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes.
M. Kininis, G. D. Isaacs, L. J. Core, N. Hah, and W. L. Kraus (2009)
Mol. Cell. Biol.
29, 1123-1133
|Abstract »|Full Text »|PDF »
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.