Home LiteratureArticle Details
PMID: 22986266 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Review

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans.

Nature reviews. Genetics ·Vol. 13 ·No. 10 ·2012-10-00 ·Pages 720-31

Adelman K, Lis JT

Abstract

Recent years have witnessed a sea change in our understanding of transcription regulation: whereas traditional models focused solely on the events that brought RNA polymerase II (Pol II) to a gene promoter to initiate RNA synthesis, emerging evidence points to the pausing of Pol II during early elongation as a widespread regulatory mechanism in higher eukaryotes. Current data indicate that pausing is particularly enriched at genes in signal-responsive pathways. Here the evidence for pausing of Pol II from recent high-throughput studies will be discussed, as well as the potential interconnected functions of promoter-proximally paused Pol II.

MeSH Terms
Animals Binding Sites Gene Expression Regulation/genetics Humans Models, Biological Promoter Regions, Genetic/genetics Protein Binding/physiology RNA Polymerase II/metabolism,physiology Regulatory Sequences, Nucleic Acid/genetics,physiology Transcription, Genetic/physiology
Chemicals
RNA Polymerase II
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Adelman Karen
Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA. adelmank@niehs.nih.gov
Lis John T
References (98)
98 references, click to expand
  1. Stability of Drosophila RNA polymerase II elongation complexes in vitro.
    Mol Cell Biol. 1992 May;12(5):2067-77 PMID: 1373806
  2. Synchronous and stochastic patterns of gene activation in the Drosophila embryo.
    Science. 2009 Jul 24;325(5939):471-3 PMID: 19628867
  3. Controlling the elongation phase of transcription with P-TEFb.
    Mol Cell. 2006 Aug 4;23(3):297-305 PMID: 16885020
  4. Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene.
    Mol Cell Biol. 2006 Aug;26(16):6094-104 PMID: 16880520
  5. Hold back of RNA polymerase II at the transcription start site mediates down-regulation of c-myc in vivo.
    EMBO J. 1992 Sep;11(9):3307-14 PMID: 1505520
  6. Serine-7 but not serine-5 phosphorylation primes RNA polymerase II CTD for P-TEFb recognition.
    Nat Commun. 2012 May 15;3:842 PMID: 22588304
  7. A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification.
    Blood. 2007 Dec 15;110(13):4445-54 PMID: 17855633
  8. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4.
    Mol Cell. 2005 Aug 19;19(4):535-45 PMID: 16109377
  9. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons.
    Mol Cell. 2010 Nov 24;40(4):571-81 PMID: 21095587
  10. Ending the message: poly(A) signals then and now.
    Genes Dev. 2011 Sep 1;25(17):1770-82 PMID: 21896654
  11. Purification of P-TEFb, a transcription factor required for the transition into productive elongation.
    J Biol Chem. 1995 May 26;270(21):12335-8 PMID: 7759473
  12. The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.
    Cell. 1988 Sep 9;54(6):795-804 PMID: 3136931
  13. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.
    Cell. 1999 Apr 2;97(1):41-51 PMID: 10199401
  14. Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription.
    Biochim Biophys Acta. 2012 Jul;1819(7):700-6 PMID: 22406341
  15. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia.
    Mol Cell. 2010 Feb 12;37(3):429-37 PMID: 20159561
  16. NF-kappaB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II.
    Mol Cell. 2001 Aug;8(2):327-37 PMID: 11545735
  17. c-Myc regulates transcriptional pause release.
    Cell. 2010 Apr 30;141(3):432-45 PMID: 20434984
  18. Promoter-associated pausing in promoter architecture and postinitiation transcriptional regulation.
    Cold Spring Harb Symp Quant Biol. 1998;63:347-56 PMID: 10384299
  19. Independent recruitment in vivo by Gal4 of two complexes required for transcription.
    Mol Cell. 2003 May;11(5):1301-9 PMID: 12769853
  20. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.
    Mol Cell Biol. 2008 May;28(10):3290-300 PMID: 18332113
  21. DNA sequence requirements for generating paused polymerase at the start of hsp70.
    Genes Dev. 1992 Feb;6(2):284-95 PMID: 1737619
  22. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.
    Nature. 2011 Mar 3;471(7336):115-8 PMID: 21368835
  23. Updating the RNA polymerase CTD code: adding gene-specific layers.
    Trends Genet. 2012 Jul;28(7):333-41 PMID: 22622228
  24. Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks.
    Genes Dev. 2012 May 1;26(9):933-44 PMID: 22549956
  25. Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila.
    Nucleic Acids Res. 1998 Feb 15;26(4):919-24 PMID: 9461448
  26. Promoter elements associated with RNA Pol II stalling in the Drosophila embryo.
    Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7762-7 PMID: 18505835
  27. Pause sites promote transcriptional termination of mammalian RNA polymerase II.
    Mol Cell Biol. 2006 May;26(10):3986-96 PMID: 16648491
  28. The glucocorticoid receptor inhibits NFkappaB by interfering with serine-2 phosphorylation of the RNA polymerase II carboxy-terminal domain.
    Genes Dev. 2000 Sep 15;14(18):2314-29 PMID: 10995388
  29. Promoter-proximal Pol II: when stalling speeds things up.
    Cell Cycle. 2008 Jun 1;7(11):1539-44 PMID: 18469524
  30. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I.
    Nature. 1980 Aug 28;286(5776):854-60 PMID: 6774262
  31. Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product.
    Nature. 1987 Dec 3-9;330(6147):489-93 PMID: 2825027
  32. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription.
    Mol Cell. 2010 May 14;38(3):428-38 PMID: 20471948
  33. Regulation of gene expression via the core promoter and the basal transcriptional machinery.
    Dev Biol. 2010 Mar 15;339(2):225-9 PMID: 19682982
  34. Control of inducible gene expression by signal-dependent transcriptional elongation.
    Cell. 2009 Jul 10;138(1):129-45 PMID: 19596240
  35. Inducible gene expression: diverse regulatory mechanisms.
    Nat Rev Genet. 2010 Jun;11(6):426-37 PMID: 20421872
  36. Promoter melting and TFIID complexes on Drosophila genes in vivo.
    Genes Dev. 1992 Nov;6(11):2190-200 PMID: 1427079
  37. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.
    Science. 2008 Dec 19;322(5909):1845-8 PMID: 19056941
  38. HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID, and RNA polymerase II binding sites.
    Genes Dev. 1995 Nov 15;9(22):2756-69 PMID: 7590251
  39. Clustering of RNA polymerase B molecules in the 5' moiety of the adult beta-globin gene of hen erythrocytes.
    Nucleic Acids Res. 1981 Jun 11;9(11):2589-98 PMID: 6269056
  40. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
    Nature. 2007 Aug 2;448(7153):553-60 PMID: 17603471
  41. Progression through the RNA polymerase II CTD cycle.
    Mol Cell. 2009 Nov 25;36(4):541-6 PMID: 19941815
  42. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells.
    Mol Cell Biol. 1986 Nov;6(11):3984-9 PMID: 3099167
  43. In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes.
    Proc Natl Acad Sci U S A. 1993 Sep 1;90(17):7923-7 PMID: 8367444
  44. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro.
    EMBO J. 1998 Dec 15;17(24):7395-403 PMID: 9857195
  45. A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
    Cell. 2006 Apr 21;125(2):315-26 PMID: 16630819
  46. The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo.
    Mol Cell. 2011 Jun 24;42(6):837-44 PMID: 21700228
  47. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription.
    Mol Cell. 2012 May 11;46(3):311-24 PMID: 22483619
  48. High-resolution mapping of DNase I-hypersensitive sites of Drosophila heat shock genes in Drosophila melanogaster and Saccharomyces cerevisiae.
    Mol Cell Biol. 1984 Sep;4(9):1853-63 PMID: 6436689
  49. Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.
    Mol Cell Biol. 2007 Jul;27(14):5090-104 PMID: 17515612
  50. Phage lambda gene Q antiterminator recognizes RNA polymerase near the promoter and accelerates it through a pause site.
    Cell. 1985 Aug;42(1):259-69 PMID: 2990726
  51. A transcription reinitiation intermediate that is stabilized by activator.
    Nature. 2000 Nov 9;408(6809):225-9 PMID: 11089979
  52. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription.
    Mol Cell. 2005 Aug 19;19(4):523-34 PMID: 16109376
  53. Elongation and premature termination of transcripts initiated from c-fos and c-myc promoters show dissimilar patterns.
    Oncogene. 1995 Jan 19;10(2):319-28 PMID: 7838531
  54. A chromatin landmark and transcription initiation at most promoters in human cells.
    Cell. 2007 Jul 13;130(1):77-88 PMID: 17632057
  55. Transcriptional activation by recruitment.
    Nature. 1997 Apr 10;386(6625):569-77 PMID: 9121580
  56. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.
    Nat Genet. 2007 Dec;39(12):1512-6 PMID: 17994019
  57. RNA polymerase is poised for activation across the genome.
    Nat Genet. 2007 Dec;39(12):1507-11 PMID: 17994021
  58. Pre-mRNA processing reaches back to transcription and ahead to translation.
    Cell. 2009 Feb 20;136(4):688-700 PMID: 19239889
  59. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase.
    Mol Cell. 2006 Dec 8;24(5):735-746 PMID: 17157256
  60. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.
    Dev Cell. 2010 Apr 20;18(4):544-55 PMID: 20412770
  61. Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.
    EMBO J. 1995 Jun 1;14(11):2570-9 PMID: 7781610
  62. Imaging biological structures with fluorescence photoactivation localization microscopy.
    Nat Protoc. 2009;4(3):291-308 PMID: 19214181
  63. Three functional classes of transcriptional activation domain.
    Mol Cell Biol. 1996 May;16(5):2044-55 PMID: 8628270
  64. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II.
    Proc Natl Acad Sci U S A. 2004 May 18;101(20):7572-7 PMID: 15136722
  65. Mechanisms of transcriptional activation in vivo: two steps forward.
    Trends Genet. 1996 Aug;12(8):311-5 PMID: 8783941
  66. Postinitiation transcriptional control in Drosophila melanogaster.
    Mol Cell Biol. 1990 Nov;10(11):6041-5 PMID: 2172790
  67. A high-resolution map of active promoters in the human genome.
    Nature. 2005 Aug 11;436(7052):876-80 PMID: 15988478
  68. Paused RNA polymerase II as a developmental checkpoint.
    Cell. 2011 May 13;145(4):502-11 PMID: 21565610
  69. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.
    Genes Dev. 1998 Feb 1;12(3):343-56 PMID: 9450929
  70. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.
    Cell. 2010 Nov 12;143(4):540-51 PMID: 21074046
  71. Dynamic regulation of nucleosome positioning in the human genome.
    Cell. 2008 Mar 7;132(5):887-98 PMID: 18329373
  72. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region.
    Genes Dev. 1992 Nov;6(11):2201-13 PMID: 1427080
  73. Functional association of Gdown1 with RNA polymerase II poised on human genes.
    Mol Cell. 2012 Jan 13;45(1):38-50 PMID: 22244331
  74. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.
    Science. 2010 Jan 15;327(5963):335-8 PMID: 20007866
  75. A slow RNA polymerase II affects alternative splicing in vivo.
    Mol Cell. 2003 Aug;12(2):525-32 PMID: 14536091
  76. Structural insights to how mammalian capping enzyme reads the CTD code.
    Mol Cell. 2011 Jul 22;43(2):299-310 PMID: 21683636
  77. Nucleosomes unfold completely at a transcriptionally active promoter.
    Mol Cell. 2003 Jun;11(6):1587-98 PMID: 12820971
  78. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).
    Genes Dev. 2011 Jul 15;25(14):1486-98 PMID: 21764852
  79. Control of formation of two distinct classes of RNA polymerase II elongation complexes.
    Mol Cell Biol. 1992 May;12(5):2078-90 PMID: 1569941
  80. Determinants of nucleosome organization in primary human cells.
    Nature. 2011 May 22;474(7352):516-20 PMID: 21602827
  81. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter.
    J Biol Chem. 2002 Oct 18;277(42):40156-62 PMID: 12177005
  82. Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling.
    Proc Natl Acad Sci U S A. 2009 Oct 27;106(43):18207-12 PMID: 19820169
  83. P-TEFb is critical for the maturation of RNA polymerase II into productive elongation in vivo.
    Mol Cell Biol. 2008 Feb;28(3):1161-70 PMID: 18070927
  84. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex.
    Mol Cell Biol. 2003 Mar;23(6):1863-73 PMID: 12612062
  85. The DNA-encoded nucleosome organization of a eukaryotic genome.
    Nature. 2009 Mar 19;458(7236):362-6 PMID: 19092803
  86. GAGA factor and the TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 promoter.
    Mol Cell Biol. 2002 Sep;22(17):6148-57 PMID: 12167709
  87. Nucleosome displacement in transcription.
    Genes Dev. 2006 Aug 1;20(15):2009-17 PMID: 16882978
  88. DRB-induced premature termination of late adenovirus transcription.
    Nature. 1978 Apr 13;272(5654):590-3 PMID: 643052
  89. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly.
    Genes Dev. 2008 Jul 15;22(14):1921-33 PMID: 18628398
  90. Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing.
    J Mol Biol. 1995 Oct 6;252(5):522-35 PMID: 7563071
  91. Functions of DNA methylation: islands, start sites, gene bodies and beyond.
    Nat Rev Genet. 2012 May 29;13(7):484-92 PMID: 22641018
  92. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.
    Cell. 2009 Jul 10;138(1):114-28 PMID: 19596239
  93. High nucleosome occupancy is encoded at human regulatory sequences.
    PLoS One. 2010 Feb 09;5(2):e9129 PMID: 20161746
  94. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP.
    Mol Cell. 2010 May 14;38(3):439-51 PMID: 20471949
  95. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.
    Genes Dev. 2011 Apr 1;25(7):742-54 PMID: 21460038
  96. Transcriptional regulation and the role of diverse coactivators in animal cells.
    FEBS Lett. 2005 Feb 7;579(4):909-15 PMID: 15680973
  97. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter.
    Mol Cell. 2003 Jun;11(6):1599-607 PMID: 12820972
  98. Human mediator subunit MED26 functions as a docking site for transcription elongation factors.
    Cell. 2011 Jul 8;146(1):92-104 PMID: 21729782
Article Info
Journal
Nature reviews. Genetics
Abbr.
Nat Rev Genet
ISSN
1471-0064
Published
2012-10-00
Pages
720-31
Language
English
Region
England
NLM ID
100962779
PMCID
PMC3552498
Subset
IM
Grants
Intramural NIH HHS · ZIA ES101987-07 · United States
NIGMS NIH HHS · GM25232 · United States
NIGMS NIH HHS · R37 GM025232 · United States
Intramural NIH HHS · Z01 ES101987 · United States
NIGMS NIH HHS · R01 GM025232 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com