Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Getting up to speed with transcription elongation by RNA polymerase II

Key Points

  • RNA polymerase II (Pol II) elongation is a highly regulated process.

  • Regulation of transcription is often mediated at the level of promoter-proximal pausing of Pol II, in which Pol II is paused approximately 30–60 nucleotides downstream of the transcription start site (TSS) and awaits recruitment of kinase positive transcription elongation factor-b (P-TEFb).

  • P-TEFb is the main factor required to release paused Pol II from the promoter-proximal region, and can directly or indirectly be recruited by many factors, including bromodomain-containing protein 4 (BRD4) and the super elongation complex (SEC).

  • Elongation rates throughout the gene body are not uniform but vary between, and within genes, and can range from 1 to 6 kb per minute.

  • Transient slowdown of Pol II is observed up to 15 kb downstream of the TSS, at exons and near the poly(A) cleavage site.

  • Elongation rates can affect co-transcriptional RNA processes such as splicing and termination, as well as genome stability.

Abstract

Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: RNA polymerase II recruitment, initiation and gene entry, pausing and release.
Figure 2: The cascade of events that precede productive elongation by RNA polymerase II.
Figure 3: RNA polymerase II elongation rate throughout a gene.

References

  1. 1

    Kwak, H. & Lis, J. T. Control of transcriptional elongation. Annu. Rev. Genet. 47, 483–508 (2013).

    CAS  Article  Google Scholar 

  2. 2

    Adelman, K. & Lis, J. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nature Rev. Genet. 13, 720–731 (2012).

    CAS  Google Scholar 

  3. 3

    Kwak, H., Fuda, N. J., Core, L. J. & Lis, J. T. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 339, 950–953 (2013). In this study, pausing was mapped at the genome-wide level with base-pair resolution, showing the dependency of strong promoter-proximal pausing on core promoter elements.

    CAS  PubMed  PubMed Central  Google Scholar 

  4. 4

    Li, J. & Gilmour, D. Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 32, 1829–1841 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5

    Weber, C. M., Ramachandran, S. & Henikoff, S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol. Cell 53, 819–830 (2014).

    CAS  PubMed  Google Scholar 

  6. 6

    Peterlin, B. & Price, D. Controlling the elongation phase of transcription with P-TEFb. Mol. Cell 23, 297–305 (2006).

    CAS  Google Scholar 

  7. 7

    Zhou, Q., Li, T. & Price, D. H. RNA polymerase II elongation control. Annu. Rev. Biochem. 81, 119–143 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8

    Lis, J., Mason, P., Peng, J., Price, D. & Werner, J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14, 792–803 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Jonkers, I., Kwak, H. & Lis, J. T. Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. eLife 3, e02407 (2014). This study measures elongation rates genome-wide and shows that the half-lives of paused Pol II complexes on 3,181 genes are uniformly long with an average of 7 minutes.

    PubMed  PubMed Central  Google Scholar 

  10. 10

    Danko, C. et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell 50, 212–222 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Alexander, R., Innocente, S., Barrass, J. & Beggs, J. Splicing-dependent RNA polymerase pausing in yeast. Mol. Cell 40, 582–593 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Veloso, A. et al. Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications. Genome Res. 24, 896–905 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Fuchs, G. et al. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol. 15, R69 (2014).

    PubMed  PubMed Central  Google Scholar 

  14. 14

    Saponaro, M. et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 157, 1037–1049 (2014). This manuscript documents that RECQL5 slows down transcript elongation and suppresses genome rearrangements at common fragile sites.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Dujardin, G. et al. How slow RNA polymerase II elongation favors alternative exon skipping. Mol. Cell 54, 683–690 (2014).

    CAS  PubMed  Google Scholar 

  16. 16

    Schor, I., Fiszbein, A., Petrillo, E. & Kornblihtt, A. Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation. EMBO J. 32, 2264–2274 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Mata, M. de la et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525–532 (2003).

    PubMed  Google Scholar 

  18. 18

    Moehle, E. A., Braberg, H., Krogan, N. J. & Guthrie, C. Adventures in time and space: splicing efficiency and RNA polymerase II elongation rate. RNA Biol. 11, 313–319 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19

    Plant, K., Dye, M., Lafaille, C. & Proudfoot, N. Strong polyadenylation and weak pausing combine to cause efficient termination of transcription in the human gamma-globin gene. Mol. Cell. Biol. 25, 3276–3285 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Gromak, N., West, S. & Proudfoot, N. Pause sites promote transcriptional termination of mammalian, RNA polymerase II. Mol. Cell. Biol. 26, 3986–3996 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Skourti-Stathaki, K., Kamieniarz-Gdula, K. & Proudfoot, N. J. R-loops induce repressive chromatin marks over mammalian gene terminators. Nature 516, 436–439 (2014).

    CAS  Article  Google Scholar 

  22. 22

    Hazelbaker, D., Marquardt, S., Wlotzka, W. & Buratowski, S. Kinetic competition between RNA Polymerase II and Sen1-dependent transcription termination. Mol. Cell 49, 55–66 (2013).

    CAS  Google Scholar 

  23. 23

    Sainsbury, S., Bernecky, S. & Cramer, P. Structural basis of transcription initiation by RNA polymerase II. Nature Rev. Mol. Cell. Biol. 16, 129–143 (2015).

    CAS  Google Scholar 

  24. 24

    Porrua, O. & Libri, D. Transcription termination and the control of the transcriptome: why, where and how to stop. Nature Rev. Mol. Cell. Biol. 16, 190–202 (2015).

    CAS  Google Scholar 

  25. 25

    Venkatesh, S. S. & Workman, J. L. Histone exchange, chromatin structure and the regulation of transcription. Nature Rev. Mol. Cell. Biol. 16, 178–189 (2015).

    CAS  Google Scholar 

  26. 26

    Ehrensberger, A. H., Kelly, G. P. & Svejstrup, J. Q. Mechanistic interpretation of promoter-proximal peaks and RNAPII density maps. Cell 154, 713–715 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    Venters, B. & Pugh, B. Genomic organization of human transcription initiation complexes. Nature 502, 53–58 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28

    Core, L. J. et al. Defining the status of RNA polymerase at promoters. Cell Rep. 2, 1025–1035 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29

    Rahl, P. et al. c-Myc regulates transcriptional pause release. Cell 141, 432–445 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Henriques, T. et al. Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol. Cell 52, 517–528 (2013). This study reports that promoter-paused elongation complexes are highly stable, with half-lives of minutes in D. melanogaster.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31

    Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845–1848 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Min, I. M. et al. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 25, 742–754 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Nechaev, S. et al. Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327, 335–338 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Gilchrist, D. et al. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell 143, 540–551 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Lee, H., Kraus, K., Wolfner, M. & Lis, J. DNA sequence requirements for generating paused polymerase at the start of hsp70. Genes Dev. 6, 284–295 (1992).

    CAS  PubMed  Google Scholar 

  36. 36

    Shopland, L., Hirayoshi, K., Fernandes, M. & Lis, J. 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. 9, 2756–2769 (1995).

    CAS  PubMed  Google Scholar 

  37. 37

    Kouzine, F. et al. Global regulation of promoter melting in naive lymphocytes. Cell 153, 988–999 (2013). This genome-wide analysis of resting lymphocytes identifies promoter melting as a third major rate-limiting step in transcription (following PIC formation and pause release).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901–1904 (2002).

    CAS  PubMed  Google Scholar 

  39. 39

    Brannan, K. et al. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Mol. Cell 46, 311–324 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40

    Wagschal, A. et al. Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII. Cell 150, 1147–1157 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Cheng, B. et al. Functional association of Gdown1 with RNA polymerase II poised on human genes. Mol. Cell 45, 38–50 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. 42

    Jishage, M. et al. Transcriptional regulation by Pol II(G.) Involving mediator and competitive interactions of Gdown1 and TFIIF with pol II. Mol. Cell 45, 51–63 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43

    Davis, M., Guo, J., Price, D. & Luse, D. Functional interactions of the RNA polymerase II-interacting proteins Gdown1 and TFIIF. J. Biol. Chem. 289, 11143–11152 (2014).

    Google Scholar 

  44. 44

    Chen, F., Gao, X. & Shilatifard, A. Stably paused genes revealed through inhibition of transcription initiation by the TFIIH inhibitor triptolide. Genes Dev. 29, 39–47 (2015).

    PubMed  PubMed Central  Google Scholar 

  45. 45

    Buckley, M. S., Kwak, H., Zipfel, W. R. & Lis, J. T. Kinetics of promoter Pol II on Hsp70 reveal stable pausing and key insights into its regulation. Genes Dev. 28, 14–19 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Saunders, A., Core, L., Sutcliffe, C., Lis, J. & Ashe, H. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev. 27, 1146–1158 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Rougvie, A. E. & Lis, J. T. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell 54, 795–804 (1988).

    CAS  PubMed  Google Scholar 

  48. 48

    Guenther, M., Levine, S., Boyer, L., Jaenisch, R. & Young, R. A. Chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49

    Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nature Genet. 39, 1512–1516 (2007).

    CAS  PubMed  Google Scholar 

  50. 50

    Lagha, M. et al. Paused pol II coordinates tissue morphogenesis in the Drosophila embryo. Cell 153, 976–987 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Kapanidis, A. N. et al. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144–1147 (2006).

    PubMed  PubMed Central  Google Scholar 

  52. 52

    Pal, M., Ponticelli, A. & Luse, D. The role of the transcription bubble & TFIIB in promoter clearance by RNA polymerase II. Mol. Cell 19, 101–110 (2005).

    CAS  Google Scholar 

  53. 53

    Strobel, E. & Roberts, J. Regulation of promoter-proximal transcription elongation: enhanced DNA scrunching drives λQ antiterminator-dependent escape from a σ70-dependent pause. Nucleic Acids Res. 42, 5097–5108 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Hendrix, D. A., Hong, J.-W. W., Zeitlinger, J., Rokhsar, D. S. & Levine, M. S. Promoter elements associated with RNA pol II stalling in the Drosophila embryo. Proc. Natl Acad. Sci. USA 105, 7762–7767 (2008).

    CAS  PubMed  Google Scholar 

  55. 55

    Core, L. et al. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genet. 46, 1311–1320 (2014).

    CAS  PubMed  Google Scholar 

  56. 56

    Li, J. et al. Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Mol. Cell 50, 711–722 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57

    Hargreaves, D., Horng, T. & Medzhitov, R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138, 129–145 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Heinz, S., Romanoski, C. E., Benner, C. & Glass, C. K. The selection and function of cell type-specific enhancers. Nature Rev. Mol. Cell. Biol. 16, 144–154 (2015).

    CAS  Google Scholar 

  59. 59

    Allen, B. L. & Taatjes, D. J. The Mediator complex: a central integrator of transcription. Nature Rev. Mol. Cell. Biol. 16, 155–166 (2015).

    CAS  Google Scholar 

  60. 60

    Takahashi, H. et al. Human mediator subunit MED26 functions as a docking site for transcription elongation factors. Cell 146, 92–104 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. 61

    Ghavi-Helm, Y. et al. Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96–100 (2014).

    CAS  Google Scholar 

  62. 62

    Lee, C. et al. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila. Mol. Cell. Biol. 28, 3290–3300 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63

    Farkas, G., Leibovitch, B. & Elgin, S. Chromatin organization and transcriptional control of gene expression in Drosophila. Gene 253, 117–136 (2000).

    CAS  PubMed  Google Scholar 

  64. 64

    Chopra, V. S. et al. Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3. Dev. Biol. 317, 660–670 (2008).

    CAS  PubMed  Google Scholar 

  65. 65

    Blau, J. et al. Three functional classes of transcriptional activation domain. Mol. Cell. Biol. 16, 2044–2055 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Krumm, A., Hickey, L. B. & Groudine, M. Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. Genes Dev. 9, 559–572 (1995).

    CAS  PubMed  Google Scholar 

  67. 67

    Bunch, H. et al. TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release. Nature Struct. Mol. Biol. 21, 876–883 (2014).

    CAS  Google Scholar 

  68. 68

    Jiang, L. et al. Polo-like kinase 1 inhibits the activity of positive transcription elongation factor of RNA Pol II b (P-TEFb). PloS ONE 8, e72289 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69

    Smith, E., Lin, C. & Shilatifard, A. The super elongation complex (SEC) and MLL in development and disease. Genes Dev. 25, 661–672 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. 70

    Itzen, F., Greifenberg, A., Bosken, C. & Geyer, M. Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation. Nucleic Acids Res. 42, 7577–7590 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71

    Jang, M. et al. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol. Cell 19, 523–534 (2005).

    CAS  Google Scholar 

  72. 72

    Zou, Z. et al. Brd4 maintains constitutively active NF-κB in cancer cells by binding to acetylated RelA. Oncogene 33, 2395–2404 (2014).

    CAS  PubMed  Google Scholar 

  73. 73

    Huang, B., Yang, X.-D. D., Zhou, M.-M. M., Ozato, K. & Chen, L.-F. F. Brd4 coactivates transcriptional activation of NF-κB via specific binding to acetylated RelA. Mol. Cell. Biol. 29, 1375–1387 (2009).

    CAS  Google Scholar 

  74. 74

    Luo, Z. et al. The super elongation complex family of RNA polymerase II elongation factors: gene target specificity and transcriptional output. Mol. Cell. Biol. 32, 2608–2617 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75

    Lin, C. et al. Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC). Genes Dev. 25, 1486–1498 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. 76

    Smith, E. et al. The little elongation complex regulates small nuclear RNA transcription. Mol. Cell 44, 954–965 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Lin, C. et al. 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 37, 429–437 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78

    Luo, Z., Lin, C. & Shilatifard, A. The super elongation complex (SEC) family in transcriptional control. Nature Rev. Mol. Cell. Biol. 13, 543–547 (2012).

    CAS  Google Scholar 

  79. 79

    Gardini, A. et al. Integrator regulates transcriptional initiation and pause release following activation. Mol. Cell 56, 128–139 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80

    Kim, J., Guermah, M. & Roeder, R. G. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140, 491–503 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. 81

    Wier, A., Mayekar, M., Héroux, A., Arndt, K. & VanDemark, A. Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin. Proc. Natl Acad. Sci. USA 110, 17290–17295 (2013).

    CAS  PubMed  Google Scholar 

  82. 82

    He, N. et al. Human Polymerase-Associated Factor complex (PAFc) connects the Super Elongation Complex (SEC) to RNA polymerase II on chromatin. Proc. Natl Acad. Sci. USA 108, E636–645 (2011).

    CAS  Google Scholar 

  83. 83

    Flajollet, S. et al. The elongation complex components BRD4 and MLLT3/AF9 are transcriptional coactivators of nuclear retinoid receptors. PloS ONE 8, e64880 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Diamant, G. & Dikstein, R. Transcriptional control by NF-κB: elongation in focus. Biochim. Biophys. Acta 1829, 937–945 (2013).

    CAS  PubMed  Google Scholar 

  85. 85

    Nowak, D. et al. RelA Ser276 phosphorylation is required for activation of a subset of NF-κB-dependent genes by recruiting cyclin-dependent kinase 9/cyclin T1 complexes. Mol. Cell. Biol. 28, 3623–3638 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86

    Barboric, M., Nissen, R. M., Kanazawa, S., Jabrane-Ferrat, N. & Peterlin, B. M. NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol. Cell 8, 327–337 (2001).

    CAS  Google Scholar 

  87. 87

    Mertz, J. et al. Targeting MYC dependence in cancer by inhibiting BET bromodomains. Proc. Natl Acad. Sci. USA 108, 16669–16674 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013). This study shows that exceptionally high levels of the co-activators Mediator and BRD4 are associated with super-enhancers that drive the expression of key oncogenes.

    PubMed  PubMed Central  Google Scholar 

  89. 89

    Delmore, J. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90

    Oeckinghaus, A., Hayden, M. & Ghosh, S. Crosstalk in NF-κB signaling pathways. Nature Immunol. 12, 695–708 (2011).

    CAS  Google Scholar 

  91. 91

    Fang, L. et al. ATM regulates NF-κB-dependent immediate-early genes via RelA Ser 276 phosphorylation coupled to CDK9 promoter recruitment. Nucleic Acids Res. 42, 8416–8432 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92

    McNamara, R. P., McCann, J. L., Gudipaty, S. A. & D'Orso, I. Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation. Cell Rep. 5, 1256–1268 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. 93

    Gilchrist, D. et al. Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks. Genes Dev. 26, 933–944 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94

    Ji, X. et al. SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell 153, 855–868 (2013). This study implicates an RNA-binding protein that was traditionally thought to function in splicing in the regulated release of paused Pol II to productive elongation.

    CAS  PubMed  PubMed Central  Google Scholar 

  95. 95

    Barboric, M. et al. 7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development. Proc. Natl Acad. Sci. USA 106, 7798–7803 (2009).

    CAS  PubMed  Google Scholar 

  96. 96

    Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).

    CAS  Google Scholar 

  97. 97

    Whyte, W. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. 98

    Brown, J. D. et al. NF-κB directs dynamic super enhancer formation in inflammation and atherogenesis. Mol. Cell 56, 219–231 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99

    Lai, F. et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494, 497–501 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. 100

    Yamaguchi, Y., Inukai, N., Narita, T., Wada, T. & Handa, H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase, II complex and RNA. Mol. Cell. Biol. 22, 2918–2927 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. 101

    Schaukowitch, K. et al. Enhancer RNA facilitates NELF release from immediate early genes. Mol. Cell 56, 29–42 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. 102

    Schaaf, C. A. et al. Genome-wide control of RNA polymerase II activity by cohesin. PLoS Genet. 9, e1003382 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. 103

    Thummel, C. S., Burtis, K. C. & Hogness, D. S. Spatial and temporal patterns of E74 transcription during Drosophila development. Cell 61, 101–111 (1990).

    CAS  PubMed  Google Scholar 

  104. 104

    Heidemann, M., Hintermair, C., Voß, K. & Eick, D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim. Biophys. Acta 1829, 55–62 (2013).

    CAS  Google Scholar 

  105. 105

    Glover-Cutter, K., Kim, S., Espinosa, J. & Bentley, D. RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nature Struct. Mol. Biol. 15, 71–78 (2007).

    Google Scholar 

  106. 106

    Martin, R., Rino, J., Carvalho, C., Kirchhausen, T. & Carmo-Fonseca, M. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep. 4, 1144–1155 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. 107

    Zentner, G. & Henikoff, S. Regulation of nucleosome dynamics by histone modifications. Nature Struct. Mol. Biol. 20, 259–266 (2013).

    CAS  Google Scholar 

  108. 108

    Bintu, L. et al. Nucleosomal elements that control the topography of the barrier to transcription. Cell 151, 738–749 (2012). In this study, optical tweezers were used to measure the movement of individual transcribing Pol II complexes through nucleosomes in real-time and thereby describes the energetic barriers in nucleosomes that could contribute to pausing.

    CAS  PubMed  PubMed Central  Google Scholar 

  109. 109

    Ardehali, M. B. et al. Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J. 28, 1067–1077 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. 110

    Wu, L., Li, L., Zhou, B., Qin, Z. & Dou, Y. H2B ubiquitylation promotes RNA pol II processivity via PAF1 and pTEFb. Mol. Cell 54, 920–931 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. 111

    Jung, I. et al. H2B monoubiquitylation is a 5′-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res. 22, 1026–1035 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. 112

    Shilatifard, A., Conaway, R. C. & Conaway, J. W. The RNA polymerase II elongation complex. Annu. Rev. Biochem. 72, 693–715 (2003).

    CAS  PubMed  Google Scholar 

  113. 113

    Amit, M. et al. Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep. 1, 543–556 (2012).

    CAS  PubMed  Google Scholar 

  114. 114

    Tilgner, H. et al. Nucleosome positioning as a determinant of exon recognition. Nature Struct. Mol. Biol. 16, 996–1001 (2009).

    CAS  Google Scholar 

  115. 115

    Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron structure. Nature Struct. Mol. Biol. 16, 990–995 (2009).

    CAS  Google Scholar 

  116. 116

    Close, P. et al. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484, 386–389 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. 117

    Huff, J., Plocik, A., Guthrie, C. & Yamamoto, K. Reciprocal intronic and exonic histone modification regions in humans. Nature Struct. Mol. Biol. 17, 1495–1499 (2010).

    CAS  Google Scholar 

  118. 118

    Saint-André, V., Batsché, E., Rachez, C. & Muchardt, C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nature Struct. Mol. Biol. 18, 337–344 (2011).

    Google Scholar 

  119. 119

    Schor, I. E., Rascovan, N., Pelisch, F., Alló, M. & Kornblihtt, A. R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl Acad. Sci. USA 106, 4325–4330 (2009).

    CAS  PubMed  Google Scholar 

  120. 120

    Ip, J. et al. Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation. Genome Res. 21, 390–401 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  121. 121

    Hein, P. P. et al. RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement. Nature Struct. Mol. Biol. 21, 794–802 (2014).

    CAS  Google Scholar 

  122. 122

    Skourti-Stathaki, K., Proudfoot, N. & Gromak, N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2- dependent termination. Mol. Cell 42, 794–805 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 123

    Ozer, A., Pagano, J. M. & Lis, J. T. New technologies provide quantum changes in the scale, speed, and success of SELEX methods and aptamer characterization. Mol. Ther. Nucleic Acids 3, e183 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. 124

    Lee, T. I. & Young, R. A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237–1251 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. 125

    Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524–528 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. 126

    Dawson, M. et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478, 529–533 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. 127

    Singh, J. & Padgett, R. Rates of in situ transcription and splicing in large human genes. Nature Struct. Mol. Biol. 16, 1128–1133 (2009).

    CAS  Google Scholar 

  128. 128

    Churchman, L. & Weissman, J. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469, 368–373 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. 129

    Yao, J., Munson, K., Webb, W. & Lis, J. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442, 1050–1053 (2006).

    CAS  Google Scholar 

  130. 130

    Boireau, S. et al. The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 179, 291–304 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  131. 131

    Brody, Y. et al. The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing. PLoS Biol. 9, e1000573 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. 132

    Darzacq, X. et al. In vivo dynamics of RNA polymerase II transcription. Nature Struct. Mol. Biol. 14, 796–806 (2007).

    CAS  Google Scholar 

  133. 133

    Tennyson, C. N., Klamut, H. J. & Worton, R. G. The human dystrophin gene requires 16 hours to be transcribed and is cotranscriptionally spliced. Nature Genet. 9, 184–190 (1995).

    CAS  PubMed  Google Scholar 

  134. 134

    Mason, P. & Struhl, K. Distinction & relationship between elongation rate & processivity of RNA polymerase II in vivo. Mol. Cell 17, 831–840 (2005).

    CAS  PubMed  Google Scholar 

  135. 135

    Ameur, A. et al. Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nature Struct. Mol. Biol. 18, 1435–1440 (2011).

    CAS  Google Scholar 

Download references

Acknowledgements

The authors thank C. Danko, F. Duarte and D. Mahat for their critical evaluation of the manuscript. J.T.L. was supported by NIGMS (National Institute of General Medical Sciences) from the US National Institutes of Health under award GM25232. I.J. was supported by a European Research Council Advanced Grant (ERCadv-671274). The content is solely the responsibility of the authors and does not necessarily represent the official views of the US National Institutes of Health or the European Research Council.

Author information

Affiliations

Authors

Corresponding author

Correspondence to John T. Lis.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides

Glossary

DRB

A small drug that inhibits P-TEFb kinase activity. It is used to characterize pausing and elongation complexes, and to measure elongation rates genome-wide.

Carboxy-terminal domain (CTD) of Pol II

The CTD of Pol II, which is positioned at the end of the largest Pol II subunit, is an unstructured, yet evolutionarily conserved, domain that comprises many tandem copies of the consensus heptapeptide YSPTSPS. Phosphorylation of these repeats is crucial for the regulation of Pol II function.

+1 nucleosome

The first well-positioned nucleosome downstream of the transcription start site, which can form a barrier for elongating Pol II and might increase Pol II promoter-proximal pausing. The position of the +1 nucleosome depends on transcription, nucleosome remodelling, and DNA sequences.

Pre-initiation complex

(PIC). A complex consisting of general transcription factors and Pol II that binds at the transcription start site, before DNA melting and transcription initiation.

Open promoters

Promoters that are nucleosome-free and easily accessible to transcription factors and Pol II. These promoters are primed for, or undergo, active transcription.

DNA melting

The process of unwinding and 'opening' double-stranded DNA at the transcription start site by general transcription factors to form a transcription bubble, which allows initiation of Pol II activity.

General transcription factors

(GTFs). Factors that bind the core promoter region, facilitate DNA melting and transcription bubble formation, and position Pol II to initiate transcription and escape the promoter region.

Enhancers

Regulatory regions that bind sequence-specific TFs and have potential transcription start sites and can interact with gene promoters three dimensionally to regulate gene expression.

Mediator

A multisubunit co-activator complex that can interact with TFs, GTFs and Pol II and is essential for transcription. Mediator has been shown to mediate interaction between enhancers and gene promoters, for example at super-enhancers.

Enhancer RNAs

(eRNAs). RNAs that derive from the transcription of enhancers. Some of these enhancer-derived RNAs contribute to enhancer function.

Histone chaperones

Proteins that facilitate the movement of Pol II through chromatin by loosening the nucleosome–DNA interactions and then restoring these in the wake of Pol II.

R-loops

An RNA–DNA hybrid structure formed during the transcription of a sequence with high GC-content that has the potential to pause Pol II. R-loops are associated with transcription termination and genome instability.

Exon skipping

A form of alternative splicing, in which an exon is 'skipped' and removed as part of the flanking introns during transcription.

MLL–ELL fusions

A fusion formed between the MLL gene (which encodes mixed-lineage leukaemia) and the ELL gene (which encodes eleven-nineteen Lys-rich leukaemia) that greatly increases the leukaemogenic potential of a cell.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jonkers, I., Lis, J. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 16, 167–177 (2015). https://doi.org/10.1038/nrm3953

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing