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.

  • Review Article
  • Published:

Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

An Author Correction to this article was published on 13 October 2022

This article has been updated

Abstract

Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some lncRNA synthesis may reflect transcriptional ‘noise’, recent studies define unique functions for either specific lncRNAs or for the process of lncRNA synthesis. Notably, the transcription, processing and metabolism of lncRNAs are regulated differently from protein-coding genes. In this Review, we provide insight into the regulation of lncRNA transcription and processing gleaned from the application of recently devised nascent transcriptomics technology. We first compare and contrast different methodologies for studying nascent transcription. We then discuss the molecular mechanisms regulating lncRNA transcription, especially transcription initiation and termination, which emphasize fundamental differences in their expression as compared with protein-coding genes. When perturbed, lncRNA misregulation leads to genomic stress such as transcription–replication conflict and R-loop-mediated DNA damage. We discuss many unresolved but important questions about the synthesis and potential functions of lncRNAs.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Unstable lncRNAs and other mammalian transcription units.
Fig. 2: Nascent RNA analysis in mammalian cells.
Fig. 3: Regulation of transcription initiation of lncRNAs.
Fig. 4: Different mechanisms of transcription termination of lncRNAs in mammals.
Fig. 5: Factors affecting pc-gene transcription readthrough.
Fig. 6: Mechanisms leading to premature transcription termination.
Fig. 7: ncRNA transcription associated with DNA damage.

Similar content being viewed by others

Change history

References

  1. Grummt, I. Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus. Genes Dev. 17, 1691–1702 (2003).

    Article  CAS  PubMed  Google Scholar 

  2. Moss, T. & Stefanovsky, V. Y. At the center of eukaryotic life. Cell 109, 545–548 (2002).

    Article  CAS  PubMed  Google Scholar 

  3. Boisvert, F. M., van Koningsbruggen, S., Navascues, J. & Lamond, A. I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574–585 (2007).

    Article  CAS  PubMed  Google Scholar 

  4. Turowski, T. W. & Tollervey, D. Transcription by RNA polymerase III: insights into mechanism and regulation. Biochem. Soc. Trans. 44, 1367–1375 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Huang, L. et al. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol. 16, 91–93 (2009).

    Article  CAS  PubMed  Google Scholar 

  6. Ream, T. S. et al. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell 33, 192–203 (2009).

    Article  CAS  PubMed  Google Scholar 

  7. Gallego-Bartolome, J. et al. Co-targeting RNA polymerases IV and V promotes efficient De Novo DNA methylation in arabidopsis. Cell 176, 1068–1082.e19 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Moir, R. D. & Willis, I. M. Regulation of pol III transcription by nutrient and stress signaling pathways. Biochim. Biophys. Acta 1829, 361–375 (2013).

    Article  CAS  PubMed  Google Scholar 

  9. Pombo, A. et al. Regional specialization in human nuclei: visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 18, 2241–2253 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Proudfoot, N. J., Furger, A. & Dye, M. J. Integrating mRNA processing with transcription. Cell 108, 501–512 (2002).

    Article  CAS  PubMed  Google Scholar 

  11. Peck, S. A., Hughes, K. D., Victorino, J. F. & Mosley, A. L. Writing a wrong: coupled RNA polymerase II transcription and RNA quality control. Wiley Interdiscip. Rev. RNA 10, e1529 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  12. Wickramasinghe, V. O. & Laskey, R. A. Control of mammalian gene expression by selective mRNA export. Nat. Rev. Mol. Cell Biol. 16, 431–442 (2015).

    Article  CAS  PubMed  Google Scholar 

  13. Statello, L., Guo, C. J., Chen, L. L. & Huarte, M. Gene regulation by long non-coding RNAs and its biological functions. Nat. Rev. Mol. Cell Biol. 22, 96–118 (2021).

    Article  CAS  PubMed  Google Scholar 

  14. Treiber, T., Treiber, N. & Meister, G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat. Rev. Mol. Cell Biol. 20, 5–20 (2019).

    Article  CAS  PubMed  Google Scholar 

  15. Ozata, D. M., Gainetdinov, I., Zoch, A., O’Carroll, D. & Zamore, P. D. PIWI-interacting RNAs: small RNAs with big functions. Nat. Rev. Genet. 20, 89–108 (2019).

    Article  CAS  PubMed  Google Scholar 

  16. Morais, P., Adachi, H. & Yu, Y. T. Spliceosomal snRNA epitranscriptomics. Front. Genet. 12, 652129 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Hon, C. C. et al. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature 543, 199–204 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Fang, S. et al. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res. 46, D308–D314 (2018).

    Article  CAS  PubMed  Google Scholar 

  20. Clark, M. B. et al. Genome-wide analysis of long noncoding RNA stability. Genome Res. 22, 885–898 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Schlackow, M. et al. Distinctive patterns of transcription and RNA Processing for Human lincRNAs. Mol. Cell 65, 25–38 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ulitsky, I. & Bartel, D. P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Pefanis, E. et al. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 161, 774–789 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Andersson, R. et al. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat. Commun. 5, 5336 (2014).

    Article  CAS  PubMed  Google Scholar 

  25. Kamieniarz-Gdula, K. & Proudfoot, N. J. Transcriptional control by premature termination: a forgotten mechanism. Trends Genet. 35, 553–564 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Wu, M. et al. The RNA exosome shapes the expression of key protein-coding genes. Nucleic Acids Res. 48, 8509–8528 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. West, S., Gromak, N. & Proudfoot, N. J. Human 5′ -> 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432, 522–525 (2004).

    Article  CAS  PubMed  Google Scholar 

  28. Proudfoot, N. J. Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science 352, aad9926 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Eaton, J. D. & West, S. An end in sight? Xrn2 and transcriptional termination by RNA polymerase II. Transcription 9, 321–326 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Stark, R., Grzelak, M. & Hadfield, J. RNA sequencing: the teenage years. Nat. Rev. Genet. 20, 631–656 (2019).

    Article  CAS  PubMed  Google Scholar 

  32. Elion, E. A. & Warner, J. R. An RNA polymerase I enhancer in Saccharomyces cerevisiae. Mol. Cell. Biol. 6, 2089–2097 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Birse, C. E., Minvielle-Sebastia, L., Lee, B. A., Keller, W. & Proudfoot, N. J. Coupling termination of transcription to messenger RNA maturation in yeast. Science 280, 298–301 (1998).

    Article  CAS  PubMed  Google Scholar 

  34. Birse, C. E., Lee, B. A., Hansen, K. & Proudfoot, N. J. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J. 16, 3633–3643 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Dye, M. J. & Proudfoot, N. J. Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II. Cell 105, 669–681 (2001).

    Article  CAS  PubMed  Google Scholar 

  36. Groudine, M., Eisenman, R. & Weintraub, H. Chromatin structure of endogenous retroviral genes and activation by an inhibitor of DNA methylation. Nature 292, 311–317 (1981).

    Article  CAS  PubMed  Google Scholar 

  37. Core, L. J. & Lis, J. T. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 319, 1791–1792 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Chu, T. et al. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nat. Genet. 50, 1553–1564 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Barbieri, E. et al. Rapid and scalable profiling of nascent RNA with fastGRO. Cell Rep. 33, 108373 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Windhager, L. et al. Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res 22, 2031–2042 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Schwalb, B. et al. TT-seq maps the human transient transcriptome. Science 352, 1225–1228 (2016).

    Article  CAS  PubMed  Google Scholar 

  43. Herzog, V. A. et al. Thiol-linked alkylation of RNA to assess expression dynamics. Nat. Methods 14, 1198–1204 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Schofield, J. A., Duffy, E. E., Kiefer, L., Sullivan, M. C. & Simon, M. D. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nat. Methods 15, 221–225 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  46. Mayer, A. et al. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell 161, 541–554 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  48. Nojima, T. et al. Mammalian NET-Seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161, 526–540 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Kindgren, P., Ivanov, M. & Marquardt, S. Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis. Nucleic Acids Res. 48, 2332–2347 (2020).

    Article  CAS  PubMed  Google Scholar 

  50. Zhu, J., Liu, M., Liu, X. & Dong, Z. RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis. Nat. Plants 4, 1112–1123 (2018).

    Article  CAS  PubMed  Google Scholar 

  51. Zaborowska, J., Egloff, S. & Murphy, S. The pol II CTD: new twists in the tail. Nat. Struct. Mol. Biol. 23, 771–777 (2016).

    Article  CAS  PubMed  Google Scholar 

  52. Harlen, K. M. & Churchman, L. S. The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat. Rev. Mol. Cell Biol. 18, 263–273 (2017).

    Article  CAS  PubMed  Google Scholar 

  53. Bentley, D. L. Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163–175 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Chen, Y. et al. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat. Genet. 48, 984–994 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Sousa-Luis, R. et al. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. Mol. Cell 81, 1935–1950.e6 (2021). New technologies to profile full-length, nascent transcripts, highlighting co-transcriptional RNA cleavage and splicing kinetics.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Hirabayashi, S. et al. NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements. Nat. Genet. 51, 1369–1379 (2019).

    Article  CAS  PubMed  Google Scholar 

  58. Jiao, X. et al. 5′ end nicotinamide adenine dinucleotide cap in human cells promotes RNA Decay through DXO-Mediated deNADding. Cell 168, 1015–1027.e10 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Wissink, E. M., Vihervaara, A., Tippens, N. D. & Lis, J. T. Nascent RNA analyses: tracking transcription and its regulation. Nat. Rev. Genet. 20, 705–723 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Lim, B. Imaging transcriptional dynamics. Curr. Opin. Biotechnol. 52, 49–55 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Shah, S. et al. Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Cell 174, 363–376.e16 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Wan, Y. et al. Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell 184, 2878–2895.e20 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Chen, B. et al. Live cell imaging and proteomic profiling of endogenous NEAT1 lncRNA by CRISPR/Cas9-mediated knock-in. Protein Cell 11, 641–660 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Uszczynska-Ratajczak, B., Lagarde, J., Frankish, A., Guigo, R. & Johnson, R. Towards a complete map of the human long non-coding RNA transcriptome. Nat. Rev. Genet. 19, 535–548 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. So, B. R. & Dreyfuss, G. Myriad RNAs and RNA-binding proteins control cell functions, explain diseases, and guide new therapies. Cold Spring Harb. Symp. Quant. Biol. 84, 239–242 (2019).

    Article  PubMed  Google Scholar 

  66. Quinodoz, S. A. et al. RNA promotes the formation of spatial compartments in the nucleus. Cell 184, 5775–5790.e30 (2021).

    Article  CAS  PubMed  Google Scholar 

  67. Markaki, Y. et al. Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell 184, 6174–6192.e32 (2021).

    Article  CAS  PubMed  Google Scholar 

  68. Hallegger, M. et al. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 184, 4680–4696.e22 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Bhat, P., Honson, D. & Guttman, M. Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nat. Rev. Mol. Cell Biol. 22, 653–670 (2021).

    Article  CAS  PubMed  Google Scholar 

  70. Roden, C. & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).

    Article  CAS  PubMed  Google Scholar 

  71. Zaret, K. S. Pioneer transcription factors initiating gene network changes. Annu Rev. Genet 54, 367–385 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Lim, B. & Levine, M. S. Enhancer-promoter communication: hubs or loops? Curr. Opin. Genet Dev. 67, 5–9 (2021).

    Article  CAS  PubMed  Google Scholar 

  73. Preker, P. et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 322, 1851–1854 (2008).

    Article  CAS  PubMed  Google Scholar 

  74. Li, W., Notani, D. & Rosenfeld, M. G. Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat. Rev. Genet. 17, 207–223 (2016).

    Article  CAS  PubMed  Google Scholar 

  75. Duina, A. A. Histone chaperones Spt6 and FACT: similarities and differences in modes of action at transcribed genes. Genet Res. Int. 2011, 625210 (2011).

    PubMed  PubMed Central  Google Scholar 

  76. Doris, S. M. et al. Spt6 is required for the fidelity of promoter selection. Mol. Cell 72, 687–699.e6 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Hainer, S. J. et al. Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev. 29, 362–378 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Whitehouse, I., Rando, O. J., Delrow, J. & Tsukiyama, T. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450, 1031–1035 (2007).

    Article  CAS  PubMed  Google Scholar 

  79. Marquardt, S. et al. A chromatin-based mechanism for limiting divergent noncoding transcription. Cell 157, 1712–1723 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Garcia-Muse, T. & Aguilera, A. R loops: from physiological to pathological roles. Cell 179, 604–618 (2019).

    Article  CAS  PubMed  Google Scholar 

  81. Skourti-Stathaki, K. & Proudfoot, N. J. A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression. Genes Dev. 28, 1384–1396 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Chen, L. et al. R-ChIP using inactive RNase H reveals dynamic coupling of r-loops with transcriptional pausing at gene promoters. Mol. Cell 68, 745–757.e5 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Tan-Wong, S. M., Dhir, S. & Proudfoot, N. J. R-loops promote antisense transcription across the mammalian genome. Mol. Cell 76, 600–616.e6 (2019). Discovery that many lncRNAs derive from R-loop-associated Pol II promoter activity.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Mele, M. et al. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res. 27, 27–37 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Sun, Y. et al. Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proc. Natl Acad. Sci. USA 115, E1419–E1428 (2018). Cryo-EM 3D structure of CPSF directly interacting with a PAS.

    CAS  PubMed  Google Scholar 

  86. Clerici, M., Faini, M., Muckenfuss, L. M., Aebersold, R. & Jinek, M. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat. Struct. Mol. Biol. 25, 135–138 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Eaton, J. D. & West, S. Termination of transcription by RNA polymerase II: BOOM! Trends Genet. 36, 664–675 (2020).

    Article  CAS  PubMed  Google Scholar 

  88. Cortazar, M. A. et al. Control of RNA Pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism. Mol. Cell 76, 896–908.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Hu, S. et al. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape. Mol. Cell 81, 4425–4439.e6 (2021).

    Article  CAS  PubMed  Google Scholar 

  90. Eaton, J. D., Francis, L., Davidson, L. & West, S. A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes. Genes Dev. 34, 132–145 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Parua, P. K. et al. A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II. Nature 558, 460–464 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Kecman, T. et al. Elongation/termination factor exchange mediated by PP1 phosphatase orchestrates transcription termination. Cell Rep. 25, 259–269.e5 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Mischo, H. E. & Proudfoot, N. J. Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. Biochim. Biophys. Acta 1829, 174–185 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Vasiljeva, L., Kim, M., Mutschler, H., Buratowski, S. & Meinhart, A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat. Struct. Mol. Biol. 15, 795–804 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Vasiljeva, L. & Buratowski, S. Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol. Cell 21, 239–248 (2006).

    Article  CAS  PubMed  Google Scholar 

  96. Mischo, H. E. et al. Yeast Sen1 helicase protects the genome from transcription-associated instability. Mol. Cell 41, 21–32 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Grzechnik, P., Gdula, M. R. & Proudfoot, N. J. Pcf11 orchestrates transcription termination pathways in yeast. Genes Dev. 29, 849–861 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Hatchi, E. et al. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol. Cell 57, 636–647 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  101. Rondon, A. G., Mischo, H. E., Kawauchi, J. & Proudfoot, N. J. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol. Cell 36, 88–98 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Nedea, E. et al. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3′-ends. J. Biol. Chem. 278, 33000–33010 (2003).

    Article  CAS  PubMed  Google Scholar 

  103. Lidschreiber, M. et al. The APT complex is involved in non-coding RNA transcription and is distinct from CPF. Nucleic Acids Res. 46, 11528–11538 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Baillat, D. et al. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005). Purification of the Integrator complex, showing its role in U snRNA 3′-end formation.

    Article  CAS  PubMed  Google Scholar 

  105. Kirstein, N., Gomes Dos Santos, H., Blumenthal, E. & Shiekhattar, R. The Integrator complex at the crossroad of coding and noncoding RNA. Curr. Opin. Cell Biol. 70, 37–43 (2021).

    Article  CAS  PubMed  Google Scholar 

  106. Egloff, S. et al. Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 318, 1777–1779 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Egloff, S. Role of Ser7 phosphorylation of the CTD during transcription of snRNA genes. RNA Biol. 9, 1033–1038 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Egloff, S. et al. The integrator complex recognizes a new double mark on the RNA polymerase II carboxyl-terminal domain. J. Biol. Chem. 285, 20564–20569 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Fianu, I. et al. Structural basis of Integrator-mediated transcription regulation. Science 374, 883–887 (2021).

    Article  CAS  PubMed  Google Scholar 

  110. Lai, F., Gardini, A., Zhang, A. & Shiekhattar, R. Integrator mediates the biogenesis of enhancer RNAs. Nature 525, 399–403 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Nojima, T. et al. Deregulated expression of mammalian lncRNA through Loss of SPT6 induces R-loop formation, replication stress, and cellular senescence. Mol. Cell 72, 970–984.e7 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Barra, J. et al. Integrator restrains paraspeckles assembly by promoting isoform switching of the lncRNA NEAT1. Sci. Adv. 6, eaaz9072 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Lykke-Andersen, S. et al. Integrator is a genome-wide attenuator of non-productive transcription. Mol. Cell 81, 514–529.e6 (2021).

    Article  CAS  PubMed  Google Scholar 

  114. Beckedorff, F. et al. The human integrator complex facilitates transcriptional elongation by endonucleolytic cleavage of nascent transcripts. Cell Rep. 32, 107917 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Austenaa, L. M. et al. Transcription of mammalian cis-regulatory elements is restrained by actively enforced early termination. Mol. Cell 60, 460–474 (2015). This article shows the role of Restrictor subunit WDR82 in mammalian lncRNA termination.

    Article  CAS  PubMed  Google Scholar 

  116. Brewer-Jensen, P. et al. Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination. RNA 22, 139–154 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Searles, L. L. & Voelker, R. A. Molecular characterization of the Drosophila vermilion locus and its suppressible alleles. Proc. Natl Acad. Sci. USA 83, 404–408 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Austenaa, L. M. I. et al. A first exon termination checkpoint preferentially suppresses extragenic transcription. Nat. Struct. Mol. Biol. 28, 337–346 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Estell, C., Davidson, L., Steketee, P. C., Monier, A. & West, S. ZC3H4 restricts non-coding transcription in human cells. eLife 10, e67305 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Ghazal, G. et al. Yeast RNase III triggers polyadenylation-independent transcription termination. Mol. Cell 36, 99–109 (2009).

    Article  CAS  PubMed  Google Scholar 

  121. Kawauchi, J., Mischo, H., Braglia, P., Rondon, A. & Proudfoot, N. J. Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination. Genes Dev. 22, 1082–1092 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Morlando, M. et al. Primary microRNA transcripts are processed co-transcriptionally. Nat. Struct. Mol. Biol. 15, 902–909 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Ballarino, M. et al. Coupled RNA processing and transcription of intergenic primary microRNAs. Mol. Cell. Biol. 29, 5632–5638 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Dhir, A., Dhir, S., Proudfoot, N. J. & Jopling, C. L. Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. Nat. Struct. Mol. Biol. 22, 319–327 (2015). Shows the role of Microprocessor in lncRNA termination.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Eaton, J. D. et al. Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity. Genes Dev. 32, 127–139 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Hintermair, C. et al. Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation. EMBO J. 31, 2784–2797 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Nemec, C. M. et al. Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner. Proc. Natl Acad. Sci. USA 114, E3944–E3953 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Harlen, K. M. et al. Comprehensive RNA Polymerase II interactomes reveal distinct and varied roles for each phospho-CTD Residue. Cell Rep. 15, 2147–2158 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Jasnovidova, O., Krejcikova, M., Kubicek, K. & Stefl, R. Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p. EMBO Rep. 18, 906–913 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13, 67–76 (2004).

    Article  CAS  PubMed  Google Scholar 

  131. Sanchez, A. M., Shuman, S. & Schwer, B. RNA polymerase II CTD interactome with 3′ processing and termination factors in fission yeast and its impact on phosphate homeostasis. Proc. Natl Acad. Sci. USA 115, E10652–E10661 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Kamieniarz-Gdula, K. et al. Selective roles of vertebrate PCF11 in premature and full-length transcript termination. Mol. Cell 74, 158–172.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Schuller, R. et al. Heptad-specific phosphorylation of RNA polymerase II CTD. Mol. Cell 61, 305–314 (2016).

    Article  PubMed  Google Scholar 

  134. Yurko, N. M. & Manley, J. L. The RNA polymerase II CTD “orphan” residues: emerging insights into the functions of Tyr-1, Thr-4, and Ser-7. Transcription 9, 30–40 (2018).

    Article  CAS  PubMed  Google Scholar 

  135. Collin, P., Jeronimo, C., Poitras, C. & Robert, F. RNA polymerase II CTD tyrosine 1 is required for efficient termination by the Nrd1-Nab3-Sen1 pathway. Mol. Cell 73, 655–669.e7 (2019).

    Article  CAS  PubMed  Google Scholar 

  136. Descostes, N. et al. Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells. eLife 3, e02105 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  137. Shah, N. et al. Tyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals. Mol. Cell 69, 48–61.e6 (2018).

    Article  CAS  PubMed  Google Scholar 

  138. Shearwin, K. E., Callen, B. P. & Egan, J. B. Transcriptional interference-a crash course. Trends Genet. 21, 339–345 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. DeGennaro, C. M. et al. Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol. Cell. Biol. 33, 4779–4792 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Bortvin, A. & Winston, F. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272, 1473–1476 (1996).

    Article  CAS  PubMed  Google Scholar 

  141. Zumer, K. et al. Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Mol. Cell 81, 3096–3109.e8 (2021).

    Article  CAS  PubMed  Google Scholar 

  142. Narain, A. et al. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol. Cell 81, 3110–3127.e14 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Arnold, M., Bressin, A., Jasnovidova, O., Meierhofer, D. & Mayer, A. A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3′-processing and termination. Mol. Cell 81, 3589–3603.e13 (2021).

    Article  CAS  PubMed  Google Scholar 

  144. Yoh, S. M., Lucas, J. S. & Jones, K. A. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev. 22, 3422–3434 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Rutkowski, A. J. et al. Widespread disruption of host transcription termination in HSV-1 infection. Nat. Commun. 6, 7126 (2015). First description of host genome termination defects caused by HSV-1 infection.

    Article  PubMed  Google Scholar 

  146. Hennig, T. et al. HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes. PLoS Pathog. 14, e1006954 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  147. Wyler, E. et al. Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection. Genome Biol. 18, 209 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  148. Wang, X. et al. Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27. Nat. Commun. 11, 293 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  149. Chen, I. H., Sciabica, K. S. & Sandri-Goldin, R. M. ICP27 interacts with the RNA export factor Aly/REF to direct herpes simplex virus type 1 intronless mRNAs to the TAP export pathway. J. Virol. 76, 12877–12889 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Hardy, W. R. & Sandri-Goldin, R. M. Herpes simplex virus inhibits host cell splicing, and regulatory protein ICP27 is required for this effect. J. Virol. 68, 7790–7799 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Sciabica, K. S., Dai, Q. J. & Sandri-Goldin, R. M. ICP27 interacts with SRPK1 to mediate HSV splicing inhibition by altering SR protein phosphorylation. EMBO J. 22, 1608–1619 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Tang, S., Patel, A. & Krause, P. R. Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner. Proc. Natl Acad. Sci. USA 113, 12256–12261 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Nojima, T. et al. Herpesvirus protein ICP27 switches PML isoform by altering mRNA splicing. Nucleic Acids Res. 37, 6515–6527 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Bauer, D. L. V. et al. Influenza virus mounts a two-pronged attack on host RNA polymerase II transcription. Cell Rep. 23, 2119–2129.e3 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Nemeroff, M. E., Barabino, S. M., Li, Y., Keller, W. & Krug, R. M. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3′end formation of cellular pre-mRNAs. Mol. Cell 1, 991–1000 (1998).

    Article  CAS  PubMed  Google Scholar 

  156. Vilborg, A., Passarelli, M. C., Yario, T. A., Tycowski, K. T. & Steitz, J. A. Widespread inducible transcription downstream of human genes. Mol. Cell 59, 449–461 (2015). Discovery that cellular stress can induce Pol II termination defects.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Rosa-Mercado, N. A. et al. Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Mol. Cell 81, 502–513.e4 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Grosso, A. R. et al. Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. eLife 4, e09214 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  159. Maher, C. A. et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 458, 97–101 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Kannan, K. et al. Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proc. Natl Acad. Sci. USA 108, 9172–9177 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Frye, M., Harada, B. T., Behm, M. & He, C. RNA modifications modulate gene expression during development. Science 361, 1346–1349 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Anreiter, I., Mir, Q., Simpson, J. T., Janga, S. C. & Soller, M. New twists in detecting mRNA modification dynamics. Trends Biotechnol. 39, 72–89 (2021).

    Article  CAS  PubMed  Google Scholar 

  163. Jonkhout, N. et al. The RNA modification landscape in human disease. RNA 23, 1754–1769 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Ke, S. et al. m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 31, 990–1006 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Pontier, D. et al. The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci. Alliance 2, e201900393 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  166. Parker, M. T. et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife 9, e49658 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Kasowitz, S. D. et al. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 14, e1007412 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Larke, M. S. C. et al. Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Mol. Cell 81, 983–997.e7 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Thomas, Q. A. et al. Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis. Nat. Commun. 11, 2589 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Kaida, D. et al. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468, 664–668 (2010). U1 snRNA blocks premature intronic polyadenylation genome-wide, called telescripting.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  172. Berg, M. G. et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150, 53–64 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  173. Oh, J. M. et al. U1 snRNP telescripting regulates a size-function-stratified human genome. Nat. Struct. Mol. Biol. 24, 993–999 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  174. So, B. R. et al. A complex of U1 snRNP with cleavage and polyadenylation factors controls telescripting, regulating mRNA transcription in human cells. Mol. Cell 76, 590–599.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Almada, A. E., Wu, X., Kriz, A. J., Burge, C. B. & Sharp, P. A. Promoter directionality is controlled by U1 snRNP and polyadenylation signals. Nature 499, 360–363 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Ntini, E. et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat. Struct. Mol. Biol. 20, 923–928 (2013).

    Article  CAS  PubMed  Google Scholar 

  177. Gregersen, L. H. et al. SCAF4 and SCAF8, mRNA anti-terminator proteins. Cell 177, 1797–1813.e18 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  178. Shi, Y. & Manley, J. L. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev. 29, 889–897 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Wang, R., Zheng, D., Wei, L., Ding, Q. & Tian, B. Regulation of intronic polyadenylation by PCF11 impacts mRNA expression of long genes. Cell Rep. 26, 2766–2778.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. Liu, H., Liu, K. & Dong, Z. Targeting CDK12 for cancer therapy: function, mechanism, and drug discovery. Cancer Res. 81, 18–26 (2021).

    Article  CAS  PubMed  Google Scholar 

  181. Chou, J., Quigley, D. A., Robinson, T. M., Feng, F. Y. & Ashworth, A. Transcription-associated cyclin-dependent kinases as targets and biomarkers for cancer therapy. Cancer Discov. 10, 351–370 (2020).

    Article  CAS  PubMed  Google Scholar 

  182. Tellier, M. et al. CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Res. 48, 7712–7727 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Krajewska, M. et al. CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation. Nat. Commun. 10, 1757 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  184. Kotake, Y. et al. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol. 3, 570–575 (2007).

    Article  CAS  PubMed  Google Scholar 

  185. Caizzi, L. et al. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol. Cell 81, 1920–1934.e9 (2021).

    Article  CAS  PubMed  Google Scholar 

  186. Elrod, N. D. et al. The integrator complex attenuates promoter-proximal transcription at protein-coding genes. Mol. Cell 76, 738–752.e7 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Tatomer, D. C. et al. The Integrator complex cleaves nascent mRNAs to attenuate transcription. Genes Dev. 33, 1525–1538 (2019). Integrator promotes nascent RNA cleavage to induce PTT in Drosophila melanogaster.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  188. Skaar, J. R. et al. The Integrator complex controls the termination of transcription at diverse classes of gene targets. Cell Res. 25, 288–305 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Zheng, H. et al. Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase. Science 370, eabb5872 (2020).

    Article  CAS  PubMed  Google Scholar 

  190. Huang, K. L. et al. Integrator recruits protein phosphatase 2A to prevent pause release and facilitate transcription termination. Mol. Cell 80, 345–358.e9 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Vervoort, S. J. et al. The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 184, 3143–3162.e32 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Natoli, G. & Andrau, J. C. Noncoding transcription at enhancers: general principles and functional models. Annu. Rev. Genet 46, 1–19 (2012).

    Article  CAS  PubMed  Google Scholar 

  193. Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  194. De Santa, F. et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 8, e1000384 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  195. Shlyueva, D., Stampfel, G. & Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 15, 272–286 (2014).

    Article  CAS  PubMed  Google Scholar 

  196. Cinghu, S. et al. Intragenic enhancers attenuate host gene expression. Mol. Cell 68, 104–117.e6 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Swamynathan, S. K. & Piatigorsky, J. Orientation-dependent influence of an intergenic enhancer on the promoter activity of the divergently transcribed mouse Shsp/alpha B-crystallin and Mkbp/HspB2 genes. J. Biol. Chem. 277, 49700–49706 (2002).

    Article  CAS  PubMed  Google Scholar 

  198. Ortega, P., Merida-Cerro, J. A., Rondon, A. G., Gomez-Gonzalez, B. & Aguilera, A. DNA-RNA hybrids at DSBs interfere with repair by homologous recombination. eLife 10, e69881 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Scully, R., Panday, A., Elango, R. & Willis, N. A. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat. Rev. Mol. Cell Biol. 20, 698–714 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Francia, S. et al. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488, 231–235 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  201. Ketley, R. F. & Gullerova, M. Jack of all trades? The versatility of RNA in DNA double-strand break repair. Essays Biochem. 64, 721–735 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  202. Burger, K., Schlackow, M. & Gullerova, M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res. 47, 3467–3484 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Pessina, F. et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 21, 1286–1299 (2019). DNA DSBs initiate Pol II transcription to promote DNA repair.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  204. Vitor, A. C. et al. Single-molecule imaging of transcription at damaged chromatin. Sci. Adv. 5, eaau1249 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  205. Storici, F., Bebenek, K., Kunkel, T. A., Gordenin, D. A. & Resnick, M. A. RNA-templated DNA repair. Nature 447, 338–341 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Keskin, H. et al. Transcript-RNA-templated DNA recombination and repair. Nature 515, 436–439 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  207. Wei, W. et al. A role for small RNAs in DNA double-strand break repair. Cell 149, 101–112 (2012).

    Article  CAS  PubMed  Google Scholar 

  208. Michalik, K. M., Bottcher, R. & Forstemann, K. A small RNA response at DNA ends in Drosophila. Nucleic Acids Res. 40, 9596–9603 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  209. Hatchi, E. et al. BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature 591, 665–670 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Sikorski, T. W. et al. Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol. Cell 44, 397–409 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. D’Alessandro, G. et al. BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment. Nat. Commun. 9, 5376 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  212. Lu, W. T. et al. Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair. Nat. Commun. 9, 532 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  213. Ohle, C. et al. Transient RNA-DNA hybrids are required for efficient double-strand break repair. Cell 167, 1001–1013.e7 (2016).

    Article  CAS  PubMed  Google Scholar 

  214. Liu, S. et al. RNA polymerase III is required for the repair of DNA double-strand breaks by homologous recombination. Cell 184, 1314–1329.e10 (2021).

    Article  CAS  PubMed  Google Scholar 

  215. Gomez-Gonzalez, B. & Aguilera, A. Transcription-mediated replication hindrance: a major driver of genome instability. Genes Dev. 33, 1008–1026 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Teloni, F. et al. Efficient Pre-mRNA cleavage prevents replication-stress-associated genome instability. Mol. Cell 73, 670–683.e12 (2019). This study demonstrates interconnections between DNA replication, pre-mRNA 3′-end cleavage and DNA damage.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  217. Macheret, M. & Halazonetis, T. D. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress. Nature 555, 112–116 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  218. Bayona-Feliu, A., Barroso, S., Munoz, S. & Aguilera, A. The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts. Nat. Genet 53, 1050–1063 (2021).

    Article  CAS  PubMed  Google Scholar 

  219. Wong, A. K. et al. BRG1, a component of the SWI-SNF complex, is mutated in multiple human tumor cell lines. Cancer Res. 60, 6171–6177 (2000).

    CAS  PubMed  Google Scholar 

  220. Centore, R. C., Sandoval, G. J., Soares, L. M. M., Kadoch, C. & Chan, H. M. Mammalian SWI/SNF chromatin remodeling complexes: emerging mechanisms and therapeutic strategies. Trends Genet. 36, 936–950 (2020).

    Article  CAS  PubMed  Google Scholar 

  221. Archacki, R. et al. Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res. 45, 3116–3129 (2017).

    CAS  PubMed  Google Scholar 

  222. Drexler, H. L., Choquet, K. & Churchman, L. S. Splicing kinetics and coordination revealed by direct nascent RNA sequencing through nanopores. Mol. Cell 77, 985–998.e8 (2020).

    Article  CAS  PubMed  Google Scholar 

  223. Herzel, L., Straube, K. & Neugebauer, K. M. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res. 28, 1008–1019 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Oesterreich, F. C. et al. Splicing of nascent RNA coincides with intron exit from RNA Polymerase II. Cell 165, 372–381 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  225. Reimer, K. A., Mimoso, C. A., Adelman, K. & Neugebauer, K. M. Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis. Mol. Cell 81, 998–1012.e7 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. Maier, K. C., Gressel, S., Cramer, P. & Schwalb, B. Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms. Genome Res. 30, 1332–1344 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Liu, H. et al. Accurate detection of m6A RNA modifications in native RNA sequences. Nat. Commun. 10, 4079 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  228. Shi, J. et al. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat. Cell Biol. 23, 424–436 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are indebted to L. Vasilieva, S. West, K. Kamieniarz-Gdula and H. Mischo for advice on this Review. The N.J.P. laboratory was supported by grants from the European Research Council (Advanced Grant no. 339170), the Wellcome Trust (Investigator Award no. 107928/Z/15/Z) and currently by the Wellcome Trust (Investigator Award no. 219443/Z/19/Z). The T.N. laboratory is supported by MEXT/JSPS Kakenhi (no. 19K24692) and JST FOREST program (no. JPMJFR2050). The authors apologize for not citing all the literature in this ever-expanding research area due to space limitations.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of the article.

Corresponding authors

Correspondence to Takayuki Nojima or Nick J. Proudfoot.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Molecular Cell Biology thanks Stephen Buratowski, Sebastian Marquardt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Glossary

Small nuclear RNA

(snRNA). Non-coding nuclear RNAs of about 150 nt. Uridine (U)-rich snRNAs are core components of the spliceosome; other snRNAs function in RNA processing and transcription regulation.

Steady-state RNA levels

Levels of fully processed RNA, determined by a balance between synthesis and degradation.

Functional PAS

Functional polyadenylation sites (PAS) recruit cleavage and polyadenylation complex to transcript 3′ end sites.

Cryptic PAS

Polyadenylation sites (PAS) that are generally inactive and located within protein-coding gene introns. Splicing disruption can activate cryptic PAS.

Nascent RNA

The initial transcript made by RNA polymerase, which has not yet undergone processing.

Torpedo mechanism

Following 3′-end RNA cleavage, the 5′ product is released as polyadenylated mRNA, leaving the 3′ product still attached to elongating polymerase II (Pol II). This product is degraded 5′-3′ by 5′-3′ exoribonuclease 2 (XRN2); if XRN2 reaches Pol II, it somehow triggers Pol II release from DNA.

Template switching

During cDNA synthesis, reverse transcriptase adds untemplated nucleotides (usually CCC) to the cDNA 3′ end, to which an adaptor with 3′ GGG can hybridize to prime the synthesis of the complementary DNA strand.

Transcription foci

Nuclear particles (often condensates) in which RNA synthesis has just occurred that then recruit further multiple chromatin-associated RNA and RNA-binding proteins together with the polymerase II elongation complex forming a membrane-less particle.

Pioneer transcription factors

Factors that are capable of directly binding DNA sequences buried within compact chromatin. Upon binding, they recruit chromatin remodelling and modification factors to allow chromatin opening and gene expression.

General transcription factors

(GTFs). Factors that bind DNA cooperatively to form a multisubunit complex at gene promoters, resulting in polymerase II recruitment and the formation of a pre-initiation complex.

Enhancer RNAs

(eRNAs). RNAs synthesized by Pol II at nucleosome depleted regions of enhancers. Enhancers display bidirectional promoter activity in synthesising eRNA.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Nojima, T., Proudfoot, N.J. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 23, 389–406 (2022). https://doi.org/10.1038/s41580-021-00447-6

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41580-021-00447-6

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