Causes and consequences of rna polymerase ii stalling during transcript elongation

ABSTRACT The journey of RNA polymerase II (Pol II) as it transcribes a gene is anything but a smooth ride. Transcript elongation is discontinuous and can be perturbed by intrinsic regulatory

barriers, such as promoter-proximal pausing, nucleosomes, RNA secondary structures and the underlying DNA sequence. More substantial blocking of Pol II translocation can be caused by other

physiological circumstances and extrinsic obstacles, including other transcribing polymerases, the replication machinery and several types of DNA damage, such as bulky lesions and DNA

double-strand breaks. Although numerous different obstacles cause Pol II stalling or arrest, the cell somehow distinguishes between them and invokes different mechanisms to resolve each

roadblock. Resolution of Pol II blocking can be as straightforward as temporary backtracking and transcription elongation factor S-II (TFIIS)-dependent RNA cleavage, or as drastic as

premature transcription termination or degradation of polyubiquitylated Pol II and its associated nascent RNA. In this Review, we discuss the current knowledge of how these different Pol II

stalling contexts are distinguished by the cell, how they overlap with each other, how they are resolved and how, when unresolved, they can cause genome instability. Access through your

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RNA POLYMERASE CLAMP TO DISRUPT POST-TERMINATION COMPLEXES AND PREVENT CYTOTOXIC R-LOOP FORMATION Article 08 January 2025 RNA 3′END TAILING SAFEGUARDS CELLS AGAINST PRODUCTS OF PERVASIVE

TRANSCRIPTION TERMINATION Article Open access 01 December 2024 MECHANISM OF POLYADENYLATION-INDEPENDENT RNA POLYMERASE II TERMINATION Article Open access 18 October 2024 REFERENCES *

Bentley, D. L. & Groudine, M. A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells. _Nature_ 321, 702–706 (1986). CAS  PubMed 

Google Scholar  * Eick, D. & Bornkamm, G. W. Transcriptional arrest within the first exon is a fast control mechanism in c-myc gene expression. _Nucleic Acids Res._ 14, 8331–8346 (1986).

CAS  PubMed  PubMed Central  Google Scholar  * Core, L. & Adelman, K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. _Genes Dev._ 33, 960–982 (2019). CAS 

PubMed  PubMed Central  Google Scholar  * Garcia-Muse, T. & Aguilera, A. Transcription-replication conflicts: how they occur and how they are resolved. _Nat. Rev. Mol. Cell Biol._ 17,

553–563 (2016). CAS  PubMed  Google Scholar  * Martinez-Rucobo, F. W. & Cramer, P. Structural basis of transcription elongation. _Biochim. Biophys. Acta_ 1829, 9–19 (2013). CAS  PubMed 

Google Scholar  * Kilchert, C., Wittmann, S. & Vasiljeva, L. The regulation and functions of the nuclear RNA exosome complex. _Nat. Rev. Mol. Cell Biol._ 17, 227–239 (2016). CAS  PubMed

  Google Scholar  * Dangkulwanich, M. et al. Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism. _eL__ife_ 2,

e00971 (2013). PubMed  PubMed Central  Google Scholar  * Nudler, E. RNA polymerase backtracking in gene regulation and genome instability. _Cell_ 149, 1438–1445 (2012). CAS  PubMed  Google

Scholar  * Bar-Nahum, G. et al. A ratchet mechanism of transcription elongation and its control. _Cell_ 120, 183–193 (2005). CAS  PubMed  Google Scholar  * Abbondanzieri, E. A., Greenleaf,

W. J., Shaevitz, J. W., Landick, R. & Block, S. M. Direct observation of base-pair stepping by RNA polymerase. _Nature_ 438, 460–465 (2005). CAS  PubMed  PubMed Central  Google Scholar 

* Liu, X., Bushnell, D. A. & Kornberg, R. D. RNA polymerase II transcription: structure and mechanism. _Biochim. Biophys. Acta_ 1829, 2–8 (2013). CAS  PubMed  Google Scholar  *

Brueckner, F. et al. Structure-function studies of the RNA polymerase II elongation complex. _Acta Crystallogr. D Biol. Crystallogr._ 65, 112–120 (2009). CAS  PubMed  PubMed Central  Google

Scholar  * Adelman, K. et al. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. _Proc. Natl Acad. Sci. USA_ 99, 13538–13543 (2002). CAS  PubMed  PubMed

Central  Google Scholar  * Galburt, E. A. et al. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. _Nature_ 446, 820–823 (2007). CAS  PubMed  Google

Scholar  * Ishibashi, T. et al. Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics. _Proc. Natl Acad. Sci. USA_

111, 3419–3424 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Conaway, R. C. & Conaway, J. W. The hunt for RNA polymerase II elongation factors: a historical perspective. _Nat.

Struct. Mol. Biol._ 26, 771–776 (2019). CAS  PubMed  Google Scholar  * Nudler, E., Mustaev, A., Lukhtanov, E. & Goldfarb, A. The RNA-DNA hybrid maintains the register of transcription by

preventing backtracking of RNA polymerase. _Cell_ 89, 33–41 (1997). CAS  PubMed  Google Scholar  * Cheung, A. C. & Cramer, P. Structural basis of RNA polymerase II backtracking, arrest

and reactivation. _Nature_ 471, 249–253 (2011). CAS  PubMed  Google Scholar  * Vos, S. M., Farnung, L., Urlaub, H. & Cramer, P. Structure of paused transcription complex Pol

II-DSIF-NELF. _Nature_ 560, 601–606 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Sekimizu, K., Kobayashi, N., Mizuno, D. & Natori, S. Purification of a factor from Ehrlich

ascites tumor cells specifically stimulating RNA polymerase II. _Biochem_ 15, 5064–5070 (1976). CAS  Google Scholar  * Rappaport, J., Reinberg, D., Zandomeni, R. & Weinmann, R.

Purification and functional characterization of transcription factor SII from calf thymus. Role in RNA polymerase II elongation. _J. Biol. Chem._ 262, 5227–5232 (1987). CAS  PubMed  Google

Scholar  * Reinberg, D. & Roeder, R. G. Factors involved in specific transcription by mammalian RNA polymerase II. Transcription factor IIS stimulates elongation of RNA chains. _J. Biol.

Chem._ 262, 3331–3337 (1987). CAS  PubMed  Google Scholar  * Reines, D. Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. _J. Biol. Chem._ 267,

3795–3800 (1992). CAS  PubMed  Google Scholar  * Reines, D., Chamberlin, M. J. & Kane, C. M. Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a

block to transcription in a human gene in vitro. _J. Biol. Chem._ 264, 10799–10809 (1989). CAS  PubMed  Google Scholar  * Izban, M. G. & Luse, D. S. The RNA polymerase II ternary complex

cleaves the nascent transcript in a 3’–5’ direction in the presence of elongation factor SII. _Genes Dev._ 6, 1342–1356 (1992). CAS  PubMed  Google Scholar  * Izban, M. G. & Luse, D. S.

Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. _J. Biol. Chem._ 267, 13647–13655 (1992). CAS  PubMed

  Google Scholar  * Gu, W. & Reines, D. Identification of a decay in transcription potential that results in elongation factor dependence of RNA polymerase II. _J. Biol. Chem._ 270,

11238–11244 (1995). CAS  PubMed  Google Scholar  * Wang, D. et al. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. _Science_ 324, 1203–1206

(2009). CAS  PubMed  PubMed Central  Google Scholar  * Kettenberger, H., Armache, K. J. & Cramer, P. Complete RNA polymerase II elongation complex structure and its interactions with NTP

and TFIIS. _Mol. Cell_ 16, 955–965 (2004). CAS  PubMed  Google Scholar  * Kettenberger, H., Armache, K. J. & Cramer, P. Architecture of the RNA polymerase II-TFIIS complex and

implications for mRNA cleavage. _Cell_ 114, 347–357 (2003). CAS  PubMed  Google Scholar  * Lisica, A. et al. Mechanisms of backtrack recovery by RNA polymerases I and II. _Proc. Natl Acad.

Sci. USA_ 113, 2946–2951 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Sigurdsson, S., Dirac-Svejstrup, A. B. & Svejstrup, J. Q. Evidence that transcript cleavage is essential

for RNA polymerase II transcription and cell viability. _Mol. Cell_ 38, 202–210 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Zatreanu, D. et al. Elongation factor TFIIS prevents

transcription stress and R-loop accumulation to maintain genome stability. _Mol. Cell_ 76, 57–69 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Sheridan, R. M., Fong, N.,

D’Alessandro, A. & Bentley, D. L. Widespread backtracking by RNA Pol II is a major effector of gene activation, 5’ pause release, termination, and transcription elongation rate. _Mol.

Cell_ 73, 107–118 e104 (2019). ZATREANU ET AL. (2019) AND SHERIDAN ET AL. (2019) ANALYSE GENOME-WIDE EFFECTS ON TRANSCRIPTION OF THE EXPRESSION OF A DOMINANT-NEGATIVE TFIIS MUTANT. CAS 

PubMed  Google Scholar  * 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  * 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). CAS  PubMed  PubMed Central  Google Scholar  * Nojima, T. et al. Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA

processing. _Cell_ 161, 526–540 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Mayer, A. et al. Native elongating transcript sequencing reveals human transcriptional activity at

nucleotide resolution. _Cell_ 161, 541–554 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Kamieniarz-Gdula, K. & Proudfoot, N. J. Transcriptional control by premature

termination: a forgotten mechanism. _Trends Genet._ 35, 553–564 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Kumar, A., Clerici, M., Muckenfuss, L. M., Passmore, L. A. & Jinek,

M. Mechanistic insights into mRNA 3′-end processing. _Curr. Opin. Struct. Biol._ 59, 143–150 (2019). CAS  PubMed  PubMed Central  Google Scholar  * 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). PubMed  PubMed Central  Google

Scholar  * Gilmour, D. S. & Lis, J. T. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells. _Mol. Cell Biol._ 6, 3984–3989

(1986). CAS  PubMed  PubMed Central  Google Scholar  * Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. _Nat. Rev. Genet._ 13,

720–731 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Zeitlinger, J. et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. _Nat.

Genet._ 39, 1512–1516 (2007). CAS  PubMed  PubMed Central  Google Scholar  * 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  Google Scholar  * Krebs, A. R. et al. Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused

promoters. _Mol. Cell_ 67, 411–422 e414 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Erickson, B., Sheridan, R. M., Cortazar, M. & Bentley, D. L. Dynamic turnover of paused

Pol II complexes at human promoters. _Genes Dev._ 32, 1215–1225 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Steurer, B. et al. Live-cell analysis of endogenous GFP-RPB1 uncovers

rapid turnover of initiating and promoter-paused RNA polymerase II. _Proc. Natl Acad. Sci. USA_ 115, E4368–E4376 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Gressel, S. et al.

CDK9-dependent RNA polymerase II pausing controls transcription initiation. _eLife_ https://doi.org/10.7554/eLife.29736 (2017). Article  PubMed  PubMed Central  Google Scholar  * Marshall,

N. F. & Price, D. H. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. _J. Biol. Chem._ 270, 12335–12338 (1995). CAS  PubMed  Google

Scholar  * Wada, T. et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. _Genes Dev._ 12, 343–356

(1998). CAS  PubMed  PubMed Central  Google Scholar  * Yamaguchi, Y. et al. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. _Cell_

97, 41–51 (1999). CAS  PubMed  Google Scholar  * Wu, C. H. et al. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. _Genes Dev._ 17, 1402–1414 (2003). CAS 

PubMed  PubMed Central  Google Scholar  * Peterlin, B. M. & Price, D. H. Controlling the elongation phase of transcription with P-TEFb. _Mol. Cell_ 23, 297–305 (2006). CAS  PubMed 

Google Scholar  * Missra, A. & Gilmour, D. S. Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II

transcription elongation complex. _Proc. Natl Acad. Sci. USA_ 107, 11301–11306 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Vos, S. M. et al. Structure of activated transcription

complex Pol II-DSIF-PAF-SPT6. _Nature_ 560, 607–612 (2018). VOS ET AL. (_NATURE_ 560, 601–606, 2018) AND VOS ET AL. (_NATURE_ 560, 607–612, 2018) PROVIDE STRUCTURAL INSIGHT INTO THE

MECHANISMS REGULATING PROMOTER-PROXIMAL PAUSING AND THE TRANSITION TO PRODUCTIVE ELONGATION DURING THE EARLY STAGES OF TRANSCRIPTION. CAS  PubMed  Google Scholar  * Vos, S. M., Farnung, L.,

Linden, A., Urlaub, H. & Cramer, P. Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. _Nat. Struct. Mol. Biol._ 27, 668–677 (2020). CAS

  PubMed  Google Scholar  * Hendrix, D. A., Hong, J. 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  PubMed Central  Google Scholar  * Fant, C. B. et al. TFIID enables RNA polymerase II promoter-proximal pausing. _Mol. Cell_

78, 785–793 e788 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Renner, D. B., Yamaguchi, Y., Wada, T., Handa, H. & Price, D. H. A highly purified RNA polymerase II elongation

control system. _J. Biol. Chem._ 11, 42601–42609 (2001). Google Scholar  * Cheng, B. & Price, D. H. Properties of RNA polymerase II elongation complexes before and after the

P-TEFb-mediated transition into productive elongation. _J. Biol. Chem._ 282, 21901–21912 (2007). CAS  PubMed  Google Scholar  * 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  * Adelman, K. et al. Efficient release from promoter-proximal

stall sites requires transcript cleavage factor TFIIS. _Mol. Cell_ 17, 103–112 (2005). CAS  PubMed  Google Scholar  * 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). CAS  PubMed  PubMed Central  Google Scholar  * Lai, W. K. M. & Pugh, B. F. Understanding

nucleosome dynamics and their links to gene expression and DNA replication. _Nat. Rev. Mol. Cell Biol._ 18, 548–562 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Lorch, Y.,

LaPointe, J. W. & Kornberg, R. D. Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones. _Cell_ 49, 203–210 (1987). CAS  PubMed

  Google Scholar  * Izban, M. G. & Luse, D. S. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific

pausing. _Genes Dev._ 5, 683–696 (1991). CAS  PubMed  Google Scholar  * Bondarenko, V. A. et al. Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. _Mol.

Cell_ 24, 469–479 (2006). CAS  PubMed  Google Scholar  * Kulaeva, O. I. et al. Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II. _Nat. Struct. Mol. Biol._

16, 1272–1278 (2009). CAS  PubMed  PubMed Central  Google Scholar  * Kulaeva, O. I. & Studitsky, V. M. Mechanism of histone survival during transcription by RNA polymerase II.

_Transcription_ 1, 85–88 (2010). PubMed  PubMed Central  Google Scholar  * Kujirai, T. et al. Structural basis of the nucleosome transition during RNA polymerase II passage. _Science_ 362,

595–598 (2018). THIS STUDY REVEALS DIFFERENT CONFORMATIONS OF POL II AS IT TRANSCRIBES NUCLEOSOMAL DNA, AND HOW HISTONE–DNA INTERACTIONS CONTRIBUTE TO NUCLEOSOME-DEPENDENT TRANSCRIPTION

STALLING. CAS  PubMed  Google Scholar  * Farnung, L., Vos, S. M. & Cramer, P. Structure of transcribing RNA polymerase II-nucleosome complex. _Nat. Commun._ 9, 5432 (2018). CAS  PubMed 

PubMed Central  Google Scholar  * Crickard, J. B., Lee, J., Lee, T. H. & Reese, J. C. The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome.

_Nucleic Acids Res._ 45, 6362–6374 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Kujirai, T. & Kurumizaka, H. Transcription through the nucleosome. _Curr. Opin. Struct. Biol._

61, 42–49 (2020). CAS  PubMed  Google Scholar  * Teves, S. S., Weber, C. M. & Henikoff, S. Transcribing through the nucleosome. _Trends Biochem. Sci._ 39, 577–586 (2014). CAS  PubMed 

Google Scholar  * Svejstrup, J. Q. Chromatin elongation factors. _Curr. Opin. Genet. Dev._ 12, 156–161 (2002). CAS  PubMed  Google Scholar  * Kireeva, M. L. et al. Nature of the nucleosomal

barrier to RNA polymerase II. _Mol. Cell_ 18, 97–108 (2005). CAS  PubMed  Google Scholar  * Mavrich, T. N. et al. Nucleosome organization in the Drosophila genome. _Nature_ 453, 358–362

(2008). CAS  PubMed  PubMed Central  Google Scholar  * Schones, D. E. et al. Dynamic regulation of nucleosome positioning in the human genome. _Cell_ 132, 887–898 (2008). CAS  PubMed  Google

Scholar  * Aoi, Y. et al. NELF regulates a promoter-proximal step distinct from RNA Pol II pause-release. _Mol. Cell_ 78, 261–274 e265 (2020). CAS  PubMed  PubMed Central  Google Scholar  *

Chen, Z. et al. High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier. _eLife_ https://doi.org/10.7554/eLife.48281 (2019). Article  PubMed  PubMed

Central  Google Scholar  * Kireeva, M. L., Komissarova, N., Waugh, D. S. & Kashlev, M. The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II

elongation complex. _J. Biol. Chem._ 275, 6530–6536 (2000). CAS  PubMed  Google Scholar  * Saeki, H. & Svejstrup, J. Q. Stability, flexibility, and dynamic interactions of colliding RNA

polymerase II elongation complexes. _Mol. Cell_ 35, 191–205 (2009). CAS  PubMed  PubMed Central  Google Scholar  * Zhang, J. & Landick, R. A two-way street: regulatory interplay between

RNA polymerase and nascent RNA structure. _Trends Biochem. Sci._ 41, 293–310 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Zamft, B., Bintu, L., Ishibashi, T. & Bustamante, C.

Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases. _Proc. Natl Acad. Sci. USA_ 109, 8948–8953 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Turowski,

T. W. et al. Nascent transcript folding plays a major role in determining RNA polymerase elongation rates. _Mol. Cell_ 79, 488–503 (2020). CAS  PubMed  PubMed Central  Google Scholar  *

Churchman, L. S. & Weissman, J. S. Nascent transcript sequencing visualizes transcription at nucleotide resolution. _Nature_ 469, 368–373 (2011). KWAK ET AL. (2013), NOJIMA ET AL.

(2015), MAYER ET AL. (2015) AND CHURCHMAN AND WEISSMAN (2011) DESCRIBE NASCENT-TRANSCRIPTOME SEQUENCING METHODS THAT HAVE REVOLUTIONIZED OUR UNDERSTANDING OF POL II DYNAMICS AT EUKARYOTIC

GENES. CAS  PubMed  Google Scholar  * Tome, J. M., Tippens, N. D. & Lis, J. T. Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and

enhancers. _Nat. Genet._ 50, 1533–1541 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Watts, J. A. et al. cis elements that mediate RNA polymerase II pausing regulate human gene

expression. _Am. J. Hum. Genet._ 105, 677–688 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Szlachta, K. et al. Alternative DNA secondary structure formation affects RNA polymerase

II promoter-proximal pausing in human. _Genome Biol._ 19, 89 (2018). PubMed  PubMed Central  Google Scholar  * Gregersen, L. H. & Svejstrup, J. Q. The cellular response to

transcription-blocking DNA damage. _Trends Biochem. Sci._ 43, 327–341 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Lans, H., Hoeijmakers, J. H. J., Vermeulen, W. & Marteijn, J.

A. The DNA damage response to transcription stress. _Nat. Rev. Mol. Cell Biol._ 20, 766–784 (2019). CAS  PubMed  Google Scholar  * Machour, F. E. & Ayoub, N. Transcriptional regulation

at DSBs: mechanisms and consequences. _Trends Genet_. https://doi.org/10.1016/j.tig.2020.01.001 (2020). * Caron, P. et al. WWP2 ubiquitylates RNA polymerase II for DNA-PK-dependent

transcription arrest and repair at DNA breaks. _Genes Dev._ 33, 684–704 (2019). CAS  PubMed  PubMed Central  Google Scholar  * García-Muse, T. & Aguilera, A. Transcription–replication

conflicts: how they occur and how they are resolved. _Nat. Rev. Mol. Cell Biol._ 17, 553–563 (2016). PubMed  Google Scholar  * Gomez-Gonzalez, B. & Aguilera, A. Transcription-mediated

replication hindrance: a major driver of genome instability. _Genes Dev._ 33, 1008–1026 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Hamperl, S. & Cimprich, KarleneA. Conflict

resolution in the genome: how transcription and replication make it work. _Cell_ 167, 1455–1467 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Marchal, C., Sima, J. & Gilbert, D.

M. Control of DNA replication timing in the 3D genome. _Nat. Rev. Mol. Cell Biol._ 20, 721–737 (2019). CAS  PubMed  Google Scholar  * Rivera-Mulia, J. C. & Gilbert, D. M. Replication

timing and transcriptional control: beyond cause and effect — part III. _Curr. Opin. Cell Biol._ 40, 168–178 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Meryet-Figuiere, M. et al.

Temporal separation of replication and transcription during S-phase progression. _Cell Cycle_ 13, 3241–3248 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Helmrich, A., Ballarino,

M., Nudler, E. & Tora, L. Transcription-replication encounters, consequences and genomic instability. _Nat. Struct. Mol. Biol._ 20, 412–418 (2013). CAS  PubMed  Google Scholar  *

Helmrich, A., Ballarino, M. & Tora, L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. _Mol. Cell_ 44,

966–977 (2011). CAS  PubMed  Google Scholar  * Azvolinsky, A., Giresi, P. G., Lieb, J. D. & Zakian, V. A. Highly transcribed RNA polymerase II genes are impediments to replication fork

progression in Saccharomyces cerevisiae. _Mol. Cell_ 34, 722–734 (2009). CAS  PubMed  PubMed Central  Google Scholar  * Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T. & Cimprich,

K. A. Transcription-replication conflict orientation modulates R-loop levels and activates distinct DNA damage responses. _Cell_ 170, 774–786 e719 (2017). CAS  PubMed  PubMed Central 

Google Scholar  * Sanchez, A. et al. Transcription-replication conflicts as a source of common fragile site instability caused by BMI1-RNF2 deficiency. _PLoS Genet._ 16, e1008524 (2020). CAS

  PubMed  PubMed Central  Google Scholar  * Shao, X., Joergensen, A. M., Howlett, N. G., Lisby, M. & Oestergaard, V. H. A distinct role for recombination repair factors in an early

cellular response to transcription–replication conflicts. _Nucleic Acids Res._ 48, 5467–5484 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Takeuchi, Y., Horiuchi, T. &

Kobayashi, T. Transcription-dependent recombination and the role of fork collision in yeast rDNA. _Genes Dev._ 17, 1497–1506 (2003). CAS  PubMed  PubMed Central  Google Scholar  * Prado, F.

& Aguilera, A. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. _EMBO J._ 24, 1267–1276 (2005). CAS  PubMed  PubMed Central  Google

Scholar  * Teloni, F. et al. Efficient pre-mRNA cleavage prevents replication-stress-associated genome instability. _Mol. Cell_ 73, 670–683 e612 (2019). CAS  PubMed  PubMed Central  Google

Scholar  * 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.e97 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Kanagaraj, R. et al. RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive

elongation phase of transcription. _Nucleic Acids Res._ 38, 8131–8140 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Aygun, O. et al. Direct inhibition of RNA polymerase II

transcription by RECQL5. _J. Biol. Chem._ 284, 23197–23203 (2009). PubMed  PubMed Central  Google Scholar  * Saponaro, M. et al. RECQL5 controls transcript elongation and suppresses genome

instability associated with transcription stress. _Cell_ 157, 1037–1049 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Prescott, E. M. & Proudfoot, N. J. Transcriptional

collision between convergent genes in budding yeast. _Proc. Natl Acad. Sci. USA_ 99, 8796–8801 (2002). CAS  PubMed  PubMed Central  Google Scholar  * Garcia-Rubio, M. L. & Aguilera, A.

Topological constraints impair RNA polymerase II transcription and causes instability of plasmid-borne convergent genes. _Nucleic Acids Res._ 40, 1050–1064 (2012). CAS  PubMed  Google

Scholar  * Hobson, D. J., Wei, W., Steinmetz, L. M. & Svejstrup, J. Q. RNA polymerase II collision interrupts convergent transcription. _Mol. Cell_ 48, 365–374 (2012). CAS  PubMed 

PubMed Central  Google Scholar  * Kulaeva, O. I., Hsieh, F.-K. & Studitsky, V. M. RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones. _Proc. Natl

Acad. Sci. USA_ 107, 11325–11330 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Cui, F., Cole, H. A., Clark, D. J. & Zhurkin, V. B. Transcriptional activation of yeast genes

disrupts intragenic nucleosome phasing. _Nucleic Acids Res._ 40, 10753–10764 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Cole, H. A., Ocampo, J., Iben, J. R., Chereji, R. V. &

Clark, D. J. Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases. _Nucleic Acids Res._ 42, 12512–12522 (2014). CAS

  PubMed  PubMed Central  Google Scholar  * Pannunzio, N. R. & Lieber, M. R. Dissecting the roles of divergent and convergent transcription in chromosome instability. _Cell Rep._ 14,

1025–1031 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Kamieniarz-Gdula, K. et al. Selective roles of vertebrate PCF11 in premature and full-length transcript termination. _Mol.

Cell_ 74, 158–172 e159 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Cinghu, S. et al. Intragenic enhancers attenuate host gene expression. _Mol. Cell_ 68, 104–117 e106 (2017). CAS

  PubMed  PubMed Central  Google Scholar  * Mayne, L. V. & Lehmann, A. R. Failure of RNA synthesis to recover after UV irradiation: an early defect in cells from individuals with

Cockayne’s syndrome and xeroderma pigmentosum. _Cancer Res._ 42, 1473–1478 (1982). CAS  PubMed  Google Scholar  * Tufegdzic Vidakovic, A. et al. Regulation of the RNAPII pool is integral to

the DNA damage response. _Cell_ 180, 1245–1261 e1221 (2020). THIS STUDY SHOWS THAT REGULATION OF GLOBAL POL II LEVELS IS ESSENTIAL TO CONTROL TRANSCRIPTION ACTIVITY IN RESPONSE TO UV-INDUCED

DNA DAMAGE. CAS  PubMed  PubMed Central  Google Scholar  * Chiou, Y. Y., Hu, J., Sancar, A. & Selby, C. P. RNA polymerase II is released from the DNA template during

transcription-coupled repair in mammalian cells. _J. Biol. Chem._ 293, 2476–2486 (2018). CAS  PubMed  Google Scholar  * Lavigne, M. D., Konstantopoulos, D., Ntakou-Zamplara, K. Z., Liakos,

A. & Fousteri, M. Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate. _Nat. Commun._ 8, 2076 (2017). PubMed  PubMed

Central  Google Scholar  * Borisova, M. E. et al. p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. _Nat. Commun._ 9, 1017 (2018). PubMed  PubMed Central 

Google Scholar  * Bugai, A. et al. P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress. _Mol. Cell_ 74, 254–267.e210 (2019). CAS  PubMed  PubMed

Central  Google Scholar  * Andrade-Lima, L. C., Veloso, A., Paulsen, M. T., Menck, C. F. & Ljungman, M. DNA repair and recovery of RNA synthesis following exposure to ultraviolet light

are delayed in long genes. _Nucleic Acids Res._ 43, 2744–2756 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Williamson, L. et al. UV irradiation induces a non-coding RNA that

functionally opposes the protein encoded by the same gene. _Cell_ 168, 843–855 e813 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Wilson, M. D., Harreman, M. & Svejstrup, J. Q.

Ubiquitylation and degradation of elongating RNA polymerase II: the last resort. _Biochim. Biophys. Acta_ 1829, 151–157 (2013). CAS  PubMed  Google Scholar  * Venema, J., Mullenders, L. H.,

Natarajan, A. T., van Zeeland, A. A. & Mayne, L. V. The genetic defect in Cockayne syndrome is associated with a defect in repair of UV-induced DNA damage in transcriptionally active

DNA. _Proc. Natl Acad. Sci. USA_ 87, 4707–4711 (1990). CAS  PubMed  PubMed Central  Google Scholar  * Troelstra, C. et al. ERCC6, a member of a subfamily of putative helicases, is involved

in Cockayne’s syndrome and preferential repair of active genes. _Cell_ 71, 939–953 (1992). CAS  PubMed  Google Scholar  * Selby, C. P. & Sancar, A. Cockayne syndrome group B protein

enhances elongation by RNA polymerase II. _Proc. Natl Acad. Sci. USA_ 94, 11205–11209 (1997). CAS  PubMed  PubMed Central  Google Scholar  * Xu, J. et al. Structural basis for the initiation

of eukaryotic transcription-coupled DNA repair. _Nature_ 551, 653–657 (2017). STRUCTURAL ANALYSIS OF THE YEAST CSB HOMOLOGUE RAD26 PROVIDES INSIGHT INTO HOW CSB MIGHT FUNCTION IN THE

REGULATION OF POL II STALLING AND TC-NER. CAS  PubMed  PubMed Central  Google Scholar  * Charlet-Berguerand, N. et al. RNA polymerase II bypass of oxidative DNA damage is regulated by

transcription elongation factors. _EMBO J._ 25, 5481–5491 (2006). CAS  PubMed  PubMed Central  Google Scholar  * Kuraoka, I. et al. RNA polymerase II bypasses 8-oxoguanine in the presence of

transcription elongation factor TFIIS. _DNA Repair_ 6, 841–851 (2007). CAS  PubMed  Google Scholar  * Kathe, S. D., Shen, G. P. & Wallace, S. S. Single-stranded breaks in DNA but not

oxidative DNA base damages block transcriptional elongation by RNA polymerase II in HeLa cell nuclear extracts. _J. Biol. Chem._ 279, 18511–18520 (2004). CAS  PubMed  Google Scholar  *

Jansen, L. E. et al. Spt4 modulates Rad26 requirement in transcription-coupled nucleotide excision repair. _EMBO J._ 19, 6498–6507 (2000). CAS  PubMed  PubMed Central  Google Scholar  *

Ding, B., LeJeune, D. & Li, S. The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. _J. Biol. Chem._ 285,

5317–5326 (2010). CAS  PubMed  Google Scholar  * Li, W., Giles, C. & Li, S. Insights into how Spt5 functions in transcription elongation and repressing transcription coupled DNA repair.

_Nucleic Acids Res._ 42, 7069–7083 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Duan, M., Selvam, K., Wyrick, J. J. & Mao, P. Genome-wide role of Rad26 in promoting

transcription-coupled nucleotide excision repair in yeast chromatin. _Proc. Natl Acad. Sci. USA_ 117, 18608–18616 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Gaillard, H. et al.

Genome-wide analysis of factors affecting transcription elongation and DNA repair: a new role for PAF and Ccr4-not in transcription-coupled repair. _PLoS Genet._ 5, e1000364 (2009). PubMed 

PubMed Central  Google Scholar  * Selby, C. P. & Sancar, A. Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the

ternary transcription complex of stalled RNA polymerase II. _J. Biol. Chem._ 272, 1885–1890 (1997). CAS  PubMed  Google Scholar  * Selby, C. P. & Sancar, A. Molecular mechanism of

transcription-repair coupling. _Science_ 260, 53–58 (1993). CAS  PubMed  Google Scholar  * Caron, P., van der Linden, J. & van Attikum, H. Bon voyage: a transcriptional journey around

DNA breaks. _DNA Repair_ 82, 102686 (2019). CAS  PubMed  Google Scholar  * Shanbhag, N. M., Rafalska-Metcalf, I. U., Balane-Bolivar, C., Janicki, S. M. & Greenberg, R. A. ATM-dependent

chromatin changes silence transcription in cis to DNA double-strand breaks. _Cell_ 141, 970–981 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Gao, L. & Gross, D. S. Sir2

silences gene transcription by targeting the transition between RNA polymerase II initiation and elongation. _Mol. Cell Biol._ 28, 3979–3994 (2008). CAS  PubMed  PubMed Central  Google

Scholar  * Awwad, S. W., Abu-Zhayia, E. R., Guttmann-Raviv, N. & Ayoub, N. NELF-E is recruited to DNA double-strand break sites to promote transcriptional repression and repair. _EMBO

Rep._ 18, 745–764 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Pankotai, T., Bonhomme, C., Chen, D. & Soutoglou, E. DNAPKcs-dependent arrest of RNA polymerase II transcription

in the presence of DNA breaks. _Nat. Struct. Mol. Biol._ 19, 276–282 (2012). CAS  PubMed  Google Scholar  * Burger, K., Ketley, R. F. & Gullerova, M. Beyond the trinity of ATM, ATR, and

DNA-PK: multiple kinases shape the DNA damage response in concert with RNA metabolism. _Front. Mol. Biosci._ 6, 61 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Hustedt, N. &

Durocher, D. The control of DNA repair by the cell cycle. _Nat. Cell Biol._ 19, 1–9 (2016). PubMed  Google Scholar  * Skourti-Stathaki, K., Proudfoot, Nicholas, 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). CAS  PubMed  PubMed Central  Google Scholar  *

Cohen, S. et al. Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations. _Nat. Commun._ 9, 533 (2018). PubMed  PubMed Central  Google Scholar  *

Francia, S. et al. Site-specific DICER and DROSHA RNA products control the DNA-damage response. _Nature_ 488, 231–235 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Michelini, F. et

al. Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks. _Nat. Cell Biol._ 19, 1400–1411 (2017). CAS  PubMed  PubMed

Central  Google Scholar  * 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). CAS  PubMed  PubMed Central  Google Scholar  * 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). CAS  PubMed  PubMed Central  Google Scholar  * Ohle, C. et al. Transient RNA-DNA hybrids are required for efficient

double-strand break repair. _Cell_ 167, 1001–1013 e1007 (2016). CAS  PubMed  Google Scholar  * Bregman, D. B. et al. UV-induced ubiquitination of RNA polymerase II: a novel modification

deficient in Cockayne syndrome cells. _Proc. Natl Acad. Sci. USA_ 93, 11586–11590 (1996). CAS  PubMed  PubMed Central  Google Scholar  * Ratner, J. N., Balasubramanian, B., Corden, J.,

Warren, S. L. & Bregman, D. B. Ultraviolet radiation-induced ubiquitination and proteasomal degradation of the large subunit of RNA polymerase II. Implications for transcription-coupled

DNA repair. _J. Biol. Chem._ 273, 5184–5189 (1998). CAS  PubMed  Google Scholar  * Beaudenon, S. L., Huacani, M. R., Wang, G., McDonnell, D. P. & Huibregtse, J. M. Rsp5 ubiquitin-protein

ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. _Mol. Cell Biol._ 19, 6972–6979 (1999). CAS  PubMed  PubMed Central 

Google Scholar  * Lee, K. B., Wang, D., Lippard, S. J. & Sharp, P. A. Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro. _Proc. Natl Acad. Sci.

USA_ 99, 4239–4244 (2002). CAS  PubMed  PubMed Central  Google Scholar  * Ribar, B., Prakash, L. & Prakash, S. ELA1 and CUL3 are required along with ELC1 for RNA polymerase II

polyubiquitylation and degradation in DNA-damaged yeast cells. _Mol. Cell Biol._ 27, 3211–3216 (2007). CAS  PubMed  PubMed Central  Google Scholar  * Ribar, B., Prakash, L. & Prakash, S.

Requirement of ELC1 for RNA polymerase II polyubiquitylation and degradation in response to DNA damage in Saccharomyces cerevisiae. _Mol. Cell Biol._ 26, 3999–4005 (2006). CAS  PubMed 

PubMed Central  Google Scholar  * Lommel, L., Bucheli, M. E. & Sweder, K. S. Transcription-coupled repair in yeast is independent from ubiquitylation of RNA pol II: implications for

Cockayne’s syndrome. _Proc. Natl Acad. Sci. USA_ 97, 9088–9092 (2000). CAS  PubMed  PubMed Central  Google Scholar  * Woudstra, E. C. et al. A Rad26-Def1 complex coordinates repair and RNA

pol II proteolysis in response to DNA damage. _Nature_ 415, 929–933 (2002). CAS  PubMed  Google Scholar  * Nakazawa, Y. et al. Ubiquitination of DNA damage-stalled RNAPII promotes

transcription-coupled repair. _Cell_ 180, 1228–1244.e1224 (2020). CAS  PubMed  Google Scholar  * Nguyen, V. T. et al. In vivo degradation of RNA polymerase II largest subunit triggered by

α-amanitin. _Nucleic Acids Res._ 24, 2924–2929 (1996). CAS  PubMed  PubMed Central  Google Scholar  * Mitsui, A. & Sharp, P. A. Ubiquitination of RNA polymerase II large subunit signaled

by phosphorylation of carboxyl-terminal domain. _Proc. Natl Acad. Sci. USA_ 96, 6054–6059 (1999). CAS  PubMed  PubMed Central  Google Scholar  * Anindya, R., Aygun, O. & Svejstrup, J.

Q. Damage-induced ubiquitylation of human RNA polymerase II by the ubiquitin ligase Nedd4, but not cockayne syndrome proteins or BRCA1. _Mol. Cell_ 28, 386–397 (2007). CAS  PubMed  Google

Scholar  * Poli, J. et al. Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress. _Genes Dev._ 30, 337–354

(2016). CAS  PubMed  PubMed Central  Google Scholar  * Kuehner, J. N., Kaufman, J. W. & Moore, C. Stimulation of RNA polymerase II ubiquitination and degradation by yeast mRNA 3’-end

processing factors is a conserved DNA damage response in eukaryotes. _DNA Repair_ 57, 151–160 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Luo, Z., Zheng, J., Lu, Y. & Bregman,

D. B. Ultraviolet radiation alters the phosphorylation of RNA polymerase II large subunit and accelerates its proteasome-dependent degradation. _Mutat. Res._ 486, 259–274 (2001). CAS 

PubMed  Google Scholar  * Somesh, B. P. et al. Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest. _Cell_ 121, 913–923 (2005).

CAS  PubMed  Google Scholar  * Lafon, A. et al. INO80 chromatin remodeler facilitates release of RNA polymerase II from chromatin for ubiquitin-mediated proteasomal degradation. _Mol. Cell_

60, 784–796 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Verma, R., Oania, R., Fang, R., Smith, G. T. & Deshaies, R. J. Cdc48/p97 mediates UV-dependent turnover of RNA Pol II.

_Mol. Cell_ 41, 82–92 (2011). CAS  PubMed  PubMed Central  Google Scholar  * Proudfoot, N. J. Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. _Science_

352, aad9926 (2016). PubMed  PubMed Central  Google Scholar  * 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.e894 (2019). CAS  PubMed  PubMed Central  Google Scholar  * 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). CAS  PubMed  PubMed Central  Google Scholar  * Dubbury, S. J.,

Boutz, P. L. & Sharp, P. A. CDK12 regulates DNA repair genes by suppressing intronic polyadenylation. _Nature_ 564, 141–145 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Yang,

Y. et al. PAF complex plays novel subunit-specific roles in alternative cleavage and polyadenylation. _PLoS Genet._ 12, e1005794 (2016). PubMed  PubMed Central  Google Scholar  * Devany, E.

et al. Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. _Cell Discov._ 2, 16013 (2016). CAS  PubMed  PubMed Central  Google

Scholar  * Fong, N. et al. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. _Genes Dev._ 28, 2663–2676 (2014). PubMed  PubMed Central  Google Scholar  *

Fong, N. et al. Effects of transcription elongation rate and Xrn2 exonuclease activity on RNA polymerase II termination suggest widespread kinetic competition. _Mol. Cell_ 60, 256–267

(2015). CAS  PubMed  PubMed Central  Google Scholar  * 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  * Elrod, N. D. et al. The integrator complex attenuates promoter-proximal transcription at

protein-coding genes. _Mol. Cell_ 76, 738–752 e737 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Tatomer, D. C. et al. The integrator complex cleaves nascent mRNAs to attenuate

transcription. _Genes Dev._ 33, 1525–1538 (2019). ELROD ET AL. (2019) AND TATOMER ET AL. (2019) PROVIDE EVIDENCE THAT THE INTEGRATOR RNA CLEAVAGE COMPLEX MEDIATES PREMATURE TERMINATION OF

PROMOTER-PROXIMAL POL II PAUSING, THEREBY ATTENUATING TRANSCRIPTION. CAS  PubMed  PubMed Central  Google Scholar  * 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). CAS  PubMed  Google Scholar  * Jonkers, I., Kwak, H. & Lis, J. T. Genome-wide dynamics of Pol II

elongation and its interplay with promoter proximal pausing, chromatin, and exons. _eL__ife_ 3, e02407 (2014). PubMed  PubMed Central  Google Scholar  * Shao, W. & Zeitlinger, J. Paused

RNA polymerase II inhibits new transcriptional initiation. _Nat. Genet._ 49, 1045–1051 (2017). CAS  PubMed  Google Scholar  * 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). CAS  PubMed  Google Scholar  * Lai, F., Gardini, A., Zhang, A. &

Shiekhattar, R. Integrator mediates the biogenesis of enhancer RNAs. _Nature_ 525, 399–403 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Stadelmayer, B. et al. Integrator complex

regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. _Nat. Commun._ 5, 5531 (2014). CAS  PubMed  Google Scholar  * Yamamoto, J. et al. DSIF and NELF

interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. _Nat. Commun._ 5, 4263 (2014). CAS  PubMed  Google Scholar  * Beckedorff, F. et al. The human

integrator complex facilitates transcriptional elongation by endonucleolytic cleavage of nascent transcripts. _Cell Rep._ 32, 107917 (2020). CAS  PubMed  PubMed Central  Google Scholar  *

Lykke-Andersen, S. et al. Integrator is a genome-wide attenuator of non-productive transcription. Preprint at _bioRxiv_ https://doi.org/10.1101/2020.07.17.208702 (2020). Article  Google

Scholar  * Vervoort, S. J. et al. A PP2A-Integrator complex fine-tunes transcription by opposing CDK9. Preprint at _bioRxiv_ https://doi.org/10.1101/2020.07.12.199372 (2020). Article  Google

Scholar  * Huang, K. L. et al. Integrator recruits protein phosphatase 2A to prevent pause release and facilitate transcription termination. _Mol. Cell_

https://doi.org/10.1016/j.molcel.2020.08.016 (2020). Article  PubMed  PubMed Central  Google Scholar  * Eaton, J. D. et al. Xrn2 accelerates termination by RNA polymerase II, which is

underpinned by CPSF73 activity. _Genes Dev._ 32, 127–139 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Mischo, H. E. et al. Yeast Sen1 helicase protects the genome from

transcription-associated instability. _Mol. Cell_ 41, 21–32 (2011). CAS  PubMed  PubMed Central  Google Scholar  * Alzu, A. et al. Senataxin associates with replication forks to protect fork

integrity across RNA-polymerase-II-transcribed genes. _Cell_ 151, 835–846 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Li, W., Selvam, K., Rahman, S. A. & Li, S. Sen1, the

yeast homolog of human senataxin, plays a more direct role than Rad26 in transcription coupled DNA repair. _Nucleic Acids Res._ 44, 6794–6802 (2016). CAS  PubMed  PubMed Central  Google

Scholar  * Han, Z. et al. Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. _EMBO J._ 39, e101548

(2020). CAS  PubMed  PubMed Central  Google Scholar  * Huertas, P. & Aguilera, A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and

transcription-associated recombination. _Mol. Cell_ 12, 711–721 (2003). CAS  PubMed  Google Scholar  * Garcia-Muse, T. & Aguilera, A. R loops: from physiological to pathological roles.

_Cell_ 179, 604–618 (2019). CAS  PubMed  Google Scholar  * Lai, F., Damle, S. S., Ling, K. K. & Rigo, F. Directed RNase H cleavage of nascent transcripts causes transcription

termination. _Mol. Cell_ 77, 1032–1043 e1034 (2020). CAS  PubMed  Google Scholar  * Lee, J. S. & Mendell, J. T. Antisense-mediated transcript knockdown triggers premature transcription

termination. _Mol. Cell_ 77, 1044–1054 e1043 (2020). CAS  PubMed  PubMed Central  Google Scholar  * Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and

analysis. _Protein Sci._ 27, 14–25 (2018). CAS  PubMed  Google Scholar  * Crickard, J. B., Fu, J. & Reese, J. C. Biochemical analysis of yeast suppressor of Ty 4/5 (Spt4/5) reveals the

importance of nucleic acid interactions in the prevention of RNA polymerase II arrest. _J. Biol. Chem._ 291, 9853–9870 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Zhu, W. et al.

DSIF contributes to transcriptional activation by DNA-binding activators by preventing pausing during transcription elongation. _Nucleic Acids Res._ 35, 4064–4075 (2007). CAS  PubMed  PubMed

Central  Google Scholar  * Dutta, A. et al. Ccr4-Not and TFIIS function cooperatively to rescue arrested RNA polymerase II. _Mol. Cell Biol._ 35, 1915–1925 (2015). CAS  PubMed  PubMed

Central  Google Scholar  * 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  * Schweikhard, V. et al. Transcription factors TFIIF and TFIIS promote transcript elongation by RNA polymerase II by

synergistic and independent mechanisms. _Proc. Natl Acad. Sci. USA_ 111, 6642–6647 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Swanson, M. S., Malone, E. A. & Winston, F.

SPT5, an essential gene important for normal transcription in Saccharomyces cerevisiae, encodes an acidic nuclear protein with a carboxy-terminal repeat. _Mol. Cell Biol._ 11, 4286 (1991).

CAS  PubMed  PubMed Central  Google Scholar  * Bernecky, C., Plitzko, J. M. & Cramer, P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.

_Nat. Struct. Mol. Biol._ 24, 809–815 (2017). CAS  PubMed  Google Scholar  * Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J. M. & Cramer, P. Structure of transcribing mammalian RNA

polymerase II. _Nature_ 529, 551–554 (2016). CAS  PubMed  Google Scholar  * Rondon, A. G., Garcia-Rubio, M., Gonzalez-Barrera, S. & Aguilera, A. Molecular evidence for a positive role

of Spt4 in transcription elongation. _EMBO J._ 22, 612–620 (2003). CAS  PubMed  PubMed Central  Google Scholar  * Guo, S. et al. A regulator of transcriptional elongation controls vertebrate

neuronal development. _Nature_ 408, 366–369 (2000). CAS  PubMed  Google Scholar  * Andrulis, E. D., Guzman, E., Doring, P., Werner, J. & Lis, J. T. High-resolution localization of

Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. _Genes Dev._ 14, 2635–2649 (2000). CAS  PubMed  PubMed Central  Google

Scholar  * Kaplan, C. D., Morris, J. R., Wu, C. & Winston, F. Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D.

melanogaster. _Genes Dev._ 14, 2623–2634 (2000). CAS  PubMed  PubMed Central  Google Scholar  * Shetty, A. et al. Spt5 plays vital roles in the control of sense and antisense transcription

elongation. _Mol. Cell_ 66, 77–88 e75 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Baluapuri, A. et al. MYC recruits SPT5 to RNA polymerase II to promote processive transcription

elongation. _Mol. Cell_ 74, 674–687 e611 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Bacon, C. W. & D’Orso, I. CDK9: a signaling hub for transcriptional control.

_Transcription_ 10, 57–75 (2019). CAS  PubMed  Google Scholar  * Chen, F. X., Smith, E. R. & Shilatifard, A. Born to run: control of transcription elongation by RNA polymerase II. _Nat.

Rev. Mol. Cell Biol._ 19, 464–478 (2018). CAS  PubMed  Google Scholar  * Van Oss, S. B., Cucinotta, C. E. & Arndt, K. M. Emerging insights into the roles of the Paf1 complex in gene

regulation. _Trends Biochem. Sci._ 42, 788–798 (2017). PubMed  PubMed Central  Google Scholar  * Basu, S., Nandy, A. & Biswas, D. Keeping RNA polymerase II on the run: functions of MLL

fusion partners in transcriptional regulation. _Biochim. Biophys. Acta Gene Regul. Mech._ 1863, 194563 (2020). CAS  PubMed  Google Scholar  * Buratowski, S. Progression through the RNA

polymerase II CTD cycle. _Mol. Cell_ 36, 541–546 (2009). CAS  PubMed  PubMed Central  Google Scholar  * Eick, D. & Geyer, M. The RNA polymerase II carboxy-terminal domain (CTD) code.

_Chem. Rev._ 113, 8456–8490 (2013). CAS  PubMed  Google Scholar  * 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). CAS  PubMed  Google Scholar  * Zehring, W. A., Lee, J. M., Weeks, J. R., Jokerst, R. S. & Greenleaf, A. L. The

C-terminal repeat domain of RNA polymerase II largest subunit is essential in vivo but is not required for accurate transcription initiation in vitro. _Proc. Natl Acad. Sci. USA_ 85,

3698–3702 (1988). CAS  PubMed  PubMed Central  Google Scholar  * Nonet, M., Sweetser, D. & Young, R. A. Functional redundancy and structural polymorphism in the large subunit of RNA

polymerase II. _Cell_ 50, 909–915 (1987). CAS  PubMed  Google Scholar  * Saldi, T., Cortazar, M. A., Sheridan, R. M. & Bentley, D. L. Coupling of RNA polymerase II transcription

elongation with pre-mRNA splicing. _J. Mol. Biol._ 428, 2623–2635 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Boehning, M. et al. RNA polymerase II clustering through

carboxy-terminal domain phase separation. _Nat. Struct. Mol. Biol._ 25, 833–840 (2018). CAS  PubMed  Google Scholar  * Mayfield, J. E., Burkholder, N. T. & Zhang, Y. J. Dephosphorylating

eukaryotic RNA polymerase II. _Biochim. Biophys. Acta_ 1864, 372–387 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Lee, J. M. & Greenleaf, A. L. CTD kinase large subunit is

encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. _Gene Expr._ 1, 149–167 (1991). CAS  PubMed  Google Scholar  * Bartkowiak, B. et al. CDK12 is a transcription

elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. _Genes Dev._ 24, 2303–2316 (2010). CAS  PubMed  PubMed Central  Google Scholar  * Greenleaf, A. L. Human CDK12 and

CDK13, multi-tasking CTD kinases for the new millenium. _Transcription_ 10, 91–110 (2019). CAS  PubMed  Google Scholar  * Krajewska, M. et al. CDK12 loss in cancer cells affects DNA damage

response genes through premature cleavage and polyadenylation. _Nat. Commun._ 10, 1757 (2019). PubMed  PubMed Central  Google Scholar  * Fan, Z. et al. CDK13 cooperates with CDK12 to control

global RNA polymerase II processivity. _Sci. Adv._ 6, eaaz5041 (2020). CAS  PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS The authors thank members of the

Svejstrup laboratory for helpful comments and suggestions, and especially L. Gregersen and A. Tufegdzic Vidakovic for their critical reading of the manuscript. The authors apologize to those

authors whose work could not be cited due to space constraints. M.N.G was supported by an EMBO Postdoctoral Fellowship (EMBO ALTF 2020-260). AUTHOR INFORMATION Author notes * These authors

contributed equally: Melvin Noe Gonzalez, Daniel Blears. AUTHORS AND AFFILIATIONS * Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK Melvin Noe Gonzalez, 

Daniel Blears & Jesper Q. Svejstrup * Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark Melvin Noe Gonzalez, Daniel Blears & Jesper Q.

Svejstrup Authors * Melvin Noe Gonzalez View author publications You can also search for this author inPubMed Google Scholar * Daniel Blears View author publications You can also search for

this author inPubMed Google Scholar * Jesper Q. Svejstrup View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS The authors contributed equally

to all aspects of the article. CORRESPONDING AUTHOR Correspondence to Jesper Q. Svejstrup. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL

INFORMATION PEER REVIEW INFORMATION _Nature Reviews Molecular Cell Biology_ thanks the anonymous reviewers 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 * General transcription factors Transcription factors that are

recruited to the promoter during transcription initiation and are necessary for the formation of the pre-initiation complex. * Pre-initiation complexes (PICs). Complexes of general

transcription factors and RNA polymerase II that assemble at gene promoters during transcription initiation. * Transcription pausing Transient series of Pol II stalling events, followed by

resumption of transcription. * Processive Refers to the extent to which RNA polymerase II performs consecutive nucleotide incorporations and forward translocation without dissociating from

the DNA. * Promoter-proximal pausing Widespread, regulatory stalling of RNA polymerase II in animal cells shortly downstream of transcription start sites. * Transcription arrest Blocking of

transcript elongation by RNA polymerase II by an unsurmountable obstacle. * Genome instability A cellular genotoxic state that may include changes in DNA sequence and/or chromosomal

rearrangements. * Transcription stalling The point at which forward translocation by RNA polymerase II is blocked, leading to secondary events that include backtracking, arrest or

transcription resumption. * Transcription stress Collective term for events in which RNA polymerase II becomes stalled or arrested during transcript elongation. * Premature termination

Termination of transcription anywhere between the transcription start site and the canonical polyadenylation site, by means of RNA cleavage and RNA polymerase II dissociation. * R-loop

Three-stranded RNA–DNA hybrid structure formed by hybridization of nascent RNA to the DNA strand from which it was transcribed. * Transcription start site The DNA base position that is

complimentary to the first incorporated RNA nucleoside triphosphate. * Pol II C-terminal domain The highly conserved C-terminal domain (CTD) of RBP1, the catalytic subunit of RNA polymerase

II (Pol II). Post-translational modification of the CTD is an important mechanism of transcription regulation. * Core promoter elements Consensus DNA sequences located at gene promoters

which direct the assembly of the pre-initiation complex and transcription initiation. * Nucleosome dyad Central position within the nucleosome structure, at which a twofold topological

symmetry is exhibited. * SHL Superhelical locations on the nucleosome structure, spaced by approximately 10 bp. SHL(0) marks the nucleosome dyad. * Transcription readthrough Continuation of

transcription beyond (downstream) of canonical termination regions. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Noe Gonzalez, M., Blears, D. &

Svejstrup, J.Q. Causes and consequences of RNA polymerase II stalling during transcript elongation. _Nat Rev Mol Cell Biol_ 22, 3–21 (2021). https://doi.org/10.1038/s41580-020-00308-8

Download citation * Accepted: 08 October 2020 * Published: 18 November 2020 * Issue Date: January 2021 * DOI: https://doi.org/10.1038/s41580-020-00308-8 SHARE THIS ARTICLE Anyone you share

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