Transcription competes with other DNA-dependent processes, such as DNA repair, for access to its substrate, DNA. However, the principles governing the interplay between these processes remain poorly understood. Evidence suggests that the BRCA1-BARD1 complex, a key player in the DNA damage response, may act as a mediator of this crosstalk. In this study, we investigated the molecular mechanism underpinning the interaction between RNA polymerase II (RNAPII) and the BRCA1-BARD1 complex, as well as its functional implications. Our findings reveal that the tandem BRCT domain of BRCA1 binds the Ser5-phosphorylated CTD of RNAPII, utilizing a mechanism previously established for other BRCA1 BRCT ligands. Furthermore, we demonstrate that this interaction is critical for the organization of RNAPII into condensates with liquid-like properties. Analysis of disease-associated variants within the BRCT repeats further supports the biological relevance of this condensation. Collectively, our results suggest that the BRCA1-BARD1 complex may coordinate transcription and DNA repair by facilitating the organization of RNAPII into transcription factories.

CEITEC Central European Institute of Technology Masaryk University Brno Czechia

CEITEC Central European Institute of Technology Masaryk University Brno Czechia; National Centre for Biomolecular Research Faculty of Science Masaryk University Brno Czechia

Zobrazit více v PubMed

Gaillard H., Aguilera A. Transcription as a threat to genome integrity. Annu. Rev. Biochem. 2016;85:291–317. PubMed

Sollier J., Stork C.T., García-Rubio M.L., Paulsen R.D., Aguilera A., Cimprich K.A. Transcription-coupled nucleotide excision repair factors promote R-Loop-Induced genome instability. Mol. Cell. 2014;56:777–785. PubMed PMC

García-Muse T., Aguilera A. Transcription–replication conflicts: how they occur and how they are resolved. Nat. Rev. Mol. Cell Biol. 2016;17:553–563. PubMed

Hamperl S., Cimprich K.A. Conflict resolution in the genome: how transcription and replication make it work. Cell. 2016;167:1455–1467. PubMed PMC

Crossley M.P., Bocek M., Cimprich K.A. R-Loops as cellular regulators and genomic threats. Mol. Cell. 2019;73:398–411. PubMed PMC

Stoy H., Zwicky K., Kuster D., Lang K.S., Krietsch J., Crossley M.P., et al. Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids. Nat. Struct. Mol. Biol. 2023;30:348–359. PubMed PMC

Aguilera A., García-Muse T.R. Loops: from transcription byproducts to threats to genome stability. Mol. Cell. 2012;46:115–124. PubMed

Gan W., Guan Z., Liu J., Gui T., Shen K., Manley J.L., Li X. R-loop-mediated genomic instability is caused by impairment of replication fork progression. Genes Dev. 2011;25:2041–2056. PubMed PMC

Wahba L., Amon J.D., Koshland D., Vuica-Ross M. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol. Cell. 2011;44:978–988. PubMed PMC

Parajuli S., Teasley D.C., Murali B., Jackson J., Vindigni A., Stewart S.A. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork. J. Biol. Chem. 2017;292:15216–15224. PubMed PMC

Zhao H., Zhu M., Limbo O., Russell P. RNase H eliminates r-loops that disrupt DNA replication but is nonessential for efficient DSB repair. EMBO Rep. 2018;19 PubMed PMC

Boleslavska B., Oravetzova A., Shukla K., Nascakova Z., Ibini O.N., Hasanova Z., et al. DDX17 helicase promotes resolution of R-loop-mediated transcription–replication conflicts in human cells. Nucleic Acids Res. 2022;50:12274–12290. PubMed PMC

Song C., Hotz-Wagenblatt A., Voit R., Grummt I. SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability. Genes Dev. 2017;31:1370–1381. PubMed PMC

Mersaoui S.Y., Yu Z., Coulombe Y., Karam M., Busatto F.F., Masson J.Y., Richard S. Arginine methylation of the DDX5 helicase RGG RG motif by PRMT5 regulates resolution of RNA:DNA hybrids. EMBO J. 2019;38 PubMed PMC

Chang E.Y.-C., Novoa C.A., Aristizabal M.J., Coulombe Y., Segovia R., Chaturvedi R., et al. RECQ-like helicases Sgs1 and BLM regulate R-loop–associated genome instability. J. Cell Biol. 2017;216:3991–4005. PubMed PMC

Rao S., Andrs M., Shukla K., Isik E., König C., Schneider S., et al. Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation. Nucleic Acids Res. 2024;52:10355–10369. PubMed PMC

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. 2011;42:794–805. PubMed PMC

Hasanova Z., Klapstova V., Porrua O., Stefl R., Sebesta M. Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor. Nucleic Acids Res. 2023;51:2818–2837. PubMed PMC

McDevitt S., Rusanov T., Kent T., Chandramouly G., Pomerantz R.T. How RNA transcripts coordinate DNA recombination and repair. Nat. Commun. 2018;9:1091. PubMed PMC

Marnef A., Legube G. R-loops as Janus-faced modulators of DNA repair. Nat. Cell Biol. 2021;23:305–313. PubMed

Jimeno S., Prados-Carvajal R., Huertas P. The role of RNA and RNA-related proteins in the regulation of DNA double strand break repair pathway choice. DNA Repair (Amst). 2019;81 PubMed

Ohle C., Tesorero R., Schermann G., Dobrev N., Sinning I., Fischer T. Transient RNA-DNA hybrids are required for efficient double-strand break repair. Cell. 2016;167:1001–1013.e7. PubMed

Niehrs C., Luke B. Regulatory R-loops as facilitators of gene expression and genome stability. Nat. Rev. Mol. Cell Biol. 2020;21:167–178. PubMed PMC

Pessina F., Giavazzi F., Yin Y., Gioia U., Vitelli V., Galbiati A., et al. Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors. Nat. Cell Biol. 2019;21:1286–1299. PubMed PMC

Bonath F., Domingo-Prim J., Tarbier M., Friedländer M.R., Visa N. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Res. 2018;46:11869–11882. PubMed PMC

Burger K., Schlackow M., Gullerova M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res. 2019;47:3467–3484. PubMed PMC

Ajit K., Alagia A., Burger K., Gullerova M. Tyrosine 1-phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage. Genome Res. 2024;34:201–216. PubMed PMC

Long Q., Ajit K., Sedova K., Haluza V., Stefl R., Dokaneheifard S., et al. Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks. Nucleic Acids Res. 2024;52:13036–13056. PubMed PMC

Scully R., Anderson S.F., Chao D.M., Wei W., Ye L., Young R.A., et al. BRCA1 is a component of the RNA polymerase II holoenzyme. Proc. Natl. Acad. Sci. U. S. A. 1997;94:5605–5610. PubMed PMC

Krum S.A., Miranda G.A., Lin C., Lane T.F. BRCA1 associates with processive RNA polymerase II. J. Biol. Chem. 2003;278:52012–52020. PubMed

Bennett C.B., Westmoreland T.J., Verrier C.S., Blanchette C.A.B., Sabin T.L., Phatnani H.P., et al. Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction. PLoS One. 2008;3 PubMed PMC

Gilmore B.L., Winton C.E., Demmert A.C., Tanner J.R., Bowman S., Karageorge V., et al. A molecular toolkit to visualize native protein assemblies in the context of human disease. Sci. Rep. 2015;5 PubMed PMC

Rodriguez M., Yu X., Chen J., Songyang Z. Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. J. Biol. Chem. 2003;278:52914–52918. PubMed

Herold S., Kalb J., Büchel G., Ade C.P., Baluapuri A., Xu J., et al. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature. 2019;567:545–549. PubMed PMC

Yu X., Chini C.C.S., He M., Mer G., Chen J. The BRCT domain is a phospho-protein binding domain. Science. 2003;302:639–642. PubMed

Yuan Z., Kumar E.A., Kizhake S., Natarajan A. Structure–activity relationship studies to probe the phosphoprotein binding site on the carboxy terminal domains of the breast cancer susceptibility gene 1. J. Med. Chem. 2011;54:4264–4268. PubMed PMC

Manke I.A., Lowery D.M., Nguyen A., Yaffe M.B. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science. 2003;302:636–639. PubMed

Shiozaki E.N., Gu L., Yan N., Shi Y. Structure of the BRCT repeats of BRCA1 bound to a BACH1 phosphopeptide. Mol. Cell. 2004;14:405–412. PubMed

Clapperton J.A., Manke I.A., Lowery D.M., Ho T., Haire L.F., Yaffe M.B., Smerdon S.J. Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat. Struct. Mol. Biol. 2004;11:512–518. PubMed

Liu X., Ladias J.A.A. Structural basis for the BRCA1 BRCT interaction with the proteins ATRIP and BAAT1. Biochemistry. 2013;52:7618–7627. PubMed

Shen Y., Tong L. Structural evidence for direct interactions between the BRCT domains of human BRCA1 and a phospho-peptide from human ACC1. Biochemistry. 2008;47:5767–5773. PubMed PMC

Edwards R.A., Lee M.S., Tsutakawa S.E., Williams R.S., Nazeer I., Kleiman F.E., et al. The BARD1 C-Terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry. 2008;47:11446–11456. PubMed PMC

Birrane G., Varma A.K., Soni A., Ladias J.A.A. Crystal structure of the BARD1 BRCT domains. Biochemistry. 2007;46:7706–7712. PubMed

Tarsounas M., Sung P. The antitumorigenic roles of BRCA1–BARD1 in DNA repair and replication. Nat. Rev. Mol. Cell Biol. 2020;21:284–299. PubMed PMC

Zhao W., Steinfeld J.B., Liang F., Chen X., Maranon D.G., Jian Ma C., et al. BRCA1–BARD1 promotes RAD51-mediated homologous DNA pairing. Nature. 2018;550:360–365. PubMed PMC

Nakamura K., Saredi G., Becker J.R., Foster B.M., Nguyen N.V., Beyer T.E., et al. H4K20me0 recognition by BRCA1–BARD1 directs homologous recombination to sister chromatids. Nat. Cell Biol. 2019;21:311–318. PubMed PMC

Bunting S.F., Callén E., Wong N., Chen H.T., Polato F., Gunn A., et al. 53BP1 inhibits homologous recombination in Brca1-Deficient cells by blocking resection of DNA breaks. Cell. 2010;141:243–254. PubMed PMC

Botuyan M.V., Lee J., Ward I.M., Kim J.E., Thompson J.R., Chen J., Mer G. Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair. Cell. 2006;127:1361–1373. PubMed PMC

Chapman J.R., Sossick A.J., Boulton S.J., Jackson S.P. BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J. Cell Sci. 2012;125:3529–3534. PubMed PMC

Escribano-Díaz C., Orthwein A., Fradet-Turcotte A., Xing M., Young J.T.F., Tkáč J., et al. A cell cycle-dependent regulatory circuit composed of 53BP1-RIF1 and BRCA1-CtIP controls DNA repair pathway choice. Mol. Cell. 2013;49:872–883. PubMed

Densham R.M., Garvin A.J., Stone H.R., Strachan J., Baldock R.A., Daza-Martin M., et al. Human BRCA1–BARD1 ubiquitin ligase activity counteracts chromatin barriers to DNA resection. Nat. Struct. Mol. Biol. 2016;23:647–655. PubMed PMC

Kalb R., Mallery D.L., Larkin C., Huang J.T.J., Hiom K. BRCA1 is a Histone-H2A-Specific ubiquitin ligase. Cell Rep. 2014;8:999–1005. PubMed PMC

Ceppi I., Dello Stritto M.R., Mütze M., Braunshier S., Mengoli V., Reginato G., et al. Mechanism of BRCA1–BARD1 function in DNA end resection and DNA protection. Nature. 2024;634:492–500. PubMed PMC

Salunkhe S., Daley J.M., Kaur H., Tomimatsu N., Xue C., Raina V.B., et al. Promotion of DNA end resection by BRCA1–BARD1 in homologous recombination. Nature. 2024;634:482–491. PubMed PMC

Cruz-García A., López-Saavedra A., Huertas P. BRCA1 accelerates CtIP-Mediated DNA-end resection. Cell Rep. 2014;9:451–459. PubMed

Chong S., Dugast-Darzacq C., Liu Z., Dong P., Dailey G.M., Cattoglio C., et al. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science. 2018;361 PubMed PMC

Sabari B.R., Dall'Agnese A., Boija A., Klein I.A., Coffey E.L., Shrinivas K., et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361 PubMed PMC

Boija A., Klein I.A., Sabari B.R., Dall'Agnese A., Coffey E.L., Zamudio A.V., et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell. 2018;175:1842–1855.e16. PubMed PMC

Wei M.-T., Chang Y.C., Shimobayashi S.F., Shin Y., Strom A.R., Brangwynne C.P. Nucleated transcriptional condensates amplify gene expression. Nat. Cell Biol. 2020;22:1187–1196. PubMed

Han X., Yu D., Gu R., Jia Y., Wang Q., Jaganathan A., et al. Roles of the BRD4 short isoform in phase separation and active gene transcription. Nat. Struct. Mol. Biol. 2020;27:333–341. PubMed

Shrinivas K., Sabari B.R., Coffey E.L., Klein I.A., Boija A., Zamudio A.V., et al. Enhancer features that drive formation of transcriptional condensates. Mol. Cell. 2019;75:549–561.e7. PubMed PMC

Cho W.-K., Spille J.H., Hecht M., Lee C., Li C., Grube V., Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361:412–415. PubMed PMC

Lewis B.A., Das S.K., Jha R.K., Levens D. Self-assembly of promoter DNA and RNA Pol II machinery into transcriptionally active biomolecular condensates. Sci. Adv. 2023;9 PubMed PMC

Shao W., Bi X., Pan Y., Gao B., Wu J., Yin Y., et al. Phase separation of RNA-binding protein promotes polymerase binding and transcription. Nat. Chem. Biol. 2022;18:70–80. PubMed

Flores-Solis D., Lushpinskaia I.P., Polyansky A.A., Changiarath A., Boehning M., Mirkovic M., et al. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nat. Commun. 2023;14:5979. PubMed PMC

Fijen C., Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021;105 PubMed PMC

Dall’Agnese G., Dall'Agnese A., Banani S.F., Codrich M., Malfatti M.C., Antoniali G., Tell G. Role of condensates in modulating DNA repair pathways and its implication for chemoresistance. J. Biol. Chem. 2023;299 PubMed PMC

Wang Y.-L., Zhao W.W., Bai S.M., Feng L.L., Bie S.Y., Gong L., et al. MRNIP condensates promote DNA double-strand break sensing and end resection. Nat. Commun. 2022;13:2638. PubMed PMC

Qin C., Wang Y.L., Zhou J.Y., Shi J., Zhao W.W., Zhu Y.X., et al. RAP80 phase separation at DNA double-strand break promotes BRCA1 recruitment. Nucleic Acids Res. 2023;51:9733–9747. PubMed PMC

Long Q., Sebesta M., Sedova K., Haluza V., Alagia A., Liu Z., et al. The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell Rep. 2023;42 PubMed PMC

Kilic S., Lezaja A., Gatti M., Bianco E., Michelena J., Imhof R., Altmeyer M. Phase separation of 53BP1 determines liquid-like behavior of DNA repair compartments. EMBO J. 2019;38 PubMed PMC

Chiba N., Parvin J.D. The BRCA1 and BARD1 association with the RNA polymerase II holoenzyme. Cancer Res. 2002;62:4222–4228. PubMed

Starita L.M., Horwitz A.A., Keogh M.C., Ishioka C., Parvin J.D., Chiba N. BRCA1/BARD1 ubiquitinate phosphorylated RNA polymerase II. J. Biol. Chem. 2005;280:24498–24505. PubMed

Thanassoulas A., Nomikos M., Theodoridou M., Yannoukakos D., Mastellos D., Nounesis G. Thermodynamic study of the BRCT domain of BARD1 and its interaction with the -pSER-X-X-Phe- motif-containing BRIP1 peptide. Biochim. Biophys. Acta. 2010;1804:1908–1916. PubMed

Botuyan M.V.E., Nominé Y., Yu X., Juranic N., Macura S., Chen J., Mer G. Structural basis of BACH1 phosphopeptide recognition by BRCA1 tandem BRCT domains. Structure. 2004;12:1137–1146. PubMed PMC

Williams R.S., Green R., Glover J.N. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat. Struct. Biol. 2001;8:838–842. PubMed

Williams R.S., Lee M.S., Hau D.D., Glover J.N.M. Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1. Nat. Struct. Mol. Biol. 2004;11:519–525. PubMed

Varma A.K., Brown R.S., Birrane G., Ladias J.A.A. Structural basis for cell cycle checkpoint control by the BRCA1−CtIP complex. Biochemistry. 2005;44:10941–10946. PubMed

Abramson J., Adler J., Dunger J., Evans R., Green T., Pritzel A., et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 2024;630:493–500. PubMed PMC

Cramer P. Organization and regulation of gene transcription. Nature. 2019;573:45–54. PubMed

Boehning M., Dugast-Darzacq C., Rankovic M., Hansen A.S., Yu T., Marie-Nelly H., et al. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nat. Struct. Mol. Biol. 2018;25:833–840. PubMed

Cisse I.I., Izeddin I., Causse S.Z., Boudarene L., Senecal A., Muresan L., et al. Real-time dynamics of RNA polymerase II clustering in live human cells. Science. 2013;341:664–667. PubMed

Iborra F.J., Pombo A., Jackson D.A., Cook P.R. Active RNA polymerases are localized within discrete transcription ‘factories’ in human nuclei. J. Cell Sci. 1996;109:1427–1436. PubMed

Guo Y.E., Manteiga J.C., Henninger J.E., Sabari B.R., Dall'Agnese A., Hannett N.M., et al. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates. Nature. 2019;572:543–548. PubMed PMC

Wu D., Huang H., Chen T., Gai X., Li Q., Wang C., et al. The BRCA1/BARD1 complex recognizes pre-ribosomal RNA to facilitate homologous recombination. Cell Discov. 2023;9:99. PubMed PMC

Düster R., Kaltheuner I.H., Schmitz M., Geyer M. 1,6-Hexanediol, commonly used to dissolve liquid–liquid phase separated condensates, directly impairs kinase and phosphatase activities. J. Biol. Chem. 2021;296 PubMed PMC

Patel A., Malinovska L., Saha S., Wang J., Alberti S., Krishnan Y., Hyman A.A. ATP as a biological hydrotrope. Science. 2017;356:753–756. PubMed

Linhartova K., Falginella F.L., Matl M., Sebesta M., Vácha R., Stefl R. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nat. Commun. 2024;15:9163. PubMed PMC

Yamane K., Katayama E., Tsuruo T. The BRCT regions of tumor suppressor BRCA1 and of XRCC1 show DNA end binding activity with a multimerizing feature. Biochem. Biophys. Res. Commun. 2000;279:678–684. PubMed

Hu Z., Mi S., Zhao T., Peng C., Peng Y., Chen L., et al. BGL3 lncRNA mediates retention of the BRCA1/BARD1 complex at DNA damage sites. EMBO J. 2020;39 PubMed PMC

Mark W.-Y., Liao J.C.C., Lu Y., Ayed A., Laister R., Szymczyna B., et al. Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein–protein and Protein–DNA interactions? J. Mol. Biol. 2005;345:275–287. PubMed

Naseem R., Sturdy A., Finch D., Jowitt T., Webb M. Mapping and conformational characterization of the DNA-binding region of the breast cancer susceptibility protein BRCA1. Biochem. J. 2006;395:529–535. PubMed PMC

Paull T.T., Cortez D., Bowers B., Elledge S.J., Gellert M. Direct DNA binding by Brca1. Proc. Natl. Acad. Sci. U. S. A. 2001;98:6086–6091. PubMed PMC

Zhang Q., Kim W., Panina S.B., Mayfield J.E., Portz B., Zhang Y.J. Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription. Nat. Commun. 2024;15:7985. PubMed PMC

Rawat P., Boehning M., Hummel B., Aprile-Garcia F., Pandit A.S., Eisenhardt N., et al. Stress-induced nuclear condensation of NELF drives transcriptional downregulation. Mol. Cell. 2021;81:1013–1026.e11. PubMed PMC

Tate J.G., Bamford S., Jubb H.C., Sondka Z., Beare D.M., Bindal N., et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2019;47:D941–D947. PubMed PMC

Pei G., Lyons H., Li P., Sabari B.R. Transcription regulation by biomolecular condensates. Nat. Rev. Mol. Cell Biol. 2024;26:213–236. PubMed PMC

Wu W., Nishikawa H., Hayami R., Sato K., Honda A., Aratani S., et al. BRCA1 ubiquitinates RPB8 in response to DNA damage. Cancer Res. 2007;67:951–958. PubMed

Kleiman F.E., Wu-Baer F., Fonseca D., Kaneko S., Baer R., Manley J.L. BRCA1/BARD1 inhibition of mRNA 3′ processing involves targeted degradation of RNA polymerase II. Genes Dev. 2005;19:1227–1237. PubMed PMC

Anindya R., Aygün 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. 2007;28:386–397. PubMed

Nakazawa Y., Hara Y., Oka Y., Komine O., van den Heuvel D., Guo C., et al. Ubiquitination of DNA damage-stalled RNAPII promotes transcription-coupled repair. Cell. 2020;180:1228–1244.e24. PubMed

Tufegdžić Vidaković A., Mitter R., Kelly G.P., Neumann M., Harreman M., Rodríguez-Martínez M., et al. Regulation of the RNAPII pool is integral to the DNA damage response. Cell. 2020;180:1245–1261.e21. PubMed PMC

Witus S.R., Stewart M.D., Klevit R.E. The BRCA1/BARD1 ubiquitin ligase and its substrates. Biochem. J. 2021;478:3467–3483. PubMed PMC

Hashizume R., Fukuda M., Maeda I., Nishikawa H., Oyake D., Yabuki Y., et al. The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation. J. Biol. Chem. 2001;276:14537–14540. PubMed

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. 2017;18:263–273. PubMed

Komarnitsky P., Cho E.-J., Buratowski S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 2000;14:2452–2460. PubMed PMC

Mayer A., Lidschreiber M., Siebert M., Leike K., Söding J., Cramer P. Uniform transitions of the general RNA polymerase II transcription complex. Nat. Struct. Mol. Biol. 2010;17:1272–1278. PubMed

Li M., Yu X. Function of BRCA1 in the DNA damage response is mediated by ADP-Ribosylation. Cancer Cell. 2013;23:693–704. PubMed PMC

Billing D., Horiguchi M., Wu-Baer F., Taglialatela A., Leuzzi G., Nanez S.A., et al. The BRCT domains of the BRCA1 and BARD1 tumor suppressors differentially regulate homology-directed repair and stalled fork protection. Mol. Cell. 2018;72:127–139.e8. PubMed PMC

Dai L., Dai Y., Han J., Huang Y., Wang L., Huang J., Zhou Z. Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin. Mol. Cell. 2021;81:2765–2777.e6. PubMed

Burdett H., Foglizzo M., Musgrove L.J., Kumar D., Clifford G., Campbell L.J., et al. BRCA1–BARD1 combines multiple chromatin recognition modules to bridge nascent nucleosomes. Nucleic Acids Res. 2023;51:11080–11103. PubMed PMC

Stiller J.W., Hall B.D. Evolution of the RNA polymerase II C-terminal domain. Proc. Natl. Acad. Sci. U. S. A. 2002;99:6091–6096. PubMed PMC

Ling Y.H., Ye Z., Liang C., Yu C., Park G., Corden J.L., Wu C. Disordered C-terminal domain drives spatiotemporal confinement of RNAPII to enhance search for chromatin targets. Nat. Cell Biol. 2024;26:581–592. PubMed PMC

Quintero-Cadena P., Lenstra T.L., Sternberg P.W. RNA pol II length and disorder enable cooperative scaling of transcriptional bursting. Mol. Cell. 2020;79:207–220.e8. PubMed

Fabbro M., Rodriguez J.A., Baer R., Henderson B.R. BARD1 induces BRCA1 intranuclear foci formation by increasing RING-dependent BRCA1 nuclear import and inhibiting BRCA1 nuclear export. J. Biol. Chem. 2002;277:21315–21324. PubMed

Sung P., Dutta A., Ji J.H., Fang Q., Zhou S., Liang F., et al. 2024. Mechanism of SETX-BRCA1-BARD1 complex in resolution of R-loops and transcription-replication conflicts. DOI

Brázda P., Krejčíková M., Kasiliauskaite A., Šmiřáková E., Klumpler T., Vácha R., et al. Yeast Spt6 reads multiple phosphorylation patterns of RNA polymerase II C-Terminal domain in vitro. J. Mol. Biol. 2020;432:4092–4107. PubMed PMC

Aslanidis C., de Jong P.J. Ligation-independent cloning of PCR products (LIC-PCR) Nucleic Acids Res. 1990;18:6069–6074. PubMed PMC

Lamprecht M.R., Sabatini D.M., Carpenter A.E. CellProfilerTM: free, versatile software for automated biological image analysis. Biotechniques. 2007;42:71–75. PubMed

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. PubMed PMC

Kabsch W. XDS. Acta Crystallogr. D Biol. Crystallogr. 2010;66:125–132. PubMed PMC

Agirre J., Atanasova M., Bagdonas H., Ballard C.B., Baslé A., Beilsten-Edmands J., et al. The CCP 4 suite: integrative software for macromolecular crystallography. Acta Crystallogr. D Struct. Biol. 2023;79:449–461. PubMed PMC

McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Crystallogr. 2007;40:658–674. PubMed PMC

Murshudov G.N., Skubák P., Lebedev A.A., Pannu N.S., Steiner R.A., Nicholls R.A., et al. REFMAC 5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 2011;67:355–367. PubMed PMC

Emsley P., Lohkamp B., Scott W.G., Cowtan K. Features and development of coot. Acta Crystallogr. D Biol. Crystallogr. 2010;66:486–501. PubMed PMC

Goddard T.D., Huang C.C., Meng E.C., Pettersen E.F., Couch G.S., Morris J.H., Ferrin T.E. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 2018;27:14–25. PubMed PMC

Tauriello G., Waterhouse A.M., Haas J., Behringer D., Bienert S., Garello T., Schwede T. ModelArchive: a deposition database for computational macromolecular structural models. J. Mol. Biol. 2025;437 PubMed