title: BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair.
abstract: The mechanisms contributing to transcription-associated genomic instability are both complex and incompletely understood. Although R-loops are normal transcriptional intermediates, they are also associated with genomic instability. Here, we show that BRCA1 is recruited to R-loops that form normally over a subset of transcription termination regions. There it mediates the recruitment of a specific, physiological binding partner, senataxin (SETX). Disruption of this complex led to R-loop-driven DNA damage at those loci as reflected by adjacent γ-H2AX accumulation and ssDNA breaks within the untranscribed strand of relevant R-loop structures. Genome-wide analysis revealed widespread BRCA1 binding enrichment at R-loop-rich termination regions (TRs) of actively transcribed genes. Strikingly, within some of these genes in BRCA1 null breast tumors, there are specific insertion/deletion mutations located close to R-loop-mediated BRCA1 binding sites within TRs. Thus, BRCA1/SETX complexes support a DNA repair mechanism that addresses R-loop-based DNA damage at transcriptional pause sites.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address: elodiey_hatchi@dfci.harvard.edu.
authors.forename: Elodie
authors.initials: E
authors.lastname: Hatchi
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
authors.forename: Konstantina
authors.initials: K
authors.lastname: Skourti-Stathaki
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
authors.forename: Steffen
authors.initials: S
authors.lastname: Ventz
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
authors.forename: Luca
authors.initials: L
authors.lastname: Pinello
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: Yen
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
authors.forename: Kinga
authors.initials: K
authors.lastname: Kamieniarz-Gdula
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
authors.forename: Stoil
authors.initials: S
authors.lastname: Dimitrov
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
authors.forename: Shailja
authors.initials: S
authors.lastname: Pathania
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
authors.forename: Kristine M
authors.initials: KM
authors.lastname: McKinney
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Eaton
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory (CSAIL), MIT, Cambridge, MA 02139, USA.
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Hill
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Parmigiani
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Proudfoot
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA. Electronic address: david_livingston@dfci.harvard.edu.
authors.forename: David M
authors.initials: DM
authors.lastname: Livingston
mesh_terms: D019313:BRCA1 Protein / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D004249:DNA Damage; D004265:DNA Helicases; D004260:DNA Repair; D006367:HeLa Cells; D006801:Humans; D008957:Models, Genetic; D064251:Multifunctional Enzymes; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D019313:BRCA1 Protein; C492913:BRCA1 protein, human; D064251:Multifunctional Enzymes; C484368:SETX protein, human; D004265:DNA Helicases; D020365:RNA Helicases