BRCA1
BRCA1 DNA repair associated | BRCC1, FANCS, PPP1R53, RNF53

This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]

Member of: DE-6 DE-6.1 Developmental clusters: GC4
Biological processes 105 terms
BRCA1-A complex (GO:0070531)BRCA1-A complex (GO:0070531)BRCA1-BARD1 complex (GO:0031436)BRCA1-BARD1 complex (GO:0031436)DNA binding (GO:0003677)DNA binding (GO:0003677)DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA damage tolerance (GO:0006301)DNA repair (GO:0006281)DNA repair (GO:0006281)DNA strand resection involved in replication fork processing (GO:0110025)RNA binding (GO:0003723)RNA polymerase binding (GO:0070063)XY body (GO:0001741)cellular response to indole-3-methanol (GO:0071681)cellular response to ionizing radiation (GO:0071479)cellular response to tumor necrosis factor (GO:0071356)chordate embryonic development (GO:0043009)chromatin remodeling (GO:0006338)chromosome (GO:0005694)chromosome (GO:0005694)chromosome segregation (GO:0007059)condensed chromosome (GO:0000793)condensed nuclear chromosome (GO:0000794)cytoplasm (GO:0005737)cytoplasm (GO:0005737)damaged DNA binding (GO:0003684)double-strand break repair (GO:0006302)double-strand break repair (GO:0006302)double-strand break repair (GO:0006302)double-strand break repair (GO:0006302)double-strand break repair via homologous recombination (GO:0000724)double-strand break repair via homologous recombination (GO:0000724)enzyme binding (GO:0019899)gamma-tubulin ring complex (GO:0000931)histone H2AK127 ubiquitin ligase activity (GO:0140863)histone H2AK129 ubiquitin ligase activity (GO:0140864)homologous recombination (GO:0035825)identical protein binding (GO:0042802)intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)lateral element (GO:0000800)metal ion binding (GO:0046872)mitotic G2 DNA damage checkpoint signaling (GO:0007095)mitotic G2 DNA damage checkpoint signaling (GO:0007095)mitotic G2/M transition checkpoint (GO:0044818)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of cell cycle (GO:0045786)negative regulation of cell growth (GO:0030308)negative regulation of centriole replication (GO:0046600)negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)negative regulation of fatty acid biosynthetic process (GO:0045717)negative regulation of gene expression via chromosomal CpG island methylation (GO:0044027)negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)negative regulation of reactive oxygen species metabolic process (GO:2000378)nuclear body (GO:0016604)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)p53 binding (GO:0002039)plasma membrane (GO:0005886)positive regulation of DNA repair (GO:0045739)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of angiogenesis (GO:0045766)positive regulation of gene expression (GO:0010628)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of vascular endothelial growth factor production (GO:0010575)protein K6-linked ubiquitination (GO:0085020)protein autoubiquitination (GO:0051865)protein binding (GO:0005515)protein ubiquitination (GO:0016567)protein ubiquitination (GO:0016567)protein-containing complex (GO:0032991)regulation of DNA damage checkpoint (GO:2000001)regulation of DNA repair (GO:0006282)regulation of cell cycle (GO:0051726)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)response to ionizing radiation (GO:0010212)ribonucleoprotein complex (GO:1990904)sex-chromosome dosage compensation (GO:0007549)transcription cis-regulatory region binding (GO:0000976)transcription cis-regulatory region binding (GO:0000976)transcription coactivator activity (GO:0003713)transcription coactivator activity (GO:0003713)transcription coactivator activity (GO:0003713)tubulin binding (GO:0015631)ubiquitin ligase complex (GO:0000151)ubiquitin protein ligase activity (GO:0061630)ubiquitin protein ligase binding (GO:0031625)ubiquitin-modified histone reader activity (GO:0061649)ubiquitin-protein transferase activity (GO:0004842)ubiquitin-protein transferase activity (GO:0004842)ubiquitin-protein transferase activity (GO:0004842)ubiquitin-protein transferase activity (GO:0004842)zinc ion binding (GO:0008270)zinc ion binding (GO:0008270)
Expression (TPM)
BRCA1 — as a Regulated Gene

TFs regulating BRCA1 0 TFs

Transcription factors with Perturb-seq knockdown data for BRCA1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = BRCA1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to BRCA1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of BRCA1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr17:42,832,889–42,833,841 292.0 kb Distal (>10kb) Multiome 980
chr17:42,964,237–42,964,843 160.9 kb Distal (>10kb) Multiome 655
chr17:42,979,966–42,981,044 144.9 kb Distal (>10kb) Multiome 843
chr17:42,997,598–42,998,917 127.1 kb Distal (>10kb) Multiome 1112
chr17:43,021,026–43,022,568 103.0 kb Distal (>10kb) Multiome 973
chr17:43,024,255–43,025,752 100.3 kb Distal (>10kb) Multiome 811
chr17:43,124,981–43,125,702 119 bp At TSS Multiome 837
chr17:43,169,744–43,171,576 45.8 kb Distal (>10kb) Multiome 1018
chr17:43,211,494–43,212,392 86.6 kb Distal (>10kb) Multiome 586
chr17:43,359,784–43,361,254 235.7 kb Distal (>10kb) Multiome 981
chr17:43,367,132–43,369,458 243.8 kb Distal (>10kb) Multiome 1146
chr17:43,388,101–43,389,658 264.0 kb Distal (>10kb) Multiome 770
chr17:43,396,555–43,396,987 271.4 kb Distal (>10kb) Multiome 27
chr17:43,398,359–43,400,469 273.5 kb Distal (>10kb) Multiome 827
chr17:43,403,154–43,404,714 278.6 kb Distal (>10kb) Multiome 252
chr17:43,406,748–43,407,604 281.8 kb Distal (>10kb) Multiome 102

Genome Browser

Genomic view of the BRCA1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr17:42,822,889 – 43,417,604
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq