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]
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.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
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 |
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.