This gene belongs to the ubiquitin C-terminal hydrolase subfamily of deubiquitinating enzymes that are involved in the removal of ubiquitin from proteins. The encoded enzyme binds to the breast cancer type 1 susceptibility protein (BRCA1) via the RING finger domain of the latter and acts as a tumor suppressor. In addition, the enzyme may be involved in regulation of transcription, regulation of cell cycle and growth, response to DNA damage and chromatin dynamics. Germline mutations in this gene may be associated with tumor predisposition syndrome (TPDS), which involves increased risk of cancers including malignant mesothelioma, uveal melanoma and cutaneous melanoma. [provided by RefSeq, May 2013]
Transcription factors with Perturb-seq knockdown data for BAP1. 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 = BAP1 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 BAP1, 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 |
|---|---|---|---|---|
| chr3:52,128,194–52,128,700 | 281.6 kb | Distal (>10kb) Multiome | 376 | |
| chr3:52,153,766–52,155,196 | 255.3 kb | Distal (>10kb) Multiome | 896 | |
| chr3:52,197,554–52,198,856 | 211.9 kb | Distal (>10kb) Multiome | 731 | |
| chr3:52,238,767–52,239,716 | 170.7 kb | Distal (>10kb) Multiome | 763 | |
| chr3:52,245,446–52,246,450 | 164.0 kb | Distal (>10kb) Multiome | 553 | |
| chr3:52,277,664–52,279,184 | 131.3 kb | Distal (>10kb) Multiome | 844 | |
| chr3:52,287,499–52,288,336 | 122.0 kb | Distal (>10kb) Multiome HiCAR | 778 | |
| chr3:52,409,430–52,411,187 | 353 bp | At TSS Multiome | 813 | |
| chr3:52,412,177–52,412,350 | 2.2 kb | Proximal (<10kb) | 116 | |
| chr3:52,444,941–52,445,411 | 35.2 kb | Distal (>10kb) Multiome | 426 | |
| chr3:52,455,213–52,455,878 | 45.6 kb | Distal (>10kb) Multiome | 630 | |
| chr3:52,518,607–52,519,389 | 109.0 kb | Distal (>10kb) Multiome | 176 | |
| chr3:52,533,486–52,535,316 | 124.0 kb | Distal (>10kb) Multiome | 648 | |
| chr3:52,536,232–52,537,450 | 126.6 kb | Distal (>10kb) Multiome | 901 | |
| chr3:52,685,427–52,686,463 | 275.9 kb | Distal (>10kb) Multiome | 933 | |
| chr3:52,705,495–52,706,415 | 296.0 kb | Distal (>10kb) Multiome | 862 |
Genomic view of the BAP1 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.