The protein encoded by this gene belongs to the B-cell CLL/lymphoma 2 and adenovirus E1B 19 kDa interacting family, whose members play roles in many cellular processes including apotosis, cell transformation, and synaptic function. Several functions for this protein have been demonstrated including suppression of Ras homolog family member A activity, which results in reduced stress fiber formation and suppression of oncogenic cellular transformation. A high molecular weight isoform of this protein has also been shown to colocalize with Adaptor protein complex 2, beta-Adaptin and endodermal markers, suggesting an involvement in post-endocytic trafficking. In prostate cancer cells, this gene acts as a tumor suppressor and its expression is regulated by prostate cancer antigen 3, a non-protein coding gene on the opposite DNA strand in an intron of this gene. Prostate cancer antigen 3 regulates levels of this gene through formation of a double-stranded RNA that undergoes adenosine deaminase actin on RNA-dependent adenosine-to-inosine RNA editing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
Transcription factors with Perturb-seq knockdown data for PRUNE2. 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 = PRUNE2 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 PRUNE2, 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 |
|---|---|---|---|---|
| chr9:76,393,705–76,395,262 | 511.7 kb | Distal (>10kb) Multiome | 993 | |
| chr9:76,458,756–76,460,917 | 446.9 kb | Distal (>10kb) Multiome HiCAR | 663 | |
| chr9:76,905,420–76,906,943 | 191 bp | At TSS Multiome | 534 | |
| chr9:77,011,944–77,012,817 | 106.1 kb | Distal (>10kb) Multiome | 473 | |
| chr9:77,015,830–77,017,016 | 110.3 kb | Distal (>10kb) Multiome | 167 | |
| chr9:77,018,024–77,021,113 | 112.7 kb | Distal (>10kb) Multiome | 262 | |
| chr9:77,038,220–77,038,935 | 132.4 kb | Distal (>10kb) Multiome | 155 | |
| chr9:77,128,274–77,128,777 | 222.5 kb | Distal (>10kb) Multiome | 81 | |
| chr9:77,176,705–77,178,700 | 271.2 kb | Distal (>10kb) Multiome | 914 |
Genomic view of the PRUNE2 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.