Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodimeric protein of 40-kD (DFFB) and 45-kD (DFFA) subunits. DFFA is the substrate for caspase-3 and triggers DNA fragmentation during apoptosis. DFF becomes activated when DFFA is cleaved by caspase-3. The cleaved fragments of DFFA dissociate from DFFB, the active component of DFF. DFFB has been found to trigger both DNA fragmentation and chromatin condensation during apoptosis. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for DFFA. 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 = DFFA 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 DFFA, 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 |
|---|---|---|---|---|
| chr1:10,209,800–10,211,585 | 262.1 kb | Distal (>10kb) Multiome | 934 | |
| chr1:10,398,334–10,400,006 | 73.5 kb | Distal (>10kb) Multiome | 1064 | |
| chr1:10,430,062–10,431,244 | 41.9 kb | Distal (>10kb) Multiome | 1007 | |
| chr1:10,472,017–10,472,900 | 8 bp | At TSS Multiome | 872 | |
| chr1:10,474,760–10,475,474 | 2.5 kb | Proximal (<10kb) Multiome | 744 | |
| chr1:10,638,357–10,639,497 | 166.7 kb | Distal (>10kb) Multiome | 126 | |
| chr1:10,679,481–10,679,929 | 207.3 kb | Distal (>10kb) Multiome | 463 | |
| chr1:10,693,857–10,695,287 | 222.3 kb | Distal (>10kb) Multiome | 382 | |
| chr1:10,704,382–10,704,894 | 232.2 kb | Distal (>10kb) Multiome | 393 |
Genomic view of the DFFA 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.