Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site. This gene encodes a protein shown to have a weak class II AP endonuclease activity. Most of the encoded protein is located in the nucleus but some is also present in mitochondria. This protein may play an important role in both nuclear and mitochondrial base excision repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
Transcription factors with Perturb-seq knockdown data for APEX2. 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 = APEX2 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 APEX2, 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 |
|---|---|---|---|---|
| chrX:54,807,568–54,809,334 | 191.7 kb | Distal (>10kb) Multiome | 567 | |
| chrX:54,921,216–54,922,087 | 78.5 kb | Distal (>10kb) Multiome | 165 | |
| chrX:54,999,711–55,000,618 | 269 bp | At TSS Multiome | 555 | |
| chrX:55,120,460–55,121,511 | 120.6 kb | Distal (>10kb) Multiome | 226 | |
| chrX:55,152,693–55,153,258 | 152.6 kb | Distal (>10kb) Multiome | 44 | |
| chrX:55,160,695–55,161,885 | 160.8 kb | Distal (>10kb) Multiome | 679 |
Genomic view of the APEX2 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.