The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. The AP sites are the most frequent pre-mutagenic lesions that can prevent normal DNA replication. Splice variants have been found for this gene; all encode the same protein. Disruptions in the biological functions related to APEX are associated with many various malignancies and neurodegenerative diseases.[provided by RefSeq, Dec 2019]
Transcription factors with Perturb-seq knockdown data for APEX1. 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 = APEX1 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 APEX1, 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 |
|---|---|---|---|---|
| chr14:20,332,742–20,333,665 | 122.0 kb | Distal (>10kb) Multiome | 694 | |
| chr14:20,342,187–20,344,100 | 111.9 kb | Distal (>10kb) Multiome | 1112 | |
| chr14:20,412,688–20,413,758 | 41.9 kb | Distal (>10kb) Multiome | 865 | |
| chr14:20,454,384–20,455,825 | 151 bp | At TSS Multiome | 1012 | |
| chr14:20,460,777–20,462,259 | 6.4 kb | Proximal (<10kb) Multiome | 995 | |
| chr14:20,468,846–20,470,856 | 14.2 kb | Distal (>10kb) Multiome | 950 | |
| chr14:20,494,584–20,495,486 | 39.8 kb | Distal (>10kb) Multiome | 201 | |
| chr14:20,609,147–20,610,547 | 154.9 kb | Distal (>10kb) Multiome HiCAR | 852 | |
| chr14:20,612,915–20,614,464 | 158.4 kb | Distal (>10kb) Multiome | 1003 | |
| chr14:20,624,684–20,626,122 | 170.1 kb | Distal (>10kb) Multiome | 728 | |
| chr14:20,630,325–20,631,286 | 175.5 kb | Distal (>10kb) Multiome | 507 | |
| chr14:20,631,700–20,633,862 | 178.0 kb | Distal (>10kb) Multiome | 757 | |
| chr14:20,642,696–20,643,499 | 187.8 kb | Distal (>10kb) Multiome | 52 | |
| chr14:20,644,459–20,645,301 | 189.5 kb | Distal (>10kb) Multiome | 52 | |
| chr14:20,652,905–20,654,391 | 198.1 kb | Distal (>10kb) Multiome | 320 | |
| chr14:20,657,425–20,658,132 | 202.6 kb | Distal (>10kb) Multiome | 320 | |
| chr14:20,662,835–20,663,940 | 208.1 kb | Distal (>10kb) Multiome | 587 | |
| chr14:20,681,216–20,685,294 | 229.2 kb | Distal (>10kb) Multiome | 1181 | |
| chr14:20,705,982–20,707,066 | 251.2 kb | Distal (>10kb) Multiome | 110 | |
| chr14:20,732,350–20,732,945 | 277.4 kb | Distal (>10kb) Multiome | 51 |
Genomic view of the APEX1 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.