The protein encoded by this gene removes 5' overhanging flaps in DNA repair and processes the 5' ends of Okazaki fragments in lagging strand DNA synthesis. Direct physical interaction between this protein and AP endonuclease 1 during long-patch base excision repair provides coordinated loading of the proteins onto the substrate, thus passing the substrate from one enzyme to another. The protein is a member of the XPG/RAD2 endonuclease family and is one of ten proteins essential for cell-free DNA replication. DNA secondary structure can inhibit flap processing at certain trinucleotide repeats in a length-dependent manner by concealing the 5' end of the flap that is necessary for both binding and cleavage by the protein encoded by this gene. Therefore, secondary structure can deter the protective function of this protein, leading to site-specific trinucleotide expansions. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for FEN1. 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 = FEN1 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 FEN1, 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 |
|---|---|---|---|---|
| chr11:61,508,087–61,510,095 | 284.3 kb | Distal (>10kb) Multiome | 740 | |
| chr11:61,567,110–61,568,033 | 225.4 kb | Distal (>10kb) Multiome | 1078 | |
| chr11:61,580,454–61,581,871 | 211.6 kb | Distal (>10kb) Multiome | 760 | |
| chr11:61,587,343–61,588,726 | 204.6 kb | Distal (>10kb) Multiome | 271 | |
| chr11:61,680,168–61,680,631 | 112.6 kb | Distal (>10kb) Multiome | 532 | |
| chr11:61,747,560–61,748,157 | 45.1 kb | Distal (>10kb) Multiome | 493 | |
| chr11:61,752,190–61,753,041 | 40.4 kb | Distal (>10kb) Multiome | 329 | |
| chr11:61,777,258–61,777,759 | 15.5 kb | Distal (>10kb) Multiome | 149 | |
| chr11:61,792,046–61,793,394 | 178 bp | At TSS Multiome | 896 | |
| chr11:61,814,541–61,817,407 | 22.3 kb | Distal (>10kb) Multiome | 1128 | |
| chr11:61,827,285–61,829,337 | 35.0 kb | Distal (>10kb) Multiome | 728 | |
| chr11:61,871,019–61,871,621 | 78.4 kb | Distal (>10kb) Multiome | 443 | |
| chr11:61,890,974–61,892,214 | 98.8 kb | Distal (>10kb) Multiome HiCAR | 619 | |
| chr11:61,898,986–61,899,424 | 106.3 kb | Distal (>10kb) Multiome | 498 | |
| chr11:61,917,152–61,917,983 | 124.6 kb | Distal (>10kb) Multiome | 465 | |
| chr11:61,955,466–61,956,219 | 162.9 kb | Distal (>10kb) Multiome | 217 | |
| chr11:61,966,654–61,968,718 | 174.7 kb | Distal (>10kb) Multiome | 939 | |
| chr11:61,971,541–61,972,360 | 179.1 kb | Distal (>10kb) Multiome | 877 |
Genomic view of the FEN1 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.