The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 (MIM 610602) and ALKBH3 are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).[supplied by OMIM, Mar 2008]
Transcription factors with Perturb-seq knockdown data for ALKBH3. 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 = ALKBH3 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 ALKBH3, 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 |
|---|---|---|---|---|
| chr11:43,643,882–43,644,534 | 236.7 kb | Distal (>10kb) Multiome | 809 | |
| chr11:43,680,105–43,681,375 | 200.2 kb | Distal (>10kb) Multiome | 774 | |
| chr11:43,880,452–43,881,136 | 66 bp | At TSS Multiome | 939 | |
| chr11:43,890,306–43,890,462 | 9.5 kb | Proximal (<10kb) | 104 | |
| chr11:43,942,022–43,943,596 | 61.6 kb | Distal (>10kb) Multiome | 499 | |
| chr11:44,065,829–44,066,798 | 185.4 kb | Distal (>10kb) Multiome | 696 | |
| chr11:44,078,830–44,079,335 | 198.2 kb | Distal (>10kb) Multiome | 60 | |
| chr11:44,095,519–44,096,650 | 215.0 kb | Distal (>10kb) Multiome | 621 |
Genomic view of the ALKBH3 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.