This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha (DNMT3A), and reduces DNMT3A-mediated CpG island methylation. It is suggested that silencing of this gene, resulting in acceleration of DNA methylation, may have a role in oncogenesis. [provided by RefSeq, Oct 2011]
Transcription factors with Perturb-seq knockdown data for SALL3. 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 = SALL3 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 SALL3, 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 |
|---|---|---|---|---|
| chr18:78,972,886–78,974,829 | 5.4 kb | Proximal (<10kb) | 174 | |
| chr18:78,977,520–78,977,712 | 2.6 kb | Proximal (<10kb) | 20 | |
| chr18:78,977,822–78,978,220 | 2.1 kb | Proximal (<10kb) | 33 | |
| chr18:78,978,336–78,981,364 | 168 bp | At TSS Multiome | 292 | |
| chr18:78,984,810–78,985,736 | 4.9 kb | Proximal (<10kb) Multiome | 173 | |
| chr18:78,986,067–78,986,483 | 5.8 kb | Proximal (<10kb) | 137 | |
| chr18:79,068,341–79,069,941 | 89.0 kb | Distal (>10kb) Multiome | 886 | |
| chr18:79,246,410–79,246,885 | 266.4 kb | Distal (>10kb) Multiome | 387 |
Genomic view of the SALL3 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.