CpG methylation is an epigenetic modification that is important for embryonic development, imprinting, and X-chromosome inactivation. Studies in mice have demonstrated that DNA methylation is required for mammalian development. This gene encodes a DNA methyltransferase that is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes to the cytoplasm and nucleus and its expression is developmentally regulated. [provided by RefSeq, Mar 2016]
Transcription factors with Perturb-seq knockdown data for DNMT3A. 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 = DNMT3A 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 DNMT3A, 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 |
|---|---|---|---|---|
| chr2:24,971,247–24,972,384 | 370.5 kb | Distal (>10kb) Multiome | 1032 | |
| chr2:25,041,314–25,043,455 | 300.4 kb | Distal (>10kb) Multiome | 743 | |
| chr2:25,131,383–25,132,709 | 210.1 kb | Distal (>10kb) Multiome | 162 | |
| chr2:25,161,156–25,161,629 | 181.0 kb | Distal (>10kb) Multiome | 112 | |
| chr2:25,168,208–25,168,958 | 173.9 kb | Distal (>10kb) Multiome | 225 | |
| chr2:25,215,506–25,216,577 | 126.3 kb | Distal (>10kb) Multiome | 303 | |
| chr2:25,228,812–25,229,707 | 113.4 kb | Distal (>10kb) Multiome | 332 | |
| chr2:25,250,582–25,253,280 | 90.0 kb | Distal (>10kb) Multiome | 927 | |
| chr2:25,256,230–25,257,422 | 85.7 kb | Distal (>10kb) Multiome | 198 | |
| chr2:25,259,433–25,260,091 | 82.7 kb | Distal (>10kb) Multiome | 160 | |
| chr2:25,276,533–25,277,585 | 65.1 kb | Distal (>10kb) Multiome | 258 | |
| chr2:25,314,940–25,315,608 | 27.4 kb | Distal (>10kb) Multiome | 196 | |
| chr2:25,339,832–25,342,944 | 1 bp | At TSS Multiome | 921 | |
| chr2:25,361,777–25,362,353 | 19.6 kb | Distal (>10kb) Multiome | 654 | |
| chr2:25,376,446–25,377,553 | 34.5 kb | Distal (>10kb) Multiome | 758 | |
| chr2:27,250,040–27,250,883 | 1908.0 kb | Distal (>10kb) Multiome HiCAR | 559 |
Genomic view of the DNMT3A 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.