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 which is thought to function in de novo methylation, rather than maintenance methylation. The protein localizes primarily to the nucleus and its expression is developmentally regulated. Mutations in this gene cause the immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome. Eight alternatively spliced transcript variants have been described. The full length sequences of variants 4 and 5 have not been determined. [provided by RefSeq, May 2011]
Transcription factors with Perturb-seq knockdown data for DNMT3B. 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 = DNMT3B 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 DNMT3B, 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 |
|---|---|---|---|---|
| chr20:32,482,216–32,484,943 | 278.7 kb | Distal (>10kb) Multiome | 976 | |
| chr20:32,521,770–32,522,231 | 240.4 kb | Distal (>10kb) Multiome | 550 | |
| chr20:32,535,878–32,537,141 | 225.8 kb | Distal (>10kb) Multiome | 665 | |
| chr20:32,582,894–32,585,976 | 179.1 kb | Distal (>10kb) Multiome | 755 | |
| chr20:32,742,092–32,742,834 | 20.0 kb | Distal (>10kb) Multiome | 246 | |
| chr20:32,743,843–32,744,515 | 18.4 kb | Distal (>10kb) Multiome | 356 | |
| chr20:32,758,671–32,759,012 | 3.4 kb | Proximal (<10kb) | 82 | |
| chr20:32,761,666–32,763,859 | 114 bp | At TSS Multiome | 903 | |
| chr20:32,764,497–32,765,161 | 2.4 kb | Proximal (<10kb) Multiome | 223 | |
| chr20:32,819,557–32,820,685 | 57.6 kb | Distal (>10kb) Multiome | 907 | |
| chr20:32,950,448–32,950,932 | 188.3 kb | Distal (>10kb) Multiome | 85 | |
| chr20:32,974,370–32,975,976 | 212.7 kb | Distal (>10kb) Multiome | 138 | |
| chr20:32,976,142–32,976,882 | 214.2 kb | Distal (>10kb) Multiome | 240 | |
| chr20:33,014,111–33,015,188 | 252.2 kb | Distal (>10kb) Multiome | 255 |
Genomic view of the DNMT3B 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.