DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. This gene belongs to a family of nuclear proteins which are characterized by the presence of a methyl-CpG binding domain (MBD). The encoded protein is a subunit of the NuRD, a multisubunit complex containing nucleosome remodeling and histone deacetylase activities. Unlike the other family members, the encoded protein is not capable of binding to methylated DNA. The protein mediates the association of metastasis-associated protein 2 with the core histone deacetylase complex. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]
Transcription factors with Perturb-seq knockdown data for MBD3. 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 = MBD3 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 MBD3, 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 |
|---|---|---|---|---|
| chr19:1,354,303–1,355,411 | 238.0 kb | Distal (>10kb) Multiome | 688 | |
| chr19:1,383,122–1,384,333 | 209.2 kb | Distal (>10kb) Multiome | 1228 | |
| chr19:1,401,101–1,401,839 | 191.3 kb | Distal (>10kb) Multiome | 540 | |
| chr19:1,406,589–1,408,783 | 185.4 kb | Distal (>10kb) Multiome | 911 | |
| chr19:1,415,008–1,415,721 | 177.4 kb | Distal (>10kb) Multiome | 597 | |
| chr19:1,437,988–1,438,998 | 154.5 kb | Distal (>10kb) Multiome | 1076 | |
| chr19:1,444,785–1,447,383 | 147.6 kb | Distal (>10kb) Multiome | 797 | |
| chr19:1,455,191–1,456,421 | 137.0 kb | Distal (>10kb) Multiome | 491 | |
| chr19:1,468,941–1,469,903 | 123.6 kb | Distal (>10kb) Multiome | 242 | |
| chr19:1,470,088–1,471,597 | 122.1 kb | Distal (>10kb) Multiome | 544 | |
| chr19:1,478,772–1,479,848 | 113.5 kb | Distal (>10kb) Multiome | 857 | |
| chr19:1,489,566–1,491,829 | 102.0 kb | Distal (>10kb) Multiome | 836 | |
| chr19:1,507,230–1,508,699 | 84.7 kb | Distal (>10kb) Multiome | 596 | |
| chr19:1,512,960–1,513,686 | 79.7 kb | Distal (>10kb) Multiome | 541 | |
| chr19:1,523,798–1,524,624 | 68.8 kb | Distal (>10kb) Multiome | 263 | |
| chr19:1,566,277–1,568,916 | 26.1 kb | Distal (>10kb) Multiome | 748 | |
| chr19:1,592,085–1,593,444 | 116 bp | At TSS Multiome | 883 | |
| chr19:1,604,859–1,606,501 | 12.8 kb | Distal (>10kb) Multiome | 902 | |
| chr19:1,651,519–1,653,514 | 60.1 kb | Distal (>10kb) Multiome | 909 | |
| chr19:1,725,307–1,726,101 | 132.9 kb | Distal (>10kb) Multiome | 455 | |
| chr19:1,811,638–1,813,347 | 219.8 kb | Distal (>10kb) Multiome HiCAR | 782 | |
| chr19:1,826,853–1,827,379 | 234.4 kb | Distal (>10kb) Multiome | 193 | |
| chr19:1,848,048–1,848,953 | 255.8 kb | Distal (>10kb) Multiome | 819 | |
| chr19:1,851,701–1,852,216 | 259.1 kb | Distal (>10kb) Multiome | 115 | |
| chr19:1,855,082–1,856,620 | 262.6 kb | Distal (>10kb) Multiome | 476 | |
| chr19:1,861,439–1,865,723 | 271.1 kb | Distal (>10kb) Multiome | 891 | |
| chr19:1,875,645–1,876,693 | 283.4 kb | Distal (>10kb) Multiome | 887 | |
| chr19:1,885,058–1,885,861 | 292.7 kb | Distal (>10kb) Multiome | 495 |
Genomic view of the MBD3 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.