The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
Transcription factors with Perturb-seq knockdown data for MBD4. 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 = MBD4 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 MBD4, 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 |
|---|---|---|---|---|
| chr3:129,160,815–129,162,244 | 278.6 kb | Distal (>10kb) Multiome | 917 | |
| chr3:129,183,284–129,184,525 | 256.1 kb | Distal (>10kb) Multiome | 966 | |
| chr3:129,249,227–129,250,064 | 190.5 kb | Distal (>10kb) Multiome | 767 | |
| chr3:129,278,315–129,279,976 | 161.2 kb | Distal (>10kb) Multiome | 767 | |
| chr3:129,305,525–129,306,095 | 134.2 kb | Distal (>10kb) Multiome | 342 | |
| chr3:129,314,154–129,316,995 | 125.1 kb | Distal (>10kb) Multiome | 949 | |
| chr3:129,343,720–129,344,497 | 95.9 kb | Distal (>10kb) Multiome | 346 | |
| chr3:129,344,512–129,344,822 | 95.3 kb | Distal (>10kb) Multiome | 58 | |
| chr3:129,359,825–129,360,642 | 79.6 kb | Distal (>10kb) Multiome | 65 | |
| chr3:129,399,193–129,399,868 | 40.4 kb | Distal (>10kb) Multiome | 625 | |
| chr3:129,428,173–129,429,050 | 11.3 kb | Distal (>10kb) Multiome | 504 | |
| chr3:129,439,426–129,440,695 | 160 bp | At TSS Multiome | 875 | |
| chr3:129,444,041–129,444,682 | 4.0 kb | Proximal (<10kb) | 67 | |
| chr3:129,448,229–129,448,626 | 8.2 kb | Proximal (<10kb) | 197 | |
| chr3:129,534,465–129,535,515 | 94.9 kb | Distal (>10kb) Multiome | 397 | |
| chr3:129,602,230–129,602,769 | 162.5 kb | Distal (>10kb) Multiome | 70 | |
| chr3:129,605,081–129,607,497 | 166.9 kb | Distal (>10kb) Multiome | 686 | |
| chr3:129,626,284–129,628,391 | 186.8 kb | Distal (>10kb) Multiome | 862 | |
| chr3:129,699,077–129,699,564 | 259.3 kb | Distal (>10kb) Multiome | 166 |
Genomic view of the MBD4 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.