DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. The protein encoded by this gene may function as a mediator of the biological consequences of the methylation signal. It is also reported that the this protein functions as a demethylase to activate transcription, as DNA methylation causes gene silencing. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2011]
Transcription factors with Perturb-seq knockdown data for MBD2. 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 = MBD2 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 MBD2, 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 |
|---|---|---|---|---|
| chr18:54,223,556–54,225,199 | 49 bp | At TSS Multiome | 810 | |
| chr18:54,227,157–54,227,856 | 2.5 kb | Proximal (<10kb) | 13 | |
| chr18:54,228,186–54,228,761 | 3.6 kb | Proximal (<10kb) | 179 | |
| chr18:54,232,950–54,233,129 | 8.3 kb | Proximal (<10kb) | 30 | |
| chr18:54,235,612–54,236,484 | 11.5 kb | Distal (>10kb) Multiome | 178 | |
| chr18:54,246,611–54,248,045 | 22.6 kb | Distal (>10kb) Multiome | 501 | |
| chr18:54,268,849–54,270,571 | 45.0 kb | Distal (>10kb) Multiome | 936 | |
| chr18:54,357,058–54,358,694 | 133.3 kb | Distal (>10kb) Multiome | 739 | |
| chr18:54,480,384–54,481,350 | 256.2 kb | Distal (>10kb) Multiome | 108 |
Genomic view of the MBD2 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.