This gene is a classical cadherin from the cadherin superfamily. The encoded protein is a calcium-dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Based on studies in chicken and mouse, this cadherin is thought to play an important role during brain segmentation and neuronal outgrowth. In addition, a role in kidney and muscle development is indicated. Of particular interest are studies showing stable cis-heterodimers of cadherins 2 and 4 in cotransfected cell lines. Previously thought to interact in an exclusively homophilic manner, this is the first evidence of cadherin heterodimerization. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
Transcription factors with Perturb-seq knockdown data for CDH4. 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 = CDH4 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 CDH4, 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 |
|---|---|---|---|---|
| chr20:61,156,243–61,157,039 | 95.7 kb | Distal (>10kb) Multiome | 119 | |
| chr20:61,251,919–61,252,530 | 74 bp | At TSS Multiome | 126 | |
| chr20:61,252,683–61,254,102 | 423 bp | At TSS | 187 | |
| chr20:61,436,457–61,437,279 | 184.7 kb | Distal (>10kb) Multiome | 339 | |
| chr20:61,510,812–61,511,547 | 258.7 kb | Distal (>10kb) Multiome | 30 | |
| chr20:61,511,661–61,512,178 | 259.7 kb | Distal (>10kb) Multiome | 29 |
Genomic view of the CDH4 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.