This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. Members of this family are important during development, and have been associated with X-linked visceral heterotaxy and holoprosencephaly type 5. This gene is closely linked to the gene encoding zinc finger protein of the cerebellum 1, a related family member on chromosome 3. Heterozygous deletion of these linked genes is involved in Dandy-Walker malformation, which is a congenital cerebellar malformation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Dec 2009]
Transcription factors with Perturb-seq knockdown data for ZIC4. 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 = ZIC4 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 ZIC4, 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 |
|---|---|---|---|---|
| chr3:147,341,284–147,342,319 | 50.5 kb | Distal (>10kb) Multiome HiCAR | 153 | |
| chr3:147,377,268–147,378,505 | 14.3 kb | Distal (>10kb) Multiome HiCAR | 219 | |
| chr3:147,383,715–147,383,923 | 8.5 kb | Proximal (<10kb) | 42 | |
| chr3:147,384,080–147,385,652 | 7.5 kb | Proximal (<10kb) Multiome HiCAR | 161 | |
| chr3:147,387,708–147,388,496 | 3.9 kb | Proximal (<10kb) | 83 | |
| chr3:147,388,657–147,389,385 | 3.0 kb | Proximal (<10kb) | 108 | |
| chr3:147,389,823–147,390,190 | 2.2 kb | Proximal (<10kb) | 61 | |
| chr3:147,390,694–147,392,937 | 66 bp | At TSS Multiome | 431 | |
| chr3:147,393,089–147,393,978 | 1.2 kb | Proximal (<10kb) Multiome | 259 | |
| chr3:147,394,484–147,395,479 | 2.1 kb | Proximal (<10kb) | 203 | |
| chr3:147,395,609–147,398,664 | 5.0 kb | Proximal (<10kb) Multiome | 361 | |
| chr3:147,404,629–147,406,048 | 7.4 kb | Proximal (<10kb) | 119 | |
| chr3:147,407,129–147,407,537 | 9.9 kb | Proximal (<10kb) | 55 | |
| chr3:147,407,896–147,411,733 | 16.9 kb | Distal (>10kb) Multiome | 449 | |
| chr3:147,418,882–147,421,916 | 27.0 kb | Distal (>10kb) Multiome HiCAR | 338 |
Genomic view of the ZIC4 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.