This gene encodes a protein containing zinc finger motifs and a cysteine peptidase domain. The encoded protein functions as a K63-specific de-ubiquitinating enzyme that specifically cleaves long K63-linked polyubiquitin chains in the middle of a chain (i.e. "endo cleavage) rather than by removing the terminal ubiquitin from a chain. This enzyme is thought to be involved in the regulation of DNA repair by cleaving K63-linked ubiquitin chains at repair foci. This protein is related to proteases for the ubiquitin-like modifiers Ufm1 (ubiquitin fold modifier 1) and Atg8/Gabarapl2, but does not have any activity on these modifiers. [provided by RefSeq, Mar 2018]
Transcription factors with Perturb-seq knockdown data for ZUP1. 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 = ZUP1 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 ZUP1, 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 |
|---|---|---|---|---|
| chr6:116,370,005–116,371,990 | 297.8 kb | Distal (>10kb) Multiome | 655 | |
| chr6:116,461,655–116,462,775 | 206.5 kb | Distal (>10kb) Multiome | 421 | |
| chr6:116,570,743–116,571,945 | 97.4 kb | Distal (>10kb) Multiome | 1041 | |
| chr6:116,615,808–116,617,150 | 52.4 kb | Distal (>10kb) Multiome | 493 | |
| chr6:116,668,238–116,668,984 | 70 bp | At TSS Multiome | 746 | |
| chr6:116,680,569–116,682,340 | 12.4 kb | Distal (>10kb) Multiome | 965 | |
| chr6:116,764,518–116,766,081 | 96.8 kb | Distal (>10kb) Multiome | 447 | |
| chr6:116,876,238–116,878,022 | 208.4 kb | Distal (>10kb) Multiome | 339 |
Genomic view of the ZUP1 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.