This gene encodes the homolog of the Drosophila melanogaster Nipped-B gene product and fungal Scc2-type sister chromatid cohesion proteins. The Drosophila protein facilitates enhancer-promoter communication of remote enhancers and plays a role in developmental regulation. It is also homologous to a family of chromosomal adherins with broad roles in sister chromatid cohesion, chromosome condensation, and DNA repair. The human protein has a bipartite nuclear targeting sequence and a putative HEAT repeat. Condensins, cohesins and other complexes with chromosome-related functions also contain HEAT repeats. Mutations in this gene result in Cornelia de Lange syndrome, a disorder characterized by dysmorphic facial features, growth delay, limb reduction defects, and cognitive disability. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for NIPBL. 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 = NIPBL 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 NIPBL, 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 |
|---|---|---|---|---|
| chr5:36,596,123–36,596,706 | 280.4 kb | Distal (>10kb) Multiome | 93 | |
| chr5:36,606,440–36,607,386 | 270.2 kb | Distal (>10kb) Multiome | 471 | |
| chr5:36,618,961–36,619,487 | 257.7 kb | Distal (>10kb) Multiome | 147 | |
| chr5:36,689,905–36,690,922 | 186.4 kb | Distal (>10kb) Multiome | 674 | |
| chr5:36,692,732–36,693,630 | 183.6 kb | Distal (>10kb) Multiome | 332 | |
| chr5:36,701,409–36,702,282 | 175.0 kb | Distal (>10kb) Multiome | 152 | |
| chr5:36,744,113–36,746,060 | 132.1 kb | Distal (>10kb) Multiome HiCAR | 801 | |
| chr5:36,870,542–36,870,736 | 6.0 kb | Proximal (<10kb) | 228 | |
| chr5:36,875,320–36,875,597 | 1.2 kb | Proximal (<10kb) | 305 | |
| chr5:36,875,838–36,877,715 | 29 bp | At TSS Multiome | 929 | |
| chr5:36,878,770–36,879,061 | 2.0 kb | Proximal (<10kb) | 201 | |
| chr5:37,086,434–37,087,024 | 209.8 kb | Distal (>10kb) Multiome | 249 | |
| chr5:37,090,010–37,091,198 | 213.6 kb | Distal (>10kb) Multiome | 257 |
Genomic view of the NIPBL 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.