Nop56p is a yeast nucleolar protein that is part of a complex with the nucleolar proteins Nop58p and fibrillarin. Nop56p is required for assembly of the 60S ribosomal subunit and is involved in pre-rRNA processing. The protein encoded by this gene is similar in sequence to Nop56p and is also found in the nucleolus. Expansion of a GGCCTG repeat from 3-8 copies to 1500-2500 copies in an intron of this gene results in spinocerebellar ataxia 36. Multiple transcript variants encoding several different isoforms have been found for this gene, but the full-length nature of most of them has not been determined. [provided by RefSeq, Jul 2016]
Transcription factors with Perturb-seq knockdown data for NOP56. 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 = NOP56 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 NOP56, 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 |
|---|---|---|---|---|
| chr20:2,470,152–2,471,296 | 181.8 kb | Distal (>10kb) Multiome | 1126 | |
| chr20:2,508,648–2,509,663 | 143.6 kb | Distal (>10kb) Multiome | 854 | |
| chr20:2,524,432–2,525,455 | 128.0 kb | Distal (>10kb) Multiome | 724 | |
| chr20:2,536,033–2,536,583 | 116.3 kb | Distal (>10kb) Multiome | 42 | |
| chr20:2,651,802–2,653,286 | 90 bp | At TSS Multiome | 1060 | |
| chr20:2,658,803–2,659,102 | 6.2 kb | Proximal (<10kb) | 315 | |
| chr20:2,663,925–2,664,409 | 11.6 kb | Distal (>10kb) Multiome | 908 | |
| chr20:2,692,159–2,694,013 | 40.0 kb | Distal (>10kb) Multiome | 584 | |
| chr20:2,752,636–2,753,047 | 100.1 kb | Distal (>10kb) Multiome | 395 | |
| chr20:2,800,326–2,801,021 | 148.1 kb | Distal (>10kb) Multiome | 349 | |
| chr20:2,840,006–2,841,330 | 188.0 kb | Distal (>10kb) Multiome | 997 | |
| chr20:2,872,329–2,874,047 | 220.9 kb | Distal (>10kb) Multiome | 980 |
Genomic view of the NOP56 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.