The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]
Transcription factors with Perturb-seq knockdown data for NUP54. 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 = NUP54 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 NUP54, 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 |
|---|---|---|---|---|
| chr4:75,848,100–75,848,739 | 300.1 kb | Distal (>10kb) Multiome | 281 | |
| chr4:75,939,639–75,941,475 | 207.5 kb | Distal (>10kb) Multiome | 762 | |
| chr4:75,990,621–75,991,159 | 157.5 kb | Distal (>10kb) Multiome | 782 | |
| chr4:76,087,045–76,087,527 | 61.2 kb | Distal (>10kb) Multiome | 438 | |
| chr4:76,147,405–76,148,870 | 6 bp | At TSS Multiome | 1076 | |
| chr4:76,212,911–76,214,625 | 65.3 kb | Distal (>10kb) Multiome | 798 | |
| chr4:76,251,398–76,252,255 | 103.3 kb | Distal (>10kb) Multiome | 710 | |
| chr4:76,305,965–76,307,583 | 158.1 kb | Distal (>10kb) Multiome | 793 |
Genomic view of the NUP54 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.