This gene encodes a member of the steroid-thyroid hormone-retinoid receptor superfamily. Expression is induced by phytohemagglutinin in human lymphocytes and by serum stimulation of arrested fibroblasts. The encoded protein acts as a nuclear transcription factor. Translocation of the protein from the nucleus to mitochondria induces apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]
Transcription factors with Perturb-seq knockdown data for NR4A1. 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 = NR4A1 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 NR4A1, 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 |
|---|---|---|---|---|
| chr12:51,813,977–51,815,076 | 222.8 kb | Distal (>10kb) Multiome | 486 | |
| chr12:51,820,355–51,822,541 | 216.2 kb | Distal (>10kb) Multiome | 412 | |
| chr12:51,846,754–51,849,656 | 190.0 kb | Distal (>10kb) Multiome | 440 | |
| chr12:51,863,484–51,864,666 | 173.0 kb | Distal (>10kb) Multiome | 326 | |
| chr12:51,887,921–51,888,408 | 149.1 kb | Distal (>10kb) Multiome | 151 | |
| chr12:51,951,120–51,952,143 | 85.6 kb | Distal (>10kb) Multiome | 587 | |
| chr12:52,005,871–52,007,901 | 30.4 kb | Distal (>10kb) Multiome | 293 | |
| chr12:52,010,041–52,010,749 | 26.8 kb | Distal (>10kb) Multiome | 443 | |
| chr12:52,014,577–52,015,139 | 22.3 kb | Distal (>10kb) Multiome | 72 | |
| chr12:52,022,754–52,024,212 | 13.4 kb | Distal (>10kb) Multiome | 630 | |
| chr12:52,025,442–52,026,162 | 11.4 kb | Distal (>10kb) Multiome | 629 | |
| chr12:52,029,773–52,030,002 | 7.2 kb | Proximal (<10kb) | 149 | |
| chr12:52,032,739–52,033,401 | 4.1 kb | Proximal (<10kb) Multiome | 640 | |
| chr12:52,036,744–52,037,531 | 40 bp | At TSS Multiome | 625 | |
| chr12:52,050,161–52,052,728 | 14.1 kb | Distal (>10kb) Multiome | 861 | |
| chr12:52,069,275–52,070,473 | 32.5 kb | Distal (>10kb) Multiome HiCAR | 901 | |
| chr12:52,119,893–52,120,359 | 83.0 kb | Distal (>10kb) Multiome HiCAR | 380 | |
| chr12:52,163,813–52,164,287 | 127.0 kb | Distal (>10kb) Multiome | 450 | |
| chr12:52,232,988–52,233,518 | 195.9 kb | Distal (>10kb) Multiome | 170 | |
| chr12:52,308,190–52,308,768 | 271.4 kb | Distal (>10kb) Multiome | 295 |
Genomic view of the NR4A1 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.