The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
Transcription factors with Perturb-seq knockdown data for NANOG. 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 = NANOG 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 NANOG, 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 |
|---|---|---|---|---|
| chr12:7,638,028–7,638,994 | 149.1 kb | Distal (>10kb) Multiome | 360 | |
| chr12:7,639,859–7,640,636 | 147.4 kb | Distal (>10kb) Multiome | 28 | |
| chr12:7,709,770–7,710,489 | 77.7 kb | Distal (>10kb) Multiome HiCAR | 82 | |
| chr12:7,787,660–7,788,021 | at TSS | At TSS | 43 | |
| chr12:7,789,219–7,789,438 | 1.4 kb | Proximal (<10kb) | 68 | |
| chr12:7,859,953–7,860,905 | 72.6 kb | Distal (>10kb) Multiome | 344 | |
| chr12:7,906,949–7,907,466 | 119.5 kb | Distal (>10kb) Multiome | 435 | |
| chr12:7,935,022–7,936,948 | 148.5 kb | Distal (>10kb) Multiome | 450 | |
| chr12:7,937,904–7,938,471 | 150.3 kb | Distal (>10kb) Multiome | 193 | |
| chr12:7,959,506–7,960,170 | 172.0 kb | Distal (>10kb) Multiome | 284 | |
| chr12:7,960,785–7,961,174 | 173.1 kb | Distal (>10kb) Multiome | 471 | |
| chr12:7,970,302–7,971,168 | 183.0 kb | Distal (>10kb) Multiome | 619 | |
| chr12:7,994,878–7,995,556 | 207.5 kb | Distal (>10kb) Multiome | 262 | |
| chr12:8,018,686–8,019,483 | 231.3 kb | Distal (>10kb) Multiome | 217 | |
| chr12:8,026,338–8,027,323 | 239.1 kb | Distal (>10kb) Multiome | 935 | |
| chr12:8,032,354–8,033,866 | 244.9 kb | Distal (>10kb) Multiome | 673 | |
| chr12:8,081,804–8,082,716 | 294.4 kb | Distal (>10kb) Multiome | 840 |
Genomic view of the NANOG 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.