This gene encodes a member of the Kruppel family of zinc finger proteins. The encoded transcription factor is activated by the sonic hedgehog signal transduction cascade and regulates stem cell proliferation. The activity and nuclear localization of this protein is negatively regulated by p53 in an inhibitory loop. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Transcription factors with Perturb-seq knockdown data for GLI1. 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 = GLI1 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 GLI1, 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 |
|---|---|---|---|---|
| chr12:57,215,826–57,217,972 | 243.1 kb | Distal (>10kb) Multiome HiCAR | 525 | |
| chr12:57,224,526–57,225,152 | 234.8 kb | Distal (>10kb) Multiome | 267 | |
| chr12:57,225,987–57,227,617 | 232.7 kb | Distal (>10kb) Multiome | 236 | |
| chr12:57,229,358–57,230,407 | 229.8 kb | Distal (>10kb) Multiome HiCAR | 739 | |
| chr12:57,237,805–57,241,749 | 220.6 kb | Distal (>10kb) Multiome HiCAR | 846 | |
| chr12:57,242,371–57,244,402 | 216.0 kb | Distal (>10kb) Multiome HiCAR | 596 | |
| chr12:57,430,384–57,431,415 | 28.8 kb | Distal (>10kb) Multiome | 879 | |
| chr12:57,452,962–57,453,212 | 6.6 kb | Proximal (<10kb) | 369 | |
| chr12:57,454,516–57,456,639 | 3.4 kb | Proximal (<10kb) Multiome | 841 | |
| chr12:57,458,743–57,463,318 | 501 bp | At TSS Multiome | 994 | |
| chr12:57,475,229–57,476,151 | 15.7 kb | Distal (>10kb) Multiome | 194 | |
| chr12:57,487,577–57,488,336 | 28.1 kb | Distal (>10kb) Multiome | 784 | |
| chr12:57,519,488–57,521,440 | 60.9 kb | Distal (>10kb) Multiome HiCAR | 1029 | |
| chr12:57,521,541–57,523,658 | 63.0 kb | Distal (>10kb) Multiome HiCAR | 960 | |
| chr12:57,546,771–57,547,419 | 87.4 kb | Distal (>10kb) Multiome | 623 | |
| chr12:57,549,654–57,550,343 | 90.3 kb | Distal (>10kb) Multiome | 366 | |
| chr12:57,583,383–57,583,948 | 123.7 kb | Distal (>10kb) Multiome | 353 | |
| chr12:57,590,813–57,591,877 | 131.3 kb | Distal (>10kb) Multiome | 738 | |
| chr12:57,604,466–57,605,404 | 145.1 kb | Distal (>10kb) Multiome | 337 | |
| chr12:57,609,052–57,609,957 | 149.6 kb | Distal (>10kb) Multiome | 83 | |
| chr12:57,610,841–57,611,876 | 151.7 kb | Distal (>10kb) Multiome | 558 | |
| chr12:57,621,603–57,622,199 | 162.1 kb | Distal (>10kb) Multiome | 446 | |
| chr12:57,631,837–57,633,369 | 173.4 kb | Distal (>10kb) Multiome | 706 | |
| chr12:57,693,486–57,694,647 | 234.2 kb | Distal (>10kb) Multiome | 757 | |
| chr12:57,726,079–57,726,879 | 266.5 kb | Distal (>10kb) Multiome | 597 | |
| chr12:57,738,612–57,739,176 | 279.2 kb | Distal (>10kb) Multiome | 201 | |
| chr12:57,744,434–57,745,735 | 285.2 kb | Distal (>10kb) Multiome | 822 | |
| chr12:57,751,806–57,753,147 | 292.7 kb | Distal (>10kb) Multiome | 1030 | |
| chr12:57,754,455–57,756,188 | 295.1 kb | Distal (>10kb) Multiome | 616 | |
| chr12:57,756,649–57,757,193 | 297.2 kb | Distal (>10kb) Multiome | 315 |
Genomic view of the GLI1 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.