Homeodomain proteins are sequence-specific transcription factors that share a highly conserved DNA-binding domain and play fundamental roles in cell proliferation, differentiation, and death. PKNOX2 belongs to the TALE (3-amino acid loop extension) class of homeodomain proteins characterized by a 3-amino acid extension between alpha helices 1 and 2 within the homeodomain (Imoto et al., 2001 [PubMed 11549286]).[supplied by OMIM, Oct 2009]
Transcription factors with Perturb-seq knockdown data for PKNOX2. 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 = PKNOX2 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 PKNOX2, 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 |
|---|---|---|---|---|
| chr11:124,875,886–124,877,815 | 288.2 kb | Distal (>10kb) Multiome | 769 | |
| chr11:124,920,725–124,921,671 | 243.6 kb | Distal (>10kb) Multiome | 329 | |
| chr11:124,953,809–124,954,493 | 210.6 kb | Distal (>10kb) Multiome | 818 | |
| chr11:125,062,600–125,064,019 | 101.5 kb | Distal (>10kb) Multiome | 640 | |
| chr11:125,111,022–125,112,225 | 53.0 kb | Distal (>10kb) Multiome | 651 | |
| chr11:125,162,861–125,163,059 | 1.7 kb | Proximal (<10kb) | 47 | |
| chr11:125,163,468–125,165,998 | 20 bp | At TSS Multiome | 417 | |
| chr11:125,166,402–125,167,041 | 1.7 kb | Proximal (<10kb) | 95 | |
| chr11:125,167,297–125,167,601 | 2.6 kb | Proximal (<10kb) | 145 | |
| chr11:125,169,327–125,169,765 | 4.6 kb | Proximal (<10kb) | 49 | |
| chr11:125,224,246–125,224,764 | 59.9 kb | Distal (>10kb) Multiome | 63 | |
| chr11:125,239,981–125,240,709 | 75.6 kb | Distal (>10kb) Multiome | 103 | |
| chr11:125,262,828–125,263,907 | 98.8 kb | Distal (>10kb) Multiome | 339 | |
| chr11:125,330,306–125,331,087 | 166.1 kb | Distal (>10kb) Multiome | 104 | |
| chr11:125,369,857–125,372,110 | 205.5 kb | Distal (>10kb) Multiome HiCAR | 226 | |
| chr11:125,404,667–125,405,169 | 240.2 kb | Distal (>10kb) Multiome HiCAR | 273 | |
| chr11:125,443,557–125,444,361 | 279.3 kb | Distal (>10kb) Multiome | 142 |
Genomic view of the PKNOX2 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.