Transcription factors with Perturb-seq knockdown data for PNISR-AS1. 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 = PNISR-AS1 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 PNISR-AS1, 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 |
|---|---|---|---|---|
| chr6:99,219,557–99,220,312 | 205.8 kb | Distal (>10kb) Multiome | 105 | |
| chr6:99,348,770–99,350,367 | 75.9 kb | Distal (>10kb) Multiome | 615 | |
| chr6:99,393,480–99,394,529 | 31.7 kb | Distal (>10kb) Multiome | 782 | |
| chr6:99,424,727–99,426,355 | 291 bp | At TSS Multiome | 975 | |
| chr6:99,435,060–99,435,190 | 9.3 kb | Proximal (<10kb) | 53 | |
| chr6:99,514,702–99,516,390 | 89.8 kb | Distal (>10kb) Multiome | 945 | |
| chr6:99,520,676–99,522,033 | 95.4 kb | Distal (>10kb) Multiome | 822 | |
| chr6:99,567,957–99,569,279 | 143.0 kb | Distal (>10kb) Multiome | 1064 | |
| chr6:99,588,272–99,589,608 | 163.1 kb | Distal (>10kb) Multiome | 545 | |
| chr6:99,602,753–99,604,086 | 178.0 kb | Distal (>10kb) Multiome | 376 | |
| chr6:99,612,582–99,615,086 | 187.9 kb | Distal (>10kb) Multiome | 533 | |
| chr6:99,618,513–99,619,470 | 193.2 kb | Distal (>10kb) Multiome | 225 |
Genomic view of the PNISR-AS1 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.