Transcription factors with Perturb-seq knockdown data for CAST. 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 = CAST 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 CAST, 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 |
|---|---|---|---|---|
| chr5:96,431,257–96,433,483 | 270.0 kb | Distal (>10kb) Multiome | 402 | |
| chr5:96,434,024–96,435,283 | 268.4 kb | Distal (>10kb) Multiome | 541 | |
| chr5:96,661,819–96,663,768 | 40.6 kb | Distal (>10kb) Multiome | 856 | |
| chr5:96,699,357–96,699,773 | 3.0 kb | Proximal (<10kb) | 83 | |
| chr5:96,699,883–96,700,207 | 2.6 kb | Proximal (<10kb) | 24 | |
| chr5:96,702,491–96,703,472 | 93 bp | At TSS Multiome | 828 | |
| chr5:96,807,053–96,808,809 | 105.5 kb | Distal (>10kb) Multiome | 1054 | |
| chr5:96,934,346–96,937,145 | 232.2 kb | Distal (>10kb) Multiome | 1171 |
Genomic view of the CAST 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.