Transcription factors with Perturb-seq knockdown data for RTCA-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 = RTCA-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 RTCA-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 |
|---|---|---|---|---|
| chr1:99,969,317–99,970,703 | 296.0 kb | Distal (>10kb) Multiome | 1091 | |
| chr1:100,037,569–100,039,066 | 228.0 kb | Distal (>10kb) Multiome | 979 | |
| chr1:100,048,184–100,049,196 | 217.4 kb | Distal (>10kb) Multiome | 234 | |
| chr1:100,132,347–100,133,463 | 133.1 kb | Distal (>10kb) Multiome | 947 | |
| chr1:100,249,217–100,250,325 | 16.2 kb | Distal (>10kb) Multiome | 803 | |
| chr1:100,265,673–100,266,819 | 97 bp | At TSS Multiome | 796 | |
| chr1:100,337,594–100,338,776 | 72.0 kb | Distal (>10kb) Multiome | 109 | |
| chr1:100,350,909–100,353,664 | 86.3 kb | Distal (>10kb) Multiome | 1006 | |
| chr1:100,439,928–100,440,470 | 174.2 kb | Distal (>10kb) Multiome | 293 | |
| chr1:100,538,654–100,540,350 | 273.6 kb | Distal (>10kb) Multiome | 481 |
Genomic view of the RTCA-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.