Transcription factors with Perturb-seq knockdown data for USP3-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 = USP3-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 USP3-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 |
|---|---|---|---|---|
| chr15:63,381,566–63,382,221 | 218.9 kb | Distal (>10kb) Multiome | 358 | |
| chr15:63,396,367–63,396,999 | 204.1 kb | Distal (>10kb) Multiome | 284 | |
| chr15:63,434,760–63,435,736 | 165.8 kb | Distal (>10kb) Multiome | 102 | |
| chr15:63,466,399–63,467,254 | 134.0 kb | Distal (>10kb) Multiome | 497 | |
| chr15:63,502,962–63,505,773 | 97.5 kb | Distal (>10kb) Multiome | 1114 | |
| chr15:63,599,386–63,601,708 | 130 bp | At TSS Multiome | 832 | |
| chr15:63,610,185–63,610,522 | 9.4 kb | Proximal (<10kb) | 339 | |
| chr15:63,833,277–63,834,519 | 233.1 kb | Distal (>10kb) Multiome | 873 |
Genomic view of the USP3-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.