Transcription factors with Perturb-seq knockdown data for NACA3P. 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 = NACA3P 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 NACA3P, 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 |
|---|---|---|---|---|
| chr4:164,935,257–164,935,711 | 7.6 kb | Proximal (<10kb) | 113 | |
| chr4:164,937,672–164,938,197 | 5.1 kb | Proximal (<10kb) | 59 | |
| chr4:164,949,534–164,950,054 | 6.2 kb | Proximal (<10kb) | 95 |
Genomic view of the NACA3P 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.