Transcription factors with Perturb-seq knockdown data for BDNF-AS. 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 = BDNF-AS 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 BDNF-AS, 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 |
|---|---|---|---|---|
| chr11:26,935,672–26,936,561 | 570.6 kb | Distal (>10kb) Multiome HiCAR | 212 | |
| chr11:27,186,846–27,189,000 | 318.6 kb | Distal (>10kb) Multiome HiCAR | 303 | |
| chr11:27,248,576–27,249,774 | 257.6 kb | Distal (>10kb) Multiome | 209 | |
| chr11:27,281,350–27,282,333 | 224.9 kb | Distal (>10kb) Multiome | 322 | |
| chr11:27,304,430–27,305,242 | 202.1 kb | Distal (>10kb) Multiome | 124 | |
| chr11:27,362,704–27,363,814 | 143.6 kb | Distal (>10kb) Multiome | 933 | |
| chr11:27,443,724–27,444,393 | 62.9 kb | Distal (>10kb) Multiome | 91 | |
| chr11:27,444,522–27,445,324 | 61.7 kb | Distal (>10kb) Multiome | 199 | |
| chr11:27,471,035–27,473,509 | 34.0 kb | Distal (>10kb) Multiome | 780 | |
| chr11:27,499,199–27,499,417 | 7.4 kb | Proximal (<10kb) | 104 | |
| chr11:27,506,080–27,507,386 | 56 bp | At TSS Multiome | 861 | |
| chr11:27,628,672–27,629,755 | 122.4 kb | Distal (>10kb) Multiome | 92 | |
| chr11:27,634,338–27,635,109 | 128.0 kb | Distal (>10kb) Multiome | 115 | |
| chr11:27,698,739–27,701,728 | 192.3 kb | Distal (>10kb) Multiome | 518 | |
| chr11:27,718,043–27,719,845 | 211.9 kb | Distal (>10kb) Multiome | 477 | |
| chr11:27,721,736–27,723,344 | 215.9 kb | Distal (>10kb) Multiome | 381 | |
| chr11:27,795,831–27,797,062 | 289.7 kb | Distal (>10kb) Multiome | 361 | |
| chr11:28,922,252–28,923,991 | 1416.0 kb | Distal (>10kb) Multiome HiCAR | 261 |
Genomic view of the BDNF-AS 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.