The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]
Transcription factors with Perturb-seq knockdown data for PHF21A. 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 = PHF21A 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 PHF21A, 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 |
|---|---|---|---|---|
| chr11:45,847,011–45,848,213 | 273.8 kb | Distal (>10kb) Multiome | 845 | |
| chr11:45,885,234–45,886,606 | 235.6 kb | Distal (>10kb) Multiome | 501 | |
| chr11:45,899,383–45,900,756 | 221.3 kb | Distal (>10kb) Multiome | 534 | |
| chr11:45,917,590–45,918,966 | 202.3 kb | Distal (>10kb) Multiome | 781 | |
| chr11:45,921,513–45,923,586 | 198.8 kb | Distal (>10kb) Multiome | 624 | |
| chr11:46,120,416–46,122,472 | 351 bp | At TSS Multiome | 758 | |
| chr11:46,238,964–46,239,736 | 118.1 kb | Distal (>10kb) Multiome | 559 | |
| chr11:46,242,857–46,244,010 | 122.3 kb | Distal (>10kb) Multiome | 900 | |
| chr11:46,277,351–46,278,874 | 157.4 kb | Distal (>10kb) Multiome | 343 | |
| chr11:46,294,934–46,295,998 | 174.4 kb | Distal (>10kb) Multiome | 533 | |
| chr11:46,296,747–46,297,460 | 175.9 kb | Distal (>10kb) Multiome | 415 | |
| chr11:46,338,698–46,339,679 | 218.0 kb | Distal (>10kb) Multiome | 393 | |
| chr11:46,346,987–46,348,092 | 226.2 kb | Distal (>10kb) Multiome | 586 | |
| chr11:46,352,002–46,352,557 | 231.1 kb | Distal (>10kb) Multiome | 306 | |
| chr11:46,379,120–46,383,444 | 258.4 kb | Distal (>10kb) Multiome | 930 | |
| chr11:46,388,459–46,390,750 | 267.6 kb | Distal (>10kb) Multiome | 593 | |
| chr11:46,391,139–46,393,221 | 271.5 kb | Distal (>10kb) Multiome | 965 | |
| chr11:46,407,311–46,408,466 | 286.7 kb | Distal (>10kb) Multiome | 157 |
Genomic view of the PHF21A 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.