Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family. It has histone deacetylase activity and represses transcription when tethered to a promoter. It may participate in the regulation of transcription through its binding with the zinc-finger transcription factor YY1. This protein can also down-regulate p53 function and thus modulate cell growth and apoptosis. This gene is regarded as a potential tumor suppressor gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for HDAC3. 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 = HDAC3 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 HDAC3, 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 |
|---|---|---|---|---|
| chr5:141,407,865–141,408,477 | 228.8 kb | Distal (>10kb) Multiome | 109 | |
| chr5:141,417,522–141,418,139 | 219.1 kb | Distal (>10kb) Multiome | 106 | |
| chr5:141,475,524–141,476,908 | 160.9 kb | Distal (>10kb) Multiome | 402 | |
| chr5:141,484,493–141,485,507 | 151.9 kb | Distal (>10kb) Multiome | 189 | |
| chr5:141,508,593–141,509,337 | 127.9 kb | Distal (>10kb) Multiome | 242 | |
| chr5:141,512,198–141,512,900 | 124.3 kb | Distal (>10kb) Multiome | 300 | |
| chr5:141,513,616–141,515,069 | 122.3 kb | Distal (>10kb) Multiome | 392 | |
| chr5:141,524,502–141,525,311 | 112.0 kb | Distal (>10kb) Multiome | 605 | |
| chr5:141,557,658–141,558,135 | 78.9 kb | Distal (>10kb) Multiome | 373 | |
| chr5:141,560,663–141,561,120 | 75.9 kb | Distal (>10kb) Multiome | 327 | |
| chr5:141,617,831–141,619,550 | 17.7 kb | Distal (>10kb) Multiome | 1037 | |
| chr5:141,636,256–141,638,491 | 25 bp | At TSS Multiome | 852 | |
| chr5:141,650,837–141,651,870 | 14.6 kb | Distal (>10kb) Multiome | 438 | |
| chr5:141,680,751–141,681,516 | 44.1 kb | Distal (>10kb) Multiome | 257 | |
| chr5:141,681,692–141,682,621 | 45.4 kb | Distal (>10kb) Multiome | 554 | |
| chr5:141,692,108–141,692,560 | 55.4 kb | Distal (>10kb) Multiome | 498 | |
| chr5:141,702,181–141,702,796 | 65.6 kb | Distal (>10kb) Multiome | 351 | |
| chr5:141,795,082–141,795,688 | 158.5 kb | Distal (>10kb) Multiome | 25 | |
| chr5:141,811,578–141,812,181 | 175.0 kb | Distal (>10kb) Multiome | 243 | |
| chr5:141,816,277–141,817,287 | 180.0 kb | Distal (>10kb) Multiome | 210 | |
| chr5:141,838,853–141,839,539 | 202.4 kb | Distal (>10kb) Multiome | 185 | |
| chr5:141,845,184–141,846,305 | 208.9 kb | Distal (>10kb) Multiome | 188 | |
| chr5:141,848,609–141,851,214 | 212.5 kb | Distal (>10kb) Multiome | 892 | |
| chr5:141,858,059–141,858,606 | 221.5 kb | Distal (>10kb) Multiome | 80 | |
| chr5:141,875,925–141,877,406 | 239.4 kb | Distal (>10kb) Multiome | 506 | |
| chr5:141,877,575–141,879,487 | 241.6 kb | Distal (>10kb) Multiome | 693 | |
| chr5:141,923,268–141,924,400 | 287.1 kb | Distal (>10kb) Multiome | 922 |
Genomic view of the HDAC3 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.