HDAC5
histone deacetylase 5 | FLJ90614, KIAA0600, NY-CO-9

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 class II histone deacetylase/acuc/apha family. It possesses histone deacetylase activity and represses transcription when tethered to a promoter. It coimmunoprecipitates only with HDAC3 family member and might form multicomplex proteins. It also interacts with myocyte enhancer factor-2 (MEF2) proteins, resulting in repression of MEF2-dependent genes. This gene is thought to be associated with colon cancer. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Member of: DE-4 Developmental clusters: GC7
Biological processes 49 terms
B cell activation (GO:0042113)B cell differentiation (GO:0030183)DNA-binding transcription activator activity (GO:0001216)DNA-binding transcription factor binding (GO:0140297)DNA-binding transcription factor binding (GO:0140297)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629)cellular response to insulin stimulus (GO:0032869)cellular response to lipopolysaccharide (GO:0071222)chromatin binding (GO:0003682)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)epigenetic regulation of gene expression (GO:0040029)histone deacetylase activity (GO:0004407)histone deacetylase activity (GO:0004407)histone deacetylase activity (GO:0004407)histone deacetylase activity, hydrolytic mechanism (GO:0141221)histone deacetylase binding (GO:0042826)histone deacetylase complex (GO:0000118)histone deacetylase complex (GO:0000118)identical protein binding (GO:0042802)inflammatory response (GO:0006954)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)negative regulation of gene expression, epigenetic (GO:0045814)negative regulation of myotube differentiation (GO:0010832)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)negative regulation of transcription by RNA polymerase II (GO:0000122)neuron differentiation (GO:0030182)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein kinase C binding (GO:0005080)protein lysine deacetylase activity (GO:0033558)protein lysine deacetylase activity (GO:0033558)protein-containing complex (GO:0032991)regulation of myotube differentiation (GO:0010830)response to activity (GO:0014823)response to cocaine (GO:0042220)response to xenobiotic stimulus (GO:0009410)transcription cis-regulatory region binding (GO:0000976)transcription corepressor binding (GO:0001222)
Expression (TPM)
HDAC5 — as a Regulated Gene

TFs regulating HDAC5 0 TFs

Transcription factors with Perturb-seq knockdown data for HDAC5. 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 = HDAC5 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to HDAC5

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HDAC5, 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
chr17:43,832,658–43,833,385 290.4 kb Distal (>10kb) Multiome 455
chr17:43,900,207–43,900,990 222.9 kb Distal (>10kb) Multiome 308
chr17:43,906,025–43,906,856 217.0 kb Distal (>10kb) Multiome 353
chr17:43,907,081–43,907,899 215.9 kb Distal (>10kb) Multiome 362
chr17:43,937,932–43,938,382 185.4 kb Distal (>10kb) Multiome 757
chr17:43,952,298–43,953,752 170.5 kb Distal (>10kb) Multiome 295
chr17:43,983,489–43,984,364 139.6 kb Distal (>10kb) Multiome 743
chr17:44,004,236–44,007,875 118.9 kb Distal (>10kb) Multiome 807
chr17:44,014,255–44,015,168 108.7 kb Distal (>10kb) Multiome 1020
chr17:44,066,017–44,066,857 57.0 kb Distal (>10kb) Multiome 722
chr17:44,070,107–44,071,340 52.8 kb Distal (>10kb) Multiome 1041
chr17:44,095,480–44,096,263 27.6 kb Distal (>10kb) Multiome 713
chr17:44,110,949–44,111,605 12.4 kb Distal (>10kb) Multiome 856
chr17:44,122,999–44,124,340 172 bp At TSS Multiome 883
chr17:44,141,505–44,142,741 18.3 kb Distal (>10kb) Multiome 857
chr17:44,168,259–44,168,849 45.0 kb Distal (>10kb) Multiome 475
chr17:44,186,111–44,187,514 63.2 kb Distal (>10kb) Multiome 917
chr17:44,198,550–44,201,037 76.6 kb Distal (>10kb) Multiome 868
chr17:44,210,257–44,210,930 87.0 kb Distal (>10kb) Multiome 568
chr17:44,218,107–44,221,629 95.0 kb Distal (>10kb) Multiome 936
chr17:44,221,765–44,222,816 98.7 kb Distal (>10kb) Multiome 597
chr17:44,307,755–44,309,164 184.9 kb Distal (>10kb) Multiome 726
chr17:44,314,945–44,315,776 191.7 kb Distal (>10kb) Multiome 273
chr17:44,316,273–44,316,728 192.9 kb Distal (>10kb) Multiome 183
chr17:44,324,218–44,325,841 201.3 kb Distal (>10kb) Multiome 852
chr17:44,326,610–44,327,149 203.4 kb Distal (>10kb) Multiome 599
chr17:44,344,826–44,346,001 221.6 kb Distal (>10kb) Multiome 837
chr17:44,353,667–44,355,182 231.1 kb Distal (>10kb) Multiome 393
chr17:44,363,447–44,364,077 240.2 kb Distal (>10kb) Multiome 502
chr17:44,374,688–44,375,216 251.3 kb Distal (>10kb) Multiome 299
chr17:44,384,542–44,386,175 261.9 kb Distal (>10kb) Multiome 553

Genome Browser

Genomic view of the HDAC5 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.

chr17:43,822,658 – 44,396,175
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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