HDAC6

histone deacetylase 6 | FLJ16239, HD6, JM21, KDAC6, KIAA0901, PPP1R90

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 class II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription. [provided by RefSeq, Jul 2008]

Member of: DE-5 Developmental clusters: GC6

Biological processes 129 terms

ATPase inhibitor activity (GO:0042030)Hsp90 protein binding (GO:0051879)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)acetylspermidine deacetylase activity (GO:0047611)aggresome (GO:0016235)aggresome (GO:0016235)aggresome assembly (GO:0070842)alpha-tubulin binding (GO:0043014)axon (GO:0030424)axon (GO:0030424)axon cytoplasm (GO:1904115)axonal transport of mitochondrion (GO:0019896)beta-catenin binding (GO:0008013)beta-tubulin binding (GO:0048487)caveola (GO:0005901)cell body (GO:0044297)cell leading edge (GO:0031252)cellular response to heat (GO:0034605)cellular response to hydrogen peroxide (GO:0070301)cellular response to topologically incorrect protein (GO:0035967)centrosome (GO:0005813)centrosome (GO:0005813)ciliary basal body (GO:0036064)cilium (GO:0005929)cilium assembly (GO:0060271)cilium disassembly (GO:0061523)cilium disassembly (GO:0061523)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic ubiquitin ligase complex (GO:0000153)cytoskeleton (GO:0005856)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)deacetylase activity (GO:0019213)dendrite (GO:0030425)dendrite (GO:0030425)dynein complex binding (GO:0070840)enzyme binding (GO:0019899)enzyme binding (GO:0019899)epidermal growth factor receptor signaling pathway (GO:0007173)histone deacetylase activity (GO:0004407)histone deacetylase activity (GO:0004407)histone deacetylase binding (GO:0042826)histone deacetylase complex (GO:0000118)histone deacetylase complex (GO:0000118)inclusion body (GO:0016234)intracellular protein transport (GO:0006886)lysosome localization (GO:0032418)macroautophagy (GO:0016236)macromolecule deacylation (GO:0098732)microtubule (GO:0005874)microtubule associated complex (GO:0005875)microtubule binding (GO:0008017)microtubule binding (GO:0008017)microtubule binding (GO:0008017)microtubule cytoskeleton (GO:0015630)misfolded protein binding (GO:0051787)mitochondrion localization (GO:0051646)multivesicular body (GO:0005771)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of aggrephagy (GO:1905336)negative regulation of cellular component organization (GO:0051129)negative regulation of gene expression, epigenetic (GO:0045814)negative regulation of hydrogen peroxide metabolic process (GO:0010727)negative regulation of protein-containing complex assembly (GO:0031333)negative regulation of protein-containing complex disassembly (GO:0043242)negative regulation of proteolysis (GO:0045861)neuron projection (GO:0043005)nucleus (GO:0005634)nucleus (GO:0005634)perikaryon (GO:0043204)perikaryon (GO:0043204)perinuclear region of cytoplasm (GO:0048471)peroxidase inhibitor activity (GO:0036479)plasma membrane bounded cell projection (GO:0120025)polyamine deacetylation (GO:0106047)polyubiquitin modification-dependent protein binding (GO:0031593)polyubiquitinated misfolded protein transport (GO:0070845)positive regulation of cellular component organization (GO:0051130)positive regulation of epithelial cell migration (GO:0010634)positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)positive regulation of protein oligomerization (GO:0032461)positive regulation of protein oligomerization (GO:0032461)positive regulation of type 2 mitophagy (GO:1905091)protein binding (GO:0005515)protein deacetylation (GO:0006476)protein destabilization (GO:0031648)protein lysine deacetylase activity (GO:0033558)protein lysine deacetylase activity (GO:0033558)protein lysine deacetylase activity (GO:0033558)protein lysine deacetylase activity (GO:0033558)protein quality control for misfolded or incompletely synthesized proteins (GO:0006515)protein ubiquitination (GO:0016567)protein-containing complex (GO:0032991)regulation of androgen receptor signaling pathway (GO:0060765)regulation of autophagy (GO:0010506)regulation of autophagy of mitochondrion (GO:1903146)regulation of macroautophagy (GO:0016241)regulation of microtubule-based movement (GO:0060632)regulation of microtubule-based process (GO:0032886)regulation of protein stability (GO:0031647)response to misfolded protein (GO:0051788)response to stress (GO:0006950)spermidine deacetylation (GO:0106048)tau protein binding (GO:0048156)tau protein binding (GO:0048156)tau protein binding (GO:0048156)tau protein binding (GO:0048156)tau protein binding (GO:0048156)transcription corepressor binding (GO:0001222)tubulin deacetylase activity (GO:0042903)tubulin deacetylase activity (GO:0042903)tubulin deacetylase activity (GO:0042903)tubulin deacetylase activity (GO:0042903)tubulin deacetylase activity (GO:0042903)tubulin deacetylation (GO:0090042)tubulin deacetylation (GO:0090042)tubulin deacetylation (GO:0090042)type 2 mitophagy (GO:0061734)ubiquitin binding (GO:0043130)ubiquitin protein ligase activity (GO:0061630)ubiquitin protein ligase binding (GO:0031625)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating HDAC6 0 TFs

Transcription factors with Perturb-seq knockdown data for HDAC6. 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 = HDAC6 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

Rows:

Elements linked to HDAC6

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HDAC6, 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.

Element	Dist. to TSS	Link type	TFs
chrX:48,508,766–48,509,247	293.1 kb	Distal (>10kb) Multiome	400
chrX:48,521,369–48,522,158	280.3 kb	Distal (>10kb) Multiome	519
chrX:48,539,185–48,540,294	262.4 kb	Distal (>10kb) Multiome	658
chrX:48,574,090–48,575,023	227.4 kb	Distal (>10kb) Multiome	779
chrX:48,597,350–48,598,476	204.1 kb	Distal (>10kb) Multiome	660
chrX:48,676,132–48,677,132	125.5 kb	Distal (>10kb) Multiome	642
chrX:48,695,862–48,697,105	105.4 kb	Distal (>10kb) Multiome	600
chrX:48,737,116–48,737,756	64.7 kb	Distal (>10kb) Multiome	580
chrX:48,801,126–48,802,845	127 bp	At TSS Multiome	734
chrX:48,891,080–48,891,988	89.7 kb	Distal (>10kb) Multiome	525
chrX:48,897,163–48,898,345	95.9 kb	Distal (>10kb) Multiome	672
chrX:48,911,574–48,912,414	110.0 kb	Distal (>10kb) Multiome	671
chrX:48,917,179–48,917,999	115.4 kb	Distal (>10kb) Multiome	468
chrX:48,918,412–48,919,792	117.1 kb	Distal (>10kb) Multiome	693
chrX:48,957,469–48,959,105	156.3 kb	Distal (>10kb) Multiome	722
chrX:49,001,538–49,002,676	200.3 kb	Distal (>10kb) Multiome	540
chrX:49,039,840–49,040,493	238.1 kb	Distal (>10kb) Multiome	436
chrX:49,042,954–49,044,182	241.6 kb	Distal (>10kb) Multiome	664
chrX:49,053,328–49,054,050	251.6 kb	Distal (>10kb) Multiome	403
chrX:49,071,863–49,072,612	270.1 kb	Distal (>10kb) Multiome	107
chrX:49,073,903–49,074,451	272.1 kb	Distal (>10kb) Multiome	464
chrX:49,100,885–49,101,855	299.3 kb	Distal (>10kb) Multiome	562

Genome Browser

Genomic view of the HDAC6 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.