HTT
huntingtin | IT15, HD

Huntingtin is a disease gene linked to Huntington's disease, a neurodegenerative disorder characterized by loss of striatal neurons. This is thought to be caused by an expanded, unstable trinucleotide repeat in the huntingtin gene, which translates as a polyglutamine repeat in the protein product. A fairly broad range of trinucleotide repeats (9-35) has been identified in normal controls, and repeat numbers in excess of 40 have been described as pathological. The huntingtin locus is large, spanning 180 kb and consisting of 67 exons. The huntingtin gene is widely expressed and is required for normal development. It is expressed as 2 alternatively polyadenylated forms displaying different relative abundance in various fetal and adult tissues. The larger transcript is approximately 13.7 kb and is expressed predominantly in adult and fetal brain whereas the smaller transcript of approximately 10.3 kb is more widely expressed. The genetic defect leading to Huntington's disease may not necessarily eliminate transcription, but may confer a new property on the mRNA or alter the function of the protein. One candidate is the huntingtin-associated protein-1, highly expressed in brain, which has increased affinity for huntingtin protein with expanded polyglutamine repeats. This gene contains an upstream open reading frame in the 5' UTR that inhibits expression of the huntingtin gene product through translational repression. [provided by RefSeq, Jul 2016]

Member of: DE-8 DE-8.1
Biological processes 69 terms
Golgi apparatus (GO:0005794)Golgi organization (GO:0007030)autophagosome (GO:0005776)autophagosome (GO:0005776)axon (GO:0030424)axon (GO:0030424)axon (GO:0030424)beta-tubulin binding (GO:0048487)central nervous system development (GO:0007417)centriole (GO:0005814)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasmic vesicle (GO:0031410)cytoplasmic vesicle (GO:0031410)cytoplasmic vesicle membrane (GO:0030659)cytosol (GO:0005829)dendrite (GO:0030425)dendrite (GO:0030425)dynactin binding (GO:0034452)dynein intermediate chain binding (GO:0045505)early endosome (GO:0005769)early endosome (GO:0005769)early endosome (GO:0005769)endoplasmic reticulum (GO:0005783)endosomal transport (GO:0016197)establishment of mitotic spindle orientation (GO:0000132)heat shock protein binding (GO:0031072)identical protein binding (GO:0042802)inclusion body (GO:0016234)kinase binding (GO:0019900)late endosome (GO:0005770)microtubule-based process (GO:0007017)negative regulation of apoptotic process (GO:0043066)negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)neurogenesis (GO:0022008)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)p53 binding (GO:0002039)perinuclear region of cytoplasm (GO:0048471)perinuclear region of cytoplasm (GO:0048471)phosphoprotein phosphatase activity (GO:0004721)positive regulation of CAMKK-AMPK signaling cascade (GO:1905291)positive regulation of aggrephagy (GO:1905337)positive regulation of apoptotic process (GO:0043065)positive regulation of calcium-mediated signaling (GO:0050850)positive regulation of cilium assembly (GO:0045724)positive regulation of lipophagy (GO:1904504)positive regulation of mitophagy (GO:1901526)postsynaptic cytosol (GO:0099524)presynaptic cytosol (GO:0099523)profilin binding (GO:0005522)protein binding (GO:0005515)protein destabilization (GO:0031648)protein-containing complex (GO:0032991)protein-containing complex (GO:0032991)regulation of CAMKK-AMPK signaling cascade (GO:1905289)regulation of CAMKK-AMPK signaling cascade (GO:1905289)regulation of signal transduction (GO:0009966)retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890)synapse (GO:0045202)synaptic vesicle transport (GO:0048489)transmembrane transporter binding (GO:0044325)vesicle transport along microtubule (GO:0047496)vesicle transport along microtubule (GO:0047496)vocal learning (GO:0042297)
Expression (TPM)
HTT — as a Regulated Gene

TFs regulating HTT 0 TFs

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

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of HTT, 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
chr4:2,792,387–2,793,280 281.7 kb Distal (>10kb) Multiome 561
chr4:2,800,892–2,801,392 273.6 kb Distal (>10kb) Multiome 538
chr4:2,817,772–2,818,865 256.5 kb Distal (>10kb) Multiome 350
chr4:2,843,009–2,844,539 230.9 kb Distal (>10kb) Multiome 762
chr4:2,867,740–2,868,353 206.6 kb Distal (>10kb) Multiome 232
chr4:2,886,596–2,887,030 187.8 kb Distal (>10kb) Multiome 64
chr4:2,922,643–2,923,182 151.8 kb Distal (>10kb) Multiome 115
chr4:2,934,626–2,935,335 139.9 kb Distal (>10kb) Multiome 661
chr4:2,962,729–2,964,377 111.2 kb Distal (>10kb) Multiome 1035
chr4:3,073,152–3,075,706 395 bp At TSS Multiome 810
chr4:3,291,622–3,293,967 218.3 kb Distal (>10kb) Multiome 796

Genome Browser

Genomic view of the HTT 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.

chr4:2,782,387 – 3,303,967
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq