CHD6 chromodomain helicase DNA binding protein 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHD6provided by HGNC
Official Full Name: chromodomain helicase DNA binding protein 6provided by HGNC
Primary source: HGNC:HGNC:19057
See related: Ensembl:ENSG00000124177 MIM:616114; AllianceGenome:HGNC:19057
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CHD5; RIGB; CHD-6
Summary: This gene encodes a member of the SNF2/RAD54 helicase protein family. The encoded protein contains two chromodomains, a helicase domain, and an ATPase domain. Several multi-subunit protein complexes remodel chromatin to allow patterns of cell type-specific gene expression, and the encoded protein is thought to be a core member of one or more of these chromatin remodeling complexes. The encoded protein may function as a transcriptional repressor and is involved in the cellular repression of influenza virus replication. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in ovary (RPKM 7.0), thyroid (RPKM 6.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q12

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (41402083..41618377, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (43133884..43350249, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (40030723..40247016, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.
Title: CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells.
Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology.
Title: Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology.
Study shows that Chromodomain Helicase DNA-binding protein 6 (CHD6), distinct to other CHD enzymes, is stabilized during oxidative stress via reduced degradation and suggests that CHD6 is a key regulator of the oxidative DNA damage response.
Title: The CHD6 chromatin remodeler is an oxidative DNA damage response factor.
Data suggest that CHD6 and CHD7 both bind with high affinity to short linker DNA, whereas CHD8 requires longer DNA for binding; thus, CHD8 slides nucleosomes into positions with more flanking linker DNA than CHD7; CHD6 disrupts nucleosomes in a distinct non-sliding manner.
Title: The ATP-dependent chromatin remodeling enzymes CHD6, CHD7, and CHD8 exhibit distinct nucleosome binding and remodeling activities.
The role of CHD6 in regulating the chromatin topology of CFTR as an exemplary genetic model for this mechanism was described.
Title: CHD6 regulates the topological arrangement of the CFTR locus.
CHD6 regulates the topology of the CFTR locus
Title: CHD6 regulates the topological arrangement of the CFTR locus.
These data indicate that CHD6 degradation is a general effect exerted by influenza A viruses and suggest that this viral repressor may play an important inhibitory role since degradation and accumulation into inactive chromatin occur during the infection.
Title: CHD6, a cellular repressor of influenza virus replication, is degraded in human alveolar epithelial cells and mice lungs during infection.
CHD6 has a negative role in the influenza virus cycle because the virus replicates more efficiently in CHD6-silenced cells.
Title: CHD6 chromatin remodeler is a negative modulator of influenza virus replication that relocates to inactive chromatin upon infection.
Both RNA knockdown experiments and mutational analyses of the E2C domain suggest that binding of CHD6 to E8--E2C contributes to the transcriptional repression of the huma papillomavirus E6/E7 oncogene promoter.
Title: Interaction of the papillomavirus E8--E2C protein with the cellular CHD6 protein contributes to transcriptional repression.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Multiple loci influencing hippocampal degeneration identified by genome scan. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Z94571 (e-PCR)
- UniSTS:68658

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

Z94700 (e-PCR)
- UniSTS:30825

D10S16 (e-PCR)
- UniSTS:155756

WIAF-1711 (e-PCR)
- UniSTS:67986

AL023701 (e-PCR)
- UniSTS:2753

D20S997 (e-PCR)
- UniSTS:10704

SHGC-82496 (e-PCR)
- UniSTS:183527

Z94510 (e-PCR)
- UniSTS:78062

Z94307 (e-PCR)
- UniSTS:82167

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on DNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in cell redox homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 6

Names: ATP-dependent helicase CHD6; helicase C-terminal domain- and SNF2 N-terminal domain-containing protein; radiation-induced gene B protein

NP_115597.3

EC 3.6.4.12

XP_005260633.1

EC 3.6.4.12

XP_011527382.1

EC 3.6.4.12

XP_011527384.1

EC 3.6.4.12

XP_016883588.1

EC 3.6.4.12

XP_016883589.1

EC 3.6.4.12

XP_016883590.1

EC 3.6.4.12

XP_016883591.1

EC 3.6.4.12

XP_016883593.1

EC 3.6.4.12

XP_047296501.1

EC 3.6.4.12

XP_047296502.1

EC 3.6.4.12

XP_047296503.1

EC 3.6.4.12

XP_047296504.1

EC 3.6.4.12

XP_047296505.1

EC 3.6.4.12

XP_047296506.1

EC 3.6.4.12

XP_047296507.1

EC 3.6.4.12

XP_054180093.1

EC 3.6.4.12

XP_054180094.1

EC 3.6.4.12

XP_054180095.1

EC 3.6.4.12

XP_054180096.1

EC 3.6.4.12

XP_054180097.1

EC 3.6.4.12

XP_054180098.1

EC 3.6.4.12

XP_054180099.1

EC 3.6.4.12

XP_054180100.1

EC 3.6.4.12

XP_054180101.1

EC 3.6.4.12

XP_054180102.1

EC 3.6.4.12

XP_054180103.1

EC 3.6.4.12

XP_054180104.1

EC 3.6.4.12

XP_054180105.1

EC 3.6.4.12

XP_054180106.1

EC 3.6.4.12

XP_054180107.1

EC 3.6.4.12

XP_054180108.1

EC 3.6.4.12

XP_054180109.1

EC 3.6.4.12

XP_054180110.1

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_050686.2 RefSeqGene

Range

5000..221294

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_032221.5 → NP_115597.3 chromodomain-helicase-DNA-binding protein 6

See identical proteins and their annotated locations for NP_115597.3

Status: REVIEWED

Source sequence(s)

AL031667, AL031669, AL121674

Consensus CDS

CCDS13317.1

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

Related

ENSP00000362330.3, ENST00000373233.8

Conserved Domains (5) summary

cd00046
Location:480 → 629

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:464 → 751

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:783 → 897

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:376 → 429

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2402 → 2437

BRK; BRK domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

41402083..41618377 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440549.1 → XP_047296505.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1
XM_047440545.1 → XP_047296501.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1
XM_047440546.1 → XP_047296502.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1
XM_047440548.1 → XP_047296504.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1
XM_047440547.1 → XP_047296503.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/Swiss-Prot

Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1
XM_047440550.1 → XP_047296506.1 chromodomain-helicase-DNA-binding protein 6 isoform X5
XM_017028100.2 → XP_016883589.1 chromodomain-helicase-DNA-binding protein 6 isoform X6

Conserved Domains (5) summary

cd00046
Location:458 → 607

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:442 → 729

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:761 → 875

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:354 → 407

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2380 → 2415

BRK; BRK domain
XM_011529080.3 → XP_011527382.1 chromodomain-helicase-DNA-binding protein 6 isoform X3

Conserved Domains (5) summary

cd00046
Location:478 → 627

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:462 → 749

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:781 → 895

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:374 → 427

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2400 → 2435

BRK; BRK domain
XM_017028101.2 → XP_016883590.1 chromodomain-helicase-DNA-binding protein 6 isoform X4
XM_017028099.3 → XP_016883588.1 chromodomain-helicase-DNA-binding protein 6 isoform X1
XM_011529082.3 → XP_011527384.1 chromodomain-helicase-DNA-binding protein 6 isoform X9

Conserved Domains (2) summary

smart00592
Location:1725 → 1760

BRK; domain in transcription and CHROMO domain helicases

pfam00271
Location:106 → 220

Helicase_C; Helicase conserved C-terminal domain
XM_005260576.5 → XP_005260633.1 chromodomain-helicase-DNA-binding protein 6 isoform X11

Conserved Domains (1) summary

cl02688
Location:1051 → 1086

BRK; BRK domain
XM_017028102.2 → XP_016883591.1 chromodomain-helicase-DNA-binding protein 6 isoform X7
XM_017028104.2 → XP_016883593.1 chromodomain-helicase-DNA-binding protein 6 isoform X8
XM_047440551.1 → XP_047296507.1 chromodomain-helicase-DNA-binding protein 6 isoform X10