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

Gene ID: 84181, updated on 7-Apr-2024

Summary

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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

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Location:
20q12
Exon count:
45
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (41402083..41618377, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (43133884..43350249, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (40030723..40247016, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904985 Neighboring gene zinc finger MYM-type containing 1 pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:40020313-40020978 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:40053627-40053868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17895 Neighboring gene uncharacterized LOC124904904 Neighboring gene ribosomal protein L12 pseudogene 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:40195885-40196079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12922 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:40278687-40279204 Neighboring gene NFE2L2 motif-containing MPRA enhancer 172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17896 Neighboring gene uncharacterized LOC124904905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17899 Neighboring gene RNA, U6 small nuclear 1018, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells. Zhao D, et al. Nucleic Acids Res, 2022 Nov 28. PMID 36408932, Free PMC Article
  2. Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology. Kargapolova Y, et al. Nat Commun, 2021 May 21. PMID 34021162, Free PMC Article
  3. The CHD6 chromatin remodeler is an oxidative DNA damage response factor. Moore S, et al. Nat Commun, 2019 Jan 16. PMID 30651562, Free PMC Article
  4. CHD6 chromatin remodeler is a negative modulator of influenza virus replication that relocates to inactive chromatin upon infection. Alfonso R, et al. Cell Microbiol, 2011 Dec. PMID 21899694
  5. Interaction of the papillomavirus E8--E2C protein with the cellular CHD6 protein contributes to transcriptional repression. Fertey J, et al. J Virol, 2010 Sep. PMID 20631145, Free PMC Article

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. CHD6 regulates the topology of the CFTR locus
    Title: CHD6 regulates the topological arrangement of the CFTR locus.
  7. 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.
  8. 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.
  9. 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.
  10. 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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1335

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 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 chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell redox homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
part_of 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
XP_005260633.1
XP_011527382.1
XP_011527384.1
XP_016883588.1
XP_016883589.1
XP_016883590.1
XP_016883591.1
XP_016883593.1
XP_047296501.1
XP_047296502.1
XP_047296503.1
XP_047296504.1
XP_047296505.1
XP_047296506.1
XP_047296507.1
XP_054180093.1
XP_054180094.1
XP_054180095.1
XP_054180096.1
XP_054180097.1
XP_054180098.1
XP_054180099.1
XP_054180100.1
XP_054180101.1
XP_054180102.1
XP_054180103.1
XP_054180104.1
XP_054180105.1
XP_054180106.1
XP_054180107.1
XP_054180108.1
XP_054180109.1
XP_054180110.1

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

  1. NG_050686.2 RefSeqGene

    Range
    5000..221294
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    41402083..41618377 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. XM_047440550.1 → XP_047296506.1  chromodomain-helicase-DNA-binding protein 6 isoform X5

  7. 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

  8. 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

  9. XM_017028101.2 → XP_016883590.1  chromodomain-helicase-DNA-binding protein 6 isoform X4

  10. XM_017028099.3 → XP_016883588.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

  11. 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

  12. 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

  13. XM_017028102.2 → XP_016883591.1  chromodomain-helicase-DNA-binding protein 6 isoform X7

  14. XM_017028104.2 → XP_016883593.1  chromodomain-helicase-DNA-binding protein 6 isoform X8

  15. XM_047440551.1 → XP_047296507.1  chromodomain-helicase-DNA-binding protein 6 isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    43133884..43350249 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324124.1 → XP_054180099.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  2. XM_054324120.1 → XP_054180095.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  3. XM_054324123.1 → XP_054180098.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  4. XM_054324125.1 → XP_054180100.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  5. XM_054324126.1 → XP_054180101.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  6. XM_054324121.1 → XP_054180096.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  7. XM_054324129.1 → XP_054180104.1  chromodomain-helicase-DNA-binding protein 6 isoform X5

  8. XM_054324119.1 → XP_054180094.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  9. XM_054324122.1 → XP_054180097.1  chromodomain-helicase-DNA-binding protein 6 isoform X2

    UniProtKB/Swiss-Prot
    Q5JYQ0, Q5TGZ9, Q5TH00, Q5TH01, Q8IZR2, Q8TD26, Q8WTY0, Q9H4H6, Q9H6D4, Q9NTT7, Q9P2L1

  10. XM_054324130.1 → XP_054180105.1  chromodomain-helicase-DNA-binding protein 6 isoform X6

  11. XM_054324127.1 → XP_054180102.1  chromodomain-helicase-DNA-binding protein 6 isoform X3

  12. XM_054324128.1 → XP_054180103.1  chromodomain-helicase-DNA-binding protein 6 isoform X4

  13. XM_054324118.1 → XP_054180093.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

  14. XM_054324133.1 → XP_054180108.1  chromodomain-helicase-DNA-binding protein 6 isoform X9

  15. XM_054324135.1 → XP_054180110.1  chromodomain-helicase-DNA-binding protein 6 isoform X11

  16. XM_054324131.1 → XP_054180106.1  chromodomain-helicase-DNA-binding protein 6 isoform X7

  17. XM_054324132.1 → XP_054180107.1  chromodomain-helicase-DNA-binding protein 6 isoform X8

  18. XM_054324134.1 → XP_054180109.1  chromodomain-helicase-DNA-binding protein 6 isoform X10

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TD26.4 GenPept UniProtKB/Swiss-Prot:Q8TD26

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