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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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    See CHD6 in Genome Data Viewer
    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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