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    CHD1 chromodomain helicase DNA binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 1105, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CHD1provided by HGNC
    Official Full Name
    chromodomain helicase DNA binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:1915
    See related
    Ensembl:ENSG00000153922 MIM:602118; AllianceGenome:HGNC:1915
    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
    CHD-1; PILBOS
    Summary
    The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in bone marrow (RPKM 30.4), appendix (RPKM 9.5) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CHD1 in Genome Data Viewer
    Location:
    5q15-q21.1
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (98853985..98929007, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (99357270..99432327, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (98189689..98264711, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:98175311-98175811 Neighboring gene casein kinase 1 alpha 1 pseudogene 3 Neighboring gene uncharacterized LOC105379099 Neighboring gene RNA, U6 small nuclear 402, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:98240158-98241357 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:98264728-98265626 Neighboring gene uncharacterized LOC100289230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22838 Neighboring gene CHD1 divergent transcript Neighboring gene ribosomal protein S9 pseudogene 3

    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. Influenza Virus and Chromatin: Role of the CHD1 Chromatin Remodeler in the Virus Life Cycle. Marcos-Villar L, et al. J Virol, 2016 Jan 20. PMID 26792750, Free PMC Article
    2. SPOP and CHD1 alterations in prostate cancer: Relationship with PTEN loss, tumor grade, perineural infiltration, and PSA recurrence. Hernández-Llodrà S, et al. Prostate, 2021 Dec. PMID 34533858
    3. The Chromatin Remodeling Complex CHD1 Regulates the Primitive State of Mesenchymal Stromal Cells to Control Their Stem Cell Supporting Activity. Lee HR, et al. Stem Cells Dev, 2021 Apr 1. PMID 33593142
    4. CHD1 loss negatively influences metastasis-free survival in R0-resected prostate cancer patients and promotes spontaneous metastasis in vivo. Oh-Hohenhorst SJ, et al. Cancer Gene Ther, 2022 Jan. PMID 33414516, Free PMC Article
    5. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Zhang Z, et al. Cancer Cell, 2020 Apr 13. PMID 32220301, Free PMC Article

    See all (140) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA LINC02535 Induces Colorectal Adenocarcinoma Progression via Modulating miR-30d-5p/CHD1.
      Title: LncRNA LINC02535 Induces Colorectal Adenocarcinoma Progression via Modulating miR-30d-5p/CHD1.
    2. MiR-30a-5p/CHD1 axis enhances cisplatin sensitivity of ovarian cancer cells via inactivating the Wnt/beta-catenin pathway.
      Title: MiR-30a-5p/CHD1 axis enhances cisplatin sensitivity of ovarian cancer cells via inactivating the Wnt/β-catenin pathway.
    3. CHD1 Promotes Sensitivity to Aurora Kinase Inhibitors by Suppressing Interaction of AURKA with Its Coactivator TPX2.
      Title: CHD1 Promotes Sensitivity to Aurora Kinase Inhibitors by Suppressing Interaction of AURKA with Its Coactivator TPX2.
    4. CHD1 loss negatively influences metastasis-free survival in R0-resected prostate cancer patients and promotes spontaneous metastasis in vivo.
      Title: CHD1 loss negatively influences metastasis-free survival in R0-resected prostate cancer patients and promotes spontaneous metastasis in vivo.
    5. SPOP and CHD1 alterations in prostate cancer: Relationship with PTEN loss, tumor grade, perineural infiltration, and PSA recurrence.
      Title: SPOP and CHD1 alterations in prostate cancer: Relationship with PTEN loss, tumor grade, perineural infiltration, and PSA recurrence.
    6. MAP3K7 Loss Drives Enhanced Androgen Signaling and Independently Confers Risk of Recurrence in Prostate Cancer with Joint Loss of CHD1.
      Title: MAP3K7 Loss Drives Enhanced Androgen Signaling and Independently Confers Risk of Recurrence in Prostate Cancer with Joint Loss of CHD1.
    7. The Chromatin Remodeling Complex CHD1 Regulates the Primitive State of Mesenchymal Stromal Cells to Control Their Stem Cell Supporting Activity.
      Title: The Chromatin Remodeling Complex CHD1 Regulates the Primitive State of Mesenchymal Stromal Cells to Control Their Stem Cell Supporting Activity.
    8. Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex.
      Title: Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex.
    9. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation.
      Title: Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation.
    10. The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans.
      Title: The chromatin remodeler Chd1 regulates cohesin in budding yeast and humans.
    Submit: New GeneRIF Correction See all GeneRIFs (43)

    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

    Associated conditions

    Description Tests
    Pilarowski-Bjornsson syndrome
    MedGen: C4540131 OMIM: 617682 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart Study.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686E2337

    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 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 methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation by host of viral transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nuclear chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 1
    Names
    ATP-dependent helicase CHD1
    NP_001261.2
    NP_001351042.1
    NP_001363123.1
    XP_024310112.1
    XP_024310113.1
    XP_047272625.1
    XP_047272626.1
    XP_047272628.1
    XP_047272629.1
    XP_054207481.1
    XP_054207482.1
    XP_054207483.1
    XP_054207484.1
    XP_054207485.1
    XP_054207486.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001270.4 → NP_001261.2  chromodomain-helicase-DNA-binding protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001261.2

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS34204.1
      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
      Related
      ENSP00000483667.1, ENST00000614616.5
      Conserved Domains (8) summary
      PLN03142
      Location:464 → 1000
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:387 → 443
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:276 → 354
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam05110
      Location:1281 → 1401
      AF-4; AF-4 proto-oncoprotein
      pfam13907
      Location:1409 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam15440
      Location:1554 → 1708
      THRAP3_BCLAF1; THRAP3/BCLAF1 family
      pfam18375
      Location:1124 → 1210
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:460 → 697
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    2. NM_001364113.3 → NP_001351042.1  chromodomain-helicase-DNA-binding protein 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS93752.1
      UniProtKB/TrEMBL
      A0A087WVF4
      Related
      ENSP00000479403.2, ENST00000511067.3
      Conserved Domains (5) summary
      cd00024
      Location:306 → 355
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      pfam00385
      Location:389 → 443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam08648
      Location:1672 → 1781
      DUF1777; Protein of unknown function (DUF1777)
      pfam13907
      Location:1496 → 1586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:464 → 1000
      SNF2_N; SNF2 family N-terminal domain

    3. NM_001376194.2 → NP_001363123.1  chromodomain-helicase-DNA-binding protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055
      Consensus CDS
      CCDS34204.1
      UniProtKB/Swiss-Prot
      O14646, Q17RZ3
      Conserved Domains (8) summary
      PLN03142
      Location:464 → 1000
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18661
      Location:387 → 443
      CD2_tandem_CHD1-2_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      cd18666
      Location:276 → 354
      CD1_tandem_CHD1-2_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins
      pfam05110
      Location:1281 → 1401
      AF-4; AF-4 proto-oncoprotein
      pfam13907
      Location:1409 → 1498
      DUF4208; Domain of unknown function (DUF4208)
      pfam15440
      Location:1554 → 1708
      THRAP3_BCLAF1; THRAP3/BCLAF1 family
      pfam18375
      Location:1124 → 1210
      CDH1_2_SANT_HL1; CDH1/2 SANT-Helical linker 1
      cl28899
      Location:460 → 697
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    RNA

    1. NR_157078.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055

    2. NR_157079.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC022121, KC877055

    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

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      98853985..98929007 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416670.1 → XP_047272626.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

    2. XM_024454345.2 → XP_024310113.1  chromodomain-helicase-DNA-binding protein 1 isoform X3

      Conserved Domains (4) summary
      cd00024
      Location:306 → 355
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      pfam00385
      Location:389 → 443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam13907
      Location:1496 → 1586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:464 → 1000
      SNF2_N; SNF2 family N-terminal domain

    3. XM_024454344.2 → XP_024310112.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVF4
      Conserved Domains (5) summary
      cd00024
      Location:306 → 355
      CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
      pfam00385
      Location:389 → 443
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam08648
      Location:1672 → 1781
      DUF1777; Protein of unknown function (DUF1777)
      pfam13907
      Location:1496 → 1586
      DUF4208; Domain of unknown function (DUF4208)
      cl26465
      Location:464 → 1000
      SNF2_N; SNF2 family N-terminal domain

    4. XM_047416669.1 → XP_047272625.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

      UniProtKB/Swiss-Prot
      O14646, Q17RZ3

    5. XM_047416672.1 → XP_047272628.1  chromodomain-helicase-DNA-binding protein 1 isoform X5

    6. XM_047416673.1 → XP_047272629.1  chromodomain-helicase-DNA-binding protein 1 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      99357270..99432327 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351509.1 → XP_054207484.1  chromodomain-helicase-DNA-binding protein 1 isoform X4

    2. XM_054351508.1 → XP_054207483.1  chromodomain-helicase-DNA-binding protein 1 isoform X3

    3. XM_054351506.1 → XP_054207481.1  chromodomain-helicase-DNA-binding protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A087WVF4

    4. XM_054351507.1 → XP_054207482.1  chromodomain-helicase-DNA-binding protein 1 isoform X2

      UniProtKB/Swiss-Prot
      O14646, Q17RZ3

    5. XM_054351510.1 → XP_054207485.1  chromodomain-helicase-DNA-binding protein 1 isoform X5

    6. XM_054351511.1 → XP_054207486.1  chromodomain-helicase-DNA-binding protein 1 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14646.2 GenPept UniProtKB/Swiss-Prot:O14646

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