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

Gene ID: 1105, updated on 10-Dec-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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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
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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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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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