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    Chd2 chromodomain helicase DNA binding protein 2 [ Mus musculus (house mouse) ]

    Gene ID: 244059, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Chd2provided by MGI
    Official Full Name
    chromodomain helicase DNA binding protein 2provided by MGI
    Primary source
    MGI:MGI:2448567
    See related
    Ensembl:ENSMUSG00000078671 AllianceGenome:MGI:2448567
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CHD-2; 2810013C04Rik; 2810040A01Rik; 5630401D06Rik
    Summary
    Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and histone binding activity. Involved in gene expression and muscle organ development. Acts upstream of or within DNA damage response and hematopoietic stem cell differentiation. Located in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Used to study CHARGE syndrome. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 94. Orthologous to human CHD2 (chromodomain helicase DNA binding protein 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 9.7), limb E14.5 (RPKM 9.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Chd2 in Genome Data Viewer
    Location:
    7 D1; 7 41.85 cM
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (73076400..73191494, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (73426652..73541746, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 4930429H19 gene Neighboring gene RIKEN cDNA A730056A06 gene Neighboring gene STARR-seq mESC enhancer starr_19176 Neighboring gene repulsive guidance molecule family member A Neighboring gene predicted gene 44758 Neighboring gene STARR-seq mESC enhancer starr_19180 Neighboring gene STARR-seq mESC enhancer starr_19181 Neighboring gene STARR-seq mESC enhancer starr_19183 Neighboring gene STARR-seq mESC enhancer starr_19186 Neighboring gene STARR-seq mESC enhancer starr_19187 Neighboring gene STARR-positive B cell enhancer ABC_E6553 Neighboring gene CRISPRi-validated cis-regulatory element for Chaserr and Chd2 Neighboring gene CHD2 adjacent suppressive regulatory RNA Neighboring gene STARR-seq mESC enhancer starr_19190 Neighboring gene STARR-positive B cell enhancer ABC_E1342 Neighboring gene STARR-positive B cell enhancer ABC_E6554 Neighboring gene STARR-seq mESC enhancer starr_19193 Neighboring gene STARR-seq mESC enhancer starr_19194 Neighboring gene predicted gene, 30149 Neighboring gene STARR-seq mESC enhancer starr_19195 Neighboring gene predicted gene, 39036 Neighboring gene predicted gene, 26176

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Mutation of the SNF2 family member Chd2 affects mouse development and survival. Marfella CG, et al. J Cell Physiol, 2006 Oct. PMID 16810678
    2. Disruption of chromodomain helicase DNA binding protein 2 (CHD2) causes scoliosis. Kulkarni S, et al. Am J Med Genet A, 2008 May 1. PMID 18386809, Free PMC Article
    3. A mutation in the mouse Chd2 chromatin remodeling enzyme results in a complex renal phenotype. Marfella CG, et al. Kidney Blood Press Res, 2008. PMID 19142019, Free PMC Article
    4. Chromodomain helicase DNA-binding protein 2 affects the repair of X-ray and UV-induced DNA damage. Rajagopalan S, et al. Environ Mol Mutagen, 2012 Jan. PMID 22223433
    5. Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells. Semba Y, et al. Nucleic Acids Res, 2017 Sep 6. PMID 28549158, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Studies results provide initial insight into how Chd2 haploinsufficiency leads to aberrant cortical network function and impaired memory.
      Title: Chd2 Is Necessary for Neural Circuit Development and Long-Term Memory.
    2. Chd2 is essential in preventing suppressive chromatin formation for developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state.
      Title: Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells.
    3. inactivation of CHD2 during neurogenesis might contribute to abnormal neurodevelopment
      Title: CHD2 is Required for Embryonic Neurogenesis in the Developing Cerebral Cortex.
    4. The data indicated that MyoD determines cell fate and facilitates differentiation- dependent gene expression through Chd2-dependent deposition of H3.3 at myogenic loci prior to differentiation.
      Title: Chd2 interacts with H3.3 to determine myogenic cell fate.
    5. Study present evidence that the Chd2 mutant cells are defective in their ability to repair DNA damage induced by ionizing and ultraviolet radiation.
      Title: Chromodomain helicase DNA-binding protein 2 affects the repair of X-ray and UV-induced DNA damage.
    6. Chd2-mutant mice present with glomerulopathy, proteinuria, and significantly impaired kidney function.
      Title: A mutation in the mouse Chd2 chromatin remodeling enzyme results in a complex renal phenotype.
    7. Chd2 heterozygous mutant mice exhibit increased extramedullary hematopoiesis and susceptibility to lymphomas.
      Title: Role of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling and tumorigenesis.
    8. Our results demonstrate that mutation of Chd2 dramatically affects mammalian development and long-term survival.
      Title: Mutation of the SNF2 family member Chd2 affects mouse development and survival.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within hematopoietic stem cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in muscle organ development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleosome organization 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
    		  
    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 2
    Names
    ATP-dependent helicase CHD2
    NP_001074814.2

    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_001081345.2 → NP_001074814.2  chromodomain-helicase-DNA-binding protein 2

      See identical proteins and their annotated locations for NP_001074814.2

      Status: VALIDATED

      Source sequence(s)
      AC099699, AC154883
      Consensus CDS
      CCDS52274.1
      UniProtKB/Swiss-Prot
      E9PZM4
      Related
      ENSMUSP00000126352.3, ENSMUST00000169922.9
      Conserved Domains (7) summary
      cd00024
      Location:282 → 344
      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 ...
      cd00046
      Location:503 → 648
      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:487 → 768
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:790 → 905
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:379 → 447
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam13907
      Location:1471 → 1553
      DUF4208; Domain of unknown function (DUF4208)
      pfam17104
      Location:1042 → 1165
      DUF5102; Domain of unknown function (DUF5102)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000073.7 Reference GRCm39 C57BL/6J

      Range
      73076400..73191494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    E9PZM4.1 GenPept UniProtKB/Swiss-Prot:E9PZM4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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