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    CHR1 chromatin remodeling 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 836808, updated on 14-Nov-2024

    Summary

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    Official Symbol
    CHR1
    Official Full Name
    chromatin remodeling 1
    Primary source
    TAIR:AT5G66750
    Locus tag
    AT5G66750
    See related
    Araport:AT5G66750
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ATDDM1; CHA1; CHR01; chromatin remodeling 1; CHROMATIN REMODELING 1; DDM1; DECREASED DNA METHYLATION 1; MSN2.14; MSN2_14; SOM1; SOM4; SOMNIFEROUS 1
    Summary
    Protein is similar to SWI2/SNF2 chromatin remodeling proteins. DDM1 is appears to act as a chromatin-remodeling ATPase involved in cytosine methylation in CG and non-CG contexts. Involved in gene silencing and maintenance of DNA methylation and histone methylation. Hypomethylation of many genomic regions occurs in ddm1 mutants, and can cause several phenotypic abnormalities, but some loci, such as BONSAI (At1g73177) can be hypermethylated in ddm1 mutants after several generations, leading to different phenotypes. DDM1 might be involved in establishing a heterochromain boundary. A line expressing an RNAi targeted against DDM1 shows some resistance to agrobacterium-mediated root transformation.
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    Genomic context

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    See CHR1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    16
    Sequence:
    Chromosome: 5; NC_003076.8 (26648897..26653191)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene spindle assembly abnormal protein (DUF620) Neighboring gene tRNA-Glu Neighboring gene succinate dehydrogenase 1-1

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. Liu Y, et al. Nat Plants, 2024 Mar. PMID 38413824
    2. The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Jeddeloh JA, et al. Genes Dev, 1998 Jun 1. PMID 9620857, Free PMC Article
    3. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Johnson L, et al. Curr Biol, 2002 Aug 20. PMID 12194816
    4. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. Brzeski J, et al. J Biol Chem, 2003 Jan 10. PMID 12403775
    5. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. Soppe WJ, et al. EMBO J, 2002 Dec 2. PMID 12456661, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
      Title: Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1.
    2. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
      Title: Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation.
    3. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
      Title: Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.
    4. DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis.
      Title: DDM1-mediated R-loop resolution and H2A.Z exclusion facilitates heterochromatin formation in Arabidopsis.
    5. DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis.
      Title: DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis.
    6. Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana.
      Title: Loss of chromatin remodeler DDM1 causes segregation distortion in Arabidopsis thaliana.
    7. The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W.
      Title: The chromatin remodeler DDM1 prevents transposon mobility through deposition of histone variant H2A.W.
    8. These results suggest that DDM1 is involved in the homology directed repair such as SSA and HR, probably by modifying chromatin structure.
      Title: Mutation in DDM1 inhibits the homology directed repair of double strand breaks.
    9. Data show that chromatin remodeling 1 (DDM1) is required for telomere length maintenance.
      Title: DDM1 guards against telomere truncation in Arabidopsis.
    10. Here, the authors show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. The results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases.
      Title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_126073.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA helicase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within DNA-mediated transformation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heterochromatin formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within retrotransposition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of nucleosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    chromatin remodeling 1
    NP_201476.1
    • chromatin remodeling 1 (CHR1); FUNCTIONS IN: helicase activity, ATPase activity; INVOLVED IN: methylation-dependent chromatin silencing, DNA mediated transformation, transposition, RNA-mediated; LOCATED IN: nucleosome; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: chromatin remodeling factor17 (TAIR:AT5G18620.2); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      26648897..26653191
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_126073.3 → NP_201476.1  chromatin remodeling 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_201476.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q5C995, Q5C996, Q9XFH4
      UniProtKB/TrEMBL
      A0A178UBH1, A0A7G2FJC1
      Conserved Domains (1) summary
      PLN03142
      Location:12 → 739
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9XFH4.1

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