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    IBM1 Transcription factor jumonji (jmjC) domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 819952, updated on 18-Sep-2024

    Summary

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    Official Symbol
    IBM1
    Official Full Name
    Transcription factor jumonji (jmjC) domain-containing protein
    Primary source
    TAIR:AT3G07610
    Locus tag
    AT3G07610
    See related
    Araport:AT3G07610
    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
    increase in bonsai methylation 1
    Summary
    IBM1 likely encodes a protein with histone H3mK9 demethylation activity. It may preferentially demethylate H3mK9 at low-copy loci to protect them from silencing by nearby heterochromatin by preventing the spread of cytosine methylation. BONSAI (At1g73177) is hypermethylated in ibm1 mutants. ibm1 mutants have morphological defects that become apparent at the F3 generation, including small narrow leaves, arrested flower development, and faulty pollen development. These phenotypes cannot result solely from the BONSAI hypermethylation. Aberrant phenotypes in ibm1 mutants in both DNA methylation and plant development can be suppressed by mutations in the KYP H3K9 methyltransferase or he CMT3 non CG-cytosine methylase.
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    Genomic context

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    See IBM1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    16
    Sequence:
    Chromosome: 3; NC_003074.8 (2425884..2433113)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene Small nuclear ribonucleoprotein family protein Neighboring gene Heavy metal transport/detoxification superfamily protein Neighboring gene ncRNA Neighboring gene glycosyltransferase Neighboring gene arogenate dehydratase 2

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Dynamic evolution of the heterochromatin sensing histone demethylase IBM1. Zhang Y, et al. PLoS Genet, 2024 Jul. PMID 38991029, Free PMC Article
    2. Epigenetic regulation of high light-induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis. Fan D, et al. New Phytol, 2024 Jun. PMID 38708492
    3. Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome. Lv S, et al. ISME J, 2022 Nov. PMID 35908110, Free PMC Article
    4. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns. Rigal M, et al. EMBO J, 2012 Jun 29. PMID 22580822, Free PMC Article
    5. Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome. Inagaki S, et al. EMBO J, 2010 Oct 20. PMID 20834229, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.
      Title: Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.
    2. Epigenetic regulation of high light-induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis.
      Title: Epigenetic regulation of high light-induced anthocyanin biosynthesis by histone demethylase IBM1 in Arabidopsis.
    3. Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome.
      Title: Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome.
    4. Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis.
      Title: Contrasting epigenetic control of transgenes and endogenous genes promotes post-transcriptional transgene silencing in Arabidopsis.
    5. Results show that ibm1 mutation causes a very severe growth phenotype with a much reduced plant size and affects the expression of a large number of genes.
      Title: JMJ24 antagonizes histone H3K9 demethylase IBM1/JMJ25 function and interacts with RNAi pathways for gene silencing.
    6. The authors show that both ibm1 and edm2 mutants display defects in production of stomatal lineage cells, which is linked to DNA hypermethylation of the ERECTA family genes, including ER, ERL1 and ERL2 Stomatal phenotypes and DNA methylation levels of ER genes in ibm1 and edm2 mutants are restored by mutations in the genes encoding the histone methyltransferase KYP and DNA methyltransferase CMT3.
      Title: Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development.
    7. our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.
      Title: SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.
    8. EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation
      Title: Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.
    9. The results suggest that IBM1 regulates gene expression through two distinct pathways: direct association to protect genes from silencing by preventing the coupling of histone and DNA methylation, and indirect silencing of gene expression through RNA-directed DNA methylation-directed repression.
      Title: IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis.
    10. It was shown that the expression of the H3K9 demethylase IBM1 requires DNA methylation. Surprisingly, the regulatory methylated region is contained in an unusually large intron that is conserved in IBM1 orthologues.
      Title: DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    General gene information

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    NM_001084652.2
    NM_001202909.1
    NM_111640.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables chromatin DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K9 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K9 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within leaf development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within pollen development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stomatal lineage progression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Transcription factor jumonji (jmjC) domain-containing protein
    NP_001078121.1
    • increase in bonsai methylation 1 (IBM1); CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347); BEST Arabidopsis thaliana protein match is: transcription factor jumonji (jmjC) domain-containing protein (TAIR:AT1G62310.1); Has 3909 Blast hits to 1142 proteins in 231 species: Archae - 5; Bacteria - 1730; Metazoa - 411; Fungi - 91; Plants - 818; Viruses - 8; Other Eukaryotes - 846 (source: NCBI BLink).
    NP_001189838.1
    • increase in bonsai methylation 1 (IBM1); FUNCTIONS IN: sequence-specific DNA binding transcription factor activity, histone demethylase activity (H3-K9 specific); INVOLVED IN: flower development, DNA methylation on cytosine, leaf development, pollen development, histone H3-K9 demethylation; LOCATED IN: cellular_component unknown; EXPRESSED IN: 16 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), Transcription factor jumonji (InterPro:IPR013129); BEST Arabidopsis thaliana protein match is: Transcription factor jumonji (jmjC) domain-containing protein (TAIR:AT1G11950.1).
    NP_187418.1
    • increase in bonsai methylation 1 (IBM1); CONTAINS InterPro DOMAIN/s: Transcription factor jumonji/aspartyl beta-hydroxylase (InterPro:IPR003347), Transcription factor jumonji (InterPro:IPR013129); BEST Arabidopsis thaliana protein match is: Transcription factor jumonji (jmjC) domain-containing protein (TAIR:AT1G11950.1); Has 4122 Blast hits to 1300 proteins in 255 species: Archae - 5; Bacteria - 1758; Metazoa - 460; Fungi - 93; Plants - 912; Viruses - 8; Other Eukaryotes - 886 (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_003074.8 Reference assembly

      Range
      2425884..2433113
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_111640.2 → NP_187418.1  Transcription factor jumonji (jmjC) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_187418.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9SSE9
      UniProtKB/TrEMBL
      A0A178VP18, A0A5S9XA21
      Conserved Domains (3) summary
      smart00558
      Location:621 → 693
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam10497
      Location:149 → 211
      zf-4CXXC_R1; Zinc-finger domain of monoamine-oxidase A repressor R1
      cl21464
      Location:747 → 843
      cupin_like; Conserved domain found in cupin and related proteins

    2. NM_001084652.2 → NP_001078121.1  Transcription factor jumonji (jmjC) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001078121.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      F4JFK6, Q681X0
      Conserved Domains (2) summary
      smart00558
      Location:621 → 689
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam10497
      Location:149 → 211
      zf-4CXXC_R1; Zinc-finger domain of monoamine-oxidase A repressor R1

    3. NM_001202909.1 → NP_001189838.1  Transcription factor jumonji (jmjC) domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001189838.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VP18, A0A5S9XA21, F4JFK4
      Conserved Domains (3) summary
      smart00558
      Location:621 → 685
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      pfam10497
      Location:149 → 211
      zf-4CXXC_R1; Zinc-finger domain of monoamine-oxidase A repressor R1
      cl21464
      Location:769 → 865
      cupin_like; Conserved domain found in cupin and related proteins
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SSE9.1

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