Gene Details:

• Gene ID: AT3G07610
• Gene Symbol: IBM1
• Gene Name: increase in bonsai methylation 1
• Description: Transcription factor jumonji (jmjC) domain-containing protein;(source:Araport11)
• TAIR Accession:
• Genome: Araport11_genome_release
• Species: Arabidopsis thaliana

Transcripts:

• AT3G07610.1     AT3G07610.2     AT3G07610.3

Germplasm Phenotype:

• SALK_035608C  — The ibm1-4 mutation causes hypermethylation of the BONSAI (At1g73177) locus in the first generation in which the mutant allele becomes homozygous, and there is a higher level of H3mK9 at the BONSAI locus in ibm1-4 mutant than in wild type rosette leaves. ibm1-4 mutants have morphological defects that become apparent at the F3 generation, including small narrow leaves, arrested flower development, and faulty pollen development. The growth defects observed in ibm1-4 are exacerbated in a ddm1-1 mutant background ddm1-1has also been shown to cause BONSAI hypermethylation. Meanwhile, DNA methylation and developmental defects are suppressed in kyp (At5g13960) and cmt3 (At1g69770) mutant backgrounds.
• ibm1-1  — The ibm1-1 mutation causes hypermethylation of the BONSAI (At1g73177) locus in the first generation in which the mutant allele becomes homozygous. The BONSAI gene undergoes cytosine methylation, primarily associated with non-CG sites in the ibm1-1 mutant, whereas there is almost no evidence of cytosine methylation at this locus in wild type seedlings. Methylation at repetitive regions, including centromeric satellites, or 5S rRNA genes are not compromised in the ibm1-1 mutant. ibm1-1 mutants have morphological defects that become apparent at the F3 generation, including small narrow leaves, arrested flower development, and faulty pollen development.

Literature:

• Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.   DOI:  10.1186/gb-2002-3-4-research0016 ;  PMID:  11983057
• Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana.   DOI:  10.1126/science.1150987 ;  PMID:  18218897
• Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.   DOI:  10.1038/emboj.2010.227 ;  PMID:  20834229
• Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.   DOI:  10.1016/j.cell.2012.10.054 ;  PMID:  23313553
• SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1.   DOI:  10.1371/journal.pone.0084687 ;  PMID:  24404182
• Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA.   DOI:  10.1371/journal.pgen.1003867 ;  PMID:  24204292
• Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development.   DOI:  10.1242/dev.129932 ;  PMID:  27697902
• A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis.   DOI:  10.1073/pnas.1710683114 ;  PMID:  28808009
• Antagonistic Actions of FPA and IBM2 Regulate Transcript Processing from Genes Containing Heterochromatin.   DOI:  10.1104/pp.18.01106 ;  PMID:  30814131
• The Histone Demethylase IBM1 Positively Regulates Arabidopsis Immunity by Control of Defense Gene Expression.   DOI:  10.3389/fpls.2019.01587 ;  PMID:  31956325
• The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression.   DOI:  10.1371/journal.pgen.1008993 ;  PMID:  32925902
• Histone demethylase IBM1-mediated meiocyte gene expression ensures meiotic chromosome synapsis and recombination.   DOI:  10.1371/journal.pgen.1010041 ;  PMID:  35192603
• Dysfunction of histone demethylase IBM1 in Arabidopsis causes autoimmunity and reshapes the root microbiome.   DOI:  10.1038/s41396-022-01297-6 ;  PMID:  35908110
• Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes.   DOI:  10.1371/journal.pone.0203442 ;  PMID:  30169501

Sequence: