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

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_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.
Title: Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.
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.
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.
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.
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.
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.
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.
EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation
Title: Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns.
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.
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.

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General gene information

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NM_001084652.2

Supported by ESTs:

NM_001202909.1

Supported by ESTs:

NM_111640.2

Supported by ESTs:

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

NC_003074.8 Reference assembly

Range

2425884..2433113

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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