CMT3 chromomethylase 3 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: CMT3
Official Full Name: chromomethylase 3
Primary source: TAIR:AT1G69770
Locus tag: AT1G69770
See related: Araport:AT1G69770
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: chromomethylase 3; T6C23.3; T6C23_3
Summary: Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing.
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Genomic context

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See CMT3 in Genome Data Viewer

Location:: chromosome: 1

Exon count:: 21

Sequence:: Chromosome: 1; NC_003070.9 (26248118..26253687, complement)

Chromosome 1 - NC_003070.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress.
Title: DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress.
Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis.
Title: Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis.
CMT3-SUVH4 is the major pathway controlling silencing of the exonic Evelknievel retroelement via inducing non-CG methylation.
Title: CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA.
The results suggest that dedifferentiation is associated with Tag1 activation and that CMT3 rather than DDM1 plays a central role in restraining Tag1 activation via inducing gene body DNA methylation.
Title: Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation.
The methylation level of the Arabidopsis genome, including transposons, was significantly lower in the siz1-2 mutant than in wild-type plants. CMT3 was sumoylated by the E3 ligase activity of AtSIZ1 through a direct interaction.
Title: Arabidopsis CMT3 activity is positively regulated by AtSIZ1-mediated sumoylation.
Cmt3gene expression throughout normal development in Arabidopsis
Title: [Developmental expression of Arabidopsis methyltransferase genes MET1, DRM2 and CMT3].
gamma irradiation induced DNA hypomethylation preferentially at non-CG sites of transcriptionally inactive repeats in a locus-specific manner, which depends on CMT3 activity
Title: Characterization of non-CG genomic hypomethylation associated with gamma-ray-induced suppression of CMT3 transcription in Arabidopsis thaliana.
These results suggest that CMT3 associates with H3K9me2-containing nucleosomes through dual binding of its bromo adjacent homology and chromo domains to H3K9me2 in order to target DNA methylation.
Title: Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
A speculative model of the CMT3-induced egg cell silencing is presented here.
Title: A role for CHROMOMETHYLASE3 in mediating transposon and euchromatin silencing during egg cell reprogramming in Arabidopsis.
Three methyltransferases MET1, CMT3 and DRM1/2 are all required cooperatively for RPS methylation both at CG and non-CG sites.
Title: Cooperative activity of DNA methyltransferases for maintenance of symmetrical and non-symmetrical cytosine methylation in Arabidopsis thaliana.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_105645.4

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates	IMP Inferred from Mutant Phenotype more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of gene expression, epigenetic	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within zygote asymmetric cytokinesis in embryo sac	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: chromomethylase 3

NP_177135.1

chromomethylase 3 (CMT3); FUNCTIONS IN: DNA (cytosine-5-)-methyltransferase activity; INVOLVED IN: in 6 processes; LOCATED IN: chromatin, nucleus; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: DNA methylase, C-5 cytosine-specific (InterPro:IPR001525), Chromo domain-like (InterPro:IPR016197), Bromo adjacent homology (BAH) domain (InterPro:IPR001025), DNA methylase, C-5 cytosine-specific, active site (InterPro:IPR018117), Chromo domain (InterPro:IPR000953); BEST Arabidopsis thaliana protein match is: chromomethylase 2 (TAIR:AT4G19020.1); Has 4337 Blast hits to 3739 proteins in 974 species: Archae - 208; Bacteria - 2545; Metazoa - 230; Fungi - 161; Plants - 416; Viruses - 30; Other Eukaryotes - 747 (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_003070.9 Reference assembly

Range

26248118..26253687 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_105645.4 → NP_177135.1 chromomethylase 3 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_177135.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q94F88, Q94FN4, Q9C9L8

UniProtKB/TrEMBL

A0A654EMJ3, Q0WN75

Conserved Domains (2) summary

cd04716
Location:107 → 228

BAH_plantDCM_I; BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects ...

cl30459
Location:266 → 810

Cyt_C5_DNA_methylase; Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group ...