SUVH4 histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: SUVH4
Official Full Name: histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein
Primary source: TAIR:AT5G13960
Locus tag: AT5G13960
See related: Araport:AT5G13960
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: KRYPTONITE; KYP; MAC12.7; MAC12_7; SDG33; SET DOMAIN PROTEIN 33; SU(VAR)3-9 homolog 4
Summary: Encodes a histone 3 lysine 9 specific methyltransferase involved in the maintenance of DNA methylation. SUVH4/KYP is a SU(VAR)3-9 homolog, a SET domain protein. Known SET domain proteins are involved in epigenetic control of gene expression. There are 10 SUVH genes in Arabidopsis and members of this subfamily of the SET proteins have an additional conserved SRA domain. In kyp mutants, there is a loss of CpNpG methylation. The protein was shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the latter two. There is also evidence that KYP/SUVH4 might be involved in the telomerase-independent process known as Alternative Lengthening of Telomeres.
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Genomic context

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See SUVH4 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 14

Sequence:: Chromosome: 5; NC_003076.8 (4501362..4506250)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2.
Title: Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2.
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 histone deacetylase HDA6 can interact with the histone methyltransferases SUVH4, SUVH5, and SUVH6 (SUVH4/5/6).
Title: HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing.
The authors conclude that geminivirus TrAP attenuates the transcriptional gene silencing of the viral chromatin by inhibiting KYP activity to evade host surveillance.
Title: Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense.
The structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.
Title: Mechanism of DNA methylation-directed histone methylation by KRYPTONITE.
Genetic analysis showed that DOG1 and HUB1 are epistatic to KYP/SUVH4, suggesting that these genes regulate seed dormancy in the same genetic pathway.
Title: A novel role for histone methyltransferase KYP/SUVH4 in the control of Arabidopsis primary seed dormancy.
H3 lysine 9 methylation epigenetic modifications are reduced in an suvh4 suvh6 double mutant
Title: H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

NM_121399.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables double-stranded methylated DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K9 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables methyl-CpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpNpG binding	IDA Inferred from Direct Assay more info	PubMed
enables methyl-CpNpN binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression, epigenetic	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein

NP_196900.1

SU(VAR)3-9 homolog 4 (SUVH4); FUNCTIONS IN: double-stranded methylated DNA binding, methyl-CpNpG binding, methyl-CpG binding, histone methyltransferase activity (H3-K9 specific), methyl-CpNpN binding; INVOLVED IN: maintenance of DNA methylation, histone methylation, peptidyl-lysine methylation, histone H3-K9 methylation; LOCATED IN: nucleus; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214), SRA-YDG (InterPro:IPR003105), Pre-SET domain (InterPro:IPR007728), Post-SET domain (InterPro:IPR003616); BEST Arabidopsis thaliana protein match is: SU(VAR)3-9 homolog 6 (TAIR:AT2G22740.1); 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

NC_003076.8 Reference assembly

Range

4501362..4506250

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001343303.1 → NP_001332445.1 histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8BH29
NM_121399.3 → NP_196900.1 histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4-like protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_196900.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8GZB6, Q9C5P3, Q9FFX9

Conserved Domains (2) summary

cd10545
Location:360 → 595

SET_AtSUVH-like; SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins

pfam02182
Location:147 → 303

SAD_SRA; SAD/SRA domain