IDN2 XH/XS domain-containing protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Gene symbol: IDN2
Gene description: XH/XS domain-containing protein
Primary source: Araport:AT3G48670
Locus tag: AT3G48670
See related: TAIR:AT3G48670
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: INVOLVED IN DE NOVO 2; RDM12; RNA-DIRECTED DNA METHYLATION 12
Summary: Encodes IDN2 (INVOLVED IN DE NOVO 2), a double-stranded RNA-binding protein involved in de novo methylation and small interfering RNA (siRNA)-mediated maintenance methylation. IND2 is a component of the RNA-directed DNA methylation pathway.
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Genomic context

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See IDN2 in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 9

Sequence:: Chromosome: 3; NC_003074.8 (18030669..18034065)

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?

The findings support a model in which IDN2 interacts with RPA and facilitates the release of RPA from single-stranded DNA tails and subsequent recruitment of RAD51 at DSB sites to promote DSB repair.
Title: IDN2 Interacts with RPA and Facilitates DNA Double-Strand Break Repair by Homologous Recombination in Arabidopsis.
FDM1 interacts with itself and with IDN2. The XH domain of FDM1 mediates the FDM1-FDM1 and FDM1-IDN2 interactions.
Title: The DNA- and RNA-binding protein FACTOR of DNA METHYLATION 1 requires XH domain-mediated complex formation for its function in RNA-directed DNA methylation.
The paper presents a refined model for the pathway of RNA-directed DNA methylation and transcriptional gene silencing that positions function of IDN2 downstream of siRNA formation and points to an important role for its XH domain.
Title: IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation.
we demonstrated that the previously uncharacterized IDN2 XH domain is required for the IDN2-IDP1/IDP2 complex formation as well as for IDN2 function. IDP1 is required for de novo DNA methylation, siRNA accumulation, and transcriptional gene silencing.
Title: IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.
Data show that two partially redundant proteins termed IDN2-LIKE 1 (IDNL1; AT1G15910) and IDN2-LIKE 2 (IDNL2; AT4G00380) that are paralogous to INVOLVED IN DE NOVO 2 (IDN2) and that form a stable complex with IDN2 in vivo.
Title: INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.
IDN1 (DMS3) and IDN2 control de novo methylation and small interfering RNA (siRNA)-mediated maintenance methylation and are components of the RNA-directed DNA methylation pathway. [IDN2]
Title: IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.
RDM12 encodes an SGS3-like protein, and is a component of the RNA-directed DNA methylation pathway. [RDM12]
Title: An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis.

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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_114726.6

Supported by ESTs:

NM_202674.3

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in gene silencing by siRNA-directed DNA methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within gene silencing by siRNA-directed DNA methylation	IGI Inferred from Genetic Interaction 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 regulation of double-strand break repair via homologous recombination	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to cadmium ion	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: XH/XS domain-containing protein

NP_190436.2

INVOLVED IN DE NOVO 2 (IDN2); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to cadmium ion, chromatin silencing, DNA methylation; LOCATED IN: cellular_component unknown; EXPRESSED IN: root; CONTAINS InterPro DOMAIN/s: Domain of unknown function XS (InterPro:IPR005380), Domain of unknown function XH (InterPro:IPR005379), Domain of unknown function, putative Zinc finger, XS/XH (InterPro:IPR005381); BEST Arabidopsis thaliana protein match is: XH/XS domain-containing protein (TAIR:AT3G12550.2); Has 76122 Blast hits to 43343 proteins in 2243 species: Archae - 1068; Bacteria - 10039; Metazoa - 36284; Fungi - 4878; Plants - 2932; Viruses - 220; Other Eukaryotes - 20701 (source: NCBI BLink).

NP_974403.1

INVOLVED IN DE NOVO 2 (IDN2); FUNCTIONS IN: molecular_function unknown; INVOLVED IN: response to cadmium ion, chromatin silencing, DNA methylation; LOCATED IN: cellular_component unknown; EXPRESSED IN: root; CONTAINS InterPro DOMAIN/s: Domain of unknown function XS (InterPro:IPR005380), Domain of unknown function XH (InterPro:IPR005379), Domain of unknown function, putative Zinc finger, XS/XH (InterPro:IPR005381); BEST Arabidopsis thaliana protein match is: XH/XS domain-containing protein (TAIR:AT3G12550.2); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (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

18030669..18034065

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001339377.1 → NP_001327083.1 XH/XS domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8VZ79, Q9SMN2

UniProtKB/TrEMBL

A0A178VJW2, A0A5S9XKP9, A0A654FE09

Conserved Domains (4) summary

COG1196
Location:245 → 477

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam03470
Location:48 → 91

zf-XS; XS zinc finger domain

pfam03468
Location:124 → 235

XS; XS domain

pfam03469
Location:511 → 643

XH; XH domain
NM_114726.6 → NP_190436.2 XH/XS domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_190436.2

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8VZ79, Q9SMN2

UniProtKB/TrEMBL

A0A178VJW2, A0A5S9XKP9, A0A654FE09

Conserved Domains (4) summary

COG1196
Location:245 → 477

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam03470
Location:48 → 91

zf-XS; XS zinc finger domain

pfam03468
Location:124 → 235

XS; XS domain

pfam03469
Location:511 → 643

XH; XH domain
NM_202674.3 → NP_974403.1 XH/XS domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_974403.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q8VZ79, Q9SMN2

UniProtKB/TrEMBL

A0A178VJW2, A0A5S9XKP9, A0A654FE09

Conserved Domains (4) summary

COG1196
Location:245 → 477

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

pfam03470
Location:48 → 91

zf-XS; XS zinc finger domain

pfam03468
Location:124 → 235

XS; XS domain

pfam03469
Location:511 → 643

XH; XH domain