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

Gene ID: 824027, updated on 18-Sep-2024

Summary

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Official Symbol
IDN2
Official Full Name
XH/XS domain-containing protein
Primary source
TAIR:AT3G48670
Locus tag
AT3G48670
See related
Araport: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_003074.8Genomic Context describing neighboring genes Neighboring gene miscRNA Neighboring gene transmembrane protein, putative (DUF 3339) Neighboring gene egg cell-secreted-like protein (DUF1278) Neighboring gene gamma carbonic anhydrase-like 2

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation. Finke A, et al. Epigenetics, 2012 Aug. PMID 22810086, Free PMC Article
  2. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Zheng Z, et al. Plant J, 2010 Apr 1. PMID 20059743, Free PMC Article
  3. 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. Xie M, et al. Plant J, 2012 Nov. PMID 22757778
  4. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Ausin I, et al. Nat Struct Mol Biol, 2009 Dec. PMID 19915591, Free PMC Article
  5. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Ausin I, et al. Proc Natl Acad Sci U S A, 2012 May 29. PMID 22592791, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_114726.6
NM_202674.3

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

  1. NC_003074.8 Reference assembly

    Range
    18030669..18034065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  3. 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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8VZ79.1

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