Protein: Protein INVOLVED IN DE NOVO 2 (Protein RNA-DIRECTED DNA METHYLATION 12) (Q8VZ79)
Organism: Arabidopsis thaliana (Mouse-ear cress)
Function: Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway and downstream of small interfering RNA (siRNA) formation. Required for de novo DNA methylation, siRNA accumulation and siRNA-mediated maintenance methylation. Required for several post-transcriptional gene silencing pathways. Binds double-stranded RNAs (dsRNAs) with 5'-overhangs through its XS domain. Binds long non-coding RNA (lncRNA) in an AGO4-dependent manner and associates with DRM2, resulting in DNA methylation of RdDM target loci. Mediates the silencing of a subset of MORC6 target loci.
Sequence: MGSTVILSSDDEDSDISESEMDEYGDKMYLNLKGGKLKVRLSPQAFICPYCPNKKKTSFQYKDLLQHASGVGNSNSDKRSAKEKASHLALVKYLQQDLADSASEAEPSSKRQKNGNPIQDCDHDEKLVYPWKGIVVNIPTTKAQDGRSAGESGSKLRDEYILRGFNPTRVRPLWNYLGHSGTAIVEFNKDWNGLHNGLLFDKAYTVDGHGKKDWLKKDGPKLGLYGWIARADDYNGNNIIGENLRKTGDLKTIAELTEEEARKQELLVQNLRQLVEEKKKDMKEIEELCSVKSEELNQLMEEKEKNQQKHYRELNAIQERTMSHIQKIVDDHEKLKRLLESERKKLEIKCNELAKREVHNGTERMKLSEDLEQNASKNSSLELAAMEQQKADEEVKKLAEDQRRQKEELHEKIIRLERQRDQKQAIELEVEQLKGQLNVMKHMASDGDAEVVKEVDIIFKDLGEKEAQLADLDKFNQTLILRERRTNDELQEAHKELVNIMKEWNTNIGVKRMGELVTKPFVDAMQQKYCQQDVEDRAVEVLQLWEHYLKDSDWHPFKRVKLENEDREVEVIDDRDEKLRELKADLGDGPYNAVTKALLEINEYNPSGRYITTELWNFKADKKATLEEGVTCLLDQWEKAKRKRGMA
InterPro domains: - IPR005380: XS domain (domain) [124-235]
- IPR045177: Factor of DNA methylation 1-5/IDN2 (family) [9-645]
- IPR005379: Factor of DNA methylation 1-5/IDN2 , domain XH (domain) [511-643]
- IPR005381: Zinc finger-XS domain (domain) [48-91]
- IPR038588: XS domain superfamily (homologous_superfamily) [119-290]
Interaction partners: - Protein RNA-directed DNA methylation 3
- SWI/SNF complex subunit SWI3B
- Protein DEFECTIVE IN MERISTEM SILENCING 3
- DNA-directed RNA polymerase V subunit 1
- Protein RDM1
- DNA
- Protein CHROMATIN REMODELING 35
- Histone-lysine N-methyltransferase family member SUVH9
- Protein MICRORCHIDIA 6
- Histone-lysine N-methyltransferase family member SUVH2
Gene Ontology annotations:
Molecular Function (MF): GO:0003674 (molecular function), GO:0005488 (binding), GO:0097159 (organic cyclic compound binding), GO:1901363 (heterocyclic compound binding), GO:0005515 (protein binding), GO:0003676 (nucleic acid binding), GO:0043621 (protein self-association), GO:0003677 (DNA binding), GO:0003723 (RNA binding), GO:0003725 (double-stranded RNA binding)
Biological Process (BP): GO:0008150 (biological process), GO:0009987 (cellular process), GO:0065007 (biological regulation), GO:0050789 (regulation of biological process), GO:0048519 (negative regulation of biological process), GO:0071840 (cellular component organization or biogenesis), GO:0009892 (negative regulation of metabolic process), GO:0019222 (regulation of metabolic process), GO:0060255 (regulation of macromolecule metabolic process), GO:0016043 (cellular component organization), GO:0010605 (negative regulation of macromolecule metabolic process), GO:0006325 (chromatin organization), GO:0010629 (negative regulation of gene expression), GO:0010468 (regulation of gene expression), GO:0040029 (epigenetic regulation of gene expression), GO:0006338 (chromatin remodeling), GO:0045814 (negative regulation of gene expression, epigenetic), GO:0031047 (RNA-mediated gene silencing), GO:0031048 (RNA-mediated heterochromatin formation), GO:0031507 (heterochromatin formation), GO:0070828 (heterochromatin organization), GO:0140718 (facultative heterochromatin formation), GO:0080188 (gene silencing by RNA-directed DNA methylation), GO:0006346 (DNA methylation-dependent heterochromatin formation)
Cellular Component (CC): GO:0005575 (cellular component), GO:0110165 (cellular anatomical entity), GO:0005622 (intracellular anatomical structure), GO:0043226 (organelle), GO:0005737 (cytoplasm), GO:0043229 (intracellular organelle), GO:0005739 (mitochondrion), GO:0043227 (membrane-bounded organelle), GO:0043231 (intracellular membrane-bounded organelle)