INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 109; no. 22; pp. 8374 - 8381
• Main Authors: Ausin, Israel, Greenberg, Maxim V. C, Simanshu, Dhirendra K, Hale, Christopher J, Vashisht, Ajay A, Simon, Stacey A, Lee, Tzuu-fen, Feng, Suhua, Española, Sophia D, Meyers, Blake C, Wohlschlegel, James A, Patel, Dinshaw J, Jacobsen, Steven E
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 29.05.2012; National Acad Sciences
• Series: Inaugural Article
• Subjects: 60 APPLIED LIFE SCIENCES; Amino Acid Sequence; ARABIDOPSIS; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - chemistry; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; BASIC BIOLOGICAL SCIENCES; Binding Sites - genetics; Biological Sciences; Blotting, Northern; Blotting, Western; CYTOSINE; DNA; DNA Methylation; Flowers & plants; Flowers - genetics; Flowers - metabolism; Gene Expression Regulation, Plant; GENES; Genetic loci; genetic techniques and protocols; GENETICS; Genomes; Genomics; Genotype & phenotype; IN VIVO; Life Sciences; MACHINERY; MAINTENANCE; MASS SPECTROSCOPY; METHYLATION; MIRRORS; Models, Molecular; Molecular Sequence Data; Multiprotein Complexes - chemistry; Multiprotein Complexes - genetics; Multiprotein Complexes - metabolism; MUTANTS; Mutation; MUTATIONS; PHENOTYPE; Phenotypes; Plant Leaves - genetics; Plant Leaves - metabolism; Plants; Plants, Genetically Modified; Protein Binding; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; PROTEINS; Ribonucleic acid; RNA; RNA Interference; RNA, Plant - genetics; RNA, Plant - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Sequence Homology, Amino Acid; Sequencing; Small interfering RNA; transcription (genetics); Transcriptome - genetics
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1206638109

At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.