title: Mobile small RNAs regulate genome-wide DNA methylation.
abstract: RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21-24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euchromatic regions, lose DNA methylation in a mutant lacking 22- to 24-nt sRNAs (dicer-like 2, 3, 4 triple mutant). Transcriptome analyses identified a small number of genes whose expression in roots is associated with mobile sRNAs and connected to DNA methylation directly or indirectly. Finally, we demonstrate that sRNAs from shoots of one accession move across a graft union and target DNA methylation de novo at normally unmethylated sites in the genomes of root cells from a different accession.
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Mathew G
authors.initials: MG
authors.lastname: Lewsey
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hardcastle
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Charles W
authors.initials: CW
authors.lastname: Melnyk
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Attila
authors.initials: A
authors.lastname: Molnar
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors.forename: Adrián
authors.initials: A
authors.lastname: Valli
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Mark A
authors.initials: MA
authors.lastname: Urich
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037;
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nery
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom; dcb40@cam.ac.uk ecker@salk.edu.
authors.forename: David C
authors.initials: DC
authors.lastname: Baulcombe
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037 dcb40@cam.ac.uk ecker@salk.edu.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D056426:Genetic Loci; D018745:Genome, Plant; D018517:Plant Roots / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D018749:RNA, Plant
keywords: RNA-directed DNA methylation; plant grafting; small RNA; transcriptional gene silencing; transposable element