title: The RNAs of RNA-directed DNA methylation.
abstract: RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5' and 3' ends. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
authors: Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
authors: Jered M
authors: JM
authors: Wendte
authors: Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, IN 47405, USA. Electronic address: cpikaard@indiana.edu.
authors: Craig S
authors: CS
authors: Pikaard
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D018749:RNA, Plant; D012321:DNA-Directed RNA Polymerases
keywords: Chromatin modification; Cytosine methylation; Epigenetic regulation; Gene regulation; Noncoding RNA; RNA silencing