title: RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants.
abstract: RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)-related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.
authors.affiliation: Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan; email: marjorimatzke@gate.sinica.edu.tw , kanno0@gate.sinica.edu.tw , antoniusmatzke@gate.sinica.edu.tw.
authors.forename: Marjori A
authors.initials: MA
authors.lastname: Matzke
authors.forename: Tatsuo
authors.initials: T
authors.lastname: Kanno
authors.forename: Antonius J M
authors.initials: AJ
authors.lastname: Matzke
mesh_terms: D005075:Biological Evolution; D019175:DNA Methylation; D018744:DNA, Plant / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D019684:Magnoliopsida / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000378:metabolism; D018749:RNA, Plant / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism*
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; D012321:DNA-Directed RNA Polymerases
keywords: RNA polymerase; RNA-directed DNA methylation; epigenetics; small RNAs