title: Genetic and functional diversification of small RNA pathways in plants.
abstract: Multicellular eukaryotes produce small RNA molecules (approximately 21-24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.
authors.affiliation: Center for Gene Research and Biotechnology and Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA.
authors.forename: Zhixin
authors.initials: Z
authors.lastname: Xie
authors.forename: Lisa K
authors.initials: LK
authors.lastname: Johansen
authors.forename: Adam M
authors.initials: AM
authors.lastname: Gustafson
authors.forename: Kristin D
authors.initials: KD
authors.lastname: Kasschau
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Lellis
authors.forename: Daniel
authors.initials: D
authors.lastname: Zilberman
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.forename: James C
authors.initials: JC
authors.lastname: Carrington
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D002843:Chromatin / Q000737:chemistry; D003596:Cytosine / Q000737:chemistry; D019175:DNA Methylation; D019143:Evolution, Molecular; D005091:Exons; D017343:Genes, Plant; D049452:Green Fluorescent Proteins / Q000737:chemistry; D006570:Heterochromatin / Q000737:chemistry; D006657:Histones / Q000737:chemistry; D015151:Immunoblotting; D007438:Introns; D008745:Methylation; D035683:MicroRNAs / Q000737:chemistry*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D010944:Plants / Q000821:virology; D012313:RNA / Q000737:chemistry; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry; D011993:Recombinant Fusion Proteins / Q000737:chemistry; D012984:Software
chemical_list: D002843:Chromatin; D006570:Heterochromatin; D006657:Histones; D035683:MicroRNAs; D034741:RNA, Small Interfering; D012367:RNA, Viral; D011993:Recombinant Fusion Proteins; D049452:Green Fluorescent Proteins; D012313:RNA; D003596:Cytosine; D012324:RNA-Dependent RNA Polymerase