Genetic and functional diversification of small RNA pathways in plants.

Zhixin Xie,Lisa K Johansen,James C Carrington,Daniel Zilberman,Andrew D Lellis,Steven E Jacobsen,Adam M Gustafson,Kristin D Kasschau,Detlef Weigel Detlef Weigel

doi:10.1371/journal.pbio.0020104

Zhixin Xie, Lisa K Johansen + Show 7 more

Open Access

https://doi.org/10.1371/journal.pbio.0020104

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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.

Highlights

Eukaryotic small RNAs of approximately 21–24 nucleotides function as guide molecules in a remarkably wide range of biological processes, including developmental timing and patterning, formation of heterochromatin, genome rearrangement, and antiviral defense (Carrington and Ambros 2003; Finnegan and Matzke 2003; Lai 2003)
They are associated with both post-transcriptional forms of RNA interference (RNAi) and transcriptional silencing involving chromatin modification (Finnegan and Matzke 2003). short interfering RNA (siRNA) are processed from precursors containing extensive or exclusive double-stranded RNA structure, such as transcripts containing inverted repeats or intermediates formed during RNA virus replication
To determine whether other DCL or RNA-dependent RNA polymerase (RDR) proteins are required for miRNA formation in Arabidopsis, miR-171 and miR-159 were analyzed in four new mutants

Summary

Introduction

Eukaryotic small RNAs of approximately 21–24 nucleotides function as guide molecules in a remarkably wide range of biological processes, including developmental timing and patterning, formation of heterochromatin, genome rearrangement, and antiviral defense (Carrington and Ambros 2003; Finnegan and Matzke 2003; Lai 2003). They belong to at least two general classes, microRNA (miRNA) and short interfering RNA (siRNA). They are associated with both post-transcriptional forms of RNA interference (RNAi) and transcriptional silencing involving chromatin modification (Finnegan and Matzke 2003). siRNAs are processed from precursors containing extensive or exclusive double-stranded RNA (dsRNA) structure, such as transcripts containing inverted repeats or intermediates formed during RNA virus replication

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