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PMID: 19936292 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs.

PLoS genetics ·Vol. 5 ·No. 11 ·2009-11-00 ·Pages e1000737

Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS

Abstract

Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA-dependent RNA polymerase 2 (RDR2) is a component of the RNA-directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA-seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, >6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2-sensitive and RDR2-resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant.

MeSH Terms
Arabidopsis/enzymology,genetics Arabidopsis Proteins/genetics Base Pairing/genetics Chromatin Assembly and Disassembly/genetics DNA Transposable Elements/genetics Down-Regulation/genetics Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant/genetics Lasers Meristem/genetics Microdissection Mutation/genetics RNA, Plant/metabolism RNA, Small Interfering/genetics,metabolism RNA-Dependent RNA Polymerase/deficiency,genetics Reproducibility of Results Reverse Transcriptase Polymerase Chain Reaction Sequence Analysis, RNA
Chemicals
Arabidopsis Proteins DNA Transposable Elements RNA, Plant RNA, Small Interfering RDR2 protein, Arabidopsis RNA-Dependent RNA Polymerase
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Jia Yi
Interdepartmental Plant Biology Program, Iowa State University, Ames, Iowa, USA.
Lisch Damon R
Ohtsu Kazuhiro
Scanlon Michael J
Nettleton Daniel
Schnable Patrick S
Conflict of Interest

The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS genetics
Abbr.
PLoS Genet
ISSN
1553-7404
DOI
10.1371/journal.pgen.1000737
Published
2009-11-00
Epub
2009-00-20
Pages
e1000737
Language
English
Region
United States
NLM ID
101239074
PMCID
PMC2774947
Subset
IM
External Links
PubMed source DOI: 10.1371/journal.pgen.1000737 PMC Full Text View journal details
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