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

dc.contributor.author Jia, Yi
dc.contributor.author Nettleton, Dan
dc.contributor.author Lisch, Damon
dc.contributor.author Ohtsu, Kazuhiro
dc.contributor.author Scanlon, Michael
dc.contributor.author Nettleton, Dan
dc.contributor.author Schnable, Patrick
dc.contributor.department Statistics
dc.contributor.department Agronomy
dc.contributor.department Genetics, Development and Cell Biology
dc.contributor.department Plant Biology
dc.contributor.department Center for Plant Genomics
dc.date 2019-08-24T14:21:56.000
dc.date.accessioned 2020-07-02T06:57:12Z
dc.date.available 2020-07-02T06:57:12Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2009
dc.date.issued 2009-11-01
dc.description.abstract <p>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 <em>mediator of paramutation1</em> (<em>mop1</em>) encoded RDR2 function results in reactivation of transcriptionally silenced <em>Mu</em> 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 <em>mop1</em> 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 <em>mop1</em> 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 <em>mop1</em> mutant.</p>
dc.description.comments <p>This article is published as Jia, Yi, Damon R. Lisch, Kazuhiro Ohtsu, Michael J. Scanlon, Dan Nettleton, and Patrick S. Schnable. "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." <em>PLoS genetics</em> 5, no. 11 (2009): e1000737. doi: <a href="https://doi.org/10.1371/journal.pgen.1000737">10.1371/journal.pgen.1000737</a>.</p>
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dc.identifier archive/lib.dr.iastate.edu/stat_las_pubs/209/
dc.identifier.articleid 1207
dc.identifier.contextkey 14849504
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath stat_las_pubs/209
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/90520
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/stat_las_pubs/209/2009_Nettleton_LossDependent.PDF|||Fri Jan 14 22:30:09 UTC 2022
dc.source.uri 10.1371/journal.pgen.1000737
dc.subject.disciplines Agronomy and Crop Sciences
dc.subject.disciplines Genetics and Genomics
dc.subject.disciplines Molecular Genetics
dc.subject.disciplines Plant Biology
dc.subject.disciplines Plant Breeding and Genetics
dc.title 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
dc.type article
dc.type.genre article
dspace.entity.type Publication
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