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PMID: 17400893 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.

The Plant cell ·Vol. 19 ·No. 3 ·2007-03-00 ·Pages 926-42

Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC

Abstract

Posttranscriptional RNA silencing of many endogenous transcripts, viruses, and transgenes involves the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 (RDR6/DCL4)-dependent short interfering RNA (siRNA) biogenesis pathway. Arabidopsis thaliana contains several families of trans-acting siRNAs (tasiRNAs) that form in 21-nucleotide phased arrays through the RDR6/DCL4-dependent pathway and that negatively regulate target transcripts. Using deep sequencing technology and computational approaches, the phasing patterns of known tasiRNAs and tasiRNA-like loci from across the Arabidopsis genome were analyzed in wild-type plants and silencing-defective mutants. Several gene transcripts were found to be routed through the RDR6/DCL4-dependent pathway after initial targeting by one or multiple miRNAs or tasiRNAs, the most conspicuous example of which was an expanding clade of genes encoding pentatricopeptide repeat (PPR) proteins. Interestingly, phylogenetic analysis using Populus trichocarpa revealed evidence for small RNA-mediated regulatory mechanisms within a similarly expanded group of PPR genes. We suggest that posttranscriptional silencing mechanisms operate on an evolutionary scale to buffer the effects of rapidly expanding gene families.

MeSH Terms
Arabidopsis/genetics Arabidopsis Proteins/metabolism Base Sequence Gene Expression Regulation, Plant Genes, Plant Genome, Plant/genetics MicroRNAs/genetics,metabolism Molecular Sequence Data Nucleotides RNA, Messenger/genetics,metabolism RNA, Small Interfering/genetics,metabolism RNA-Dependent RNA Polymerase/metabolism Ribonuclease III Ribonucleases/metabolism
Chemicals
Arabidopsis Proteins MicroRNAs Nucleotides RNA, Messenger RNA, Small Interfering RDR6 protein, Arabidopsis RNA-Dependent RNA Polymerase DCL4 protein, Arabidopsis Ribonucleases Ribonuclease III
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Howell Miya D
Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
Fahlgren Noah
Chapman Elisabeth J
Cumbie Jason S
Sullivan Christopher M
Givan Scott A
Kasschau Kristin D
Carrington James C
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.107.050062
Published
2007-03-00
Epub
2007-00-30
Pages
926-42
Language
English
Region
England
NLM ID
9208688
PMCID
PMC1867363
Subset
IM
Grants
NIAID NIH HHS · R01 AI043288 · United States
NIAID NIH HHS · R21 AI043288 · United States
NIAID NIH HHS · R37 AI043288 · United States
NIAID NIH HHS · AI43288 · United States
Databases
GEO
GSE6682
External Links
PubMed source DOI: 10.1105/tpc.107.050062 PMC Full Text View journal details
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