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PMID: 15980147 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 102 ·No. 27 ·2005-07-05 ·Pages 9703-8

Williams L, Carles CC, Osmont KS, Fletcher JC

Abstract

Two classes of small RNAs, microRNAs and short-interfering RNA (siRNAs), have been extensively studied in plants and animals. In Arabidopsis, the capacity to uncover previously uncharacterized small RNAs by means of conventional strategies seems to be reaching its limits. To discover new plant small RNAs, we developed a protocol to mine an Arabidopsis nonannotated, noncoding EST database. Using this approach, we identified an endogenous small RNA, trans-acting short-interfering RNA-auxin response factor (tasiR-ARF), that shares a 21- and 22-nt region of sequence similarity with members of the ARF gene family. tasiR-ARF has characteristics of both short-interfering RNA and microRNA, recently defined as tasiRNA. Accumulation of trans-acting siRNA depends on DICER-LIKE1 and RNA-DEPENDENT RNA POLYMERASE6 but not RNA-DEPENDENT RNA POLYMERASE2. We demonstrate that tasiR-ARF targets three ARF genes, ARF2, ARF3/ETT, and ARF4, and that both the tasiR-ARF precursor and its target genes are evolutionarily conserved. The identification of tasiRNA-ARF as a low-abundance, previously uncharacterized small RNA species proves our method to be a useful tool to uncover additional small regulatory RNAs.

MeSH Terms
Arabidopsis/genetics Arabidopsis Proteins/genetics,metabolism Base Sequence Cell Cycle Proteins/metabolism Computational Biology/methods DNA Primers DNA-Binding Proteins/genetics Databases, Genetic Molecular Sequence Data Multigene Family/genetics Nuclear Proteins/genetics Nucleic Acid Amplification Techniques RNA, Small Interfering/genetics RNA-Dependent RNA Polymerase/metabolism RNA-Induced Silencing Complex/genetics,metabolism Reverse Transcriptase Polymerase Chain Reaction Ribonuclease III/metabolism Sequence Alignment Sequence Analysis, DNA
Chemicals
Arabidopsis Proteins Cell Cycle Proteins DNA Primers DNA-Binding Proteins ETT protein, Arabidopsis Nuclear Proteins RNA, Small Interfering RNA-Induced Silencing Complex RNA-Dependent RNA Polymerase DCL1 protein, Arabidopsis Ribonuclease III
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Williams Leor
United States Department of Agriculture-Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710, USA.
Carles Cristel C
Osmont Karen S
Fletcher Jennifer C
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.0504029102
Published
2005-07-05
Epub
2005-00-24
Pages
9703-8
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC1172271
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.0504029102 PMC Full Text View journal details
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