Journal article
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 - PNAS, Vol.102(27), pp.9703-9708
07/05/2005
Handle:
https://hdl.handle.net/2376/113380
PMCID: PMC1172271
PMID: 15980147
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.
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Details
- Title
- A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes
- Creators
- Leor Williams - United States Department of Agriculture–Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710; and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720Cristel C Carles - United States Department of Agriculture–Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710; and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720Karen S Osmont - United States Department of Agriculture–Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710; and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720Jennifer C Fletcher - United States Department of Agriculture–Agricultural Research Service, Plant Gene Expression Center, 800 Buchanan Street, Albany, CA 94710; and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Publication Details
- Proceedings of the National Academy of Sciences - PNAS, Vol.102(27), pp.9703-9708
- Academic Unit
- Department of Crop and Soil Sciences
- Publisher
- National Academy of Sciences
- Identifiers
- 99900547624201842
- Language
- English
- Resource Type
- Journal article