DocumentCode :
3410871
Title :
Identifyng microRNAs in plant genomes
Author :
Maher, Christopher ; Timmermans, Marja ; Stein, Lincoln ; Ware, Doreen
Author_Institution :
Cold Spring Harbor Lab., New York, NY, USA
fYear :
2004
fDate :
16-19 Aug. 2004
Firstpage :
718
Lastpage :
723
Abstract :
The ability to control gene expression during development in plants could be used for improving crop yields, resistance to disease, and environmental adaptability. It has been suggested that microRNAs, or miRNAs, control developmental processes such as meristem cell identity, organ polarity, and developmental timing by interfering with the expression of mRNAs. Our preliminary analysis focuses on the miR166 family since it has been shown to mediate repression of rolled-leaf1 (rdl1) in maize. Based on maize sequences derived from degenerate primers, we computationally identified miR166b, miR166c, miR166d, and four more closely related putative maize precursors. Patscan, a pattern-matching program that allows RNA basepairing and mismatches, was used to identify functional elements in the putative hairpins. Each hairpin was further supported by their stable secondary structures determined with Mfold. Using this pattern matching approach we expanded the analysis for 19 Arabidopsis miRNA families in rice and maize.
Keywords :
biology computing; botany; genetics; macromolecules; molecular biophysics; pattern matching; Arabidopsis miRNA families; Mfold; Patscan; RNA basepairing; RNA mismatches; degenerate primers; gene expression; hairpin; maize sequences; miR166 family; microRNAs; pattern-matching program; plant genomes; rice; stable secondary structures; Bioinformatics; Crops; Diseases; Gene expression; Genomics; Pattern analysis; Pattern matching; Process control; RNA; Timing;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE
Print_ISBN :
0-7695-2194-0
Type :
conf
DOI :
10.1109/CSB.2004.1332558
Filename :
1332558
Link To Document :
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