Identifying microRNAs in plant genomes

Christopher Maher, Marja Timmermans, Lincoln Stein, Doreen Ware

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Scopus citations

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 (rd11) 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.

Original languageEnglish
Title of host publicationProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
Pages718-723
Number of pages6
StatePublished - Dec 1 2004
EventProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States
Duration: Aug 16 2004Aug 19 2004

Publication series

NameProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004

Conference

ConferenceProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
CountryUnited States
CityStanford, CA
Period08/16/0408/19/04

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    Maher, C., Timmermans, M., Stein, L., & Ware, D. (2004). Identifying microRNAs in plant genomes. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 (pp. 718-723). (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).