Computational characterization of phased small interfering RNAs and their long non-coding RNA precursors in plants
Date
2020
Authors
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Publisher
University of Delaware
Abstract
Plants possess different classes of endogenous small interfering RNAs (siRNAs) that play roles in regulating gene expression through gene silencing. Of these, a class of phased secondary siRNAs (phasiRNAs) are of particular interest because they are preferentially and highly abundant in the reproductive tissues of grass families. Two classes of reproductive phasiRNAs have been reported so far; the 21-nt accumulate prior to meiosis and are triggered by miR2118 while the 24-nt accumulate during meiosis and are triggered by miR2275. Even though phasiRNAs have been discovered about a decade ago, their functions and mechanism of action are yet to be identified. One of the challenges in studying these phasiRNAs is that; unlike microRNA precursors that produce a single microRNA duplex, phasiRNA precursors (PHAS) produce a number of phasiRNA duplexes, and for a plant like rice, there are thousands of these PHAS loci across the genome, necessitating the initial use of computational approaches for efficient experimental design. Also, the fact that PHAS loci originate from non-coding region of the genome, simple sequence comparison approaches are not effective. I employ an integrated approach to characterize phasiRNAs and their corresponding PHAS loci; 1) I use a comparative genomics approach to systematically compare rice and maize PHAS loci together with their phasiRNA products, 2) I use a synteny approach to extend the rice and maize comparison to perform a comprehensive PHAS loci cross-species comparison across ten diverse grass species, 3) I use a network approach to get a “holistic” view of the phasiRNA pathway and in turn identify key interacting partners and their interactions. With these approaches I was able to; demonstrate a number of phasiRNA characteristics, including their cis regulatory activity, establish PHAS loci relationships across diverse grass species, identify novel co-regulatory modules involving microRNAs, Transcription Factors (TFs), and PHAS genes. Such findings are important to further our understanding of plant reproductive biology and have potential to be applicable in biotech companies to produce hybrid crops with higher yields.
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Keywords
Comparative genomics, PhasiRNA, Synteny, PhasiRNA precursors