title: PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing.
abstract: Small RNAs (sRNAs) are a class of short (20-25 nt) non-coding RNAs that play important regulatory roles in gene expression. An essential first step in understanding their function is to confidently identify sRNA targets. In plants, several classes of sRNAs such as microRNAs (miRNAs) and trans-acting small interfering RNAs have been shown to bind with near-perfect complementarity to their messenger RNA (mRNA) targets, generally leading to cleavage of the mRNA. Recently, a high-throughput technique known as Parallel Analysis of RNA Ends (PARE) has made it possible to sequence mRNA cleavage products on a large-scale. Computational methods now exist to use these data to find targets of conserved and newly identified miRNAs. Due to speed limitations such methods rely on the user knowing which sRNA sequences are likely to target a transcript. By limiting the search to a tiny subset of sRNAs it is likely that many other sRNA/mRNA interactions will be missed. Here, we describe a new software tool called PAREsnip that allows users to search for potential targets of all sRNAs obtained from high-throughput sequencing experiments. By searching for targets of a complete 'sRNAome' we can facilitate large-scale identification of sRNA targets, allowing us to discover regulatory interaction networks.
authors.affiliation: School of Computing Sciences and School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors.forename: Leighton
authors.initials: L
authors.lastname: Folkes
authors.forename: Simon
authors.initials: S
authors.lastname: Moxon
authors.forename: Hugh C
authors.initials: HC
authors.lastname: Woolfenden
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Stocks
authors.forename: Gyorgy
authors.initials: G
authors.lastname: Szittya
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D034622:RNA Interference; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012333:RNA, Messenger; D058727:RNA, Small Untranslated