PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing

Folkes, Leighton, Moxon, Simon ORCID: https://orcid.org/0000-0003-4644-1816, Woolfenden, Hugh C., Stocks, Matthew B., Szittya, Gyorgy, Dalmay, Tamas ORCID: https://orcid.org/0000-0003-1492-5429 and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2012) PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. Nucleic Acids Research, 40 (13). ISSN 0305-1048

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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.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Faculty of Science > School of Biological Sciences
Depositing User: Users 2731 not found.
Date Deposited: 15 Oct 2012 11:20
Last Modified: 10 Nov 2022 14:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/39845
DOI: 10.1093/nar/gks277

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