PAREsnip

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

Leighton Folkes, Simon Moxon, Hugh C. Woolfenden, Matthew B. Stocks, G. Szittya, Tamas Dalmay, Vincent Moulton

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Small RNAs (sRNAs) are a class of short (20-25nt) 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.

Original languageEnglish
JournalNucleic Acids Research
Volume40
Issue number13
DOIs
Publication statusPublished - Jul 2012

Fingerprint

Genome
RNA
Messenger RNA
MicroRNAs
RNA Cleavage
High-Throughput Nucleotide Sequencing
Untranslated RNA
Small Interfering RNA
Software
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

PAREsnip : A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. / Folkes, Leighton; Moxon, Simon; Woolfenden, Hugh C.; Stocks, Matthew B.; Szittya, G.; Dalmay, Tamas; Moulton, Vincent.

In: Nucleic Acids Research, Vol. 40, No. 13, 07.2012.

Research output: Contribution to journalArticle

Folkes, Leighton ; Moxon, Simon ; Woolfenden, Hugh C. ; Stocks, Matthew B. ; Szittya, G. ; Dalmay, Tamas ; Moulton, Vincent. / PAREsnip : A tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing. In: Nucleic Acids Research. 2012 ; Vol. 40, No. 13.
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