NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs

Thody, Joshua, Folkes, Leighton and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2020) NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs. Nucleic Acids Research, 48 (12). 6481–6490. ISSN 0305-1048

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Abstract

Natural antisense transcript-derived small interfering RNAs (nat-siRNAs) are a class of functional small RNA (sRNA) that have been found in both plant and animals kingdoms. In plants, these sRNAs have been shown to suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex (RISC) to their sequence-specific mRNA target(s). Current computational tools for classification of nat-siRNAs are limited in number and can be computationally infeasible to use. In addition, current methods do not provide any indication of the function of the predicted nat-siRNAs. Here, we present a new software pipeline, called NATpare, for prediction and functional analysis of nat-siRNAs using sRNA and degradome sequencing data. Based on our benchmarking in multiple plant species, NATpare substantially reduces the time required to perform prediction with minimal resource requirements allowing for comprehensive analysis of nat-siRNAs in larger and more complex organisms for the first time. We then exemplify the use of NATpare by identifying tissue and stress specific nat-siRNAs in multiple Arabidopsis thaliana datasets.

Item Type:	Article
Additional Information:	© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Faculty \ School:	Faculty of Science > School of Computing Sciences Faculty of Science > School of Biological Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Depositing User:	LivePure Connector
Date Deposited:	03 Jun 2020 00:13
Last Modified:	21 Apr 2023 00:37
URI:	https://ueaeprints.uea.ac.uk/id/eprint/75447
DOI:	10.1093/nar/gkaa448

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