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

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 silen...

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Autores principales: Thody, Joshua, Folkes, Leighton, Moulton, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337908/
https://www.ncbi.nlm.nih.gov/pubmed/32463462
http://dx.doi.org/10.1093/nar/gkaa448
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author Thody, Joshua
Folkes, Leighton
Moulton, Vincent
author_facet Thody, Joshua
Folkes, Leighton
Moulton, Vincent
author_sort Thody, Joshua
collection PubMed
description 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.
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spelling pubmed-73379082020-07-13 NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs Thody, Joshua Folkes, Leighton Moulton, Vincent Nucleic Acids Res Computational Biology 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. Oxford University Press 2020-07-09 2020-05-28 /pmc/articles/PMC7337908/ /pubmed/32463462 http://dx.doi.org/10.1093/nar/gkaa448 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Thody, Joshua
Folkes, Leighton
Moulton, Vincent
NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title_full NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title_fullStr NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title_full_unstemmed NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title_short NATpare: a pipeline for high-throughput prediction and functional analysis of nat-siRNAs
title_sort natpare: a pipeline for high-throughput prediction and functional analysis of nat-sirnas
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337908/
https://www.ncbi.nlm.nih.gov/pubmed/32463462
http://dx.doi.org/10.1093/nar/gkaa448
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