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Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their path...

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Autores principales: Chou, Min-Te, Han, Bo W., Hsiao, Chiung-Po, Zamore, Phillip D., Weng, Zhiping, Hung, Jui-Hung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632877/
https://www.ncbi.nlm.nih.gov/pubmed/26007652
http://dx.doi.org/10.1093/nar/gkv537
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author Chou, Min-Te
Han, Bo W.
Hsiao, Chiung-Po
Zamore, Phillip D.
Weng, Zhiping
Hung, Jui-Hung
author_facet Chou, Min-Te
Han, Bo W.
Hsiao, Chiung-Po
Zamore, Phillip D.
Weng, Zhiping
Hung, Jui-Hung
author_sort Chou, Min-Te
collection PubMed
description Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
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spelling pubmed-46328772015-11-04 Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs Chou, Min-Te Han, Bo W. Hsiao, Chiung-Po Zamore, Phillip D. Weng, Zhiping Hung, Jui-Hung Nucleic Acids Res Methods Online Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor. Oxford University Press 2015-09-30 2015-05-24 /pmc/articles/PMC4632877/ /pubmed/26007652 http://dx.doi.org/10.1093/nar/gkv537 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Chou, Min-Te
Han, Bo W.
Hsiao, Chiung-Po
Zamore, Phillip D.
Weng, Zhiping
Hung, Jui-Hung
Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title_full Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title_fullStr Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title_full_unstemmed Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title_short Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
title_sort tailor: a computational framework for detecting non-templated tailing of small silencing rnas
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632877/
https://www.ncbi.nlm.nih.gov/pubmed/26007652
http://dx.doi.org/10.1093/nar/gkv537
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