REPAC: analysis of alternative polyadenylation from RNA-sequencing data

Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data are limited compared to RNA-sequencing data. We developed R...

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Detalles Bibliográficos
Autores principales: Imada, Eddie L., Wilks, Christopher, Langmead, Ben, Marchionni, Luigi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912678/
https://www.ncbi.nlm.nih.gov/pubmed/36759904
http://dx.doi.org/10.1186/s13059-023-02865-5
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author Imada, Eddie L.
Wilks, Christopher
Langmead, Ben
Marchionni, Luigi
author_facet Imada, Eddie L.
Wilks, Christopher
Langmead, Ben
Marchionni, Luigi
author_sort Imada, Eddie L.
collection PubMed
description Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data are limited compared to RNA-sequencing data. We developed REPAC, a framework for the analysis of APA from RNA-sequencing data. Using REPAC, we investigate the landscape of APA caused by activation of B cells. We also show that REPAC is faster than alternative methods by at least 7-fold and that it scales well to hundreds of samples. Overall, the REPAC method offers an accurate, easy, and convenient solution for the exploration of APA. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02865-5.
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spelling pubmed-99126782023-02-11 REPAC: analysis of alternative polyadenylation from RNA-sequencing data Imada, Eddie L. Wilks, Christopher Langmead, Ben Marchionni, Luigi Genome Biol Method Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data are limited compared to RNA-sequencing data. We developed REPAC, a framework for the analysis of APA from RNA-sequencing data. Using REPAC, we investigate the landscape of APA caused by activation of B cells. We also show that REPAC is faster than alternative methods by at least 7-fold and that it scales well to hundreds of samples. Overall, the REPAC method offers an accurate, easy, and convenient solution for the exploration of APA. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02865-5. BioMed Central 2023-02-09 /pmc/articles/PMC9912678/ /pubmed/36759904 http://dx.doi.org/10.1186/s13059-023-02865-5 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Imada, Eddie L.
Wilks, Christopher
Langmead, Ben
Marchionni, Luigi
REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title_full REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title_fullStr REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title_full_unstemmed REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title_short REPAC: analysis of alternative polyadenylation from RNA-sequencing data
title_sort repac: analysis of alternative polyadenylation from rna-sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912678/
https://www.ncbi.nlm.nih.gov/pubmed/36759904
http://dx.doi.org/10.1186/s13059-023-02865-5
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AT langmeadben repacanalysisofalternativepolyadenylationfromrnasequencingdata
AT marchionniluigi repacanalysisofalternativepolyadenylationfromrnasequencingdata

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