Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC

3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of...

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Autores principales: Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, Zavolan, Mihaela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875010/
https://www.ncbi.nlm.nih.gov/pubmed/29592812
http://dx.doi.org/10.1186/s13059-018-1415-3
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author Gruber, Andreas J.
Schmidt, Ralf
Ghosh, Souvik
Martin, Georges
Gruber, Andreas R.
van Nimwegen, Erik
Zavolan, Mihaela
author_facet Gruber, Andreas J.
Schmidt, Ralf
Ghosh, Souvik
Martin, Georges
Gruber, Andreas R.
van Nimwegen, Erik
Zavolan, Mihaela
author_sort Gruber, Andreas J.
collection PubMed
description 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1415-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-58750102018-04-02 Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC Gruber, Andreas J. Schmidt, Ralf Ghosh, Souvik Martin, Georges Gruber, Andreas R. van Nimwegen, Erik Zavolan, Mihaela Genome Biol Method 3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on poly(A) site choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovers motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to polypyrimidine tract binding protein 1 as a regulator of poly(A) site choice in glioblastoma. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1415-3) contains supplementary material, which is available to authorized users. BioMed Central 2018-03-28 /pmc/articles/PMC5875010/ /pubmed/29592812 http://dx.doi.org/10.1186/s13059-018-1415-3 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Gruber, Andreas J.
Schmidt, Ralf
Ghosh, Souvik
Martin, Georges
Gruber, Andreas R.
van Nimwegen, Erik
Zavolan, Mihaela
Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title_full Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title_fullStr Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title_full_unstemmed Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title_short Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC
title_sort discovery of physiological and cancer-related regulators of 3′ utr processing with kapac
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875010/
https://www.ncbi.nlm.nih.gov/pubmed/29592812
http://dx.doi.org/10.1186/s13059-018-1415-3
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