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Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe

Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, S. cerevisiae and S. pombe. Although >80% of the mRNA genes in each sp...

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Autores principales: Liu, Xiaochuan, Hoque, Mainul, Larochelle, Marc, Lemay, Jean-François, Yurko, Nathan, Manley, James L., Bachand, François, Tian, Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630032/
https://www.ncbi.nlm.nih.gov/pubmed/28916539
http://dx.doi.org/10.1101/gr.222331.117
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author Liu, Xiaochuan
Hoque, Mainul
Larochelle, Marc
Lemay, Jean-François
Yurko, Nathan
Manley, James L.
Bachand, François
Tian, Bin
author_facet Liu, Xiaochuan
Hoque, Mainul
Larochelle, Marc
Lemay, Jean-François
Yurko, Nathan
Manley, James L.
Bachand, François
Tian, Bin
author_sort Liu, Xiaochuan
collection PubMed
description Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, S. cerevisiae and S. pombe. Although >80% of the mRNA genes in each species were found to display APA, S. pombe showed greater 3′ UTR size differences among APA isoforms than did S. cerevisiae. PASs in different locations of gene are surrounded with distinct sequences in both species and are often associated with motifs involved in the Nrd1-Nab3-Sen1 termination pathway. In S. pombe, strong motifs surrounding distal PASs lead to higher abundances of long 3′ UTR isoforms than short ones, a feature that is opposite in S. cerevisiae. Differences in PAS placement between convergent genes lead to starkly different antisense transcript landscapes between budding and fission yeasts. In both species, short 3′ UTR isoforms are more likely to be expressed when cells are growing in nutrient-rich media, although different gene groups are affected in each species. Significantly, 3′ UTR shortening in S. pombe coordinates with up-regulation of expression for genes involved in translation during cell proliferation. Using S. pombe strains deficient for Pcf11 or Pab2, we show that reduced expression of 3′-end processing factors lengthens 3′ UTR, with Pcf11 having a more potent effect than Pab2. Taken together, our data indicate that APA mechanisms in S. pombe and S. cerevisiae are largely different: S. pombe has many of the APA features of higher species, and Pab2 in S. pombe has a different role in APA regulation than its mammalian homolog, PABPN1.
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spelling pubmed-56300322018-04-01 Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe Liu, Xiaochuan Hoque, Mainul Larochelle, Marc Lemay, Jean-François Yurko, Nathan Manley, James L. Bachand, François Tian, Bin Genome Res Research Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, S. cerevisiae and S. pombe. Although >80% of the mRNA genes in each species were found to display APA, S. pombe showed greater 3′ UTR size differences among APA isoforms than did S. cerevisiae. PASs in different locations of gene are surrounded with distinct sequences in both species and are often associated with motifs involved in the Nrd1-Nab3-Sen1 termination pathway. In S. pombe, strong motifs surrounding distal PASs lead to higher abundances of long 3′ UTR isoforms than short ones, a feature that is opposite in S. cerevisiae. Differences in PAS placement between convergent genes lead to starkly different antisense transcript landscapes between budding and fission yeasts. In both species, short 3′ UTR isoforms are more likely to be expressed when cells are growing in nutrient-rich media, although different gene groups are affected in each species. Significantly, 3′ UTR shortening in S. pombe coordinates with up-regulation of expression for genes involved in translation during cell proliferation. Using S. pombe strains deficient for Pcf11 or Pab2, we show that reduced expression of 3′-end processing factors lengthens 3′ UTR, with Pcf11 having a more potent effect than Pab2. Taken together, our data indicate that APA mechanisms in S. pombe and S. cerevisiae are largely different: S. pombe has many of the APA features of higher species, and Pab2 in S. pombe has a different role in APA regulation than its mammalian homolog, PABPN1. Cold Spring Harbor Laboratory Press 2017-10 /pmc/articles/PMC5630032/ /pubmed/28916539 http://dx.doi.org/10.1101/gr.222331.117 Text en © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Liu, Xiaochuan
Hoque, Mainul
Larochelle, Marc
Lemay, Jean-François
Yurko, Nathan
Manley, James L.
Bachand, François
Tian, Bin
Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title_full Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title_fullStr Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title_full_unstemmed Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title_short Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
title_sort comparative analysis of alternative polyadenylation in s. cerevisiae and s. pombe
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630032/
https://www.ncbi.nlm.nih.gov/pubmed/28916539
http://dx.doi.org/10.1101/gr.222331.117
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