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Extensive alternative polyadenylation during zebrafish development

The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages a...

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Autores principales: Ulitsky, Igor, Shkumatava, Alena, Jan, Calvin H., Subtelny, Alexander O., Koppstein, David, Bell, George W., Sive, Hazel, Bartel, David P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460199/
https://www.ncbi.nlm.nih.gov/pubmed/22722342
http://dx.doi.org/10.1101/gr.139733.112
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author Ulitsky, Igor
Shkumatava, Alena
Jan, Calvin H.
Subtelny, Alexander O.
Koppstein, David
Bell, George W.
Sive, Hazel
Bartel, David P.
author_facet Ulitsky, Igor
Shkumatava, Alena
Jan, Calvin H.
Subtelny, Alexander O.
Koppstein, David
Bell, George W.
Sive, Hazel
Bartel, David P.
author_sort Ulitsky, Igor
collection PubMed
description The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3′ UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development.
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spelling pubmed-34601992012-10-06 Extensive alternative polyadenylation during zebrafish development Ulitsky, Igor Shkumatava, Alena Jan, Calvin H. Subtelny, Alexander O. Koppstein, David Bell, George W. Sive, Hazel Bartel, David P. Genome Res Resource The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3′ UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development. Cold Spring Harbor Laboratory Press 2012-10 /pmc/articles/PMC3460199/ /pubmed/22722342 http://dx.doi.org/10.1101/gr.139733.112 Text en © 2012, Published by Cold Spring Harbor Laboratory Press 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 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
spellingShingle Resource
Ulitsky, Igor
Shkumatava, Alena
Jan, Calvin H.
Subtelny, Alexander O.
Koppstein, David
Bell, George W.
Sive, Hazel
Bartel, David P.
Extensive alternative polyadenylation during zebrafish development
title Extensive alternative polyadenylation during zebrafish development
title_full Extensive alternative polyadenylation during zebrafish development
title_fullStr Extensive alternative polyadenylation during zebrafish development
title_full_unstemmed Extensive alternative polyadenylation during zebrafish development
title_short Extensive alternative polyadenylation during zebrafish development
title_sort extensive alternative polyadenylation during zebrafish development
topic Resource
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460199/
https://www.ncbi.nlm.nih.gov/pubmed/22722342
http://dx.doi.org/10.1101/gr.139733.112
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