Transcriptomics

Dataset Information

299

Extensive alternative polyadenylation during zebrafish development


ABSTRACT: 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 more than 78.79% of the annotated protein-coding genes in zebrafish. Most zebrafish genes undergo alternative CPA with more than a thousand genes using different dominant 3'UTRs at different stages. 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 two hours 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. 3P-Seq was used to map the 3' ends of protein-coding genes in the zebrafish genome

ORGANISM(S): Danio rerio  

SUBMITTER: David Koppstein   Alena Shkumatava  George Bell  Alexander O Subtelny  David P Bartel  Calvin H Jan  Hazel Sive  Igor Ulitsky 

PROVIDER: E-GEOD-37453 | ArrayExpress | 2012-06-17

SECONDARY ACCESSION(S): SRP012376GSE37453PRJNA160143

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Extensive alternative polyadenylation during zebrafish development.

Ulitsky Igor I   Shkumatava Alena A   Jan Calvin H CH   Subtelny Alexander O AO   Koppstein David D   Bell George W GW   Sive Hazel H   Bartel David P DP  

Genome research 20120621 10


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 anno  ...[more]

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