Dataset Information

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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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]

PMID: 22722342

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Project description:Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization. Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs. Here we describe a high-throughput method to reliably identify 3´ ends of polyadenylated RNAs. This method, called poly(A)-position profiling by sequencing (3P-Seq), was used to determine the UTRs of C. elegans. Compared to standard methods also recently applied to C. elegans UTRs, 3P-Seq identified 8775 additional UTRs while excluding thousands of shorter UTR isoforms that do not appear to be authentic. Analysis of this expanded and corrected dataset indicated that the high A/U content of C. elegans 3´UTRs facilitated genome compaction, since the elements specifying cleavage and polyadenylation, which are A/U-rich, can more readily emerge in A/U rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,000 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes utilize palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3´UTRs have median length only one-sixth that of mammalian 3´UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying posttranscriptional gene regulation. Nine samples (10 sequencing runs) from various mixed and specific stages of wild-type Caenorhabditis elegans and glp-4 mutant adults.