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| Status |
Public on Jun 17, 2012 |
| Title |
Extensive alternative polyadenylation during zebrafish development |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
3P-Seq was used to map the 3' ends of protein-coding genes in the zebrafish genome
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| Contributor(s) |
Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell G, Sive H, Bartel DP |
| Citation(s) |
22722342 |
| Submission date |
Apr 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Igor Ulitsky |
| Organization name |
Whitehead Institute for Biomedical Research
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| Street address |
9 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02472 |
| Country |
USA |
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| Platforms (2) |
| GPL9319 |
Illumina Genome Analyzer II (Danio rerio) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA160143 |
| SRA |
SRP012376 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37453_RAW.tar |
133.1 Mb |
(http)(custom) |
TAR (of BED, BW, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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