Extensive alternative polyadenylation during zebrafish development (original) (raw)

1. Alena Shkumatava1,2,3,
2. Calvin H. Jan1,2,3,4,
3. Alexander O. Subtelny1,2,3,
4. David Koppstein1,2,3,
5. George W. Bell1,
6. Hazel Sive1,3 and
7. David P. Bartel1,2,3,5
8. 1Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
9. 2Howard Hughes Medical Institute,
10. 3Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

• ↵4 Present address: Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco and California Institute for Quantitative Biosciences, San Francisco, California 94158, USA.

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 >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.

Footnotes

• ↵5 Corresponding author
  E-mail dbartel{at}wi.mit.edu

• [Supplemental material is available for this article.]

• Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.139733.112.
  Freely available online through the Genome Research Open Access option.

• Received February 27, 2012.

• Accepted June 14, 2012.

• © 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/.