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PMID: 22955139 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Dynamic landscape of tandem 3' UTRs during zebrafish development.

Genome research ·Vol. 22 ·No. 10 ·2012-10-00 ·Pages 1899-906

Li Y, Sun Y, Fu Y, Li M, Huang G, Zhang C, Liang J, Huang S, Shen G, Yuan S, Chen L, Chen S, Xu A

Abstract

Tandem 3' untranslated regions (UTRs), produced by alternative polyadenylation (APA) in the terminal exon of a gene, could have critical roles in regulating gene networks. Here we profiled tandem poly(A) events on a genome-wide scale during the embryonic development of zebrafish (Danio rerio) using a recently developed SAPAS method. We showed that 43% of the expressed protein-coding genes have tandem 3' UTRs. The average 3' UTR length follows a V-shaped dynamic pattern during early embryogenesis, in which the 3' UTRs are first shortened at zygotic genome activation, and then quickly lengthened during gastrulation. Over 4000 genes are found to switch tandem APA sites, and the distinct functional roles of these genes are indicated by Gene Ontology analysis. Three families of cis-elements, including miR-430 seed, U-rich element, and canonical poly(A) signal, are enriched in 3' UTR-shortened/lengthened genes in a stage-specific manner, suggesting temporal regulation coordinated by APA and trans-acting factors. Our results highlight the regulatory role of tandem 3' UTR control in early embryogenesis and suggest that APA may represent a new epigenetic paradigm of physiological regulations.

MeSH Terms
3' Untranslated Regions Animals Gene Expression Regulation, Developmental Molecular Sequence Annotation Poly A Polyadenylation RNA Isoforms Tandem Repeat Sequences Zebrafish/embryology,genetics
Chemicals
3' Untranslated Regions RNA Isoforms Poly A
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Li Yuxin
State Key Laboratory of Biocontrol, National Engineering Center of South China Sea for Marine Biotechnology, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, College of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou, 510006, PR China.
Sun Yu
Fu Yonggui
Li Mengzhen
Huang Guangrui
Zhang Chenxu
Liang Jiahui
Huang Shengfeng
Shen Gaoyang
Yuan Shaochun
Chen Liangfu
Chen Shangwu
Xu Anlong
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1549-5469
DOI
10.1101/gr.128488.111
Published
2012-10-00
Epub
2012-00-05
Pages
1899-906
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC3460185
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.128488.111 PMC Full Text View journal details
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