Comprehensive analysis of mRNA 3' ends during early zebrafish development reveals dynamics of 3'UTR changes on a genome-wide scale.

Eggs accumulate more than 10 000 mRNAs, from which proteins are synthesized constitutively or in a temporally controlled manner. Although changes in the translation state of these mRNAs are crucial for early development, how embryos orchestrate them remains unclear. Here, we investigated changes in mRNA 3' untranslated regions (UTRs) using 3' end-RNA sequencing of zebrafish embryos and computational methods. Consistent with our previous finding that pou5f3 mRNA is shortened at the 3'UTR during early development, thousands of mRNAs showed shortening of the 3'UTRs. Moreover, we found that most mRNAs in embryos contained several different 3' ends and their proportion was dynamically changed. These changes were coupled with protein synthesis. Our results reveal genome-wide 3'-end dynamics in the regulation of biological processes.