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 ten thousand mRNAs, from which proteins are
synthesized constitutively or in temporally controlled manners. 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 shortens the 3′UTR
during early development, thousands of mRNAs were found to shorten their
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 direction of biological
processes. The datasets consist of RNA sequencing data from
3'end-RNA sequencing of zebrafish embryos at 0, 2, and 4 hours
post-fertilization (hpf).