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

Dataset DOI: [10.5061/dryad.0zpc8678g](10.5061/dryad.0zpc8678g)

## Description of the data and file structure

3’ end-RNA sequencing libraries were constructed using the Lexogen QuantSeq 3’ mRNA-seq Library Prep Kit for Illumina platforms following the manufacturer’s instructions. RNA samples were collected at 3 separate time-points (0, 2, and 4 hours post fertilisation (hpf)) from 50 embryos each time. The experiment was repeated thrice to ensure reproducibility with different fish pairs. The quality before sequencing was ensured using Tape Station (high D1000) to confirm the DNA fragments size and purity. Sequencing was carried out by Macrogen Inc. using the Illumina HiSeqX Ten platform. The sequencing depth for each sample was set to a target of 30 million reads to ensure sufficient coverage for downstream analyses.

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