Mature mRNA processing that deletes 3′ end sequences directs translational activation and embryonic development

Eggs accumulate thousands of translationally repressed mRNAs that are translated into proteins after fertilization to direct diverse developmental processes. However, molecular mechanisms underlying the translation of stored mRNAs after fertilization remain unclear. Here, we report a previously unknown RNA processing of 3′ end sequences of mature mRNAs that activates the translation of stored mRNAs. Specifically, 9 to 72 nucleotides at the 3′ ends of zebrafish pou5f3 and mouse Pou5f1 mRNAs were deleted in the early stages of development. Reporter assays illustrated the effective translation of the truncated forms of mRNAs. Moreover, promotion and inhibition of the shortening of 3′ ends accelerated and attenuated Pou5f3 accumulation, respectively, resulting in defective development. Identification of proteins binding to unprocessed and/or processed mRNAs revealed that mRNA shortening acts as molecular switches. Comprehensive analysis revealed that >250 mRNAs underwent this processing...., , # Mature mRNA processing that deletes 3′ end sequences directs translational activation and embryonic development

Dataset DOI: [10.5061/dryad.80gb5mm26](10.5061/dryad.80gb5mm26)

## 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 2 separate time-points (0 and 4 hours post fertilisation (hpf)) from 50 embryos each time. The quality before sequencing was ensured using Tape Station (high D1000) to confirm 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.
### Files and variables

#### File: 0hpf-1\_1.fastq

**Description:** Basecalled raw file from the 0 hpf dataset (sample n°1), forward

#### File: 0hp...,