DOI: 10.5061/dryad.80gb5mm26
title: Mature mRNA processing that deletes 3′ end sequences directs translational activation and embryonic development

description: 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 &gt;250 mRNAs underwent
 this processing. Therefore, our results provide a molecular principle that
 triggers the translational activation and directs development.
description: # 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: 0hpf-1\_2.fastq **Description:** Basecalled raw file
 from the 0 hpf dataset (sample n°1), reverse #### File: 4hpf-1\_1.fastq
 **Description:** Basecalled raw file from the 4 hpf dataset (sample n°1),
 forward #### File: 4hpf-1\_2.fastq **Description:** Basecalled raw file
 from the 4 hpf dataset (sample n°1), reverse ## Code/software Raw
 sequencing reads were initially processed with the fastp tool (version
 0.23.4) to perform quality trimming and filtering of low-quality bases,
 adapters, and short reads. The resulting high-quality reads were subjected
 to a quality control check using FASTQC (version 0.11.8), and any
 problematic reads identified through the FASTQC analysis were further
 trimmed or excluded. Reads were aligned to the zebrafish genome (GRCz11)
 using STAR (version 2.7.9a) with default parameters. ## Access information
 Libraries were created for the purpose of this study hence this is the
 first upload of the raw data.