Mature mRNA processing that deletes 3′ end sequences directs translational activation and embryonic development
Data files
Jun 20, 2025 version files 6.55 GB
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0hpf-1_1.fastq
1.48 GB
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0hpf-1_2.fastq
1.48 GB
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4hpf-1_1.fastq
1.79 GB
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4hpf-1_2.fastq
1.79 GB
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README.md
1.96 KB
Abstract
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. Therefore, our results provide a molecular principle that triggers the translational activation and directs development.
Dataset DOI: 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.