Alternative 3′UTRs and RNA-binding proteins Ewsr1b, HuR, and Syncrip organize sequential waves of translation to drive embryonic development
Data files
May 23, 2026 version files 9.36 GB
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README.md
2.57 KB
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RPL11_0hpf_1.fastq
855.74 MB
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RPL11_0hpf_2.fastq
855.74 MB
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RPL11_1hpf_1.fastq
1.24 GB
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RPL11_1hpf_2.fastq
1.24 GB
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RPL11_2hpf_1.fastq
788.32 MB
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RPL11_2hpf_2.fastq
788.32 MB
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RPL11_3hpf_1.fastq
1.11 GB
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RPL11_3hpf_2.fastq
1.11 GB
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RPL11_4hpf_1.fastq
680.16 MB
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RPL11_4hpf_2.fastq
680.16 MB
Abstract
Eggs of many species accumulate thousands of dormant mRNAs that are translated after fertilization at specific times and locations to direct development. However, how embryos coordinate translation of these mRNAs remains unclear. In this study, we identify sequential waves of translation critical for proper development progression. The first wave occurs within 1 h and includes translation of ewsr1b mRNA that harbors a short 3′ untranslated region (UTR) comprising 16 nucleotides. The resulting Ewsr1b protein triggers the second translation wave through binding cytoplasmic mRNAs, including pou5f3, which encodes a transcription factor promoting zygotic genome activation. In contrast, HuR and Syncrip repress translation until the first and second waves, respectively. ewsr1b mRNA that has a long 3′UTR is translated in the second wave, and the 3′UTR’s length determines protein localization and function. Overall, our findings reveal previously unknown molecular principles that coordinate translation timings and protein functions to drive long-term, multilayered processes.
Dataset DOI: 10.5061/dryad.bzkh189q6
Description of the data and file structure
Rpl11-IP RNA sequencing libraries were constructed using the SMART-Seq mRNA LP Kit and Unique Dual Index Kits following the manufacturer’s instructions. RNA samples were collected at 5 separate time-points (0, 1, 2, 3, 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 NovaSeq X Plus platform. The sequencing depth for each sample was set to a target of 40 million reads to ensure sufficient coverage for downstream analyses.
Files and variables
File: RPL11_0hpf_1.fastq
Description: Basecalled raw file from the 0 hpf dataset, forward
File: RPL11_0hpf_2.fastq
Description: Basecalled raw file from the 0 hpf dataset, reverse
File: RPL11_1hpf_1.fastq
Description: Basecalled raw file from the 1 hpf dataset, forward
File: RPL11_1hpf_2.fastq
Description: Basecalled raw file from the 1 hpf dataset, reverse
File: RPL11_2hpf_1.fastq
Description: Basecalled raw file from the 2 hpf dataset, forward
File: RPL11_2hpf_2.fastq
Description: Basecalled raw file from the 2 hpf dataset, reverse
File: RPL11_3hpf_1.fastq
Description: Basecalled raw file from the 3 hpf dataset, forward
File: RPL11_3hpf_2.fastq
Description: Basecalled raw file from the 3 hpf dataset, reverse
File: RPL11_4hpf_1.fastq
Description: Basecalled raw file from the 4 hpf dataset, forward
File: RPL11_4hpf_2.fastq
Description: Basecalled raw file from the 4 hpf dataset, 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.