ArticleNature communications2024
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 33 citations in OpenAlex.
- Primordial Germ Cell Development in Teleosts: Their Origin, Fate and Role in Sex Determination.Stem cell reviews and reports · 2026Review
- Accurate profiling of single-cell alternative transcript start sites by correcting RNA degradation.Nature communications · 2026Article
- Cholecystokinin coordinates gonadotropin-dependent and independent pathways to orchestrate zebrafish gonadal development.Nature communications · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- A convenient single-cell assay for the newly synthesized transcriptome reveals FLI1 regulon downregulation during T cell activation.Cell reports methods · 2026Article
- Uncovering the role of integrated stress in Alzheimer's disease through single-cell and transcriptomic analysis.Scientific reports · 2026Article
- Labeling of nascent RNA in the C. elegans intestine.PloS one · 2026Article
- CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of maternal-to-zygotic transition in teleosts.The EMBO journal · 2025Article
- INTS1 is required for maintaining accurate transcriptional integrity and behavior in zebrafish.NAR genomics and bioinformatics · 2025Article
- Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish.bioRxiv : the preprint server for biology · 2025Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- Zebrafish Unga Is Required for Genomic Maintenance upon Genotoxic Stress and Male Fertility.Journal of developmental biology · 2025Article
- Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Article
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Quantitative modeling of mRNA degradation reveals tempo-dependent mRNA clearance in early embryos.Nucleic acids research · 2025Article
- Cytoplasmic mRNA decay and quality control machineries in eukaryotes.Nature reviews. Genetics · 2025Review
- Time-resolved analysis of Bacillus subtilis DB104 Spo0A-mutant transcriptome profile and enhancement of recombinant protein release.Journal of microbiology (Seoul, Korea) · 2025Article
- mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesis.PLoS biology · 2025Article
- Transcriptome and Temporal Transcriptome Analyses in Single Cells.International journal of molecular sciences · 2024Review
- Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities. Here, we combine single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell types. Our study provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.