Fishman, Lior and Modak, Avani and Nechooshtan, Gal and Razin, Talya and Erhard, Florian and Regev, Aviv and Farrell, Jeffrey A. and Rabani, Michal (2024) Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq. NATURE COMMUNICATIONS, 15 (1): 3104. ISSN 2041-1723
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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. This study analyzes the embryonic replacement of maternally contributed mRNA with new mRNA in single cells and shows dynamic spatio-temporal regulation of maternal mRNA decay and cell-type specific retention within the earliest specified cell types in zebrafish embryos.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | PROFILING REVEALS; GENE-EXPRESSION; CLEARANCE |
| Subjects: | 000 Computer science, information & general works > 004 Computer science 600 Technology > 610 Medical sciences Medicine |
| Divisions: | Informatics and Data Science > Department Computational Life Science > Chair of Computational Immunology (Prof. Dr. Florian Erhard) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 27 Jan 2026 10:58 |
| Last Modified: | 27 Jan 2026 10:58 |
| URI: | https://pred.uni-regensburg.de/id/eprint/65117 |
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