Function of maternal mrna during zebrafishembryogenesis

The National Institute of General Medical Sciences awarded Stowers Institute for Medical Research $429,000 on February 13, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate the function of maternal messenger RNA during zebrafish embryogenesis and the maternal-to-zygotic transition.

The research focuses on unraveling fundamental processes of early vertebrate embryogenesis, particularly the dynamic molecular mechanisms that regulate maternal and zygotic RNAs during the period when maternal RNAs degrade and the zygotic genome activates. The work dissects spatial and temporal regulation of maternal and zygotic transcripts, identifies functions of individual maternal RNAs, and examines their roles in gene expression, mRNA stability, and translational regulation. Recent developments include a CRISPR-Cas13d system for efficient maternal RNA knockdown in zebrafish embryos, which overcomes limitations in traditional genetic approaches by enabling systematic targeting and investigation of maternal RNAs with precision. The five-year project, running through January 31, 2031, employs integrative multi-omics approaches including RNA-seq, SLAM-seq, ribosome profiling, and quantitative proteomics to understand codon-dependent mRNA stability, maternal-zygotic gene expression, and the interplay of transcription, translation, and protein accumulation during early embryogenesis. Future work will address key questions surrounding spatial and temporal regulation of maternal RNAs and their influence on early development, including maternal RNA decay, localization, and function during the maternal-to-zygotic transition.

Performance occurs in Kansas City, Missouri.

Abstract

Our research focuses on unraveling the fundamental processes of early vertebrate embryogenesis, particularly the dynamic molecular mechanisms that regulate maternal and zygotic rnas during the maternal-to-zygotic transition (MZT). This crucial period involves the degradation of maternal rnas and activation of the zygotic genome, processes essential for proper embryonic development. Our goal is to dissect the spatial and temporal regulation of maternal and zygotic transcripts, identify the functions of individual maternal rnas, and understand their roles in gene expression, including mrna stability and translational regulation. Our recent work has established transformative tools and frameworks for investigating embryogenesis, including the development of the crispr-CAS13D system for efficient maternal RNA knockdown in zebrafish embryos. This system has overcome limitations in traditional genetic approaches, including lethal and/or masked phenotypes due to maternal contribution, enabling US to systematically target maternal rnas and investigate their functions with unprecedented precision. Through integrative multi-omics approaches-such as RNA-SEQ, slam-SEQ, ribosome profiling, and quantitative proteomics-we have made significant progress in understanding codon-dependent mrna stability, maternal-zygotic gene expression, and the interplay of transcription, translation, and protein accumulation during early embryogenesis. Over the next five years, we aim to expand these efforts by addressing key questions surrounding the spatial and temporal regulation of maternal rnas and their influence on early development. Our studies will focus on: maternal RNA decay, localization and function during MZT: investigating how maternal rnas, such as CTH1, are regulated by spatial and cell-specific decay mechanisms. This will include identifying CIS-regulatory elements in their untranslated regions and characterizing the molecular factors that mediate their localization and stability. Leveraging crispr-CAS13D and multi-omics techniques to uncover the roles of maternal rnas in zygotic genome activation and early cellular processes. Broader exploration of maternal rnas: systematically investigating additional maternal genes, including genes encoding small translated open reading frames, genes with specific temporal expression and spatially localized transcripts with critical developmental roles. The overarching vision of our research is to establish a comprehensive understanding of how gene regulation is orchestrated at multiple levels-spatial, temporal, and molecular-during the earliest stages of vertebrate development. Our work has broad implications for advancing knowledge in developmental biology, reproductive health, and gene regulation, with potential applications in areas such as fertility, regenerative medicine, and mrna-based therapeutics. By integrating cutting-edge technologies with innovative approaches, our research program is poised to uncover fundamental principles of gene regulation and mrna stability, contributing to a deeper understanding of the molecular processes that drive the transformation of a single cell into a multicellular organism.