Critical role of Spatio-Temporally Regulated Maternal RNAs in Zebrafish Embryogenesis

The maternal-to-zygotic transition shifts regulatory control from maternal to zygotic messenger RNAs (mRNA) through maternal mRNA degradation. While temporal aspects of maternal mRNA decay are known, spatial mechanisms remain underexplored. Using CRISPR-Cas9 and CRISPR-Cas13d systems, we functionally dissected the contribution of maternal versus zygotic fractions and overcame challenges of studying embryonic lethal genes. We identified differentially distributed maternal mRNAs in specific cells and evidenced the critical role of five maternal mRNAs, cth1, arl4d, abi1b, foxa and lhx1a, in embryogenesis. Further, we focused on the functionally uncharacterized cth1 gene, revealing its essential role in gametogenesis and embryogenesis. Cth1 acts as a spatio-temporal RNA decay factor regulating mRNA stability and accumulation of its targets in a spatio-temporal manner through 3UTR recognition during early development. Furthermore, Cth1 3UTR drives its spatio-temporal RNA localization. Our findings provide new insights into spatio-temporal RNA decay mechanisms and highlight dual CRISPR-Cas strategies in studying embryonic development. HighlightsO_LIDifferentially distributed marginal maternal RNAs have a critical role in early embryogenesis. C_LIO_LICas13d complements the Cas9 limitation to study the functions of embryonic lethal genes. C_LIO_LICth1 is essential for gametogenesis and early embryonic development. C_LIO_LICth1 is a maternal RNA decay factor required for spatio-temporal RNA regulation. C_LIO_LI3UTR of Cth1 drives its spatio-temporal RNA dynamics. C_LI