An interplay of multilayered regulatory mechanisms underlies the RNA solubility phase transition during vertebrate oocyte-to-embryo transition

Dynamic RNA-protein interactions influence RNA transport, storage, stability, and activity and are fundamental to a broad range of biological processes. During the oocyte-to-embryo transition (OET), fully differentiated gametes fuse and regain totipotency. Throughout the OET, the transcription remains silent. Spatiotemporal regulation of gene expression relies on the dynamic interactions between maternal transcripts and various protein complexes. Despite its fundamental importance, RNA-protein interaction dynamics at the global level during the OET remain poorly understood. Here, we leverage fractionation RNA-seq to profile RNA insolubility, a proxy for the interaction between RNAs and protein complexes, during zebrafish OET. We identify transcripts that transition between the soluble (relatively protein-free) and insoluble (heavily protein-associated) states and demonstrate that these phase transitions are driven by ribosome-dependent and ribosome-independent mechanisms. We demonstrate that the capacity of maternal RNAs to engage with protein complexes changes dynamically during the OET through remodeling of cis-regulatory features. We developed a machine-learning framework and uncovered multiple cis- and trans-regulatory features that may contribute to RNA insolubility. To validate these predictions, we examined poly(A) tail length and m6A dynamics. We found that poly(A) tail length is associated with both ribosome-dependent and ribosome-independent RNA phase transitions. In parallel, fractionation m6A-pulldown RNA-seq revealed highly dynamic changes in the m6A landscape during the OET. A correlation between m6A modifications and RNA insolubility is gradually established during the OET. Together, our findings uncover a multilayered regulatory mechanism governing RNA phase transitions during the OET, providing fundamental insights into post-transcriptional regulation of gene expression during development.