A comparative analysis across species of maternal mRNA regulation in embryos

The post-transcriptional regulation of mRNAs greatly impacts gene expression dynamics, but the underlying regulatory rules and how they change between organisms remain elusive. During early metazoan development, thousands of pre-loaded maternal transcripts are post-transcriptionally regulated within embryos, making it an ideal system to investigate the mRNA regulatory code across organisms. Here, we present QUANTA, a computational strategy to distinguish transcriptionally silent genes and analyze their post-transcriptional regulation. QUANTA uses kinetic modeling to compare total and polyA+ expression patterns of genes, and quantitatively dissect the interconnected kinetics of their mRNA polyadenylation and degradation. We validate QUANTA using native maternal genes and massively parallel mRNA reporters in zebrafish embryos. Subsequently, we used QUANTA to dissect the regulation of maternally provided mRNAs in frog, mouse and human embryos. We find that widespread polyadenylation of maternal mRNAs precedes their degradation across organisms. Moreover, both the onset of maternal mRNA degradation and its rate are proportional to the developmental pace of the organisms and diverge between orthologs. Through sequence analysis, we associate differences in regulation between maternal genes with putative regulatory signals in the 3'UTRs of each organism. In fast-developing organisms, the 3'UTR regulatory code contains signals to accelerate maternal degradation, while in slow-developing organisms, the 3'UTR signals enhance mRNA stabilization. Our work provides a general strategy to quantify mRNA degradation and polyadenylation kinetics of transcriptionally silent genes, and investigate its sequence-based rules across species and biological systems. Overall design: temporal expression profiles of mRNA reporters in a massively parallel reporter analysis (MPRA) experiment. Reporters that had different 3'UTR sequences were injected into zebrafish embryos at fertilization. Two types of reporterse were used: pre-adenylated (A+) reporters and non-adenylated (A-) reporters. Samples were collected over developmental times, as specified. Embryos were grown at different temperatures: 28C, 34C and 22C.