Transcriptomic Profiling of Early Drosophila Embryogenesis Reveals Similarities in Replication Checkpoint and Histone mRNA Processing Mutants

In higher eukaryotes, maternally provided gene products drive the initial stages of embryogenesis until the zygotic transcriptional program takes over, a developmental process called the midblastula transition (MBT). In addition to zygotic genome activation, the MBT involves alterations in cell-cycle length and the implementation DNA damage/replication checkpoints that serve to monitor genome integrity. Previous work has shown that mutations affecting histone mRNA metabolism or DNA replication checkpoint factors severely impact developmental progression through the MBT, prompting us to characterize and contrast the transcriptomic impact of these genetic perturbations. In this study, we define gene expression profiles that mark early embryogenesis in Drosophila through transcriptomic analyses of developmentally staged (early syncytial vs late blastoderm) and biochemically fractionated (nuclear vs cytoplasmic) wild-type embryo. We then compare the transcriptomic profiles of loss-of-function mutants of the dChk1/Grapes replication checkpoint kinase and the Stem Loop Binding Protein (SLBP), a key regulator of replication-dependent histone mRNAs. Our analysis of RNA spatial and temporal distribution during embryogenesis offers new insights into the dynamics of early embryogenesis. Moreover, we find that grp and slbp mutant embryos display profound and highly similar defects in gene expression, most strikingly in zygotic genome activation, compromising the transition from a maternal to a zygotic regulation of development. We performed RNA-seq (Ribodepletion, Illumina) on collections of staged (0-45 min AEL and 90-180 min AEL) and biochemically fractionnated (cytoplasmic and nuclear extracts) wt (ORER) Drosophila embryos to derive a global spatiotemporal index of RNA distributions. In addition, we generated RNA-seq data of total embryo extracts (0-180 min AEL) derived from transheterozygous mothers bearing the grpfs1, Slbp10/12 and Slbp10/15 mutations.