Continuous transcriptome analysis reveals novel patterns of early gene expression in Drosophila embryos

Early organismal development consists of transformative events that lay the foundation for body formation and long-term phenotype. Despite this understanding, the rapid progression of events and the limited material available are major barriers to studying the earliest stages. The size and accessibility of Drosophila embryos overcome some of these limitations, and several studies characterizing early transcriptional events have been reported. Unfortunately, manual embryo staging, and elaborate protocols make the techniques employed in these studies prone to human and technical errors and incompatible with routine laboratory use. Herein, we present a straight-forward and operationally simple methodology for studying the early transcription (≤3 hours) in Drosophila. This method relies on single-embryo RNA-sequencing and transcriptome ordering along a developmental trajectory (pseudo-time), thereby avoiding the need for the staging of the embryos. The obtained high-resolution and time-sensitive mRNA expression profiles uncovered the exact onset of transcription and degradation of transcripts and revealed an earlier transcription start for several zygotic genes. In addition, degradation patterns suggest that maternal mRNA decay is independent of mRNA levels. By classifying each embryo as male or female, we were also able to study sex-biased transcription between the beginning of zygotic transcription to gastrulation and identified 120 differentially expressed mRNAs. Using sex-specific transcription signatures, embryos can be sexed directly, eliminating the need for Y-chromosome genotyping. Herein, we report an accessible, single-embryo sequencing approach for high-resolution, time-sensitive transcriptome analysis. Our data provide an unparalleled resolution of gene expression during early development and enhance the current understanding of early transcriptional processes.