High resolution studies of gene expression improve our understanding of early vertebrate development
The growing ubiquity and diminishing cost of next generation sequencing allow us to study gene expression at spatial or temporal resolution unthinkable even a few years ago. I will present two studies that exploit this in different ways to improve our understanding of early vertebrate development.
Correct development of the Bilaterian body plan requires the early definition of three orthogonal axes in a stereotypical manner. In vertebrates, a first axis is established during oocyte maturation, and the other two shortly after fertilization. Although the physical processes are well described, the specific molecular determinants remain poorly characterized. Here we study the post-fertilisation distribution of maternally deposited mRNAs on all three axes of the Xenopus tropicalis 8-cell stage embryo, based on sequencing of sets of positionally-defined individual blastomeres. We find no evidence for asymmetric distribution of maternal mRNAs along the dorsal-ventral or left-right axes. As expected, we find considerable asymmetry along the animal-vegetal axis, including many mRNAs not previously reported.
The problem of using mRNA level as an indication of protein function is well understood. In a second study we use time series RNA-seq data of sufficiently high resolution to identify the transcriptional activation times of genes, and use these data to dissect the temporal structure of the maternal-zygotic transition in Xenopus tropicalis. We clarify the time of onset of zygotic transcription, suggest a simpler model for the transition, and uncover a time scale for the action of gene regulatory networks at this critical phase of development.