Genome-wide analysis of mRNA decay patterns during early Drosophila development

Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit fly development. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygotically encoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNA localization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched in transcripts with common degradation patterns and propose several proteins and microRNAs as developmental regulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of a subset of cis-regulatory sequences and trans-regulators in vivo.Our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding of mRNA decay processes in all animals. Our data also provide a valuable resource for further experimental and computational studies investigating the process of mRNA decay.The process of embryonic development, that is, the transformation of the egg into a fully formed embryo, is a heritable feature that relies on the establishment of distinct programs of gene activity in different sub-regions of the developing organism. Given that the specification and implementation of such gene regulatory programs requires as well as triggers particular spatio-temporal modulations in mRNA levels, the full understanding of the mechanisms regulating mRNA abundance is central to determine how development is molecularly controlled.In this context, much attention has been focused on the study of transcriptional regulation, leaving the processes that degrade mRNA molecules relatively unexplored; this bias does not seem fair given that the abundance of each mRNA species in the embryo is determined not only by the transcr