Abstract
The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. To identify relevant Drosophila RBPs organism-wide, we refined the RNA interactome capture method for comparative analysis of the pre- and post-MZT embryos. We determine 523 proteins as high-confidence RBPs, half of which were not previously reported to bind RNA. Comparison of the RNA interactomes of pre- and post-MZT embryos reveals high dynamicity of the RNA-bound proteome during early development, and suggests active regulation of RNA binding of some RBPs. This resource provides unprecedented insight into the system of RBPs that govern the earliest steps of Drosophila development.
Highlights
The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited messenger RNAs (mRNAs) and other molecules are degraded and replaced by products of the zygotic genome
To explore the landscape of RNA-binding proteins (RBPs) in the early Drosophila embryo we further developed the RNA interactome capture method established by Castello et al.[8,12], that was initially optimized for cell lines
Our observations call for further investigation, we find it probable that the difference in disorder of novel and previously known Drosophila RBPs is not caused by experimental bias, as other parameters such as average length, isoelectric point and hydrophobicity are similar for these two groups (Supplementary Fig. 2e–g)
Summary
The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. Beyond providing a comprehensive compendium of Drosophila melanogaster RBPs, we have applied this method to embryos at two different developmental stages employing a multiplexed proteomic approach, generating, to our knowledge, the first dynamic RNA interactome until now. Comparison of samples prepared from early and late embryos reveals that the RNA interactome undergoes important changes during development This plasticity of the RNA-bound proteome can be explained either by changes in overall protein abundance or modulation of the RNA-binding activity of RBPs. Our analysis provides new insight into the molecular features of early development by highlighting proteins that may link development to RNA metabolism
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