Cytoplasmic mechanisms of gene regulation: intersections and coordination

总结

SUMMARY Different regulatory pathways work together to coordinate gene expression, and our guiding philosophy has been that exploring the interface of different types of regulation is thus a good way to discover new and important biology. Building on discoveries from our previous MIRA award, we propose to focus on understanding how different strategies for post-transcriptional regulation—mRNA decay, translation, and protein decay—act together to control gene expression. In the first of our two themes, we will explore the idea that protein decay acts as a meta-regulator of the post-transcriptional landscape of the early embryo. Using Drosophila melanogaster as a model system, we will investigate one of the earliest steps of development, the maternal-to-zygotic transition. During this process, maternal gene products are replaced with zygotic ones, and we have discovered that removal of three maternal RNA binding proteins is critical and determined how their destruction is developmentally controlled. We propose to extend this line of investigation to other RNA binding proteins that are destroyed by distinct and unknown mechanisms in the early embryo. We want to answer three critical questions: what are the mechanisms by which these other RNA binding proteins are destroyed? How is their degradation developmentally controlled? How does their degradation in turn change post- transcription regulation? Our research is significant because our results will reveal how destruction of maternal proteins shapes the regulatory landscape of the early embryo, and they will likely provide a conceptual framework applicable to other types of developmental transitions. In the second theme, we will explore how the open reading regulates mRNA decay and translation. Poor (or “nonoptimal”) codons lead to reduced protein output, and understanding the underlying mechanisms remains an open area of research for the field. We have excitingly found that nonoptimal codon usage represses translation initiation in human cells. This pathway is at least as potent as previously described pathways like mRNA decay. Our proposed program will build upon these results at a mechanistic level and will answer the following three important questions: What is the role of the poly(A) in translational repression due to nonoptimal codons? What factors mediate translational repression? How does codon-mediated regulation change during early development? This last question represents a new direction for our lab and leverages our unique combination of skills in the Drosophila MZT and codon-mediated regulation. Our research will reveal the molecular basis for a major repressive pathway mediated by nonoptimal codons. The systems we establish have the potential to reveal other types of developmentally-coordinated translational control, and we anticipate that our research will provide a launching point to explore the how gene regulation changes in biological space and time.