SUMMARY It has been recognized for decades that post-transcriptional regulation is as important as transcription for controlling gene expression, but much of post-transcriptional regulation is a black box. Alterations in post-transcriptional regulation can lead to disease, such as neurodegeneration, developmental defects, and cancer. One area of post-transcriptional regulation that remains in its infancy of understanding is how mRNA stability is affected by other events in the mRNA life cycle, such as translation. An overarching theme has been that repression of translation initiation precedes and causes mRNA decay, but there are many contradictory examples to this generalization. Here, we focus on two systems outside this generalization. First, my lab has made a significant advance in delineating translational repression in the absence of mRNA decay during early Drosophila embryogenesis through our discovery that the post-transcriptional repressor ME31B has different regulatory impacts before and after the MZT. ME31B represses translation before the MTZT, but stimulates mRNA decay after. We have found that ME31B represses translation through an eIF4E-binding protein called Cup, which is degraded during the MZT. Thus, a critical, unresolved issue is why ME31B fails to stimulate mRNA decay before the MZT. Work from my lab and others points to a potential role for Cup in blocking mRNA decay. We will address this issue by answering two questions. 1) What is the role of Cup in embryogenesis?; 2) How is mRNA decapping generally controlled during embryogenesis? Our second area of research is understanding how translation elongation affects mRNA decay. Work in model prokaryotic and eukaryotic systems has demonstrated that codon optimality affects mRNA stability. By developing a suite of new transcriptome-wide experimental and computational tools, my lab has found that translation elongation also alters mRNA stability in humans and that these changes are mediated partially through codon usage. Here, we will answer two related questions: 3) How does translation elongation affect mRNA stability in humans?; 4) What is the role of codon optimality in controlling gene expression? To do so, we will combine genetic, genome-wide, and classical molecular biology approaches. The outcomes of our research will be an improved understanding of post-transcriptional regulation, and our insights may inform our view of how gene misregulation underlies human disease.