Mapping new dimensions in gene expression regulation

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Program Abstract Accumulation of misfolded proteins in the endoplasmic reticulum (ER) and subsequent redox imbalance activate the Unfolded Protein Response (UPR) to restore a healthy cellular proteome. Dysregulation of the UPR is key to human diseases, including neurodegeneration and cancer. The UPR involves all components of gene expression control, i.e. transcription, translation, and RNA and protein degradation, that are highly coordinated and follow intricate dynamics. At first, phosphorylation of the translation initiation factor eIF2α suppresses general protein synthesis while activating translation of specific mRNAs that encode transcription factors such as ATF4. Phosphorylation also activates the IRE1 endonuclease that splices and activates the mRNA of the XBP1 transcription factor. XBP1 and ATF4, together with ATF6 and other transcription factors, trigger a second wave of response by transcribing both UPR and apoptosis genes. Further, XBP1 activity is not only controlled by IRE1, but also by SUMOylation and acetylation. IRE1 in turn can also degrade SUMO mRNA, down-regulating this post-translational modification and creating a feedback mechanism of regulation. These processes are accompanied by extensive RNA and protein degradation that remove irreparable molecules, creating a highly interconnected system. Our recent work using time-series transcriptomics and proteomics data as well as statistical modeling showed that during ER stress, mRNAs change in a pulse-like manner, while protein concentrations adjust less rapidly and appear to switch to a new steady state. Given these intricate relationships, I argue that the time is ripe to introduce systems level analyses to studies of the UPR and assess the processes involved in its gene expression regulation in a comprehensive and unbiased way. My laboratory's expertise in quantitative mass spectrometry, next-generation sequencing, computational analysis, and experiments to evaluate new mechanisms provides the ideal background for such work. In the next five years, we will move analysis of single time points to trajectories of the stress response; we will progress from examination of concentration changes to estimating rates of RNA and protein synthesis and degradation; and we will map the protein position and changes of diverse post-translational modifications to changes in these rates. These efforts will provide valuable resources and statistics tools to the scientific community. They will also inform on regulatory principles during the UPR and support specific new routes of investigation. We are only beginning to understand the differential use and modification of components of the translation machinery, and in the next five years, we will follow up on our recent findings on ribosome modifications, differential stability of ribosome subunits, and alternative splicing of aminoacyl-tRNA synthetases under stress. Further, even well-studied factors such as ATF4 still are incompletely understood in their regulation, and we will test the role of new sequence elements in ATF4 and other genes in their effect on translation. Finally, the robustness of genes to variation, e.g. mutation, is central to understanding cellular pathology, and again, our recent work suggests that some genes are robust to variation in some rates, but not others. We will test these hypotheses in targeted studies.