Mechanisms of gene-specific and genome-wide regulation of mRNA turnover Central to the control of eukaryotic gene expression is the precise and rapid regulation of transcript abundance. RNA levels are determined by a balance of both production and degradation, and thus, it is critical to examine not only transcription but also mRNA turnover to dissect the regulatory networks that control gene expression and to understand the kinetics of the cellular response. Whereas much has been learned about the mechanisms controlling transcription, the contribution of mRNA decay to shaping the transcriptome remains poorly understood. The objective of this research proposal is to elucidate the mechanisms by which mRNA turnover regulates gene-specific and genome-wide changes in mRNA levels, and to understand how mRNA decay and transcription are coordinated to induce rapid changes in the transcriptome. The experiments described in this proposal take advantage of a non-invasive metabolic labeling approach that allows us to measure decay rates with great precision for all mRNAs in budding yeast. Yeast provides an excellent model system to characterize the regulation of mRNA turnover, and because the pathways under investigation are highly conserved across species, any mechanistic insights obtained from our studies will be directly relevant to all eukaryotes including humans. We propose a combination of innovative biochemical, genetic and cell biological approaches to address three specific aims: (1) To elucidate mechanisms that induce the turnover of specific groups of mRNAs. (2) To investigate the physiological function of the mRNA decay factor Dhh1 and to understand how Dhh1 controls translational repression and mRNA degradation. (3) To identify mechanisms of genome-wide mRNA turnover regulation. This project will lead to the discovery of novel molecular pathways that regulate mRNA decay and provide fundamental new insight into an important step in the eukaryotic gene expression program critical for all aspects of cellular and organismal physiology. Furthermore, understanding the regulation of mRNA decay will give us critical insight into how this process is misregulated in human disease.

Public Health Relevance

The precise regulation of the expression of our genes is essential to control proliferation, differentiation and development, and errors in any step of the gene expression program can have severe consequences leading to cell death or disease. This proposal addresses how cells regulate the abundance of their messenger RNAs at the level of degradation and how messenger RNA production and decay are coordinated. Since defects in gene expression are both the cause and the consequence of many diseases, our research will shed light on the regulation of a fundamental cellular process and at the same time may led to the development of new disease therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Bender, Michael T
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University of California Berkeley
Schools of Arts and Sciences
United States
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Heinrich, Stephanie; Derrer, Carina Patrizia; Lari, Azra et al. (2017) Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights. Bioessays 39:
Joyner, Ryan P; Tang, Jeffrey H; Helenius, Jonne et al. (2016) A glucose-starvation response regulates the diffusion of macromolecules. Elife 5:
Mugler, Christopher Frederick; Hondele, Maria; Heinrich, Stephanie et al. (2016) ATPase activity of the DEAD-box protein Dhh1 controls processing body formation. Elife 5: