Transcription regulation of recovery from stress

The National Institute of General Medical Sciences awarded Oakland University $565,800 on March 1, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate transcriptional regulation and chromatin structure dynamics during cellular recovery from stress, with focus on autophagy-related gene expression in yeast models.

The project examines how cells maintain chromatin integrity and recover from prolonged starvation stress, specifically investigating the roles of chromatin remodeling complexes (RSC and FACT) in modulating expression of autophagy-related genes during nutrient limitation. The research uses Saccharomyces cerevisiae as a model organism to understand mechanisms underlying cellular protein degradation and organelle recycling during stress conditions, with implications for understanding autophagy dysfunction in aging and human pathologies including neurodegeneration, cardiovascular disease, and immune disorders.

Performance occurs at Oakland University in Rochester, Michigan, over the period March 1, 2026 through February 28, 2029. This is a Project Grant, the assistance type under which NIGMS funds investigator-initiated biomedical research to advance understanding of biological processes and support disease diagnosis, treatment, and prevention discovery.

Abstract

Autophagy is an evolutionarily conserved catabolic process necessary for cellular homeostasis. Dysfunction in autophagy is linked to aging and many human pathologies, including neurodegeneration, cardiovascular diseases, and immune disorders. Cells utilize autophagy to degrade and recycle cellular components, aged or misfolded proteins, and defective organelles. Cargo targeted for autophagic degradation is delivered by autophagosomes to the vacuole in yeast and plants or to lysosomes in mammalian cells. While this process is active at a basal level, IT is significantly induced during stress, such as amino acid and nitrogen limitations. In addition, autophagy machinery is also utilized to degrade specific cargo such as ribosomes via ribophagy, or mitochondria via mitophagy. During starvation stress, the cell downregulates many genes, enhancing the expression of the genes critical for mounting a survival response. This includes increased expression of autophagy-related (ATG) genes. Dynamic changes to chromatin structure are critical for modulating gene expression. These changes are mediated by chromatin-associated factors such as histone modifiers, chromatin remodelers and histone chaperones. RSC (remodels the structure of chromatin) is an ATP- dependent chromatin remodeling complex conserved from yeast to humans. Likewise, the fact complex (SPT16/POB3 or SPT16/SSRP1) is essential for maintaining chromatin structure. Induction of autophagy during starvation leads to degradation of proteins and organelles to resupply key nutrients for survival. Prolonged starvation is likely to severely deplete cellular protein levels, including those required for genomic integrity. However, how the cell maintains its chromatin structure and its ability to recover from chronic stress remains poorly understood. In this proposal, we will use saccharomyces cerevisiae as a model organism to understand how cells recover from chronic stress, and the importance of chromatin factors, RSC and fact in this process. In the specific aim 1, we will characterize changes in chromatin structure, transcription, and histone modifications during extended starvation, and determine the role of fact and RSC in the recovery from stress. In specific aim 2, we will examine how RSC depletion affects ribophagy, and identify factors that promote this process in an RSC-dependent manner. These studies will be valuable in understanding chromatin factors' role in cell survival during prolonged stress.