The ups and downs of protein expression regulation

Gene expression is regulated by four major processes: transcription, translation, and RNA and protein degradation. These processes are adjusted, in different ways, when the cells respond to a stimulus. Many pathways are known, but their precise interaction over time is not well understood. In our lab, we use multiple time series datasets — on protein and mRNA expression changes and changes in the binding of ribosomes and other proteins — in combination with statistics approaches to disentangle the contributions of the different levels of regulation and generate hypotheses on regulatory mechanisms. We focus on yeast and mammalian cells responding to stress of the endoplasmic reticulum, but have expanded these studies in a variety of directions.