Chromatin Remodeling and Transcriptional Memory: A Dissertation

Abstract

Transcriptional regulation of gene expression is critical for all unicellular and multicellular organisms. The ability to selectively induce or repress expression of only a few genes from the entire genome gives cells the ability to respond to changing environmental conditions, grow and proliferate. Multicellular organisms begin life as a single totipotent cell, which undergoes many cell divisions during embryonic and later postnatal development. During this process, the dividing cells of the embryo progressively lose their pluripotency and adopt restricted cell fates. Cell fate restriction leads different cell types to gain unique transcriptional profiles. This transcriptional profile or gene expression pattern not only defines the cell types and restricts the ways in which they can respond to signals, it also has to be faithfully re-established in the progeny of these fate-restricted cells when they divide. Different mechanisms have evolved in multicellular organisms to propagate transcriptional memory of cell identity. Most of mechanisms involve modifications of chromatin such as epigenetic modification of DNA or alterations of associated histones. In contrast to multicellular organisms which have considerable cellular diversity and a long lifespan for which cell fates and transcriptional memory needs to be maintained, single celled budding yeast, Sachharomyces cerevisiae have a life cycle of about 90 minutes in normal nutrient rich conditions. However, even budding yeast have tremendous potential to respond to changing environmental conditions like nutrient availability by inducing expression of various genes. We observed that members of the GAL gene cluster, which encodes genes induced in response to and for metabolizing the sugar galactose, showed heritable transcriptional memory of previous activation. This dissertation thesis describes the studies I have done for my graduate research to define this phenomenon of transcriptional memory at the yeast GALgenes and to determine the mechanism by which it can be formed and inherited. Chapter I gives an introduction to different mechanisms of establishing transcriptional memory in unicellular and multicellular organisms. Chromatin based mechanisms have been well studied in multicellular organisms but not observed in budding yeast. We compare chromatin based or nuclear inheritance with cytoplasmic inheritance that can be observed in yeast. Chapter II describes work done to define the phenomenon of transcriptional memory at GAL1 gene. We define this as a faster rate of induction of the GAL1 gene, compared to a naïve gene, after a brief period of repression. We show that this cellular memory persists through mitosis and can be passed on to the next generation. We also show that chromatin remodeling enzymes appear to be required for rapid reinduction, raising the question if yeast may also possess chromatin associated, nuclear mechanisms for cellular memory. Chapter III describes experiments that show that cellular memory observed at GAL1 is cytoplasmic in nature and also compares our work with similar examples observed recently by other groups. Finally, Chapter IV offers a perspective of the significance of such cellular memory mechanisms in budding yeast and outlines some potential further experiments to better understand the control of GAL1 induction kinetics.