How and when heterochromatin is formed is a fascinating subject linking studies of gene expression to broader issues like cell cycle progression, nuclear structure and chromosome segregation. The research in my lab focuses on the role of the cell cycle and DNA replication in assembly or maintenance of chromatin structures and the effects of these structures on DNA replication. We are interested in how heterochromatin initially forms on DNA, why heterochromatin formation is regulated by the cell cycle, how transcription of genes is prevented in silenced regions, and whether heterochromatin formation is influenced by or influences events such as DNA damage and the initiation of DNA replication. We are also intrigued by how these complex structures are maintained throughout the cell cycle and are duplicated and inherited each time the chromosome itself is replicated and the cell divides.  We investigate the regulation of such epigenetic processes in two systems: the silent mating-type loci of budding yeast Saccharomyces cerevisiae and the life cycle of the human tumor virus, Epstein-Barr virus, EBV.

Silencing in Saccharomyces cerevisiae

Silenced chromatin in S. cerevisiae, is akin to heterochromatin in organisms such as maize, flies, and mammals.  S. cerevisiae uses epigenetically inherited chromosomal structures to regulate a variety of cellular activities such as controlling cell-type specific gene expression, modulating ribosomal RNA levels, and preserving telomere structure and stability.  Silenced regions in S. cerevisiae that are regulated, in part, by the Silent Information Regulator, or Sir, proteins include the silent mating-type loci, HML and HMR, the rDNA locus and the telomeres.

To mediate silencing at a given site on a chromosome, an organism must first have a way to recruit the proteins that compose silenced chromatin to that locus.  In yeast, the silent mating-type loci are flanked by regulatory sites known as silencers.  Silencers contain binding sites for the Origin Recognition Complex (ORC), and the transcriptional regulators Rap1p and Abf1p.  In addition, the Sir proteins, Sir1p, Sir2p, Sir3p and Sir4p, are structural components of silenced chromatin in yeast.  Unlike ORC, Rap1p and Abf1p, however, the Sir proteins do not bind to DNA site-specifically.  Instead, Sir proteins associate with silencers through protein-protein interactions between each other, proteins bound at silencers, and histones H3 and H4. Once initiated at silencers, silencing spreads along the chromosome over several kilobases of DNA. The establishment of silencing requires passage through S phase, yet surprisingly, does not require the passage of the DNA replication fork. Furthermore, once established, the silenced state of this region of DNA is maintained throughout the cell cycle and can be stably inherited in subsequent generations. Several proteins involved in silencing in yeast have homologs in other phyla and in humans where some have been implicated in cancer. Thus, many of the strategies employed by yeast to repress gene expression are likely utilized by other eukaryotes as well.

Heritable Repression of Epstein-Barr Viral Gene Expression

Epstein-Barr virus, EBV, is a human gamma herpes virus (lymphocryptovirus) that causes infectious mononucleosis and is causally associated with Burkitt’s lymphoma, nasopharangeal carcinoma, hairy oral leukoplakia, Hodgkin’s lymphoma, and T cell lymphomas as well as various B cell lymphoproliferations in immunodeficient and immunocompromised hosts. When EBV infects primary human B cells, it efficiently induces them to proliferate indefinitely thereby causing "immortalization" of these cells. During latent infection, the viral genome is replicated semi-conservatively by the host cellular machinery. Also during latency, EBV generally maintains its genome extrachromosomally within the proliferating host cell and expresses only a small fraction of the genes it encodes. Rarely, EBV’s remaining genes become activated and the virus undergoes lytic replication. These two phases of EBV’s life cycle, latent and lytic, are governed by different modes of DNA replication and by expression of distinct viral genes. We study mechanisms that regulate the stably heritable repressed state of viral genes during latency and the roles of host cellular proteins in this process.