Jason Brickner - US grants

[unreadable] DESCRIPTION (provided by applicant): The sub-nuclear localization of DNA is highly regulated in all eukaryotes and has important but poorly understood effects on transcription and chromatin structure. The localization of DNA to the nuclear periphery has a clear role in establishing transcriptional repression (Fisher and Merkenschlager, 2002). My studies in Saccharomyces cerevisiae revealed that certain genes are also recruited to the nuclear periphery upon activation (Brickner and Walter, 2004). My work also established that localization to the nuclear periphery promotes transcriptional activation (Brickner and Walter, 2004). Genome-wide studies in yeast indicate that many transcriptionally active genes localize at the nuclear periphery (Casolari et al., 2004). Transcriptional activation of the (3-globin locus in mice also occurs at the nuclear periphery, suggesting that this phenomenon is conserved between yeast and mammals (Ragoczy et al., 2006). My lab has extended these studies and we have discovered that gene recruitment to the nuclear periphery serves as a form of cellular memory of recent transcription, marking recently repressed genes to allow more rapid reactivation. The ultimate objective of this proposal is to understand two fundamental questions in cell biology: how is the nucleus spatially organized and how does this organization affect transcription? We will focus on the dynamic recruitment of the INO1 and GAL1 genes to the nuclear periphery in Saccharomyces cerevisiae. Yeast offers a powerful combination of molecular genetics and biochemistry and will provide an ideal model system for studying this process. We will define the functional outcome of gene recruitment to the nuclear periphery and the molecular mechanisms used to affect relocalization. Finally, we will define the biochemical function of Scs2, a nuclear envelope membrane protein that plays important roles in both transcriptional activation and repression at the nuclear periphery. This work will provide the first understanding of a mechanism of regulating gene expression that may be defective in two human diseases. A number of acute myeloid leukemias result from fusion of DMA binding domains with nuclear pore proteins, presumably leading to relocalization of target genes to the nuclear periphery and alterations in gene expression (Lawrence et al., 1999; Nakamura et al., 1996). Mutations in the human homologue of Scs2 result in an inherited form of amyotrophic lateral sclerosis (Nishimura et al., 2004). Understanding the role of DMA localization in controlling gene expression may illuminate the cellular and molecular defects in these diseases. [unreadable] [unreadable] [unreadable]

DESCRIPTION (provided by applicant): This proposal requests continued funding for the Cellular and Molecular Basis of Disease (CMBD) Training Program at Northwestern University. The CMBD program supports comprehensive pre-doctoral graduate training in the life sciences, focusing on the cellular, molecular and biochemical mechanisms used in biological systems and targeted in diseases impacting human health. The CMBD program has provided intradepartmental and interdisciplinary training opportunities for Northwestern life science graduate students for the past 30 years, and has been a centerpiece for cross campus interactions at Northwestern. CMBD trainees are selected primarily from two integrated interdepartmental programs: the Interdepartmental Biological Sciences Graduate Program (IBiS) on the Evanston campus and the Driskill Graduate Training Program in the Life Sciences (DGP) on the Chicago Medical School campus. Students are appointed in the spring quarter of their second year, after they have completed their core coursework and joined their dissertation research laboratories, and they are typically supported for two or three years. As a University-wide training program with 18 trainee positions and a broad spectrum of faculty, CMBD has taken a leadership role in fostering communication and collaboration between researchers on the two campuses, and many collaborative interactions have arisen directly from the monthly student- oriented CMBD Research in Progress meetings. CMBD also facilitates student interactions with scientists at other institutions, both by providing the opportunity for CMBD trainees to present their research at national meetings and conferences, and by bringing outstanding research scientists to Northwestern, through the CMBD seminar and symposia programs. CMBD provides for training of students in the ethical conduct of research, and offers trainees the opportunity to participate in several outstanding career development forums at Northwestern University, most prominently the Bio- Opportunities program. Graduates of the CMBD program have continued as successful and productive scientists at many other institutions and in diverse careers, contributing in important ways to cell and molecular biology research on a national level.

DESCRIPTION (provided by applicant): Gene expression is regulated by transcription factors, chromatin structure and higher order organization. The positioning of genes within the nucleus and with respect to each other often correlates with their expression. However, the molecular mechanisms that control gene positioning within the nucleus, and the functional significance of gene positioning, are unclear. As a model to understand gene positioning, we have focused on the molecular mechanisms by which genes move from the nucleoplasm to the nuclear periphery upon activation in Saccharomyces cerevisiae. Targeting to the nuclear periphery involves a physical interaction with the nuclear pore complex (NPC) and is mediated by cis-acting Gene Recruitment Sequences (GRSs). GRSs function as DNA zip codes: they are necessary and sufficient to induce interaction with the NPC and localization at the nuclear periphery. Furthermore, zip codes confer interchromosomal clustering of genes at the nuclear periphery. This suggests that the yeast genome encodes its spatial organization and that cis-acting DNA sequences control interchromosomal clustering of genes through interaction with the NPC. We have identified several DNA zip codes and a protein that recognizes the GRS I zip code to mediate targeting to the nuclear periphery and interchromosomal clustering. The proposed studies will 1) determine the molecular mechanism by which the GRS I DNA zip code mediates targeting to the nuclear periphery and promotes transcription, 2) determine the genome-wide scope of GRS I zip code-mediated targeting and 3) test the hypothesis that DNA zip codes impact the global organization of the yeast genome.

? DESCRIPTION (provided by applicant): Understanding the molecular basis of epigenetic mechanisms that control the transcriptional response of cells to environmental signals is essential to understand how environment, aging and lifestyle impact physiology. My lab has discovered an evolutionarily conserved mechanism of epigenetically inherited transcriptional memory that involves the interaction of genes with nuclear pore proteins (8-10). Using both the INO1 gene from yeast and interferon ?-inducible genes in HeLa cells as models for transcriptional memory, we find that previously expressed genes interact with nuclear pore proteins for 4- 7 generations and this leads to an altered chromatin structure in the promoters of these genes. This allows RNA polymerase II to bind to these promoters, poising them for re-activation. We have now find that the scope of genes regulated by transcriptional memory includes dozens of stress-induced genes in yeast that utilize the same system. Therefore, transcriptional memory is a universal, ancient and conserved mechanism by which cells can integrate previous experience to affect future physiology. The goals of this work are to determine the molecular mechanisms that control establishment and inheritance of transcriptional memory in yeast and human cells.

Project Summary Understanding the molecular control of transcriptional responses of cells to environmental signals is essential to understand how environment, aging and lifestyle impact physiology. My lab has discovered that the position of genes is actively controlled by cells and that this impacts transcription in several ways. Although we study this phenomenon in the simple budding yeast, it is conserved to more complex animals, including humans. We recently showed that a majority of transcription factors control the interaction of genes with the Nuclear Pore Complex (NPC), impacting the spatial arrangement of genes and the interaction of chromosomes. Furthermore, we have shown that this interaction with the NPC can either promote stronger transcription and alter chromatin structure to poise genes for future expression. Thus, transcription factor-mediated targeting to the NPC likely has broad effects on both the spatial organization of the genome and gene expression. The goals of this work are to determine the molecular mechanisms by which transcription factors and NPCs spatially arrange the yeast genome and to understand how these interactions impact gene expression and chromatin structure.