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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM080484-05
Application #
8102770
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2007-08-01
Project End
2012-07-31
Budget Start
2011-08-01
Budget End
2012-07-31
Support Year
5
Fiscal Year
2011
Total Cost
$277,111
Indirect Cost
Name
Northwestern University at Chicago
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
160079455
City
Evanston
State
IL
Country
United States
Zip Code
60201
Brickner, Jason (2017) Genetic and epigenetic control of the spatial organization of the genome. Mol Biol Cell 28:364-369
Sood, Varun; Cajigas, Ivelisse; D'Urso, Agustina et al. (2017) Epigenetic Transcriptional Memory of GAL Genes Depends on Growth in Glucose and the Tup1 Transcription Factor in Saccharomyces cerevisiae. Genetics 206:1895-1907
Kim, Seungsoo; Liachko, Ivan; Brickner, Donna G et al. (2017) The dynamic three-dimensional organization of the diploid yeast genome. Elife 6:
D'Urso, Agustina; Brickner, Jason H (2017) Memory Is the Treasury and Guardian of All Things. Mol Cell 66:5-6
D'Urso, Agustina; Brickner, Jason H (2017) Epigenetic transcriptional memory. Curr Genet 63:435-439
Satomura, Atsushi; Brickner, Jason H (2017) Nuclear Pore Complexes: A Scaffold Regulating Developmental Transcription? Trends Cell Biol 27:621-622
D'Urso, Agustina; Takahashi, Yoh-Hei; Xiong, Bin et al. (2016) Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. Elife 5:
Randise-Hinchliff, Carlo; Brickner, Jason H (2016) Transcription factors dynamically control the spatial organization of the yeast genome. Nucleus 7:369-74
Brickner, Donna Garvey; Sood, Varun; Tutucci, Evelina et al. (2016) Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell 27:2980-93
Randise-Hinchliff, Carlo; Coukos, Robert; Sood, Varun et al. (2016) Strategies to regulate transcription factor-mediated gene positioning and interchromosomal clustering at the nuclear periphery. J Cell Biol 212:633-46

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