The long-term aim of my research program is to develop a quantitative understanding of gene regulation in vivo. This project focuses on the earliest steps in gene regulation, namely, how gene regulatory proteins gain access to their DMA target sites in chromatin. Access to target sites inside nucleosomes can occur spontaneously, and can be catalyzed by ATP-dependent nucleosome remodeling factors. We are studying both of these mechanisms. Studies in Aim 1 will characterize the spontaneous invasion of nucleosomes by site-specific DMA binding proteins. We will investigate the kinetics for spontaneous access at interior sites in nucleosomes, the effects of higher order chromatin folding on site accessibility, and the rules governing cooperative binding to nucleosomes. Studies in Aim 2 will address how the Drosophila ISWI/Acf1 nucleosome remodeling machine functions as a machine to catalyze and drive the movement of nucleosomes from one position on DNA to another. We will characterize the protein domain organization of this machine, and the interactions between parts of the machine with each other, and between the machine and the ATP and chromatin substrates. We will characterize how the machine changes conformation through a catalytic cycle, and the changes that the machine induces in nucleosomes. Finally, structural changes taking place within the machine throughout a catalytic cycle will be correlated in time, with those in the nucleosome, to develop a detailed picture of the functioning of this broad class of machine. Relevance: The proper regulation of genes is essential for the development and health of all organisms. Understanding how regulatory proteins find and bind to their DNA target sites will lead, over the long term, to new diagnostics and therapeutics. Studies of ATP-dependent nucleosome remodeling factors have a specific relevance to human development and health, as mutations in these factors are responsible for a wide range of human developmental diseases and cancers, including: Williams syndrome, Schimke immunoosseous dysplasia, Cockayne syndrome, X-linked a thalassaemia, mental retardation, malignant rhabdoid tumors, chronic myeloid leukemia, and prostate and lung carcinomas. ? ? ?

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics A Study Section (MGA)
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Carter, Anthony D
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Northwestern University at Chicago
Schools of Arts and Sciences
United States
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Moyle-Heyrman, Georgette; Viswanathan, Ramya; Widom, Jonathan et al. (2012) Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA. J Biol Chem 287:9002-12
Moyle-Heyrman, Georgette; Tims, Hannah S; Widom, Jonathan (2011) Structural constraints in collaborative competition of transcription factors against the nucleosome. J Mol Biol 412:634-46
Tims, Hannah S; Gurunathan, Kaushik; Levitus, Marcia et al. (2011) Dynamics of nucleosome invasion by DNA binding proteins. J Mol Biol 411:430-48
Poirier, Michael G; Oh, Eugene; Tims, Hannah S et al. (2009) Dynamics and function of compact nucleosome arrays. Nat Struct Mol Biol 16:938-44
Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-6
Field, Yair; Fondufe-Mittendorf, Yvonne; Moore, Irene K et al. (2009) Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet 41:438-45
Morozov, Alexandre V; Fortney, Karissa; Gaykalova, Daria A et al. (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37:4707-22
Segal, Eran; Widom, Jonathan (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19:65-71
Shen, Hong Ming; Poirier, Michael G; Allen, Michael J et al. (2009) The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription. J Exp Med 206:1057-71
Segal, Eran; Widom, Jonathan (2009) From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 10:443-56

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