The DNA of a single eukaryotic cell is over two meters in length, but compacts in the cell nucleus approximately 100,000 fold by a hierarchical scheme of packaging into nucleoprotein assemblies (""""""""chromatin"""""""") of increasing complexity and largely unknown architecture. Compaction beyond the nucleosome, the basic repeating unit of chromatin, is promoted by linker histone H1, with profound implications for the transcriptional competence of the underlying DNA. The location and mode of interaction of linker histones with the nucleosome is a subject of intense debate, as is the question of how sequence-specific DNA binding proteins recognize their binding site in the context of a nucleosome. Structural models are lacking for both types of interaction. ? ? The objective of this proposal is to determine the structure of two transcriptional regulators (the global regulator H1 and the specific transcription activator FoxA) in complex with the nucleosome, using x-ray crystallography and biophysical methods. It is proposed to investigate the role of linker histone tails in the organization of linker DNA, and to test the hypothesis that histone variants have evolved to modulate interaction with linker histones. These studies will culminate in a long-overdue structure of the nucleosome-H1 complex, which will reveal the location and mode of interaction of this key organizer of chromatin structure and function (specific aim 1).
In specific aim 2, the interaction of the transcription activator FoxA with highly defined nucleosomes will be studied. The hypotheses that the histone octamer contributes to FoxA binding, and that the histone tails modulate accessibility of nucleosomal DNA will be tested. Structural studies will illuminate the mechanism by which FoxA engages and opens chromatin, and the results will represent a paradigm for the mechanism by which the pervasive Fox (Forkhead) factors function in diverse biological regulatory contexts. Together, the proposed studies will provide insight into chromatin higher order structure DNA recognition in a natural chromatin context, and are thus essential to understand how the information stored in the genome is organized and accessed. In particular, the following specific aims are proposed: ? ? 1) Test the hypothesis that linker histone interacts with core histones and organizes the path of linker DNA. ? ? 1.A. Biophysical investigation of linker histone binding to nucleosomes; test the hypothesis that histone variants have evolved to modulate the interaction with linker histones. ? ? 1.B. Determine the crystal structure of H1-bound nucleosomes. ? ? 2) Test the hypothesis that FoxA binding results in an altered nucleosome structure. ? ? 2.A. Biophysical analysis of the binding of FoxA to mono-nucleosomes with defined binding sites. ? ? 2.B. Determine the crystal structure of the FoxA-nucleosome complex. ? ?

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function C Study Section (MSFC)
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Preusch, Peter C
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Colorado State University-Fort Collins
Schools of Arts and Sciences
Fort Collins
United States
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Muthurajan, U; Mattiroli, F; Bergeron, S et al. (2016) In Vitro Chromatin Assembly: Strategies and Quality Control. Methods Enzymol 573:3-41
Muthurajan, Uma M; McBryant, Steven J; Lu, Xu et al. (2011) The linker region of macroH2A promotes self-association of nucleosomal arrays. J Biol Chem 286:23852-64
Bohm, Vera; Hieb, Aaron R; Andrews, Andrew J et al. (2011) Nucleosome accessibility governed by the dimer/tetramer interface. Nucleic Acids Res 39:3093-102
Andrews, Andrew J; Luger, Karolin (2011) A coupled equilibrium approach to study nucleosome thermodynamics. Methods Enzymol 488:265-85
Yang, Chenghua; van der Woerd, Mark J; Muthurajan, Uma M et al. (2011) Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes. Nucleic Acids Res 39:4122-35
Subramanian, Vidya; Williams, Robert M; Boger, Dale L et al. (2010) Methods to characterize the effect of DNA-modifying compounds on nucleosomal DNA. Methods Mol Biol 613:173-92
Hansen, Jeffrey C; Nyborg, Jennifer K; Luger, Karolin et al. (2010) Histone chaperones, histone acetylation, and the fluidity of the chromogenome. J Cell Physiol 224:289-99
Watanabe, Shinya; Resch, Michael; Lilyestrom, Wayne et al. (2010) Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochim Biophys Acta 1799:480-6
Andrews, Andrew J; Chen, Xu; Zevin, Alexander et al. (2010) The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions. Mol Cell 37:834-42
Lilyestrom, Wayne; van der Woerd, Mark J; Clark, Nicholas et al. (2010) Structural and biophysical studies of human PARP-1 in complex with damaged DNA. J Mol Biol 395:983-94

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