The physical organization of chromosomes is intimately tied to gene regulation. Chromatin remodeling refers to the dynamic compaction and decondensation of eukaryotic chromosomes through the covalent modification and physical movement of nucleosomes. Knowledge of the processes that drive remodeling are essential for gaining a more insightful understanding of human diseases that result from disruptions of normal gene regulation, such as cancer and inherited developmental disorders. Relatively little is known regarding the mechanism of by which ATP- dependent remodeling factors alter nucleosome structure, with no understanding of how distinct remodeler domains functionally interact to promote remodeling, how key remodeler domains are positioned in space with respect to one another, nor how remodelers embrace the nucleosome substrate. The long-term objective of this proposal is to establish a biochemical and biophysical framework necessary for describing and understanding the process of chromatin remodeling. This proposal focuses on the CHD1 chromatin remodeling factor, with specific aims to (1) dissect the CHD1 remodeling cycle by characterizing partially dysfunctional variants, (2) determine the architecture of the CHD1 remodeler using X-ray crystallography, and (3) determine the organization of a CHD1:nucleosome complex using small angle X-ray scattering (SAXS) and DNA footprinting. By coupling functional studies of CHD1 with structural information gained through X-ray crystallography, SAXS, and DNA footprinting, we expect to elucidate key steps of the remodeling reaction. In the future, a deeper understanding of chromatin remodeling will be essential for developing therapeutics that manipulate genome-wide gene expression for treatment of human disease. Nearly all cells in the human body possess the same set of genes, yet only a subset of these genes are turned "on" in any particular tissue. The "on" and "off" states of genes are regulated in a complex and ill-defined manner that directly correlates with the physical packaging of chromosomes, called the chromatin structure. Understanding the process by which chromosomes can be unpackaged and repackaged by so-called chromatin remodeling factors is necessary for understanding and therefore combatting many diseases such as cancer where there are imbalances in gene expression.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM084192-05
Application #
8248770
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Preusch, Peter C
Project Start
2008-04-01
Project End
2013-08-31
Budget Start
2012-03-01
Budget End
2013-08-31
Support Year
5
Fiscal Year
2012
Total Cost
$278,572
Indirect Cost
$102,154
Name
Johns Hopkins University
Department
Physiology
Type
Schools of Arts and Sciences
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Patel, Ashok; Chakravarthy, Srinivas; Morrone, Seamus et al. (2013) Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler. Nucleic Acids Res 41:1637-48
Patel, Ashok; McKnight, Jeffrey N; Genzor, Pavol et al. (2011) Identification of residues in chromodomain helicase DNA-binding protein 1 (Chd1) required for coupling ATP hydrolysis to nucleosome sliding. J Biol Chem 286:43984-93
Sharma, Amit; Jenkins, Katherine R; Heroux, Annie et al. (2011) Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J Biol Chem 286:42099-104
McKnight, Jeffrey N; Jenkins, Katherine R; Nodelman, Ilana M et al. (2011) Extranucleosomal DNA binding directs nucleosome sliding by Chd1. Mol Cell Biol 31:4746-59
Hauk, Glenn; McKnight, Jeffrey N; Nodelman, Ilana M et al. (2010) The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell 39:711-23