Organization of eukaryotic DNA into a macromolecular histone complex (chromatin) allows the cell to utilize regulatory mechanisms that control gene activation and chromosomal stability. This epigenetic process can explain how genetically equivalent stem cells differentiate into diverse cell types, how penetrance of disease is modulated by nutrition and environment, and how organogenesis, tissue formation, and aging occur. The majority of emergent research in epigenetics describes phenomenological data, but progress on the molecular understanding of the pathways has lagged. Chromatin modifying enzymes are responsible for generating and removing chemical 'marks'on histone proteins. By dynamically altering the structure and function of chromatin, these modifying enzymes regulate transcription and all DNA-templated processes. It is postulated that the complex array of posttranslational modifications (PTMs) gives rise to a 'histone code'that is a major epigenetic mechanism for controlling transcriptional programs. Mounting evidence suggests that inappropriate chromatin PTMs and misinterpretation of the code is linked to an array of diseases, including many forms of cancer and a host of developmental defects. How this histone code is 'read', 'written'or 'erased'is poorly understood. How do PTM enzymes 'read'pre-existing marks and perform the appropriate histone modification? A major roadblock towards de-coding this information has been the shear complexity of the PTMs presented on even short stretches of amino acids within histone proteins. The cataloguing of these dynamic modifications has been accomplished through use of modification-specific antibodies and mass spectral methods. However, unbiased dissection of the combinatorial PTM patterns recognized by chromatin binding proteins requires a platform for rapidly and comprehensively surveying binding affinity. To begin to address these questions, recently we have developed combinatorial PTM libraries and screening methodologies to probe the histone code recognized by chromatin proteins/enzymes. Here, we will utilize these novel methodologies to investigate how the epigenetic code is read, written or erased. We propose that a histone code is generated, read and interpreted by enzyme complexes that can discriminate the PTM codes at two molecular levels: a.) catalytic domain selectivity and b.) modular histone-binding domains that recognize distinct patterns of PTMs. Utilizing a number of innovative biochemical tools to address these questions, three major aims are proposed: 1.) To determine the mechanisms of specific but multi-site acetylation by histone acetyltransferase complexes. 2.) To elucidate the 'histone code'read by modular chromatin-binding domains. 3.) To determine the function of chromatin-binding modules in substrate selection and catalytic efficiency by chromatin PTM complexes.

Public Health Relevance

Although the human genome (DNA sequence) is a blueprint of cellular potential, our epigenome ultimately controls whether a particular gene is turned 'on'or turned 'off.'Epigenetic processes can explain how genetically equivalent cells differentiate into diverse cell types, how penetrance of disease is modulated by nutrition and environment, and how organogenesis, tissue formation, and aging occur. The epigenome consists of a complex array of specific chemical 'marks'on histone proteins, which wrap the DNA. By dynamically altering these coded marks, our cells can regulate gene expression. Mounting evidence suggests that inappropriate epigenetic marks and misinterpretation of the code is linked to an array of diseases, including many forms of cancer and a host of developmental defects. How this histone code is 'read', 'written'or 'erased'is poorly understood. Here, we will utilize recently developed technologies to address these important questions at the molecular level. Namely, we will investigate how the epigenetic code is read, written or erased by cellular enzymes that regulate this process. This fundamental knowledge has enormous potential for significantly improving health outcomes through the discovery/development of novel therapeutics that restore epigenetic pathways gone awry. Several anti-cancer drugs have already been developed to target certain enzymes involved in this pathway.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM059785-14
Application #
8307541
Study Section
Macromolecular Structure and Function E Study Section (MSFE)
Program Officer
Gerratana, Barbara
Project Start
1999-08-01
Project End
2013-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
14
Fiscal Year
2012
Total Cost
$296,060
Indirect Cost
$90,239
Name
University of Wisconsin Madison
Department
Biochemistry
Type
Schools of Medicine
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
Zhou, Xia; Fan, Lucy X; Sweeney Jr, William E et al. (2013) Sirtuin 1 inhibition delays cyst formation in autosomal-dominant polycystic kidney disease. J Clin Invest 123:3084-98
Oliver, Samuel S; Denu, John M (2011) Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language". Chembiochem 12:299-307
Arnold, Kevin M; Lee, Susan; Denu, John M (2011) Processing mechanism and substrate selectivity of the core NuA4 histone acetyltransferase complex. Biochemistry 50:727-37
Mansfield, Robyn E; Musselman, Catherine A; Kwan, Ann H et al. (2011) Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9. J Biol Chem 286:11779-91
Albaugh, Brittany N; Arnold, Kevin M; Denu, John M (2011) KAT(ching) metabolism by the tail: insight into the links between lysine acetyltransferases and metabolism. Chembiochem 12:290-8
Albaugh, Brittany N; Arnold, Kevin M; Lee, Susan et al. (2011) Autoacetylation of the histone acetyltransferase Rtt109. J Biol Chem 286:24694-701
Garske, Adam L; Oliver, Samuel S; Wagner, Elise K et al. (2010) Combinatorial profiling of chromatin binding modules reveals multisite discrimination. Nat Chem Biol 6:283-90
Oliver, Samuel S; Denu, John M (2010) Dynamic Interplay between Histone H3 Modifications and Protein Interpreters: Emerging Evidence for a "Histone Language" Chembiochem :
Kolonko, Erin M; Albaugh, Brittany N; Lindner, Scott E et al. (2010) Catalytic activation of histone acetyltransferase Rtt109 by a histone chaperone. Proc Natl Acad Sci U S A 107:20275-80
Albaugh, Brittany N; Kolonko, Erin M; Denu, John M (2010) Kinetic mechanism of the Rtt109-Vps75 histone acetyltransferase-chaperone complex. Biochemistry 49:6375-85

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