Protein modification on histone lysines is critical for controlling gene expression, which itself controls the variable and plastic expression of the proteome in diverse cell types. Modifications on lysine are chemically diverse and include acetylation, methylation, ubiquitylation and sumoylation. We and others have discovered acetyl- and methyl-lysines in many other proteins, and only some directly control gene expression;many are critical regulatory metabolic enzymes. Ubiquitylation controls the life and death of most proteins, and other protein functions. The pathways regulating diverse modifications on lysines are remarkably complex;much remains to be learned. The network of and dynamic interactions among these modification pathways is even more complex;many lysine-modifying proteins are encoded by multi-gene families, have redundant activities, and multiple substrates, only some of which are known. Cross-talk between modifications provides an extra layer of regulation. We have developed genetic, protein chip, chemical, microfiuidic and computational approaches to decrypt and abstract the complex networks defined by these signaling pathways and monitor how they change over time. This proposal extends many unique technologies developed in the last budget period, with a special focus on adapting these technologies to monitoring dynamic proteomic changes occurring in response to a range of biological stimuli. These newer approaches are complemented in this Technology Center for Networks and Pathways by application of innovative mass spectrometry technologies, including sensitive and diverse technologies for quantifying dynamics of lysine modification in cells. The yeast metabolic cycle, integrated with cell cycling and DNA integrity is a fascinating dynamic cycle that will be studied in detail with several of the technologies. Diverse Driving Biological Projects centered on lysine acetylation, methylation, ubiquitylation and SUMOylation, as well as advanced Training efforts. Including an internship for students in Puerto Rico, are integrated with the Technology Development aspects of the proposal. Technologies and resources are actively disseminated via multiple routes;both static and dynamic proteomics datasets will be centrally warehoused/disseminated.
Lysine modification on histones (and beyond) affects fundamental patterns of gene expression and is often deranged in disease states;developing technologies to monitor how they change is essential. Because lysine modification is so extensively intertwined with human health, aging and disease, the Technology Center for Networks and Pathways could have far-reaching pre-clinical and clinical impact.
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