Genomic DNA of a human cell is packaged in 23 pairs of chromosomes that are collectively called chromatin. Chromatin is not a storage space. Rather it functions as a fundamental regulator that governs global dynamic changes of gene expression. Site-specific modifications of histones - the DNA packing proteins in chromatin - play an essential role in controlling of the capacity of the human genome to store, release and inherit biological information. Studies of histone modifications previously led to the formation of the histone code hypothesis stating that patterns of histone modifications constitute a code that specifies transcriptional outcomes. While this hypothesis has played an important role in propelling the chromatin biology field in the past decade, mounting evidence argues that histone modifications exert context-dependent functions rather than a code. However, we still have very limited knowledge of how histone modifications work in concert to direct gene expression. The goal of our research in epigenetics is to understand how chromatin modifications lead to regulatory capability of chromatin that directs both gene silencing and "on demand" expression in an orderly manner. Over the past years, we have elucidated the structure and mechanism of histone modifying enzymes and histone binding protein domains. Built on the lessons learned from our own studies, as well as from those of other leading research labs in the field, we postulate that gene expression (or silencing) in chromatin proceeds with an instruction that is programmed with a set of molecular activities of the conserved functional units that are present in participating proteins, and that these basic molecular functions including chromatin modifying activities and modification-directed molecular interactions constitute alphabets of a chromatin language of gene expression. In this project, we will test and develop mechanistic models predicted by this hypothesis through the study of the structure and mechanism of tandem chromatin protein modules in the functional context of gene transcription. To tackle this highly dynamic and complex biological system, we use an integrated structural/chromatin biology approach.
The specific aims of this project are to: (1) characterize the basic mechanisms of acetylated and methylated histone recognition in gene expression;(2) investigate molecular interplay of different histone modifications;and (3) define the histone crosstalk by the tandem chromatin modules in gene transcription.

Public Health Relevance

Site-specific histone modifications determine transcriptional activation or silencing of human genes. While important histone modifying enzymes have been identified, it remains elusive as to how these epigenetic chromatin modifications work in concert to control gene expression. To address this scientific challenge, we will perform structural and functional characterization of the conserved tandem protein modules as part of a chromatin language of gene expression hypothesis, the results of which will have important implications in a better understanding of epigenetic mechanisms underlying gene transcription in a chromatin context in human biology of health and disease, particularly cancer.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Knowlton, John R
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Icahn School of Medicine at Mount Sinai
Schools of Medicine
New York
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