DNA within the eukaryotic cell nucleus is assembled with histones and other proteins to form a complicated, multifaceted complex known as chromatin. Chromatin not only serves to package the genome but elements of chromatin structure have been intimately integrated into gene control mechanisms. The core histone tail domains are essential for the formation of multiple levels of structure within chromatin and a large portion of signal transduction within the nucleus ultimately directs posttranslational modification of these domains in order to facilitate nuclear processes such as transcription. In several cases, mutations in enzymes that carry out these modifications have been linked to various diseases including cancers in humans. However, the molecular mechanisms by which the tail domains define chromatin structures - and ultimately the functionality of the underlying DNA - remain poorly understood. The primary goal of the work described in this proposal is to elucidate the molecular mechanisms by which the core histone tail domains dictate the formation of higher order chromatin structures and how acetylation of specific lysines within these domains alters tail structures and interactions to allow for gene expression.
Our aims are to 1) characterize short-range and long-range inter- nucleosomal interactions of the H3 and H4 tail domains in model nucleosomes and nucleosome arrays, 2) Determine whether linker histone H1, the architectural transcription factor HMGN or a chromatin remodeling activity specifically alters interactions of the tail domains and to 3) quantitatively assess binding of selected tail domains and the effect of acetylation on these interactions in reconstituted and native chromatin. We will use several novel approaches including site-directed chemical mapping of tail-DNA interactions, a UV laser crosslinking approach, and other chemical probing approaches to investigate structures and interactions of the tail domains. Further, we will use a chemical protection approach and NMR of specifically labeled core histones to quantitatively assess the salt-dependent binding stability of individual histone tails within nucleosomes. This work will advance our understanding of critical molecular mechanisms that impinge upon control of gene expression and ultimately diseases such as cancer.

Public Health Relevance

Within the eukaryotic cell nucleus, DNA is associated with core histones and other proteins to form a multi-faceted complex known as chromatin. This complex brings about the orderly packaging of the immense length of DNA within the tiny volume of the nucleus and is directly integrated into multiple processes including regulation of gene expression. The results of this project will illuminate the molecular mechanisms by which critical elements known as the histone tail domains define and regulate chromatin structure and gene expression and thus allow a greater understanding of fundamental processes related to cancer and genetic diseases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics C Study Section (MGC)
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Preusch, Peter C
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University of Rochester
Schools of Dentistry
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Pepenella, Sharon; Murphy, Kevin J; Hayes, Jeffrey J (2014) A distinct switch in interactions of the histone H4 tail domain upon salt-dependent folding of nucleosome arrays. J Biol Chem 289:27342-51
Pepenella, Sharon; Murphy, Kevin J; Hayes, Jeffrey J (2014) Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure. Chromosoma 123:3-13
Elliott, Giles O; Murphy, Kevin J; Hayes, Jeffrey J et al. (2013) Replication-independent nucleosome exchange is enhanced by local and specific acetylation of histone H4. Nucleic Acids Res 41:2228-38
Schlick, Tamar; Hayes, Jeff; Grigoryev, Sergei (2012) Toward convergence of experimental studies and theoretical modeling of the chromatin fiber. J Biol Chem 287:5183-91
Fang, He; Clark, David J; Hayes, Jeffrey J (2012) DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain. Nucleic Acids Res 40:1475-84
Caterino, Tamara L; Fang, He; Hayes, Jeffrey J (2011) Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain. Mol Cell Biol 31:2341-8
Caterino, Tamara L; Hayes, Jeffrey J (2011) Structure of the H1 C-terminal domain and function in chromatin condensation. Biochem Cell Biol 89:35-44
Shukla, Manu Shubhdarshan; Syed, Sajad Hussain; Goutte-Gattat, Damien et al. (2011) The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling. Nucleic Acids Res 39:2559-70
Liu, Ning; Peterson, Craig L; Hayes, Jeffrey J (2011) SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol 31:4165-75
Jagannathan, Indu; Pepenella, Sharon; Hayes, Jeffrey J (2011) Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation. J Biol Chem 286:17521-9

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