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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM052426-17
Application #
8197825
Study Section
Molecular Genetics C Study Section (MGC)
Program Officer
Preusch, Peter C
Project Start
1995-05-01
Project End
2012-11-30
Budget Start
2011-12-01
Budget End
2012-11-30
Support Year
17
Fiscal Year
2012
Total Cost
$316,738
Indirect Cost
$111,064
Name
University of Rochester
Department
Biochemistry
Type
Schools of Dentistry
DUNS #
041294109
City
Rochester
State
NY
Country
United States
Zip Code
14627
Mishra, Laxmi Narayan; Hayes, Jeffrey J (2018) A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. J Biol Chem 293:19191-19200
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Balliano, Angela; Hao, Fanfan; Njeri, Catherine et al. (2017) HMGB1 Stimulates Activity of Polymerase ? on Nucleosome Substrates. Biochemistry 56:647-656
Wakabayashi, Hironao; Tucker, Christopher; Bethlendy, Gabor et al. (2017) NuA4 histone acetyltransferase activity is required for H4 acetylation on a dosage-compensated monosomic chromosome that confers resistance to fungal toxins. Epigenetics Chromatin 10:49
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Murphy, Kevin J; Cutter, Amber R; Fang, He et al. (2017) HMGN1 and 2 remodel core and linker histone tail domains within chromatin. Nucleic Acids Res 45:9917-9930
Bednar, Jan; Garcia-Saez, Isabel; Boopathi, Ramachandran et al. (2017) Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Mol Cell 66:384-397.e8
Gatchalian, Jovylyn; Wang, Xiaodong; Ikebe, Jinzen et al. (2017) Accessibility of the histone H3 tail in the nucleosome for binding of paired readers. Nat Commun 8:1489
Mishra, Laxmi N; Pepenella, Sharon; Rogge, Ryan et al. (2016) Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays. Sci Rep 6:34808

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