Nucleosomes are the fundamental DNA packaging units of eukaryotic chromatin. Dynamic interaction between DNA and histones in the nucleosome play important roles in controlling the structure of chromatin and subsequently the accessibility of genes, which is an essential part of gene regulation. Chromatin modification such as DNA methylation and histone acetylation is a crucial element in the mechanisms of gene regulation. Abnormal levels of DNA methylation or defective histone acetylation lead to various developmental/proliferative disorders including various types of cancer, leukemia and Rubinstein-Taybi syndrome. The long-term objective of this research is to elucidate how nucleosome dynamics contribute to the mechanisms of gene regulation through chromatin modification. The goal of this project is to reveal the link between nucleosome dynamics and chromatin modification.
The aims are to test the main hypothesis that DNA methylation and histone acetylation may alter the dynamics of DNA wrapping/unwrapping around histones during nucleosome assembly/disassembly and consequently control the efficiency of nucleosome assembly/disassembly. Due to the difficulty associated with monitoring dynamic structural changes of a nucleosome based on ensemble-averaging measurements and static structural tools, the effects of chromatin modification on the nucleosome dynamics have never been clearly addressed. In order to accomplish these aims, we will employ single molecule multi-color fluorescence resonance energy transfer to monitor the real-time dynamics of DNA wrapping/unwrapping during nucleosome assembly/disassembly with and without the modifications in a single molecule level in a time resolved manner. Changes in the kinetic rates of DNA wrapping/unwrapping during nucleosome assembly/disassembly upon DNA methylation or histone acetylation will be examined in order to test the hypothesis. The proposed aims, when successfully accomplished, will greatly facilitate our understanding of the mechanisms of gene regulation by DNA methylation and histone acetylation from a dynamics perspective. Results from the project will provide a novel and unique basis for the development of diagnoses and treatments of the diseases and disorders originated from abnormal DNA methylation and defective histone acetylation.

Public Health Relevance

Defects in DNA methylation or histone acetylation lead to lethal diseases and various developmental and proliferative abnormalities including various types of cancer, leukemia and Rubinstein-Taybi syndrome. The proposed project will make a novel and unique contribution to the development of diagnoses and treatments of the diseases and disorders associated with abnormal DNA methylation and defective histone acetylation.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM097286-04
Application #
8691896
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Preusch, Peter
Project Start
2011-07-01
Project End
2016-06-30
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
4
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Pennsylvania State University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
City
University Park
State
PA
Country
United States
Zip Code
16802
Crickard, John B; Lee, Jaehyoun; Lee, Tae-Hee et al. (2017) The elongation factor Spt4/5 regulates RNA polymerase II transcription through the nucleosome. Nucleic Acids Res 45:6362-6374
Brahma, Sandipan; Udugama, Maheshi I; Kim, Jongseong et al. (2017) INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers. Nat Commun 8:15616
Lee, Jaehyoun; Lee, Tae-Hee (2017) Single-Molecule Investigations on Histone H2A-H2B Dynamics in the Nucleosome. Biochemistry 56:977-985
Yue, Hongjun; Fang, He; Wei, Sijie et al. (2016) Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. Biochemistry 55:2069-77
Kim, Jongseong; Wei, Sijie; Lee, Jaehyoun et al. (2016) Single-Molecule Observation Reveals Spontaneous Protein Dynamics in the Nucleosome. J Phys Chem B 120:8925-31
Falk, Samantha J; Lee, Jaehyoun; Sekulic, Nikolina et al. (2016) CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres. Nat Struct Mol Biol 23:204-208
Fang, He; Wei, Sijie; Lee, Tae-Hee et al. (2016) Chromatin structure-dependent conformations of the H1 CTD. Nucleic Acids Res 44:9131-9141
Wei, Sijie; Falk, Samantha J; Black, Ben E et al. (2015) A novel hybrid single molecule approach reveals spontaneous DNA motion in the nucleosome. Nucleic Acids Res 43:e111
Kim, Jongseong; Lee, Jaehyoun; Lee, Tae-Hee (2015) Lysine Acetylation Facilitates Spontaneous DNA Dynamics in the Nucleosome. J Phys Chem B 119:15001-5
Lee, Ju Yeon; Lee, Jaehyoun; Yue, Hongjun et al. (2015) Dynamics of nucleosome assembly and effects of DNA methylation. J Biol Chem 290:4291-303

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