Eukaryotic DNA is packaged into chromatin, and this chromatin has a well-defined organization. Chromatin is composed of nucleosome building blocks, whose positioning along the DNA dictates the accessibility of gene regulatory elements, and ultimately the expression levels of genes. Nucleosomes occur in regular repeating intervals on genes. These arrays are highly regulated through many mechanisms including: post- translational modifications, deposition and eviction that are facilitated by chaperones, and re-positioning facilitated by chromatin remodeling complexes. We propose to further our understanding of nucleosomal arrays on a genomic scale.
In aim 1, we will use our newly developed ultra-high resolution ChIP-exo assay to determine the subnucleosomal organization of histone marks along nucleosomal arrays across a genome.
In aim 2, we will map the nucleosomal and subnucleosomal organization of chromatin remodelers using ChIP-exo. Their placement at specific nucleosomes, and their orientation on the nucleosome surface should provide insight into how they function on a genomic scale.
In aim 3, we will use our recently developed genome-wide reconstitution of properly positioned nucleosomal arrays to probe biochemical mechanisms of chromatin remodeler-directed array formation. Completion of these aims is expected to provide an understanding of fundamental principles of nucleosomal array and their role in regulating gene expression.

Public Health Relevance

Human health is highly dependent upon the proper functioning of our genes (biological instructions). This project will contribute to a greater understanding of how genes function by determining how these genes are packaged on a global scale, and how that packaging is regulated.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG004160-08
Application #
8708927
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Pazin, Michael J
Project Start
2006-12-01
Project End
2017-06-30
Budget Start
2014-07-01
Budget End
2015-06-30
Support Year
8
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Pennsylvania State University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
City
University Park
State
PA
Country
United States
Zip Code
16802
Iwafuchi-Doi, Makiko; Donahue, Greg; Kakumanu, Akshay et al. (2016) The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell 62:79-91
de Dieuleveult, Maud; Yen, Kuangyu; Hmitou, Isabelle et al. (2016) Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature 530:113-6
Van Oss, S Branden; Shirra, Margaret K; Bataille, Alain R et al. (2016) The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6. Mol Cell 64:815-825
Krietenstein, Nils; Wal, Megha; Watanabe, Shinya et al. (2016) Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell 167:709-721.e12
Aguilar-Gurrieri, Carmen; Larabi, Amédé; Vinayachandran, Vinesh et al. (2016) Structural evidence for Nap1-dependent H2A-H2B deposition and nucleosome assembly. EMBO J 35:1465-82
Mahony, Shaun; Pugh, B Franklin (2015) Protein-DNA binding in high-resolution. Crit Rev Biochem Mol Biol 50:269-83
Rhee, Ho Sung; Bataille, Alain R; Zhang, Liye et al. (2014) Subnucleosomal structures and nucleosome asymmetry across a genome. Cell 159:1377-88
Yen, Kuangyu; Vinayachandran, Vinesh; Pugh, B Franklin (2013) SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell 154:1246-56
Yen, Kuangyu; Vinayachandran, Vinesh; Batta, Kiran et al. (2012) Genome-wide nucleosome specificity and directionality of chromatin remodelers. Cell 149:1461-73
Bryant, Jessica M; Govin, Jérôme; Zhang, Liye et al. (2012) The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Mol Cell Biol 32:2771-83

Showing the most recent 10 out of 26 publications