In eukaryotic cells, nucleosomes prevent efficient binding of transcription factors and transcription machinery to their genomic targets. A special group of transcription factors called ?pioneer factors? can invade compact chromosome and remodel nucleosomes near their binding sites, allowing the access of transcription factors and triggering their transcriptional competency. Pioneer factors play critical roles in gene regulation and cell differentiation. Mutation or mis-regulation of pioneer factors are associated with developmental diseases and many types of human cancer. Despite their essential functions, the mechanism underlying the pioneer activity is unclear. Our long-term goal is to develop a detailed mechanistic understanding of how pioneer factors access their nucleosomal binding sites, disrupt histone-DNA contacts, and activate gene expression. To achieve this goal, our overall objective in this proposal is to quantitatively measure the binding, nucleosome-depleting, and gene regulatory activities of pioneer factors under a variety of genetic and cellular conditions. We will perform these measurements into three aims. At the population level, we will determine the steady-state nucleosome-depleting activities among genome-wide TFs to understand what kind of TFs can serve as pioneers and how their nucleosome-depleting activities are regulated in vivo (aim 1). At the single cell level, we will evaluate the gene regulatory activities of pioneer factors and their cell-to-cell variability (aim 2). At the single molecule level, we will directly measure the kinetics of pioneer factor binding and invasion of the nucleosome substrates in vitro (aim 3). Completion of these aims is expected to advance the fundamental knowledge of pioneer factors and their role in chromosome opening and gene regulation. It will also contribute to future dissection of the functional roles of pioneer factors in cancer cells and the development of novel therapies to combat their dysfunction.

Public Health Relevance

Pioneer factors play essential roles in gene regulation and cell differentiation. Mutation or mis-regulation of pioneer factors are associated with various types of human diseases, especially cancer. By developing a mechanistic understanding of pioneer factors, we will contribute to the clinical applications of these factors in cancer treatment and cellular reprogramming.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM121858-03
Application #
9616197
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2017-01-01
Project End
2020-12-31
Budget Start
2019-01-01
Budget End
2019-12-31
Support Year
3
Fiscal Year
2019
Total Cost
Indirect Cost
Name
Pennsylvania State University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
003403953
City
University Park
State
PA
Country
United States
Zip Code
16802
Liu, Yu; Wolstenholme, Charles H; Carter, Gregory C et al. (2018) Modulation of Fluorescent Protein Chromophores To Detect Protein Aggregation with Turn-On Fluorescence. J Am Chem Soc 140:7381-7384
Zou, Fan; Bai, Lu (2018) Using time-lapse fluorescence microscopy to study gene regulation. Methods :
Yan, Chao; Chen, Hengye; Bai, Lu (2018) Systematic Study of Nucleosome-Displacing Factors in Budding Yeast. Mol Cell 71:294-305.e4