STUDY OF NUCLEOSOME DEPLETING FACTORS ON THE STOCHASTIC EXPRESSION OF THE YEAST HO PROMOTER

Open Access
Author:
O'Callaghan, Jessica
Area of Honors:
Biochemistry and Molecular Biology
Degree:
Bachelor of Science
Document Type:
Thesis
Thesis Supervisors:
  • Lu Bai , Thesis Supervisor
  • David Scott Gilmour, Honors Advisor
Keywords:
  • Chromatin structure
  • NDRs
  • NDFs
  • Transcription regulation
  • Gene expression
  • Single-cell fluorescence microscopy
Abstract:
Nucleosome-depleted regions (NDRs) are highly abundant in eukaryotic promoters. While it has long been established that NDRs may form from unfavorable histone-DNA interactions, this mechanism alone fails to accurately predict in vivo positioning, suggesting that other non-histone factors must play a key role in NDR formation. Some transcription factors (TFs) in yeast, termed nucleosomes-depleting factors (NDFs), including Reb1, Abf1, and Cbf1, have been proposed to effectively evict nucleosomes by either directly competing with other histones, or through recruitment of chromatin remodelers. Since nucleosomes present a significant barrier for the binding of most TFs, NDFs are likely to play a key role in chromatin reorganization activity. To determine how differences in NDF invasiveness, binding motif location, and copy number influence the nucleosomal landscape along regulatory regions in yeast, as well as the functional role of nucleosomes in transcription regulation, our research group developed a high-throughput assay to study the role of NDFs on nucleosomal coverage along the HO promoter (HOpr), whose nucleosome configuration changes throughout the cell cycle. Using this assay, we found that a single Reb1, Abf1, and Cbf1 binding motif activates HOpr in bimodal fashion, and that upstream nucleosome play a more significant role in HOpr activation than downstream ones.