title: Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression.
abstract: Studying nucleosome dynamics in promoter regions is crucial for understanding gene regulation. Nucleosomes regulate gene expression by sterically occluding transcription factors (TFs) and other non-histone proteins accessing genomic DNA. How the binding competition between nucleosomes and TFs leads to transcriptionally compatible promoter states is an open question. Here, we present a computational study of the nucleosome dynamics and organization in the promoter region of PHO5 gene in Saccharomyces cerevisiae. Introducing a model for nucleosome kinetics that takes into account ATP-dependent remodeling activity, DNA sequence effects, and kinetics of TFs (Pho4p), we compute the probability of obtaining different "promoter states" having different nucleosome configurations. Comparing our results with experimental data, we argue that the presence of local remodeling activity (LRA) as opposed to basal remodeling activity (BRA) is crucial in determining transcriptionally active promoter states. By modulating the LRA and Pho4p binding rate, we obtain different mRNA distributions-Poisson, bimodal, and long-tail. Through this work we explain many features of the PHO5 promoter such as sequence-dependent TF accessibility and the role of correlated dynamics between nucleosomes and TFs in opening/coverage of the TATA box. We also obtain possible ranges for TF binding rates and the magnitude of LRA.
authors: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
authors: Hungyo
authors: H
authors: Kharerin
authors: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
authors: Paike J
authors: PJ
authors: Bhat
authors: Department of Physics, Department of Molecular Biosciences, Northwestern University, Evanston, IL.
authors: John F
authors: JF
authors: Marko
authors: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India.
authors: Ranjith
authors: R
authors: Padinhateeri
mesh_terms: D000135:Acid Phosphatase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D004247:DNA / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D009707:Nucleosomes; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA; D000135:Acid Phosphatase; C488916:PHO5 protein, S cerevisiae