title: Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.
abstract: Nucleosome is the elementary structural unit of eukaryotic chromatin. Instability of nucleosome positioning plays critical roles in chromatin remodeling in differentiation and disease. In this study, we investigated nucleosome dynamics in the Saccharomyces cerevisiae genome using a geometric model based on Z curve theory. We identified 52,941 stable nucleosomes and 7607 dynamic nucleosomes, compiling them into a genome-wide nucleosome dynamic positioning map and constructing a user-friendly visualization platform (http://bioinfo.hrbmu.edu.cn/nucleosome). Our approach achieved a sensitivity of 90.31% and a specificity of 87.76% for S. cerevisiae. Analysis revealed transcription factor binding sites (TFBSs) were enriched in linkers. And among the sparse nucleosomes around TFBSs, dynamic nucleosomes were slightly preferred. Gene Ontology (GO) enrichment analysis indicated that stable and dynamic nucleosomes were enriched on genes involved in different biological processes and functions. This study provides an approach for comprehending chromatin remodeling and transcriptional regulation of genes.
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors: Xueting
authors: X
authors: Wu
authors: Hui
authors: H
authors: Liu
authors: Hongbo
authors: H
authors: Liu
authors: Jianzhong
authors: J
authors: Su
authors: Jie
authors: J
authors: Lv
authors: Ying
authors: Y
authors: Cui
authors: Fang
authors: F
authors: Wang
authors: Yan
authors: Y
authors: Zhang
mesh_terms: D001665:Binding Sites; D002454:Cell Differentiation / Q000235:genetics; D002843:Chromatin; D042002:Chromatin Assembly and Disassembly; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D008962:Models, Theoretical; D009707:Nucleosomes / Q000737:chemistry / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors
keywords: AUC; Chromatin remodeling; FPR; GBrowse; GO; Gene Ontology; Generic Genome Browser; NFR; Nucleosome dynamics; ROC; SGD; Saccharomyces Genome Database; TFBS; TPR; TSS; TTS; Visualization platform; Z curve model; false positive rate; nucleosome-free regions; receiver operator characteristics; the area under the ROC; transcription factor binding sites; transcription start sites; transcription termination sites; true positive rate