title: Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.
abstract: Nucleosomes, the basic unit of chromatin, have a critical role in the control of gene expression. Nucleosome positions have generally been determined by examining bulk populations of cells and then correlated with overall gene expression. Here, we describe a technique to determine nucleosome positioning in single cells by virtue of the ability of the nucleosome to protect DNA from GpC methylation. In the acid phosphatase inducible PHO5 gene, we find that there is significant cell-to-cell variation in nucleosome positions and shifts in nucleosome positioning correlate with changes in gene expression. However, nucleosome positioning is not absolute, and even with major shifts in gene expression, some cells fail to change nucleosome configuration. Mutations of the PHO5 promoter that introduce a poly(dA:dT) tract-stimulated gene expression under nonpermissive conditions led to shifts of positioned nucleosomes similar to induction of PHO5. By contrast, mutations that altered AA/TT/AT periodicity reduced gene expression upon PHO5 induction and stabilized nucleosomes in most cells, suggesting that enhanced nucleosome affinity for DNA antagonizes chromatin remodelers. Finally, we determined nucleosome positioning in two regions described as "fuzzy" or nucleosome-free when examined in a bulk assay. These regions consisted of distinct nucleosomes with a larger footprint for potential location and an increase population of cells lacking a nucleosome altogether. These data indicate an underlying complexity of nucleosome positioning that may contribute to the flexibility and heterogeneity of gene expression.
authors.affiliation: Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611;
authors.forename: Eliza C
authors.initials: EC
authors.lastname: Small
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208; and.
authors.forename: Liqun
authors.initials: L
authors.lastname: Xi
authors.affiliation: Department of Statistics, Northwestern University, Evanston, IL 60208; and.
authors.forename: Ji-Ping
authors.initials: JP
authors.lastname: Wang
authors.affiliation: Department of Molecular Biosciences, Northwestern University Weinberg College of Arts and Sciences, Evanston, IL 60208.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Widom
authors.affiliation: Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611; j-licht@northwestern.edu.
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Licht
mesh_terms: D000135:Acid Phosphatase / Q000235:genetics; D002843:Chromatin / Q000737:chemistry*; D042002:Chromatin Assembly and Disassembly; D018899:CpG Islands; D004247:DNA / Q000737:chemistry; D019175:DNA Methylation; D015966:Gene Expression Regulation, Fungal; D015723:Gene Library; D005821:Genetic Techniques; D049452:Green Fluorescent Proteins / Q000737:chemistry; D009154:Mutation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism; D010710:Phosphates / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D010710:Phosphates; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D049452:Green Fluorescent Proteins; D004247:DNA; D000135:Acid Phosphatase; C488916:PHO5 protein, S cerevisiae
keywords: chromatin structure; gene regulation