title: Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules.
abstract: DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline, we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome-depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule, and thus, single cell level, that can be used to monitor disease progression and response to therapy.
authors.affiliation: Department of Urology, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.
authors.forename: Theresa K
authors.initials: TK
authors.lastname: Kelly
authors.forename: Yaping
authors.initials: Y
authors.lastname: Liu
authors.forename: Fides D
authors.initials: FD
authors.lastname: Lay
authors.forename: Gangning
authors.initials: G
authors.lastname: Liang
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Berman
authors.forename: Peter A
authors.initials: PA
authors.lastname: Jones
mesh_terms: D000483:Alleles; D002460:Cell Line; D042002:Chromatin Assembly and Disassembly; D002874:Chromosome Mapping; D018899:CpG Islands; D004247:DNA / Q000235:genetics*; D018983:DNA Footprinting; D019175:DNA Methylation; D057890:Epigenomics / Q000379:methods*; D017353:Gene Deletion; D005786:Gene Expression Regulation; D056426:Genetic Loci; D006801:Humans; D008780:Methyltransferases; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D009707:Nucleosomes; D004247:DNA; D008780:Methyltransferases