title: Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.
abstract: The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity-nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed "fragile nucleosomes" throughout the yeast genome, nearly 1000 of which were at previously determined "nucleosome-free" loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation, and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization.
authors.affiliation: Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Yuanxin
authors.initials: Y
authors.lastname: Xi
authors.forename: Jianhui
authors.initials: J
authors.lastname: Yao
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Xiangwei
authors.initials: X
authors.lastname: He
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D004261:DNA Replication; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D018869:Heat-Shock Response; D059014:High-Throughput Nucleotide Sequencing; D008836:Micrococcal Nuclease / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000502:physiology*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic; D015854:Up-Regulation
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D008836:Micrococcal Nuclease