title: Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes.
abstract: BACKGROUND
  The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with transcriptional repression, is the most highly studied chemical modification of DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated regions (HMRs) often occur in CG islands (CGIs), however, they also occur outside of CGIs and function as cell-type specific enhancers. During the process of differentiation, reorganization of chromatin and nucleosome arrangement at regulatory regions is thought to occur in order for the establishment of cell-type specific transcriptional programs. However, the specifics regarding the organization of nucleosomes at HMRs and the potential mechanisms regulating nucleosome occupancy in these regions are unknown. Here, we have investigated nucleosome organization around hypomethylated regions (HMRs) identified in two mouse primary cells.
  
  
  RESULTS
  Microccocal nuclease (MNase) digested mononucleosomes from primary cultures of new-born female mouse dermal fibroblasts and keratinocytes were mapped and compared to the HMRs obtained from single base-pair resolution methylomes. In both cell types, we find that nucleosomes are enriched at HMR boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region. Nucleosomes are enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types suggesting that nucleosome organization surrounding HMR boundaries is independent of methylation status. In addition, we find potential transcription factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries.
  
  
  CONCLUSIONS
  Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome. Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.|Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India.
authors.forename: Raghunath
authors.initials: R
authors.lastname: Chatterjee
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.
authors.forename: Desiree
authors.initials: D
authors.lastname: Tillo
authors.affiliation: Molecular and Computational Biology, University of Southern California 1050 Childs Way, Los Angeles, California 90089 USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Smith
authors.affiliation: Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.
authors.forename: Peter
authors.initials: P
authors.lastname: FitzGerald
authors.affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Vinson
keywords: CG methylation; Epigenomics; Fibroblasts; HMR; Hypomethylated regions; Keratinocytes; Nucleosomes