title: Active human nucleolar organizer regions are interspersed with inactive rDNA repeats in normal and tumor cells.
abstract: OBJECTIVE
  The synthesis of rRNA is a key determinant of normal and malignant cell growth and subject to epigenetic regulation. Yet, the epigenomic features of rDNA arrays clustered in nucleolar organizer regions are largely unknown. We set out to explore for the first time how DNA methylation is distributed on individual rDNA arrays.
  
  
  METHODS
  Here we combined immunofluorescence detection of DNA modifications with fluorescence hybridization of single DNA fibers, metaphase immuno-FISH and methylation-sensitive restriction enzyme digestions followed by Southern blot.
  
  
  RESULTS
  We found clustering of both hypomethylated and hypermethylated repeat units and hypermethylation of noncanonical rDNA in IMR90 fibroblasts and HCT116 colorectal carcinoma cells. Surprisingly, we also found transitions between hypo- and hypermethylated rDNA repeat clusters on single DNA fibers.
  
  
  CONCLUSIONS
  Collectively, our analyses revealed co-existence of different epialleles on individual nucleolar organizer regions and showed that epi-combing is a valuable approach to analyze epigenomic patterns of repetitive DNA.
authors.affiliation: Department of Biochemistry III, Biochemistry Center Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
authors.forename: Karina
authors.initials: K
authors.lastname: Zillner
authors.affiliation: Genomic Vision, 80 Rue des Meuniers, 92220 Bagneux, France.
authors.forename: Jun
authors.initials: J
authors.lastname: Komatsu
authors.affiliation: Department of Biochemistry III, Biochemistry Center Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.|German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Filarsky
authors.affiliation: Department of Biochemistry III, Biochemistry Center Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.|University Hospital Ulm, Ulm 89070, Germany.
authors.forename: Rajakiran
authors.initials: R
authors.lastname: Kalepu
authors.affiliation: Genomic Vision, 80 Rue des Meuniers, 92220 Bagneux, France.
authors.forename: Aaron
authors.initials: A
authors.lastname: Bensimon
authors.affiliation: Department of Biochemistry III, Biochemistry Center Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.
authors.forename: Attila
authors.initials: A
authors.lastname: Németh
mesh_terms: D019175:DNA Methylation; D004275:DNA, Ribosomal / Q000737:chemistry / Q000378:metabolism*; D044127:Epigenesis, Genetic; D005260:Female; D020459:Genes, rRNA; D015894:Genome, Human; D006801:Humans; D008297:Male; D009697:Nucleolus Organizer Region; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004275:DNA, Ribosomal
keywords: DNA methylation; epigenetics; epigenomics; nucleolar organizer region; nucleolus; ribosomal DNA; single-molecule analysis