title: 4D Visualization of replication foci in mammalian cells corresponding to individual replicons.
abstract: Since the pioneering proposal of the replicon model of DNA replication 50 years ago, the predicted replicons have not been identified and quantified at the cellular level. Here, we combine conventional and super-resolution microscopy of replication sites in live and fixed cells with computational image analysis. We complement these data with genome size measurements, comprehensive analysis of S-phase dynamics and quantification of replication fork speed and replicon size in human and mouse cells. These multidimensional analyses demonstrate that replication foci (RFi) in three-dimensional (3D) preserved somatic mammalian cells can be optically resolved down to single replicons throughout S-phase. This challenges the conventional interpretation of nuclear RFi as replication factories, that is, the complex entities that process multiple clustered replicons. Accordingly, 3D genome organization and duplication can be now followed within the chromatin context at the level of individual replicons.
authors.affiliation: Department of Biology, Technische Universitaet Darmstadt, Darmstadt 64287, Germany.|Laboratory of chromosome stability, Institute of Cytology, St. Petersburg 194064, Russia.
authors.forename: V O
authors.initials: VO
authors.lastname: Chagin
authors.affiliation: Department of Biology, Technische Universitaet Darmstadt, Darmstadt 64287, Germany.|Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK.
authors.forename: C S
authors.initials: CS
authors.lastname: Casas-Delucchi
authors.affiliation: Department of Biology, Technische Universitaet Darmstadt, Darmstadt 64287, Germany.
authors.forename: M
authors.identifier: http://orcid.org/0000-0003-2340-2478
authors.initials: M
authors.lastname: Reinhart
authors.affiliation: Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, OX1 3QU Oxford, UK.|Center for Integrated Protein Science at the Department of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany.
authors.forename: L
authors.identifier: http://orcid.org/0000-0002-1612-9699
authors.initials: L
authors.lastname: Schermelleh
authors.affiliation: Center for Integrated Protein Science at the Department of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany.
authors.forename: Y
authors.initials: Y
authors.lastname: Markaki
authors.affiliation: Center for Integrated Protein Science at the Department of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Maiser
authors.affiliation: Department of Biology, Technische Universitaet Darmstadt, Darmstadt 64287, Germany.
authors.forename: J J
authors.initials: JJ
authors.lastname: Bolius
authors.affiliation: Genomic Vision, Bagneux 92220, France.
authors.forename: A
authors.initials: A
authors.lastname: Bensimon
authors.affiliation: Max Delbrueck Center for Molecular Medicine, Berlin 13125, Germany.|Charité-Universitaetsmedizin, 13353 Berlin, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Fillies
authors.affiliation: Max Delbrueck Center for Molecular Medicine, Berlin 13125, Germany.
authors.forename: P
authors.initials: P
authors.lastname: Domaing
authors.affiliation: Laboratory of chromosome stability, Institute of Cytology, St. Petersburg 194064, Russia.
authors.forename: Y M
authors.initials: YM
authors.lastname: Rozanov
authors.affiliation: Center for Integrated Protein Science at the Department of Biology, Ludwig Maximilians University Munich, Planegg-Martinsried 82152, Germany.
authors.forename: H
authors.initials: H
authors.lastname: Leonhardt
authors.affiliation: Department of Biology, Technische Universitaet Darmstadt, Darmstadt 64287, Germany.
authors.forename: M C
authors.initials: MC
authors.lastname: Cardoso
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D004261:DNA Replication; D015870:Gene Expression; D059646:Genome Size; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D007700:Kinetics; D051379:Mice; D057054:Molecular Imaging; D032446:Myoblasts / Q000378:metabolism / Q000648:ultrastructure; D018809:Proliferating Cell Nuclear Antigen / Q000235:genetics / Q000378:metabolism; D012093:Replicon; D016196:S Phase / Q000235:genetics*; D013045:Species Specificity
chemical_list: D002843:Chromatin; D018809:Proliferating Cell Nuclear Antigen