1
|
Löb D, Lengert N, Chagin VO, Reinhart M, Casas-Delucchi CS, Cardoso MC, Drossel B. 3D replicon distributions arise from stochastic initiation and domino-like DNA replication progression. Nat Commun 2016; 7:11207. [PMID: 27052359 PMCID: PMC4829661 DOI: 10.1038/ncomms11207] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 03/02/2016] [Indexed: 01/02/2023] Open
Abstract
DNA replication dynamics in cells from higher eukaryotes follows very complex but highly efficient mechanisms. However, the principles behind initiation of potential replication origins and emergence of typical patterns of nuclear replication sites remain unclear. Here, we propose a comprehensive model of DNA replication in human cells that is based on stochastic, proximity-induced replication initiation. Critical model features are: spontaneous stochastic firing of individual origins in euchromatin and facultative heterochromatin, inhibition of firing at distances below the size of chromatin loops and a domino-like effect by which replication forks induce firing of nearby origins. The model reproduces the empirical temporal and chromatin-related properties of DNA replication in human cells. We advance the one-dimensional DNA replication model to a spatial model by taking into account chromatin folding in the nucleus, and we are able to reproduce the spatial and temporal characteristics of the replication foci distribution throughout S-phase.
Collapse
Affiliation(s)
- D. Löb
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - N. Lengert
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - V. O. Chagin
- Laboratory of Chromosome Stability, Institute of Cytology, St Petersburg 194064, Russia
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. Reinhart
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - C. S. Casas-Delucchi
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M. C. Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - B. Drossel
- Department of Physics, Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| |
Collapse
|
2
|
Chagin VO, Reinhart M, Cardoso MC. High-resolution analysis of Mammalian DNA replication units. Methods Mol Biol 2016; 1300:43-65. [PMID: 25916704 DOI: 10.1007/978-1-4939-2596-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Genomic DNA of a eukaryotic cell is replicated once during the S-phase of the cell cycle to precisely maintain the complete genetic information. In the course of S-phase, semiconservative DNA synthesis is sequentially initiated and performed at thousands of discrete patches of the DNA helix termed replicons. At any given moment of S-phase, multiple replicons are active in parallel in different parts of the genome. In the last decades, tools and methods to visualize DNA synthesis inside cells have been developed. Pulse labeling with nucleotides as well as detecting components of the replication machinery yielded an overall picture of multiple discrete sites of active DNA synthesis termed replication foci (RFi) and forming spatiotemporal patterns within the cell nucleus. Recent advances in fluorescence microscopy and digital imaging in combination with computational image analysis allow a comprehensive quantitative analysis of RFi and provide valuable insights into the organization of the genomic DNA replication process and also of the genome itself. In this chapter, we describe in detail protocols for the visualization and quantification of RFi at different levels of optical and physical resolution.
Collapse
Affiliation(s)
- Vadim O Chagin
- Institute of Cytology, Russian Academy of Science, Saint Petersburg, Russia
| | | | | |
Collapse
|
3
|
Smirnov E, Borkovec J, Kováčik L, Svidenská S, Schröfel A, Skalníková M, Švindrych Z, Křížek P, Ovesný M, Hagen GM, Juda P, Michalová K, Cardoso MC, Cmarko D, Raška I. Separation of replication and transcription domains in nucleoli. J Struct Biol 2014; 188:259-66. [PMID: 25450594 DOI: 10.1016/j.jsb.2014.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 10/02/2014] [Accepted: 10/05/2014] [Indexed: 01/07/2023]
Abstract
In mammalian cells, active ribosomal genes produce the 18S, 5.8S and 28S RNAs of ribosomal particles. Transcription levels of these genes are very high throughout interphase, and the cell needs a special strategy to avoid collision of the DNA polymerase and RNA polymerase machineries. To investigate this problem, we measured the correlation of various replication and transcription signals in the nucleoli of HeLa, HT-1080 and NIH 3T3 cells using a specially devised software for analysis of confocal images. Additionally, to follow the relationship between nucleolar replication and transcription in living cells, we produced a stable cell line expressing GFP-RPA43 (subunit of RNA polymerase I, pol I) and RFP-PCNA (the sliding clamp protein) based on human fibrosarcoma HT-1080 cells. We found that replication and transcription signals are more efficiently separated in nucleoli than in the nucleoplasm. In the course of S phase, separation of PCNA and pol I signals gradually increased. During the same period, separation of pol I and incorporated Cy5-dUTP signals decreased. Analysis of single molecule localization microscopy (SMLM) images indicated that transcriptionally active FC/DFC units (i.e. fibrillar centers with adjacent dense fibrillar components) did not incorporate DNA nucleotides. Taken together, our data show that replication of the ribosomal genes is spatially separated from their transcription, and FC/DFC units may provide a structural basis for that separation.
Collapse
Affiliation(s)
- E Smirnov
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - J Borkovec
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - L Kováčik
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - S Svidenská
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - A Schröfel
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - M Skalníková
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Z Švindrych
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - P Křížek
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - M Ovesný
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - G M Hagen
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - P Juda
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - K Michalová
- Centre of Oncocytogenetics, Institute of Medical Biochemistry and Laboratory Diagnosis, General University Hospital and First Faculty of Medicine, Charles University in Prague, Czech Republic
| | - M C Cardoso
- Department of Biology, Technische Universitat Darmstadt, Darmstadt, Germany
| | - D Cmarko
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - I Raška
- Institute of Cell Biology and Pathology, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| |
Collapse
|