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FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing

Authors
  • Hennion, Magali1, 2
  • Arbona, Jean-Michel3, 4
  • Lacroix, Laurent1
  • Cruaud, Corinne5
  • Theulot, Bertrand1
  • Tallec, Benoît Le1
  • Proux, Florence1
  • Wu, Xia1
  • Novikova, Elizaveta1
  • Engelen, Stefan5
  • Lemainque, Arnaud5
  • Audit, Benjamin3
  • Hyrien, Olivier1
  • 1 Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d’Ulm, Paris, 75005, France , Paris (France)
  • 2 Current address: Epigenetics and Cell Fate Center, CNRS, Université de Paris, 35 rue Hélène Brion, Paris, 75013, France , Paris (France)
  • 3 Université de Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, Lyon, 69342, France , Lyon (France)
  • 4 Current address: Laboratory of Biology and Modelling of the Cell, Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, 46 Allée d’Italie Site Jacques Monod, Lyon, 69007, France , Lyon (France)
  • 5 Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Institut de biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, Evry, 91057, France , Evry (France)
Type
Published Article
Publication Date
May 26, 2020
Volume
21
Issue
1
Identifiers
DOI: 10.1186/s13059-020-02013-3
Source
Springer Nature
Keywords
License
Green

Abstract

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4964 and 4485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.

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