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Genome-wide mapping of individual replication fork velocities using nanopore sequencing

Author

Listed:
  • Bertrand Theulot

    (Université PSL
    Sorbonne Université, Collège Doctoral)

  • Laurent Lacroix

    (Université PSL)

  • Jean-Michel Arbona

    (Université Claude Bernard Lyon 1)

  • Gael A. Millot

    (Université Paris Cité, Bioinformatics and Biostatistics Hub)

  • Etienne Jean

    (Université PSL)

  • Corinne Cruaud

    (Université Paris-Saclay)

  • Jade Pellet

    (Université PSL)

  • Florence Proux

    (Université PSL)

  • Magali Hennion

    (Université Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS)

  • Stefan Engelen

    (Univ. Evry, Université Paris-Saclay)

  • Arnaud Lemainque

    (Université Paris-Saclay)

  • Benjamin Audit

    (ENSL, CNRS, Laboratoire de physique)

  • Olivier Hyrien

    (Université PSL)

  • Benoît Tallec

    (Université PSL)

Abstract

Little is known about replication fork velocity variations along eukaryotic genomes, since reference techniques to determine fork speed either provide no sequence information or suffer from low throughput. Here we present NanoForkSpeed, a nanopore sequencing-based method to map and extract the velocity of individual forks detected as tracks of the thymidine analogue bromodeoxyuridine incorporated during a brief pulse-labelling of asynchronously growing cells. NanoForkSpeed retrieves previous Saccharomyces cerevisiae mean fork speed estimates (≈2 kb/min) in the BT1 strain exhibiting highly efficient bromodeoxyuridine incorporation and wild-type growth, and precisely quantifies speed changes in cells with altered replisome progression or exposed to hydroxyurea. The positioning of >125,000 fork velocities provides a genome-wide map of fork progression based on individual fork rates, showing a uniform fork speed across yeast chromosomes except for a marked slowdown at known pausing sites.

Suggested Citation

  • Bertrand Theulot & Laurent Lacroix & Jean-Michel Arbona & Gael A. Millot & Etienne Jean & Corinne Cruaud & Jade Pellet & Florence Proux & Magali Hennion & Stefan Engelen & Arnaud Lemainque & Benjamin , 2022. "Genome-wide mapping of individual replication fork velocities using nanopore sequencing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31012-0
    DOI: 10.1038/s41467-022-31012-0
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    References listed on IDEAS

    as
    1. Michael Lawrence & Wolfgang Huber & Hervé Pagès & Patrick Aboyoun & Marc Carlson & Robert Gentleman & Martin T Morgan & Vincent J Carey, 2013. "Software for Computing and Annotating Genomic Ranges," PLOS Computational Biology, Public Library of Science, vol. 9(8), pages 1-10, August.
    2. Morgane Macheret & Thanos D. Halazonetis, 2018. "Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress," Nature, Nature, vol. 555(7694), pages 112-116, March.
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