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Laboratory DNA Replication and Genome Stability - LRS

Laboratoire de Cancérologie Expérimentale - LCE 

Principal investigator
Phone : +33 (0)1 46 54 84 27

Aurélie GOURET
Phone : +33 (0)1 46 54 98 66

Published on 17 March 2023

Genome integrity is constantly threatened by DNA damage originating from endogenous and environmental sources. If not promptly repaired, DNA lesions can block DNA replication and lead to replication stress, genome instability and ultimately tumorigenesis. At the same time, cancer therapy involves DNA damaging therapeutics such as cisplatin and ionizing radiation that cause replication stress. As replication stress is toxic to cells with unchecked growth, it is exploited therapeutically to kill cancer cells. However, one of the main challenges in cancer therapy remains resistance acquisition. Our overreaching goal is to understand how cells deal with replication stress, and how it impacts genome and epigenome stability as well as sensitivity to environmental insults and cancer treatments.


Cells have evolved mechanisms to respond to replication stress by tolerating DNA damage (Fig. 1). These mechanisms are a double-edge sword. On one hand, they ensure cell viability in conditions of replication stress. On the other hand, as they are potentially mutagenic, they can fuel carcinogenesis as well as contribute to the acquisition of resistance to DNA-damaging cancer therapeutics.

​Fig. 1 Mechanisms of DNA damage tolerance (Adapted from Quinet et al., 2021, credit to Dr. Meroni)

Through the development of novel single-molecule approaches based on the DNA fiber assay (Fig. 2), we have uncovered that human cells frequently employ the Repriming mechanism to respond to replication stress, at the expense of accumulating post-replicative single-stranded DNA (ssDNA) gaps (Quinet et al., 2016, 2020). We have also started deciphering the molecular bases of gap-filling mechanisms in human cells and how they impact genome stability and cell sensitivity to environmental insults and cancer therapy (Quinet et al., 2016, Tirman, Quinet et al., 2021).


Fig. 2 Single-molecule microcopy approaches based on the DNA fiber assay to study post-replicative ssDNA gap formation and repair. (A) S1-modified DNA fiber assay. The use of the ssDNA-specific S1 nuclease on the DNA fiber assay enables detection of ssDNA gaps undetectable by standard DNA fiber protocols by generating shorter tracts that are used as a read-out for the presence of gaps. (B). Gap filling or Post-Replicative Repair (PRR) assay. A thymidine analog is added to the cell culture media to be incorporated during gap filling allowing direct visualization and quantification of these events. Images adapted from Martins, Tirman et al., 2022.

By combining our previously established approaches with cutting edge microscopy, proteomics, and next-generation sequencing using human cells, we now aim at:

  • Defining the molecular steps of post-replicative ssDNA gap formation and repair
  • Elucidating the crosstalk between post-replicative gaps and chromatin dynamics
  • Investigating the response to replication stress induced by ionizing radiation and how it impacts cancer cells response to radiotherapy

Our long-term objective is to determine whether the expression of key replication stress response factors can be predictive of cancer cells response to therapy, and to identify novel strategies to improve current cancer treatments and overcome acquired resistance.

Our current projects are funded by an ATIP-Avenir grant (start date 01/01/2023), EDF (in collaboration with the team of Dr. Anna Campalans) and a Startup package for new Group leader from UMRE008/IRCM/IBFJ/CEA.

 ​Team                                                                                                                                                           Publications

​Major publications

Original articles

  1. Tirman S*, Quinet A*, Wood M, Meroni A, Cybulla E, Jackson J, Pegoraro S, Simoneau A, Zou L, Vindigni A. Temporally distinct post-replicative repair mechanisms fill PRIMPOL-dependent ssDNA gaps in human cells. Mol Cell. 2021 Oct 7;81(19):4026-404.e8 * authors contributed equally
  2.  Quinet A, Tirman S, Jackson J, Svikovic S, Lemacon D, Carvajal-Maldonado D, González-Acosta D, Vessoni AT, Cybulla E, Wood M, Tavis S, Batista LFZ, Méndez J, Sale JE, Vindigni A. PRIMPOL-mediated adaptive response suppresses replication fork reversal in BRCA-deficient cells. Mol Cell. 2020 Feb 6;77(3):1-14
  3. Chen B*, Quinet A*, Byrum AK, Jackson J, Berti M, Thangavel S, Bredemeyer AL, Hindi I, Mosammaparast N, Tyler JK, Vindigni A^, Sleckman BP^. XLF and H2AX function in series to promote replication fork stability. J Cell Biol. 2019 Jul 1;218(7):2113-2123 * authors contributed equally; ^ corresponding authors
  4. Quinet A*, Martins DJ, Vessoni AT, Biard D, Sarasin A, Stary A, Menck CFM*. Translesion synthesis mechanisms depend on the nature of DNA damage in UV-irradiated human cells. Nucleic Acids Res. 2016 Jul 8;44(12):5717-31 * corresponding authors
  5.  Quinet A*, Vessoni AT, Rocha CRR, Gottifredi V, Biard D, Sarasin A, Menck CFM*, Stary A. Gap-filling and bypass at the replication fork are both active mechanisms for tolerance of low-dose ultraviolet-induced DNA damage in the human genome. DNA Repair (Amst). 2014 Feb;14:27-38 * corresponding authors

Review articles

  1. Martins DJ*, Tirman S*, Quinet A^, Menck CFM^. Detection of post-replicative gaps accumulation and repair in human cells using the DNA fiber assay. J Vis Exp. 2022 Feb 3;(180) * authors contributed equally; ^ corresponding authors
  2. Quinet A, Tirman S, Cybulla E, Meroni A, Vindigni A. To skip or not to skip: choosing repriming to tolerate DNA damage. Mol Cell. 2021 Feb 18;81(4):649-658.
  3. Quinet A*, Lerner LK*, Martins DJ, Menck CFM. Filling gaps in translesion DNA synthesis in human cells. Mutat Res Genet Toxicol Environ Mutagen. 2018 Dec;836(Pt B):127-142. * authors contributed equally
  4. Quinet A, Vindigni A. Superfast DNA replication causes damage in cancer cells. Nature. 2018 Jul;559(7713):186-187
  5. Quinet A, Lemaçon D, Vindigni A. Replication fork reversal: players and guardians. Mol Cell. 2017 Dec 7;68(5):830-833
  6. Quinet A, Carvajal-Maldonado D, Lemaçon D, Vindigni A. DNA Fiber Analysis: Mind the Gap! Methods Enzymol, 2017;591:55-82