Cell-type-specific replication initiation programs set fragility of the fra3b fragile site

ABSTRACT Common fragile sites have long been identified by cytogeneticists as chromosomal regions prone to breakage upon replication stress1. They are increasingly recognized to be

preferential targets for oncogene-induced DNA damage in pre-neoplastic lesions2 and hotspots for chromosomal rearrangements in various cancers3. Common fragile site instability was

attributed to the fact that they contain sequences prone to form secondary structures that may impair replication fork movement, possibly leading to fork collapse resulting in DNA breaks4.

Here we show, in contrast to this view, that the fragility of _FRA3B_—the most active common fragile site in human lymphocytes—does not rely on fork slowing or stalling but on a paucity of

initiation events. Indeed, in lymphoblastoid cells, but not in fibroblasts, initiation events are excluded from a _FRA3B_ core extending approximately 700 kilobases, which forces forks

coming from flanking regions to cover long distances in order to complete replication. We also show that origins of the flanking regions fire in mid-S phase, leaving the site incompletely

replicated upon fork slowing. Notably, _FRA3B_ instability is specific to cells showing this particular initiation pattern. The fact that both origin setting5,6 and replication timing are

highly plastic7,8 in mammalian cells explains the tissue specificity of common fragile site instability we observed. Thus, we propose that common fragile sites correspond to the latest

initiation-poor regions to complete replication in a given cell type. For historical reasons, common fragile sites have been essentially mapped in lymphocytes1. Therefore, common fragile

site contribution to chromosomal rearrangements in tumours should be reassessed after mapping fragile sites in the cell type from which each tumour originates. Access through your

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BEING VIEWED BY OTHERS 3D GENOME ORGANIZATION CONTRIBUTES TO GENOME INSTABILITY AT FRAGILE SITES Article Open access 17 July 2020 MISTIMED ORIGIN LICENSING AND ACTIVATION STABILIZE COMMON

FRAGILE SITES UNDER TIGHT DNA-REPLICATION CHECKPOINT ACTIVATION Article 06 April 2023 REPLICATION STRESS INDUCES POLQ-MEDIATED STRUCTURAL VARIANT FORMATION THROUGHOUT COMMON FRAGILE SITES

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and Environment for Statistical Computing_ (R Foundation for Statistical Computing, 2006) Download references ACKNOWLEDGEMENTS We thank E. Blackburn for critical reading of the manuscript.

We thank Genomic Vision for making the DNA combing technology available to us. We acknowledge the Nikon Imaging Centre at Institut Curie-CNRS. We thank C. Rouzaud for help in combing

experiments. A.L. is supported by a grant from the ARC (Association pour la recherche sur le cancer). The M.D. team is supported by La Ligue Nationale contre le Cancer (LNCC) (Equipe

Labellisée EL2008.LNCC/MD), INCa (Institut National du Cancer) (2009-1-PLBIO-10-IC-1) and the PIC Réplication, Instabilité Chromosomique et Cancer (Institut Curie). AUTHOR INFORMATION Author

notes * Stéphane Koundrioukoff, Anne-Marie Lachagès and Nicolas Vogt: These authors contributed equally to this work. AUTHORS AND AFFILIATIONS * Institut Curie, Centre de Recherche, 26 rue

d’Ulm, 75248 Paris, France , Anne Letessier, Gaël A. Millot, Stéphane Koundrioukoff, Anne-Marie Lachagès, Nicolas Vogt, Bernard Malfoy, Olivier Brison & Michelle Debatisse * UPMC Univ.

Paris 06, F-75005 Paris, France , Anne Letessier, Gaël A. Millot, Stéphane Koundrioukoff, Anne-Marie Lachagès, Nicolas Vogt, Bernard Malfoy, Olivier Brison & Michelle Debatisse * CNRS

UMR 3244, F-75248 Paris, France , Anne Letessier, Gaël A. Millot, Stéphane Koundrioukoff, Anne-Marie Lachagès, Nicolas Vogt, Bernard Malfoy, Olivier Brison & Michelle Debatisse *

Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, 98195, Washington, USA R. Scott Hansen Authors * Anne Letessier View author

publications You can also search for this author inPubMed Google Scholar * Gaël A. Millot View author publications You can also search for this author inPubMed Google Scholar * Stéphane

Koundrioukoff View author publications You can also search for this author inPubMed Google Scholar * Anne-Marie Lachagès View author publications You can also search for this author inPubMed

 Google Scholar * Nicolas Vogt View author publications You can also search for this author inPubMed Google Scholar * R. Scott Hansen View author publications You can also search for this

author inPubMed Google Scholar * Bernard Malfoy View author publications You can also search for this author inPubMed Google Scholar * Olivier Brison View author publications You can also

search for this author inPubMed Google Scholar * Michelle Debatisse View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS A.L. performed and

analysed combing experiments. G.A.M. performed statistical and Repli-Seq analyses. S.K., A.-M.L. and O.B. performed cytogenetic analyses. N.V. and B.M. designed the Morse code. R.S.H.

contributed to Repli-Seq analysis. A.L., G.A.M., O.B. and M.D. wrote the paper. M.D. planned the project. CORRESPONDING AUTHOR Correspondence to Michelle Debatisse. ETHICS DECLARATIONS

COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION The file contains Supplementary Figures 1-9 with legends and

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ABOUT THIS ARTICLE CITE THIS ARTICLE Letessier, A., Millot, G., Koundrioukoff, S. _et al._ Cell-type-specific replication initiation programs set fragility of the _FRA3B_ fragile site.

_Nature_ 470, 120–123 (2011). https://doi.org/10.1038/nature09745 Download citation * Received: 24 September 2010 * Accepted: 08 December 2010 * Published: 23 January 2011 * Issue Date: 03

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