Publications
2018
Mapping DNA replication with nanopore sequencing.
Hennion M, Arbona JM, Cruaud C, Proux F, Le Tallec B, Novikova E, Engelen S, Lemainque A, Audit B, Hyrien O (2018) BioRxiv, Sep 25, 2018, doi : 10.1101/426858.
The eukaryotic bell-shaped temporal rate of DNA replication origin firing emanates from a balance between origin activation and passivation.
Arbona JM, Goldar A, Hyrien O, Arneodo A, Audit B (2018)
High-throughput optical mapping of replicating DNA.
De Carli F*, Menezes N*, Berrabah W, Barbe V, Genovesio A, Hyrien O (2018)Small Methods, 2018, Sep 11 ; 2(9):1800146, doi : 10.1002/smtd.201800146. * co-premiers auteurs.
Dual roles of poly(dA:dT) tracts in replication initiation and fork collapse.
Tubbs A, Sridharan S, van Wietmarschen N, Maman Y, Callen E, Stanlie A, Wu X, Yin M, Canela A, Fu H, Redon C, Pruitt SC, Jaszczynszyn Y, Aladjem MI, Aplan PD, Hyrien O, Nussenzweig A (2018),Cell, 174 (5) 1127-1142.
Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions.
Wu X*, Kabalane H*, Kahli M, Petryk N, Laperrousaz B, Jaszczyszyn Y, Drillon G, Nicolini FE, Perot G, Robert A, Fund C, Chibon F, Xia R, Wiels J, Argoul F, Maguer-Satta V, Arneodo A, Audit B, and Hyrien O (2018),Nucleic Acids Res., Nov 2 ; 46(19):10157-10172. doi : 10.1093/nar/gky797. * co-premiers auteurs.
2016
Single-molecule, antibody-free fluorescent visualisation of replication tracts along barcoded DNA molecules.
De Carli F, Gaggioli V, Millot G, Hyrien O (2016) Int. J. Dev. Biol., 60(7-8-9):297-304
How MCM loading and spreading specify eukaryotic DNA replication initiation sites.
Hyrien O (2016).F1000Research 2016, 5(F1000 Faculty Rev):2063 (doi : 10.12688/f1000research.9008.1)
Genome-wide alterations of the DNA replication program during tumor progression.
Arneodo A, Goldar A, Argoul F, Hyrien O, Audit B (2016).AIP Conference Proceedings 1760, 020002 (2016) ; doi : 10.1063/1.4960221
Deciphering DNA replication dynamics in eukaryote cell populations in relation to their averaged chromatin conformations.
Goldar A, Arneodo A, Audit B, Argoul F, Rappailles A, Guilbaud G, Petryk N, Kahli M, Hyrien O (2016). Sci. Rep., 6, 22469.
Replication landscape of the human genome.
Petryk N, Kahli M, d’Aubenton-Carafa Y, Jaszczyszyn Y, Shen Y, Sylvain M, Thermes C, Chen CL, Hyrien O (2016). Nature Comm., 7, 10208.
Up and down the slope : replication timing and fork directionality gradients in eukaryotic genomes.
Hyrien O (2016) In "The Initiation of DNA Replication in Eukaryotes" (Ed. D. Kaplan), Springer, e-Book ISBN 978-3-319-24696-3 ; Hardcover ISBN 978-3-319-24694-9.
2015
Peaks cloaked in the mist : The landscape of mammalian replication origins.
Hyrien O (2015) J. Cell Biol., 208, 147-160.
2014
From the chromatin interaction network to the organization of the human genome into replication N/U-domains.
Boulos RE, Julienne H, Baker A, Chen CL, Petryk N, Kahli M, d’Aubenton-Carafa Y, Goldar A, Jensen P, Hyrien O, Thermes C, Arneodo A, Audit B (2014) . New J. Phys.,16, 115014.
2013
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm.
Audit B, Baker A, Chen CL, Rappailles A, Guilbaud G, Julienne H, Goldar A, d’Aubenton-Carafa Y, Hyrien O, Thermes C, Arneodo A (2013) Nature Protocols, 8, 98-110.
Cdc45 is a critical effector of Myc-dependent DNA replication stress.
Srinivasan S, Wang LC, Hyrien O, Gautier J Cell Reports, (2013) 3, 1629-39.
DNA topoisomerase IIα controls replication origin cluster licensing and firing time.
Gaggioli V*, Le Viet B*, Germe T, Hyrien O Nucleic Acids Res., (2013) 41, 7313-7331.
* co-premiers auteurs.
From simple bacterial and archaeal replicons to replication N/U-domains.
Hyrien O, Rappailles A, Guilbaud G, Baker A, Chen CL, Goldar A, Petryk N, Kahli M, Ma E, d’Aubenton-Carafa Y, Audit B, Thermes C, Arneodo A (2013). J. Mol. Biol., 425, 4673-89.
2012
Replication fork polarity gradients revealed by megabase-sized replication timing domains in human cell lines.
Baker A, Audit B, Chen CL, Moindrot B, Leleu A, Guilbaud G, Rappailles A, Vaillant C, Goldar A, Mongelard F, d’Aubenton-Carafa Y, Hyrien O, Thermes C, & Arneodo A (2012). PLoS Comput. Biol. 8(4) : e1002443.
Do replication forks control late origin firing in Saccharomyces cerevisiae ?
Ma E, Hyrien O, Goldar A (2012). Nucleic Acids Res. 40(5):2010-2019.
2011
Replication fork stalling and processing at a single psoralen DNA interstrand crosslink in Xenopus egg extracts.
Le Breton C, Hennion M, Arimondo PB, Hyrien O (2011). PLoS ONE, 6, e18554.
Replication-associated mutational asymmetry in the human genome.
Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d’Aubenton-Carafa Y, Hyrien O, Arneodo A, Thermes C Mol Biol Evol, (2011) 28, 2327-2337.
Evidence for sequential and increasing origin activation along replication timing gradients in the human genome.
Guilbaud G*, Rappailles A*, Baker A, Chen CL, Arneodo A, Goldar A, d’Aubenton-Carafa Y, Thermes C, Audit B, & Hyrien O PLoS Comput. Biol. (2011) 7(12) : e1002322. * co-premiers auteurs.
2010
ATR/Chk1 pathway is essential for resumption of DNA synthesis and cell survival in UV-irradiated XP variant cells.
Despras E, Daboussi F, Hyrien O, Marheineke K & Kannouche PL (2010) Hum Mol Genet. 19, 1690-1701.
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes.
Chen C-L, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d’Aubenton-Carafa Y, Arneodo A, Hyrien O, Thermes C (2010). Genome Res., 20, 447-57.
Mathematical modelling of eukaryotic DNA replication.
Hyrien O, Goldar A (2010). Chromosome Res., 18, 147-161.
2009
Non-coding Y RNAs are required for the establishment of mammalian chromosomal DNA replication forks.
Krude T, Christov CP, Hyrien O, Marheineke K (2009) J. Cell Sci, 122, 2836-2845.
Universal temporal profile of replication origin activation in eukaryotes.
Goldar A, Marsolier-Kergoat M-C, Hyrien O (2009). PLoS ONE, 4, e5899.
Topological analysis of plasmid DNA replication intermediates using two-dimensional agarose gels.
Hyrien O (2009). In Vengrova, Sonya & Dalgaard, Jacob Z, DNA Replication, Methods and Protocols, Humana Press, Methods Mol. Biol., vol. 521, ISBN : 978-1-60327-814-0, pp. 139-167.
Use of DNA combing to study DNA replication in Xenopus and human cell-free systems.
Marheineke K, Goldar A, Krude T, Hyrien O (2009) In Vengrova, Sonya & Dalgaard, Jacob Z, DNA Replication, Methods and Protocols, Humana Press, Methods Mol. Biol., vol. 521, ISBN : 978-1-60327-814-0, pp. 575-603.
2008
An optimized easy method for preparing silanized sufaces for FISH and replication mapping on combed DNA fibers.
Labit H, Goldar A, Guilbaud G, Douarche C, Hyrien O, Marheineke K (2008). Biotechniques, 45, 649-658.
DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts.
Labit H, Perewoska I, Germe T, Hyrien O, Marheineke K (2008) Nucleic Acids Res., 36, 5623-5634.
A dynamic stochastic model for DNA replication initiation in early embryos.
Goldar A, Labit H, Marheineke K, Hyrien O (2008). PLoS ONE, 3, e2919
2006
Broadening of DNA replication origin usage during metazoan cell differentiation.
Dazy S, Gandrillon O, Hyrien O, Prioleau MN (2006) EMBO Reports, 7, 806-811.
Proliferating human cells hypomorphic for Orc2 and pre-RC formation have a defect in p53 activation and CDK2 kinase activation.
Teer JK, Machida YJ, Labit H, Novac O, Hyrien O, Marheineke K, Zannis-Hadjopoulos M, Dutta A (2006). J. Biol. Chem., 281, 6253-6260.
2005
Visualisation of bidirectional initiation of chromosomal DNA replication in the human in vitro cell free system.
Marheineke K, Hyrien O, Krude T (2005) Nucleic Acids Res., 33, 6931-6941.
Topoisomerase II-DNA complexes trapped by ICRF-193 perturb chromatin structure.
Germe T, Hyrien O (2005). EMBO Reports, 6, 729-735.
2004
Xenopus egg extracts as a model system for understanding the role of topoisomerase II in the chromosome cycle.
Hyrien O, Germe T (2004). Recent Dev. Nucleic Acids Res., 1, 75-101.
Control of replication origin density and firing time in Xenopus egg extracts : role of a caffeine-sensitive, ATR-dependent checkpoint.
Marheineke K, Hyrien O (2004) J. Biol. Chem., 27, 28071-28081.
2003
Replication of the chicken β-globin locus : early-firing origins at the 5’HS4 insulator and the ρ- and βA- globin genes show opposite epigenetic modifications.
Prioleau MN, Gendron MC, Hyrien O (2003). Mol. Cell. Biol., 23, 3536-3549.
Paradoxes of eukaryotic DNA replication : MCM proteins and the random completion problem.
Hyrien O , Marheineke K, Goldar A (2003) BioEssays, 25, 116-125.
2002
Site-specific and temporally controlled initiation of DNA replication in a human cell-free system.
Keller C, Hyrien O, Knippers R, Krude T (2002) Nucleic Acids Res. 30:2114-2123.
2001
Topoisomerase II can unlink replicating DNA by precatenane removal.
Lucas I, Germe T, Chevrier-Miller M, Hyrien O (2001) EMBO J. 20, 6509-6519.
Aphidicolin triggers a block to replication origin firing in Xenopus egg extracts.
Marheineke K, Hyrien O (2001). J. Biol. Chem., 276, 17092-17100.
2000
Hemicatenation of DNA upon inhibition of DNA replication.
Lucas I, Hyrien O (2000). Nucleic Acids Res., 28, 2187-2193.
Replication fork density increases during DNA synthesis in X. laevis egg extracts.
Herrick J, Stanislawski P, Hyrien O, Bensimon A (2000). J. Mol Biol. 300, 1133-1142.
Bi-directional replication and random termination.
Santamaría D, Viguera E, Martínez-Robles ML, Hyrien O, P.Hernández, Krimer DB, Schvartzman JB (2000). Nucleic Acids Res., 28, 2099-2107.
Mechanisms and consequences of replication fork arrest.
Hyrien O (2000). Biochimie, 82, 5-17.
Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos.
Lucas I, Chevrier-Miller M, Sogo JM, Hyrien, O. (2000). J Mol Biol, 296, 769-786.
1999
Developmental regulation of replication fork pausing in Xenopus laevis ribosomal RNA genes.
Maric C, Levacher B, Hyrien, O. (1999). J Mol Biol, 291, 775-788.
1998
Topological complexity of different populations of pBR322 as visualized by two-dimensional agarose gel electrophoresis.
Martin-Parras L, Lucas I, Martinez-Robles ML, Hernandez P, Krimer DB, Hyrien O, Schvartzman JB (1998) Nucleic Acids Res, 26, 3424-3432
Remodeling of chromatin loops does not account for specification of replication origins during Xenopus development.
Maric C, Hyrien, O. (1998). Chromosoma, 107, 155-165.
1997
Role of nuclear architecture in the initiation of eukaryotic DNA replication.
Hyrien O, Maric C, Lucas I (1997). Biochimie, 79, 541-548.
1995
Transition in specification of embryonic metazoan DNA replication origins.
Hyrien O, Maric C, Méchali M (1995) Science 270, 994-997.
