Position	MCF,ENS
Email	sylvie.hermann chez bio.ens.psl.eu
Phone

Position	Doctorante
Email	simonin chez bio.ens.psl.eu
Phone

Publications

Olivier Hyrien — 2016-04-22T13:25:41Z

2025

The double life of mammalian DNA replication origins
Hyrien O, Guilbaud G, Krude T. Genes Dev. 2025 Mar 3 ;39(5-6):304-324. doi : 10.1101/gad.352227.124

Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming
Theulot B, Tourancheau A, Simonin Chavignier E, Jean E, Arbona JM, Audit B, Hyrien O, Lacroix L, Le Tallec B. Nat Commun. 2025 Jan 2 ;16(1):242. doi : 10.1038/s41467-024-55520-3

2023

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
Arbona JM, Kabalane H, Barbier J, Goldar A, Hyrien O, Audit B. PLoS Comput Biol. 2023 May 30 ;19(5):e1011138. doi : 10.1371/journal.pcbi.1011138

Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing
Wu X, Liu Y, d'Aubenton-Carafa Y, Thermes C, Hyrien O, Chen CL, Petryk N. Nat Protoc. 2023 Jan 18. doi : 10.1038/s41596-022-00793-5

2022

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths
Jean-Michel Arbona, Hadi Kabalane, Arach Goldar, Olivier Hyrien, Benjamin Audit. bioRxiv 2021.12.15.472795 ; https://doi.org/10.1101/2021.12.15.472795

Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers
DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep. 2022 Mar 22 ;38(12):110555. https://doi.org/10.1016/j.celrep.2022.110555.

Genome-wide mapping of individual replication fork velocities using nanopore sequencing
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 Audit, Olivier Hyrien & Benoît Le Tallec. Nature communications, 13(1), 3295. https://doi.org/10.1038/s41467-022-31012-0 *joint first authors

FORK-seq : Single-Molecule Profiling of DNA Replication
Magali Hennion, Bertrand Theulot, Jean-Michel Arbona, Benjamin Audit & Olivier Hyrien. Methods Mol Biol. 2022 ;2477:107-128. https://doi.org/10.1007/978-1-0716-2257-5_8

2021

Organization of DNA Replication Origin Firing in Xenopus Egg Extracts : The Role of Intra-S Checkpoint
Diletta Ciardo, Olivier Haccard,Hemalatha Narassimprakash, Jean-Michel Arbona, Olivier Hyrien, Benjamin Audit, Kathrin Marheineke and Arach Goldar. Genes, 12(8), 1224. https://doi.org/10.3390/genes12081224

DNA molecular combing-based replication fork directionality profiling
Marion Blin, Laurent Lacroix, Nataliya Petryk, Yan Jaszczyszyn, Chun-Long Chen, Olivier Hyrien, Benoît Le Tallec. Nucleic acids research, 49(12), e69. https://doi.org/10.1093/nar/gkab219

Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones
Nina Kirstein, Alexander Buschle, Xia Wu, Stefan Krebs, Helmut Blum, Elisabeth Kremmer, Ina M Vorberg, Wolfgang Hammerschmidt, Laurent Lacroix, Olivier Hyrien,Benjamin Audit, Aloys Schepers. Elife. 2021 Mar 8 ;10:e62161. doi : 10.7554/eLife.62161.

2020

FORK-seq : replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
Hennion M, Arbona JM, Lacroix L, Cruaud C, Theulot B, Le Tallec B, Proux F, Wu X, Novikova E, Engelen S, Lemainque A, Audit B, Hyrien O (2020) Genome Biol., 2020 May 26 ;21(1):125. doi : 10.1186/s13059-020-02013-3.

2018

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. Elife. 2018 ;7:e35192. Published 2018 Jun 1. doi:10.7554/eLife.35192

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. *joint first authors.

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. * joint first authors.

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.

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