B. Pope, I. Hiratani, and D. Gilbert, Domain-wide regulation of DNA replication timing during mammalian development, Chromosome Research, vol.420, issue.9, pp.127-136, 2010.
DOI : 10.1007/s10577-009-9100-8

H. Masai, S. Matsumoto, Z. You, N. Yoshizawa-sugata, and M. Oda, Eukaryotic Chromosome DNA Replication: Where, When, and How?, Annual Review of Biochemistry, vol.79, issue.1, pp.89-130, 2010.
DOI : 10.1146/annurev.biochem.052308.103205

J. Hamlin, L. Mesner, O. Lar, R. Torres, and S. Chodaparambil, A revisionist replicon model for higher eukaryotic genomes, Journal of Cellular Biochemistry, vol.24, issue.2, pp.321-329, 2008.
DOI : 10.1002/jcb.21828

M. Raghuraman, E. Winzeler, D. Collingwood, S. Hunt, and L. Wodicka, Replication Dynamics of the Yeast Genome, Science, vol.294, issue.5540, pp.115-121, 2001.
DOI : 10.1126/science.294.5540.115

I. Hiratani, T. Ryba, M. Itoh, J. Rathjen, and M. Kulik, Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis, Genome Research, vol.20, issue.2, pp.155-169, 2010.
DOI : 10.1101/gr.099796.109

C. Heichinger, C. Penkett, J. Bahler, and P. Nurse, Genome-wide characterization of fission yeast DNA replication origins, The EMBO Journal, vol.7, issue.21, pp.5171-5179, 2006.
DOI : 10.1038/sj.emboj.7601390

D. Macalpine, H. Rodriguez, and S. Bell, Coordination of replication and transcription along a Drosophila chromosome, Genes & Development, vol.18, issue.24, pp.3094-3105, 2004.
DOI : 10.1101/gad.1246404

I. Hiratani, T. Ryba, M. Itoh, T. Yokochi, and M. Schwaiger, Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation, PLoS Biology, vol.377, issue.10, p.245, 2008.
DOI : 10.1371/journal.pbio.0060245.st001

R. Desprat, D. Thierry-mieg, N. Lailler, J. Lajugie, and C. Schildkraut, Predictable dynamic program of timing of DNA replication in human cells, Genome Research, vol.19, issue.12, pp.2288-2299, 2009.
DOI : 10.1101/gr.094060.109

K. Woodfine, H. Fiegler, D. Beare, J. Collins, and O. Mccann, Replication timing of the human genome, Human Molecular Genetics, vol.13, issue.2, pp.191-202, 2004.
DOI : 10.1093/hmg/ddh016

S. Farkash-amar, D. Lipson, A. Polten, A. Goren, and C. Helmstetter, Global organization of replication time zones of the mouse genome, Genome Research, vol.18, issue.10, pp.1562-1570, 2008.
DOI : 10.1101/gr.079566.108

C. Chen, A. Rappailles, L. Duquenne, M. Huvet, and G. Guilbaud, Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes, Genome Research, vol.20, issue.4, pp.447-457, 2010.
DOI : 10.1101/gr.098947.109

URL : https://hal.archives-ouvertes.fr/ensl-00517756

R. Hansen, S. Thomas, R. Sandstrom, T. Canfield, and R. Thurman, Sequencing newly replicated DNA reveals widespread plasticity in human replication timing, Proceedings of the National Academy of Sciences, vol.107, issue.1, pp.139-144, 2010.
DOI : 10.1073/pnas.0912402107

T. Ryba, I. Hiratani, J. Lu, M. Itoh, and M. Kulik, Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types, Genome Research, vol.20, issue.6, pp.761-770, 2010.
DOI : 10.1101/gr.099655.109

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877573

M. Yamashita, Y. Hori, T. Shinomiya, C. Obuse, and T. Tsurimoto, chromosome VI, Genes to Cells, vol.2, issue.11, pp.655-665, 1997.
DOI : 10.1046/j.1365-2443.1997.1530351.x

K. Friedman, B. Brewer, and W. Fangman, chromosome VI, Genes to Cells, vol.2, issue.11, pp.667-678, 1997.
DOI : 10.1046/j.1365-2443.1997.1520350.x

D. Czajkowsky, J. Liu, J. Hamlin, and Z. Shao, DNA Combing Reveals Intrinsic Temporal Disorder in the Replication of Yeast Chromosome VI, Journal of Molecular Biology, vol.375, issue.1, pp.12-19, 2008.
DOI : 10.1016/j.jmb.2007.10.046

P. Patel, B. Arcangioli, S. Baker, A. Bensimon, and N. Rhind, DNA Replication Origins Fire Stochastically in Fission Yeast, Molecular Biology of the Cell, vol.17, issue.1, pp.308-316, 2006.
DOI : 10.1091/mbc.E05-07-0657

N. Rhind, S. Yang, and J. Bechhoefer, Reconciling stochastic origin firing with defined replication timing, Chromosome Research, vol.78, issue.4, pp.35-43, 2010.
DOI : 10.1007/s10577-009-9093-3

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862975

S. Yang, N. Rhind, and J. Bechhoefer, Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing, Molecular Systems Biology, vol.73, p.404, 2010.
DOI : 10.1038/msb.2010.61

O. Hyrien and A. Goldar, Mathematical modelling of eukaryotic DNA replication, Chromosome Research, vol.102, issue.1, pp.147-161, 2010.
DOI : 10.1007/s10577-009-9092-4

A. De-moura, R. Retkute, M. Hawkins, and C. Nieduszynski, Mathematical modelling of whole chromosome replication, Nucleic Acids Research, vol.38, issue.17, pp.5623-5663, 2010.
DOI : 10.1093/nar/gkq343

R. Berezney, D. Dubey, and J. Huberman, Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci, Chromosoma, vol.108, issue.8, pp.471-484, 2000.
DOI : 10.1007/s004120050399

J. Huberman and A. Riggs, On the mechanism of DNA replication in mammalian chromosomes, Journal of Molecular Biology, vol.32, issue.2, pp.327-341, 1968.
DOI : 10.1016/0022-2836(68)90013-2

R. Hand, Regulation of DNA replication on subchromosomal units of mammalian cells, The Journal of Cell Biology, vol.64, issue.1, pp.89-97, 1975.
DOI : 10.1083/jcb.64.1.89

R. Hand, Eucaryotic DNA: Organization of the genome for replication, Cell, vol.15, issue.2, pp.317-325, 1978.
DOI : 10.1016/0092-8674(78)90001-6

D. Jackson and A. Pombo, Replicon Clusters Are Stable Units of Chromosome Structure: Evidence That Nuclear Organization Contributes to the Efficient Activation and Propagation of S Phase in Human Cells, The Journal of Cell Biology, vol.107, issue.6, pp.1285-1295, 1998.
DOI : 10.1083/jcb.130.6.1239

K. Marheineke and O. Hyrien, Control of Replication Origin Density and Firing Time in Xenopus Egg Extracts: ROLE OF A CAFFEINE-SENSITIVE, ATR-DEPENDENT CHECKPOINT, Journal of Biological Chemistry, vol.279, issue.27, pp.28071-28081, 2004.
DOI : 10.1074/jbc.M401574200

S. Jun, J. Herrick, A. Bensimon, and J. Bechhoefer, Persistence Length of Chromatin Determines Origin Spacing in Xenopus Early-Embryo DNA Replication: Quantitative Comparisons between Theory and Experiment, Cell Cycle, vol.3, issue.2, pp.223-229, 2004.
DOI : 10.4161/cc.3.2.655

J. Blow, P. Gillespie, D. Francis, and D. Jackson, Egg Extract Are 5???15 Kilobases Apart and Are Activated in Clusters That Fire at Different Times, The Journal of Cell Biology, vol.112, issue.1, pp.15-26, 2001.
DOI : 10.1126/science.275.5302.993

H. Nakamura, T. Morita, and C. Sato, Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus, Experimental Cell Research, vol.165, issue.2, pp.291-297, 1986.
DOI : 10.1016/0014-4827(86)90583-5

O. Keefe, R. Henderson, S. Spector, and D. , Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences, The Journal of Cell Biology, vol.116, issue.5, pp.1095-1110, 1992.
DOI : 10.1083/jcb.116.5.1095

D. Dimitrova and D. Gilbert, The Spatial Position and Replication Timing of Chromosomal Domains Are Both Established in Early G1 Phase, Molecular Cell, vol.4, issue.6, pp.983-993, 1999.
DOI : 10.1016/S1097-2765(00)80227-0

H. Ma, J. Samarabandu, R. Devdhar, R. Acharya, and P. Cheng, Spatial and Temporal Dynamics of DNA Replication Sites in Mammalian Cells, The Journal of Cell Biology, vol.1, issue.6, pp.1415-1425, 1998.
DOI : 10.1007/s004390050686

E. Manders, J. Stap, G. Brakenhoff, R. Van-driel, and J. Aten, Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy, J Cell Sci, vol.103, pp.857-862, 1992.

E. Manders, J. Stap, J. Strackee, R. Van-driel, and J. Aten, Dynamic Behavior of DNA Replication Domains, Experimental Cell Research, vol.226, issue.2, pp.328-335, 1996.
DOI : 10.1006/excr.1996.0233

D. Zink, T. Cremer, R. Saffrich, R. Fischer, and M. Trendelenburg, Structure and dynamics of human interphase chromosome territories in vivo, Human Genetics, vol.102, issue.2, pp.241-251, 1998.
DOI : 10.1007/s004390050686

N. Sadoni, M. Cardoso, E. Stelzer, H. Leonhardt, and D. Zink, Stable chromosomal units determine the spatial and temporal organization of DNA replication, Journal of Cell Science, vol.117, issue.22, pp.5353-5365, 2004.
DOI : 10.1242/jcs.01412

A. Sporbert, A. Gahl, R. Ankerhold, H. Leonhardt, and M. Cardoso, DNA Polymerase Clamp Shows Little Turnover at Established Replication Sites but Sequential De Novo Assembly at Adjacent Origin Clusters, Molecular Cell, vol.10, issue.6, pp.1355-1365, 2002.
DOI : 10.1016/S1097-2765(02)00729-3

URL : http://doi.org/10.1016/s1097-2765(02)00729-3

A. Maya-mendoza, P. Olivares-chauvet, A. Shaw, and D. Jackson, S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci, PLoS Genetics, vol.18, issue.4, p.1000900, 2010.
DOI : 10.1371/journal.pgen.1000900.s013

Z. Guan, C. Hughes, S. Kosiyatrakul, P. Norio, and R. Sen, Decreased replication origin activity in temporal transition regions, The Journal of Cell Biology, vol.18, issue.5, pp.623-635, 2009.
DOI : 10.1128/MCB.22.13.4876-4889.2002

P. Norio, S. Kosiyatrakul, Q. Yang, Z. Guan, and N. Brown, Progressive Activation of DNA Replication Initiation in Large Domains of the Immunoglobulin Heavy Chain Locus during B Cell Development, Molecular Cell, vol.20, issue.4, pp.575-587, 2005.
DOI : 10.1016/j.molcel.2005.10.029

O. Ermakova, L. Nguyen, R. Little, C. Chevillard, and R. Riblet, Evidence that a Single Replication Fork Proceeds from Early to Late Replicating Domains in the IgH Locus in a Non???B Cell Line, Molecular Cell, vol.3, issue.3, pp.321-330, 1999.
DOI : 10.1016/S1097-2765(00)80459-1

S. Farkash-amar and I. Simon, Genome-wide analysis of the replication program in mammals, Chromosome Research, vol.420, issue.1, pp.115-125, 2010.
DOI : 10.1007/s10577-009-9091-5

X. Michalet, R. Ekong, F. Fougerousse, S. Rousseaux, and C. Schurra, Dynamic Molecular Combing: Stretching the Whole Human Genome for High-Resolution Studies, Science, vol.277, issue.5331, pp.1518-1523, 1997.
DOI : 10.1126/science.277.5331.1518

K. Marheineke, A. Goldar, T. Krude, and O. Hyrien, Use of DNA combing to study DNA replication in Xenopus and human cell-free systems In, DNA Replication Methods and Protocols, pp.575-603, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00333227

S. Takebayashi, K. Sugimura, T. Saito, C. Sato, and Y. Fukushima, Regulation of replication at the R/G chromosomal band boundary and pericentromeric heterochromatin of mammalian cells, Experimental Cell Research, vol.304, issue.1, pp.162-174, 2005.
DOI : 10.1016/j.yexcr.2004.10.024

D. Housman and J. Huberman, Changes in the rate of DNA replication fork movement during S phase in mammalian cells, Journal of Molecular Biology, vol.94, issue.2, pp.173-181, 1975.
DOI : 10.1016/0022-2836(75)90076-5

J. Herrick and A. Bensimon, Global regulation of genome duplication in eukaryotes: an overview from the epifluorescence microscope, Chromosoma, vol.4, issue.9, pp.243-260, 2008.
DOI : 10.1007/s00412-007-0145-1

P. Rimmele, J. Komatsu, P. Hupe, C. Roulin, and E. Barillot, Spi-1/PU.1 Oncogene Accelerates DNA Replication Fork Elongation and Promotes Genetic Instability in the Absence of DNA Breakage, Cancer Research, vol.70, issue.17, pp.6757-6766, 2010.
DOI : 10.1158/0008-5472.CAN-09-4691

X. Ge, D. Jackson, and J. Blow, Dormant origins licensed by excess Mcm2 7 are required for human cells to survive replicative stress, Genes & Development, vol.21, issue.24, pp.3331-3341, 2007.
DOI : 10.1101/gad.457807

J. Malinsky, K. Koberna, D. Stanek, M. Masata, and I. Votruba, The supply of exogenous deoxyribonucleotides accelerates the speed of the replication fork in early S-phase, J Cell Sci, vol.114, pp.747-750, 2001.

S. Dazy, O. Gandrillon, O. Hyrien, and M. Prioleau, Broadening of DNA replication origin usage during metazoan cell differentiation, EMBO reports, vol.19, pp.806-811, 2006.
DOI : 10.1101/gad.1171404

URL : https://hal.archives-ouvertes.fr/hal-00090748

D. Gregoire, K. Brodolin, and M. Mechali, HoxB domain induction silences DNA replication origins in the locus and specifies a single origin at its boundary, EMBO reports, vol.10, pp.812-816, 2006.
DOI : 10.1128/MCB.24.8.3373-3386.2004

URL : https://hal.archives-ouvertes.fr/hal-00113404

A. Woodward, T. Gohler, M. Luciani, M. Oehlmann, and X. Ge, Excess Mcm2???7 license dormant origins of replication that can be used under conditions of replicative stress, The Journal of Cell Biology, vol.112, issue.5, pp.673-683, 2006.
DOI : 10.1126/science.280.5363.593

A. Bester, M. Roniger, Y. Oren, M. Im, and D. Sarni, Nucleotide Deficiency Promotes Genomic Instability in Early Stages of Cancer Development, Cell, vol.145, issue.3, pp.435-446, 2011.
DOI : 10.1016/j.cell.2011.03.044

C. Conti, B. Sacca, J. Herrick, C. Lalou, and Y. Pommier, Replication Fork Velocities at Adjacent Replication Origins Are Coordinately Modified during DNA Replication in Human Cells, Molecular Biology of the Cell, vol.18, issue.8, pp.3059-3067, 2007.
DOI : 10.1091/mbc.E06-08-0689

A. Letessier, G. Millot, S. Koundrioukoff, A. Lachages, and N. Vogt, Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site, Nature, vol.45, issue.7332, pp.120-123, 2011.
DOI : 10.1038/nature09745

N. Karnani, C. Taylor, A. Malhotra, and A. Dutta, Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas, Genome Research, vol.17, issue.6, pp.865-876, 2007.
DOI : 10.1101/gr.5427007

D. Gilbert, Evaluating genome-scale approaches to eukaryotic DNA replication, Nature Reviews Genetics, vol.4, issue.10, pp.673-684, 2010.
DOI : 10.1038/nrg2830

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2962615

S. Schultz, S. Desbordes, Z. Du, S. Kosiyatrakul, and I. Lipchina, Single-Molecule Analysis Reveals Changes in the DNA Replication Program for the POU5F1 Locus upon Human Embryonic Stem Cell Differentiation, Molecular and Cellular Biology, vol.30, issue.18, pp.4521-4534, 2010.
DOI : 10.1128/MCB.00380-10

L. Mesner, V. Valsakumar, N. Karnani, A. Dutta, and J. Hamlin, Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription, Genome Research, vol.21, issue.3, pp.377-389, 2011.
DOI : 10.1101/gr.111328.110

. Encode-project-consortium, E. Birney, J. Stamatoyannopoulos, A. Dutta, and R. Guigó, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, pp.799-816, 2007.

J. Cadoret, F. Meisch, V. Hassan-zadeh, I. Luyten, and C. Guillet, Genome-wide studies highlight indirect links between human replication origins and gene regulation, Proceedings of the National Academy of Sciences, vol.105, issue.41, pp.15837-15842, 2008.
DOI : 10.1073/pnas.0805208105

URL : https://hal.archives-ouvertes.fr/hal-00332341

A. Goren and H. Cedar, Replicating by the Clock, Nature Reviews Molecular Cell Biology, vol.4, issue.1, pp.25-32, 2003.
DOI : 10.1038/nrm1008

N. Gilbert, S. Boyle, H. Fiegler, K. Woodfine, and N. Carter, Chromatin Architecture of the Human Genome, Cell, vol.118, issue.5, pp.555-566, 2004.
DOI : 10.1016/j.cell.2004.08.011

B. Audit, L. Zaghloul, C. Vaillant, G. Chevereau, and Y. Aubenton-carafa, Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells, Nucleic Acids Research, vol.37, issue.18, pp.6064-6075, 2009.
DOI : 10.1093/nar/gkp631

A. Goldar, M. Marsolier-kergoat, and O. Hyrien, Universal Temporal Profile of Replication Origin Activation in Eukaryotes, PLoS ONE, vol.4, issue.6, p.5899, 2009.
DOI : 10.1371/journal.pone.0005899.g003

URL : https://hal.archives-ouvertes.fr/hal-00406221

E. Ma, O. Hyrien, and A. Goldar, Do replication forks control late origin firing in S. cerevisiae? Nucleic Acids Res;E-pub ahead of print, 2011.
DOI : 10.1093/nar/gkr982

URL : http://doi.org/10.1093/nar/gkr982

A. Goldar, H. Labit, K. Marheineke, and O. Hyrien, A Dynamic Stochastic Model for DNA Replication Initiation in Early Embryos, PLoS ONE, vol.108, issue.8, p.2919, 2008.
DOI : 10.1371/journal.pone.0002919.g009

URL : https://hal.archives-ouvertes.fr/hal-00333221

I. Lucas, M. Chevrier-miller, J. Sogo, and O. Hyrien, Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos, Journal of Molecular Biology, vol.296, issue.3, pp.769-786, 2000.
DOI : 10.1006/jmbi.2000.3500

R. Lebofsky, R. Heilig, M. Sonnleitner, J. Weissenbach, and A. Bensimon, DNA Replication Origin Interference Increases the Spacing between Initiation Events in Human Cells, Molecular Biology of the Cell, vol.17, issue.12, pp.5337-5345, 2006.
DOI : 10.1091/mbc.E06-04-0298

M. Anglana, F. Apiou, A. Bensimon, and M. Debatisse, Dynamics of DNA Replication in Mammalian Somatic Cells, Cell, vol.114, issue.3, pp.385-394, 2003.
DOI : 10.1016/S0092-8674(03)00569-5

O. Hyrien, K. Marheineke, and A. Goldar, Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem, BioEssays, vol.25, issue.2, pp.116-125, 2003.
DOI : 10.1002/bies.10208

J. Herrick, P. Stanislawski, O. Hyrien, and A. Bensimon, Replication fork density increases during DNA synthesis in X. laevis egg extracts11Edited by M. Yaniv, Journal of Molecular Biology, vol.300, issue.5, pp.1133-1142, 2000.
DOI : 10.1006/jmbi.2000.3930

J. Vincent, T. Kwong, and T. Tsukiyama, ATP-dependent chromatin remodeling shapes the DNA replication landscape, Nature Structural & Molecular Biology, vol.123, issue.5, pp.477-484, 2008.
DOI : 10.1093/nar/gkl758

D. Dimitrova and D. Gilbert, Temporally coordinated assembly and disassembly of replication factories in the absence of DNA synthesis, Nat Cell Biol, vol.2, pp.686-694, 2000.

H. Labit, A. Goldar, G. Guilbaud, C. Douarche, and O. Hyrien, A simple and optimized method of producing silanized surfaces for FISH and replication mapping on combed DNA fibers, BioTechniques, vol.45, issue.6, pp.649-658, 2008.
DOI : 10.2144/000113002

URL : https://hal.archives-ouvertes.fr/hal-00406204

A. Lengronne, P. Pasero, A. Bensimon, and E. Schwob, Monitoring S phase progression globally and locally using BrdU incorporation in TK+ yeast strains, Nucleic Acids Research, vol.29, issue.7, pp.1433-1442, 2001.
DOI : 10.1093/nar/29.7.1433

E. Despras, F. Daboussi, O. Hyrien, K. Marheineke, and P. Kannouche, ATR/Chk1 pathway is essential for resumption of DNA synthesis and cell survival in UV-irradiated XP variant cells, Human Molecular Genetics, vol.19, issue.9, pp.1690-1701, 2010.
DOI : 10.1093/hmg/ddq046

A. Bertuzzi, A. Gandolfi, A. Germani, and R. Vitelli, A general expression for sequential DNA-fluorescence histograms, Journal of Theoretical Biology, vol.102, issue.1, pp.55-67, 1983.
DOI : 10.1016/0022-5193(83)90262-X

S. Mallat, A Wavelet Tour in Signal Processing, 1998.

A. Arneodo, C. Vaillant, B. Audit, F. Argoul, and Y. Aubenton-carafa, Multi-scale coding of genomic information: From DNA sequence to genome structure and function, Physics Reports, vol.498, issue.2-3, pp.45-188, 2011.
DOI : 10.1016/j.physrep.2010.10.001

URL : https://hal.archives-ouvertes.fr/ensl-00572973

D. Karolchik, R. Baertsch, M. Diekhans, T. Furey, and A. Hinrichs, The UCSC Genome Browser Database, Nucleic Acids Research, vol.31, issue.1, pp.51-54, 2003.
DOI : 10.1093/nar/gkg129