O. Ganier, P. Prorok, I. Akerman, and M. Mechali, Metazoan DNA replication origins, Curr. Opin. Cell Biol, vol.58, pp.134-141, 2019.

C. Cayrou, The chromatin environment shapes DNA replication origin organization and defines origin classes, Genome Res, vol.25, pp.1873-1885, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01240797

C. Cayrou, New insights into replication origin characteristics in metazoans, Cell Cycle, vol.11, pp.658-667, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00668750

C. Cayrou, Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
URL : https://hal.archives-ouvertes.fr/lirmm-00631491

, Genome Res, vol.21, pp.1438-1449, 2011.

F. Comoglio, High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins, Cell Rep, vol.11, pp.821-834, 2015.

L. Krasinska, Cdk1 and Cdk2 activity levels determine the efficiency of replication origin firing in Xenopus, EMBO J, vol.27, pp.758-769, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00266277

A. R. Langley, S. Graf, J. C. Smith, and T. Krude, Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq), Nucleic Acids Res, vol.44, pp.10230-10247, 2016.

A. Tubbs, Dual roles of poly(dA:dT) tracts in replication initiation and fork collapse, Cell, vol.174, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02184422

S. Delgado, M. Gomez, A. Bird, and F. Antequera, Initiation of DNA replication at CpG islands in mammalian chromosomes, EMBO J, vol.17, pp.2426-2435, 1998.

J. Sequeira-mendes, Transcription initiation activity sets replication origin efficiency in mammalian cells, PLoS Genet, vol.5, p.1000446, 2009.

C. Costas, Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks, Nat. Struct. Mol. Biol, vol.18, pp.395-400, 2011.

F. Picard, The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells, PLoS Genet, vol.10, p.1004282, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00995097

E. Besnard, Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs, Nat. Struct. Mol. Biol, vol.19, pp.837-844, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01338204

M. Mechali, Eukaryotic DNA replication origins: many choices for appropriate answers, Nat. Rev. Mol. Cell Biol, vol.11, pp.728-738, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00529311

M. M. Martin, Genome-wide depletion of replication initiation events in highly transcribed regions, Genome Res, vol.21, pp.1822-1832, 2011.

M. Gomez and N. Brockdorff, Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage, Proc. Natl Acad. Sci. USA, vol.101, pp.6923-6928, 2004.

O. K. Smith, Distinct epigenetic features of differentiation-regulated replication origins, Epigenet. Chromatin, vol.9, p.18, 2016.

M. Giacca, Fine mapping of a replication origin of human DNA, Proc. Natl Acad. Sci. USA, vol.91, pp.7119-7123, 1994.

L. Vassilev and E. M. Johnson, An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells, Mol. Cell Biol, vol.10, pp.4899-4904, 1990.

E. M. Ladenburger, C. Keller, and R. Knippers, Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication, Mol. Cell Biol, vol.22, pp.1036-1048, 2002.

T. Taira, S. M. Iguchi-ariga, and H. Ariga, A novel DNA replication origin identified in the human heat shock protein 70 gene promoter, Mol. Cell Biol, vol.14, pp.6386-6397, 1994.

C. Cayrou, D. Gregoire, P. Coulombe, E. Danis, and M. Mechali, Genomescale identification of active DNA replication origins, Methods, vol.57, pp.158-164, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00733286

N. Petryk, Replication landscape of the human genome, Nat. Commun, vol.7, p.10208, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01412672

G. I. Dellino, Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing, Genome Res, vol.23, pp.1-11, 2013.

B. Miotto, Z. Ji, and K. Struhl, Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers, Proc. Natl Acad. Sci. USA, vol.113, pp.4810-4819, 2016.
URL : https://hal.archives-ouvertes.fr/inserm-02132558

N. Sugimoto, K. Maehara, K. Yoshida, Y. Ohkawa, and M. Fujita, Genomewide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells, Nucleic Acids Res, vol.46, pp.6683-6696, 2018.

T. Takahashi, E. Ohara, H. Nishitani, and H. Masukata, Multiple ORC-binding sites are required for efficient MCM loading and origin firing in fission yeast, EMBO J, vol.22, pp.964-974, 2003.

V. S. Chambers, High-throughput sequencing of DNA G-quadruplex structures in the human genome, Nat. Biotechnol, vol.33, pp.877-881, 2015.

A. Bedrat, L. Lacroix, and J. L. Mergny, Re-evaluation of G-quadruplex propensity with G4Hunter, Nucleic Acids Res, vol.44, pp.1746-1759, 2016.

A. Mehanna and J. F. Diffley, Pre-replicative complex assembly with purified proteins, Methods, vol.57, pp.222-226, 2012.

A. Fernandez-cid, An ORC/Cdc6/MCM2-7 complex is formed in a multistep reaction to serve as a platform for MCM double-hexamer assembly, Mol. Cell, vol.50, pp.577-588, 2013.

S. A. Samel, A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2-7 onto DNA, Genes Dev, vol.28, pp.1653-1666, 2014.

G. Coster and J. F. Diffley, Bidirectional eukaryotic DNA replication is established by quasi-symmetrical helicase loading, Science, vol.357, pp.314-318, 2017.

C. Pridgeon and D. Corne, Hypermotifs: Novel discriminatory patterns for nucleotide sequences and their application to core promoter prediction in eukaryotes, Proc. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp.420-426, 2005.

F. Massip, Evolution of replication origins in vertebrate genomes: rapid turnover despite selective constraints, Nucleic Acids Res, vol.47, pp.5114-5125, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02349718

E. Danis, Specification of a DNA replication origin by a transcription complex, Nat. Cell Biol, vol.6, pp.721-730, 2004.

M. S. Valenzuela, Preferential localization of human origins of DNA replication at the 5?-ends of expressed genes and at evolutionarily conserved DNA sequences, PLoS ONE, vol.6, p.17308, 2011.

N. Karnani, C. M. Taylor, A. Malhotra, and A. Dutta, Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection, Mol. Biol. Cell, vol.21, pp.393-404, 2010.

L. D. Mesner, Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription, Genome Res, vol.21, pp.377-389, 2011.

J. C. Cadoret, Genome-wide studies highlight indirect links between human replication origins and gene regulation, Proc. Natl Acad. Sci. USA, vol.105, pp.15837-15842, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00332341

C. Y. Mclean, GREAT improves functional interpretation of cisregulatory regions, Nat. Biotechnol, vol.28, pp.495-155, 2010.

C. Fonti and A. S. , Distinct oncogenes drive different genome and epigenome alterations in human mammary epithelial cells, Int. J Cancer, vol.145, pp.1299-1311
URL : https://hal.archives-ouvertes.fr/inserm-02177754

J. R. Dixon, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, pp.376-380, 2012.

M. S. Foulk, J. M. Urban, C. Casella, and S. A. Gerbi, Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins, Genome Res, vol.25, pp.725-735, 2015.

J. T. Yeeles, T. D. Deegan, A. Janska, A. Early, and J. F. Diffley, Regulated eukaryotic DNA replication origin firing with purified proteins, Nature, vol.519, pp.431-435, 2015.

M. Fragkos, O. Ganier, P. Coulombe, and M. Mechali, DNA replication origin activation in space and time, Nat. Rev. Mol. Cell Biol, vol.16, pp.360-374, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01159618

S. Kolesnikova and E. A. Curtis, Structure and function of multimeric Gquadruplexes, 2019.

P. Prorok, Involvement of G-quadruplex regions in mammalian replication origin activity, Nat. Commun, vol.10, p.3274, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02194008

G. Shin, D. Jeong, H. Kim, J. S. Im, and J. Lee, RecQL4 tethering on the prereplicative complex induces unscheduled origin activation and replication stress in human cells, J. Biol. Chem, vol.294, pp.16255-16265, 2019.

M. N. Sangrithi, Initiation of DNA replication requires the RECQL4 protein mutated in Rothmund-Thomson syndrome, Cell, vol.121, pp.887-898, 2005.

K. Moriyama, N. Yoshizawa-sugata, and H. Masai, Oligomer formation and Gquadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture, J. Biol. Chem, vol.293, pp.3607-3624, 2018.

M. Kliszczak, Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells, Oncotarget, vol.6, pp.40464-40479, 2015.

H. Keller, The intrinsically disordered amino-terminal region of human RecQL4: multiple DNA-binding domains confer annealing, strand exchange and G4 DNA binding, Nucleic Acids Res, vol.42, pp.12614-12627, 2014.

A. L. Valton, G4 motifs affect origin positioning and efficiency in two vertebrate replicators, EMBO J, vol.33, pp.732-746, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00987430

X. Liu, W. L. Kraus, and X. Bai, Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways, Trends Biochem. Sci, vol.40, pp.516-525, 2015.

J. Cheneby, M. Gheorghe, M. Artufel, A. Mathelier, and B. Ballester, ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments, Nucleic Acids Res, vol.46, pp.267-275, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01646201

X. Wang, Targeting of polycomb repressive complex 2 to RNA by short repeats of consecutive guanines, Mol. Cell, vol.65, pp.1056-1067, 2017.

M. Beltran, G-tract RNA removes Polycomb repressive complex 2 from genes, Nat. Struct. Mol. Biol, vol.26, pp.899-909, 2019.

M. Macheret and T. D. Halazonetis, Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress, Nature, vol.555, pp.112-116, 2018.

R. Barbet, I. Peiffer, A. Hatzfeld, P. Charbord, and J. A. Hatzfeld, Comparison of gene expression in human embryonic stem cells, hESC-derived mesenchymal stem cells and human mesenchymal stem cells, Stem Cells Int, p.368192, 2011.

L. Oburoglu, Glucose and glutamine metabolism regulate human hematopoietic stem cell lineage specification, Cell Stem Cell, vol.15, pp.169-184, 2014.
URL : https://hal.archives-ouvertes.fr/hal-02191586

M. Rodriguez-martinez, The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans, Nat. Struct. Mol. Biol, vol.24, pp.290-299, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01488419

Y. Zhang, Model-based analysis of ChIP-Seq (MACS)

, Genome Biol, vol.9, p.137, 2008.

S. Xu, S. Grullon, K. Ge, and W. Peng, Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells, Methods Mol. Biol, vol.1150, pp.97-111, 2014.

S. Heinz, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, vol.38, pp.576-589, 2010.

Y. Zeng, C. Yi, and . Sparsesvm, Fit sparse linear SVM with lasso or elasti-net regularization, 2018.

B. D. Pope, Topologically associating domains are stable units of replication-timing regulation, Nature, vol.515, pp.402-405, 2014.