Metazoan DNA replication origins, Curr. Opin. Cell Biol, vol.58, pp.134-141, 2019. ,
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
New insights into replication origin characteristics in metazoans, Cell Cycle, vol.11, pp.658-667, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00668750
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.
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. ,
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
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. ,
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
Initiation of DNA replication at CpG islands in mammalian chromosomes, EMBO J, vol.17, pp.2426-2435, 1998. ,
Transcription initiation activity sets replication origin efficiency in mammalian cells, PLoS Genet, vol.5, p.1000446, 2009. ,
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. ,
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
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
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
Genome-wide depletion of replication initiation events in highly transcribed regions, Genome Res, vol.21, pp.1822-1832, 2011. ,
Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage, Proc. Natl Acad. Sci. USA, vol.101, pp.6923-6928, 2004. ,
Distinct epigenetic features of differentiation-regulated replication origins, Epigenet. Chromatin, vol.9, p.18, 2016. ,
Fine mapping of a replication origin of human DNA, Proc. Natl Acad. Sci. USA, vol.91, pp.7119-7123, 1994. ,
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. ,
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. ,
A novel DNA replication origin identified in the human heat shock protein 70 gene promoter, Mol. Cell Biol, vol.14, pp.6386-6397, 1994. ,
Genomescale identification of active DNA replication origins, Methods, vol.57, pp.158-164, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00733286
Replication landscape of the human genome, Nat. Commun, vol.7, p.10208, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01412672
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. ,
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
Genomewide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells, Nucleic Acids Res, vol.46, pp.6683-6696, 2018. ,
Multiple ORC-binding sites are required for efficient MCM loading and origin firing in fission yeast, EMBO J, vol.22, pp.964-974, 2003. ,
High-throughput sequencing of DNA G-quadruplex structures in the human genome, Nat. Biotechnol, vol.33, pp.877-881, 2015. ,
Re-evaluation of G-quadruplex propensity with G4Hunter, Nucleic Acids Res, vol.44, pp.1746-1759, 2016. ,
Pre-replicative complex assembly with purified proteins, Methods, vol.57, pp.222-226, 2012. ,
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. ,
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. ,
Bidirectional eukaryotic DNA replication is established by quasi-symmetrical helicase loading, Science, vol.357, pp.314-318, 2017. ,
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. ,
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
Specification of a DNA replication origin by a transcription complex, Nat. Cell Biol, vol.6, pp.721-730, 2004. ,
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. ,
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. ,
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. ,
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
GREAT improves functional interpretation of cisregulatory regions, Nat. Biotechnol, vol.28, pp.495-155, 2010. ,
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
Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, vol.485, pp.376-380, 2012. ,
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. ,
Regulated eukaryotic DNA replication origin firing with purified proteins, Nature, vol.519, pp.431-435, 2015. ,
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
Structure and function of multimeric Gquadruplexes, 2019. ,
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
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. ,
Initiation of DNA replication requires the RECQL4 protein mutated in Rothmund-Thomson syndrome, Cell, vol.121, pp.887-898, 2005. ,
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. ,
Interaction of RECQ4 and MCM10 is important for efficient DNA replication origin firing in human cells, Oncotarget, vol.6, pp.40464-40479, 2015. ,
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. ,
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
Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways, Trends Biochem. Sci, vol.40, pp.516-525, 2015. ,
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
Targeting of polycomb repressive complex 2 to RNA by short repeats of consecutive guanines, Mol. Cell, vol.65, pp.1056-1067, 2017. ,
G-tract RNA removes Polycomb repressive complex 2 from genes, Nat. Struct. Mol. Biol, vol.26, pp.899-909, 2019. ,
Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress, Nature, vol.555, pp.112-116, 2018. ,
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. ,
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
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
Model-based analysis of ChIP-Seq (MACS) ,
, Genome Biol, vol.9, p.137, 2008.
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. ,
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. ,
, Fit sparse linear SVM with lasso or elasti-net regularization, 2018.
Topologically associating domains are stable units of replication-timing regulation, Nature, vol.515, pp.402-405, 2014. ,