From simple bacterial and archaeal replicons to replication N/U-domains.
暂无分享,去创建一个
A. Arneodo | B. Audit | Y. D'Aubenton-Carafa | A. Goldar | Chun-long Chen | C. Thermes | O. Hyrien | A. Baker | N. Petryk | M. Kahli | A. Rappailles | G. Guilbaud | Émilie Ma | Malik Kahli | Aurélien Rappailles
[1] M. Debatisse,et al. Replication dynamics: biases and robustness of DNA fiber analysis. , 2013, Journal of molecular biology.
[2] Conrad A. Nieduszynski,et al. Accelerated growth in the absence of DNA replication origins , 2013, Nature.
[3] H. Masai,et al. Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing. , 2013, Trends in genetics : TIG.
[4] S. Bekiranov,et al. Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins , 2013, Genome research.
[5] O. Hyrien,et al. DNA topoisomerase IIα controls replication origin cluster licensing and firing time in Xenopus egg extracts , 2013, Nucleic acids research.
[6] J. Berger,et al. Mechanisms for initiating cellular DNA replication. , 2013, Annual review of biochemistry.
[7] D. Chattoraj,et al. Evidence for Two Different Regulatory Mechanisms Linking Replication and Segregation of Vibrio cholerae Chromosome II , 2013, PLoS genetics.
[8] M. Filutowicz,et al. Plasmid R6K replication control. , 2013, Plasmid.
[9] Duncan J. Smith,et al. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. , 2013, Molecular cell.
[10] J. Berger,et al. The Bacterial DnaC Helicase Loader Is a DnaB Ring Breaker , 2013, Cell.
[11] Todd A. Stone,et al. Specificity and Function of Archaeal DNA Replication Initiator Proteins , 2013, Cell reports.
[12] O. Aparicio,et al. Location, location, location: it's all in the timing for replication origins. , 2013, Genes & development.
[13] Alain Arneodo,et al. Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm , 2012, Nature Protocols.
[14] D. Sherratt,et al. Chromosome replication and segregation in bacteria. , 2012, Annual review of genetics.
[15] Alain Arneodo,et al. Gene organization inside replication domains in mammalian genomes , 2012 .
[16] K. Shirahige,et al. Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast. , 2012, Genes & development.
[17] Vishnu Dileep,et al. Mouse Rif1 is a key regulator of the replication‐timing programme in mammalian cells , 2012, The EMBO journal.
[18] Hisao Masai,et al. Rif1 regulates the replication timing domains on the human genome , 2012, The EMBO journal.
[19] Rolf Bernander,et al. Four chromosome replication origins in the archaeon Pyrobaculum calidifontis , 2012, Molecular microbiology.
[20] Alain Arneodo,et al. 3D chromatin conformation correlates with replication timing and is conserved in resting cells , 2012, Nucleic acids research.
[21] N. Rhind,et al. Replication timing and its emergence from stochastic processes. , 2012, Trends in genetics : TIG.
[22] J. Diffley,et al. Activation of the replicative DNA helicase: breaking up is hard to do. , 2012, Current opinion in cell biology.
[23] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[24] Benjamin Audit,et al. Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines , 2012, PLoS Comput. Biol..
[25] Jared M. Peace,et al. Forkhead Transcription Factors Establish Origin Timing and Long-Range Clustering in S. cerevisiae , 2012, Cell.
[26] Katsuhiko Shirahige,et al. Rif1 is a global regulator of timing of replication origin firing in fission yeast. , 2012, Genes & development.
[27] Olivier Hyrien,et al. Do replication forks control late origin firing in Saccharomyces cerevisiae? , 2011, Nucleic acids research.
[28] S. Bell. Archaeal orc1/cdc6 proteins. , 2012, Sub-cellular biochemistry.
[29] Ryuichiro Nakato,et al. Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing , 2011, Current Biology.
[30] Alain Arneodo,et al. Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome , 2011, PLoS Comput. Biol..
[31] A. Donaldson,et al. Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast , 2011, The EMBO journal.
[32] S. Bell,et al. Molecular machines in archaeal DNA replication. , 2011, Current opinion in chemical biology.
[33] J. Hurwitz,et al. Selective Bypass of a Lagging Strand Roadblock by the Eukaryotic Replicative DNA Helicase , 2011, Cell.
[34] J. Berger,et al. DNA stretching by bacterial initiators promotes replication origin melting , 2011, Nature.
[35] Alain Arneodo,et al. Replication-associated mutational asymmetry in the human genome. , 2011, Molecular biology and evolution.
[36] J. Hamlin,et al. Cdc45 Limits Replicon Usage from a Low Density of preRCs in Mammalian Cells , 2011, PloS one.
[37] Françoise Argoul,et al. Multi-scale coding of genomic information: From DNA sequence to genome structure and function , 2011 .
[38] David M. Gilbert,et al. Evaluating genome-scale approaches to eukaryotic DNA replication , 2010, Nature Reviews Genetics.
[39] M. Méchali,et al. Eukaryotic DNA replication origins: many choices for appropriate answers , 2010, Nature Reviews Molecular Cell Biology.
[40] John Bechhoefer,et al. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing , 2010, Molecular systems biology.
[41] S. Dalton,et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. , 2010, Genome research.
[42] Laurent Farinelli,et al. Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. , 2010, Genome research.
[43] Pedro Olivares-Chauvet,et al. S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci , 2010, PLoS genetics.
[44] Alain Arneodo,et al. Wavelet-based method to disentangle transcription- and replication-associated strand asymmetries in mammalian genomes , 2010 .
[45] Bernadett Papp,et al. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. , 2010, Genome research.
[46] M. Botchan,et al. Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. , 2010, Molecular cell.
[47] Michael O Dorschner,et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing , 2009, Proceedings of the National Academy of Sciences.
[48] J. Diffley,et al. Concerted Loading of Mcm2–7 Double Hexamers around DNA during DNA Replication Origin Licensing , 2009, Cell.
[49] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[50] Alain Arneodo,et al. Open chromatin encoded in DNA sequence is the signature of ‘master’ replication origins in human cells , 2009, Nucleic acids research.
[51] Olivier Hyrien,et al. Universal Temporal Profile of Replication Origin Activation in Eukaryotes , 2009, PloS one.
[52] S. Bell,et al. Termination structures in the Escherichia coli chromosome replication fork trap. , 2009, Journal of molecular biology.
[53] Takuro Nakagawa,et al. The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus , 2009, Nature Cell Biology.
[54] D. Wigley. ORC proteins: marking the start. , 2009, Current opinion in structural biology.
[55] Olivier Hyrien,et al. Mathematical modelling of eukaryotic DNA replication , 2009, Chromosome Research.
[56] S. Bell,et al. The replication fork trap and termination of chromosome replication , 2008, Molecular microbiology.
[57] David Collingwood,et al. The Temporal Program of Chromosome Replication: Genomewide Replication in clb5Δ Saccharomyces cerevisiae , 2008, Genetics.
[58] J. Berger,et al. Structural Synergy and Molecular Crosstalk between Bacterial Helicase Loaders and Replication Initiators , 2008, Cell.
[59] E. Rocha. The organization of the bacterial genome. , 2008, Annual review of genetics.
[60] S. Bell,et al. Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius , 2008, Proceedings of the National Academy of Sciences.
[61] J. Julian Blow,et al. Replication licensing and cancer — a fatal entanglement? , 2008, Nature Reviews Cancer.
[62] Dirk Schübeler,et al. Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation , 2008, PLoS biology.
[63] Olivier Hyrien,et al. A Dynamic Stochastic Model for DNA Replication Initiation in Early Embryos , 2008, PloS one.
[64] S. Bell,et al. Extra-chromosomal elements and the evolution of cellular DNA replication machineries , 2008, Nature Reviews Molecular Cell Biology.
[65] Scott Cheng‐Hsin Yang,et al. How Xenopus laevis embryos replicate reliably: investigating the random-completion problem. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[66] Eduardo P C Rocha,et al. From GC skews to wavelets: a gentle guide to the analysis of compositional asymmetries in genomic data. , 2008, Biochimie.
[67] Zhifeng Shao,et al. DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. , 2008, Journal of molecular biology.
[68] S Nicolay,et al. DNA replication timing data corroborate in silico human replication origin predictions. , 2007, Physical review letters.
[69] J. Lobry,et al. A new method for assessing the effect of replication on DNA base composition asymmetry. , 2007, Molecular biology and evolution.
[70] Alain Arneodo,et al. Human gene organization driven by the coordination of replication and transcription. , 2007, Genome research.
[71] James M. Berger,et al. DNA replication initiation: mechanisms and regulation in bacteria , 2007, Nature Reviews Microbiology.
[72] S. Bell,et al. Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes , 2007, Proceedings of the National Academy of Sciences.
[73] J. Lawrence,et al. Mutational bias suggests that replication termination occurs near the dif site, not at Ter sites , 2007, Molecular microbiology.
[74] Jonathan A Eisen,et al. Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii , 2007, PLoS genetics.
[75] J. Walter,et al. Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. , 2007, Genes & development.
[76] John Bechhoefer,et al. How Xenopus laevis replicates DNA reliably even though its origins of replication are located and initiated stochastically. , 2006, Physical review letters.
[77] M. Touchon,et al. Similar compositional biases are caused by very different mutational effects. , 2006, Genome research.
[78] J. Berger,et al. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling , 2006, Nature Structural &Molecular Biology.
[79] S. Bell,et al. Sequential ATP hydrolysis by Cdc6 and ORC directs loading of the Mcm2-7 helicase. , 2006, Molecular cell.
[80] Alain Arneodo,et al. Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[81] S Nicolay,et al. From DNA sequence analysis to modeling replication in the human genome. , 2005, Physical review letters.
[82] J. Walter,et al. Eukaryotic origins of DNA replication: could you please be more specific? , 2005, Seminars in cell & developmental biology.
[83] J. Julian Blow,et al. Preventing re-replication of chromosomal DNA , 2005, Nature Reviews Molecular Cell Biology.
[84] M. Waldor,et al. MicroReview: Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes , 2005, Molecular microbiology.
[85] A. Markovitz. A new in vivo termination function for DNA polymerase I of Escherichia coli K12 , 2005, Molecular microbiology.
[86] M. Bulmer,et al. Strand symmetry of mutation rates in theβ-globin region , 1991, Journal of Molecular Evolution.
[87] David M. MacAlpine,et al. A genomic view of eukaryotic DNA replication , 2005, Chromosome Research.
[88] David M MacAlpine,et al. Coordination of replication and transcription along a Drosophila chromosome. , 2004, Genes & development.
[89] Nick Gilbert,et al. Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.
[90] A. Grigoriev,et al. Identification and autonomous replication capability of a chromosomal replication origin from the archaeon Sulfolobus solfataricus , 2004, Extremophiles.
[91] Rolf Bernander,et al. Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[92] Detlef D. Leipe,et al. Evolutionary history and higher order classification of AAA+ ATPases. , 2004, Journal of structural biology.
[93] M. Botchan,et al. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC–DNA binding , 2004, The EMBO journal.
[94] Rolf Bernander,et al. Identification of Two Origins of Replication in the Single Chromosome of the Archaeon Sulfolobus solfataricus , 2004, Cell.
[95] Alain Arneodo,et al. Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. , 2004, Nucleic acids research.
[96] J. Berger,et al. Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus. , 2004, Nucleic acids research.
[97] S Nicolay,et al. Transcription‐coupled TA and GC strand asymmetries in the human genome , 2003, FEBS letters.
[98] Shiladitya DasSarma,et al. An Archaeal Chromosomal Autonomously Replicating Sequence Element from an Extreme Halophile, Halobacterium sp. Strain NRC-1 , 2003, Journal of bacteriology.
[99] J. Newport,et al. CpG Methylation of DNA Restricts Prereplication Complex Assembly in Xenopus Egg Extracts , 2003, Molecular and Cellular Biology.
[100] Matthew K. Waldor,et al. Distinct Replication Requirements for the Two Vibrio cholerae Chromosomes , 2003, Cell.
[101] Olivier Hyrien,et al. Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.
[102] Alon Goren,et al. Replicating by the clock , 2003, Nature Reviews Molecular Cell Biology.
[103] Heinrich Leonhardt,et al. DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. , 2002, Molecular cell.
[104] T. Prokhorova,et al. MCM2–7 Complexes Bind Chromatin in a Distributed Pattern Surrounding the Origin Recognition Complex inXenopus Egg Extracts* , 2002, The Journal of Biological Chemistry.
[105] R. Bernander,et al. Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii , 2002 .
[106] R. Bernander,et al. Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii , 2002, Molecular microbiology.
[107] John Herrick,et al. Kinetic model of DNA replication in eukaryotic organisms. , 2001, Journal of molecular biology.
[108] J. Huberman,et al. Regulation of replication timing in fission yeast , 2001, The EMBO journal.
[109] Ronald W. Davis,et al. Replication dynamics of the yeast genome. , 2001, Science.
[110] Mark A. Ragan,et al. The complete genome of the crenarchaeon Sulfolobus solfataricus P2 , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[111] I. Kurtser,et al. Effects of replication termination mutants on chromosome partitioning in Bacillus subtilis. , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[112] A Bensimon,et al. Replication fork density increases during DNA synthesis in X. laevis egg extracts. , 2000, Journal of molecular biology.
[113] H Philippe,et al. Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. , 2000, Science.
[114] O. Hyrien,et al. Mechanisms ensuring rapid and complete DNA replication despite random initiation in Xenopus early embryos. , 2000, Journal of molecular biology.
[115] P. Forterre. Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins , 1999, Molecular microbiology.
[116] J. Blow,et al. Changes in association of the Xenopus origin recognition complex with chromatin on licensing of replication origins. , 1999, Journal of cell science.
[117] H Philippe,et al. Identification of putative chromosomal origins of replication in Archaea , 1999, Molecular microbiology.
[118] R. Chuang,et al. The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[119] Ronald Berezney,et al. Spatial and Temporal Dynamics of DNA Replication Sites in Mammalian Cells , 1998, The Journal of cell biology.
[120] A Grigoriev,et al. Analyzing genomes with cumulative skew diagrams. , 1998, Nucleic acids research.
[121] Ana Pombo,et al. 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 , 1998, The Journal of cell biology.
[122] J. Newport,et al. Identification of a Preinitiation Step in DNA Replication That Is Independent of Origin Recognition Complex and cdc6, but Dependent on cdk2 , 1998, The Journal of cell biology.
[123] W. L. Fangman,et al. Replication profile of Saccharomyces cerevisiae chromosome VI , 1997, Genes to cells : devoted to molecular & cellular mechanisms.
[124] G. Evan,et al. Interaction between the Origin Recognition Complex and the Replication Licensing Systemin Xenopus , 1996, Cell.
[125] J. Lobry. Asymmetric substitution patterns in the two DNA strands of bacteria. , 1996, Molecular biology and evolution.
[126] I. Todorov,et al. Large, complex modular structure of a fission yeast DNA replication origin , 1996, Current Biology.
[127] T. Kelly,et al. Genetic analysis of an ARS element from the fission yeast Schizosaccharomyces pombe. , 1995, The EMBO journal.
[128] M. Méchali,et al. Transition in Specification of Embryonic Metazoan DNA Replication Origins , 1995, Science.
[129] S. Bell,et al. Yeast origin recognition complex functions in transcription silencing and DNA replication. , 1993, Science.
[130] J. Rine,et al. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. , 1993, Science.
[131] M. Méchali,et al. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. , 1993, The EMBO journal.
[132] K. Nasmyth,et al. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing , 1993, Nature.
[133] C. Newlon,et al. The structure and function of yeast ARS elements. , 1993, Current opinion in genetics & development.
[134] Bruce Stillman,et al. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex , 1992, Nature.
[135] J. Blow,et al. DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts. , 1992, Nucleic acids research.
[136] M. Méchali,et al. Plasmid replication in Xenopus eggs and egg extracts: a 2D gel electrophoretic analysis. , 1992, Nucleic acids research.
[137] T. Shinomiya,et al. Analysis of chromosomal replicons in early embryos of Drosophila melanogaster by two-dimensional gel electrophoresis. , 1991, Nucleic acids research.
[138] W. L. Fangman,et al. Mapping replication origins in yeast chromosomes , 1991, BioEssays : news and reviews in molecular, cellular and developmental biology.
[139] P. Krysan,et al. Replication initiates at multiple locations on an autonomously replicating plasmid in human cells , 1991, Molecular and cellular biology.
[140] P. Kuempel,et al. The tus gene of Escherichia coli: autoregulation, analysis of flanking sequences and identification of a complementary system in Salmonella typhimurium. , 1991, Research in microbiology.
[141] P. Dijkwel,et al. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain , 1990, Cell.
[142] S. Haase,et al. Isolation of human sequences that replicate autonomously in human cells , 1989, Molecular and cellular biology.
[143] S. Shall,et al. Sequence analysis of ARS elements in fission yeast. , 1988, The EMBO journal.
[144] J. Huberman,et al. The in vivo replication origin of the yeast 2μm plasmid , 1987, Cell.
[145] W. L. Fangman,et al. The localization of replication origins on ARS plasmids in S. cerevisiae , 1987, Cell.
[146] T. Iismaa,et al. The normal replication terminus of the Bacillus subtilis chromosome, terC, is dispensable for vegetative growth and sporulation. , 1987, Journal of molecular biology.
[147] H Nakamura,et al. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. , 1986, Experimental cell research.
[148] R. Harland,et al. Regulated replication of DNA microinjected into eggs of Xenopus laevis , 1980, Cell.
[149] R. W. Davis,et al. High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. , 1979, Proceedings of the National Academy of Sciences of the United States of America.
[150] J. Louarn,et al. Evidence for a fixed termination site of chromosome replication in Escherichia coli K12. , 1977, Journal of molecular biology.
[151] P. Kuempel,et al. Terminus region of the chromosome in Escherichia coli inhibits replication forks. , 1977, Proceedings of the National Academy of Sciences of the United States of America.
[152] H. G. Callan. Review Lecture - Replication of DNA in the chromosomes of eukaryotes , 1972, Proceedings of the Royal Society of London. Series B. Biological Sciences.
[153] A. Riggs,et al. On the mechanism of DNA replication in mammalian chromosomes. , 1968, Journal of molecular biology.
[154] François Jacob,et al. On the Regulation of DNA Replication in Bacteria , 1963 .