Human ORC/MCM density is low in active genes and correlates with replication time but does not solely define replication initiation zones
暂无分享,去创建一个
H. Blum | B. Audit | W. Hammerschmidt | S. Krebs | A. Schepers | L. Lacroix | Xia Wu | O. Hyrien | N. Kirstein | Alexander Buschle
[1] B. Audit,et al. FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing , 2020, Genome Biology.
[2] Peiyao A. Zhao,et al. High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells , 2020, Genome Biology.
[3] Peiyao A. Zhao,et al. High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells , 2019, Genome Biology.
[4] A. Koren,et al. Genomic methods for measuring DNA replication dynamics , 2019, Chromosome Research.
[5] D. Gilbert,et al. Control of DNA replication timing in the 3D genome , 2019, Nature Reviews Molecular Cell Biology.
[6] Carolin A. Müller,et al. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads , 2018, Nature Methods.
[7] Dominik Boos,et al. Origin Firing Regulations to Control Genome Replication Timing , 2019, Genes.
[8] Stefan Mundlos,et al. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication , 2019, Cell.
[9] Nhuong V. Nguyen,et al. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination in sister chromatids , 2019, Nature Cell Biology.
[10] D. Fenyö,et al. Transcription shapes DNA replication initiation and termination in human cells , 2018, Nature Structural & Molecular Biology.
[11] R. Andersson,et al. MCM2 promotes symmetric inheritance of modified histones during DNA replication , 2018, Science.
[12] C. Bakkenist,et al. Regulation of the initiation of DNA replication in human cells. , 2018, DNA repair.
[13] A. Arneodo,et al. Developmental and cancer-associated plasticity of DNA replication preferentially targets GC-poor, lowly expressed and late-replicating regions , 2018, Nucleic acids research.
[14] M. Aladjem,et al. Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse , 2018, Cell.
[15] B. Fahrenkrog,et al. Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing , 2018, Nature Communications.
[16] Y. Ohkawa,et al. Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells , 2018, Nucleic acids research.
[17] Ricardo Almeida,et al. Chromatin conformation regulates the coordination between DNA replication and transcription , 2018, Nature Communications.
[18] Alessandro Costa,et al. The mechanism of eukaryotic CMG helicase activation , 2018, Nature.
[19] T. Halazonetis,et al. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress , 2018, Nature.
[20] D. Gilbert,et al. Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors , 2017, Nucleic acids research.
[21] S. Gerbi,et al. How MCM loading and spreading specify eukaryotic DNA replication initiation sites , 2016, F1000Research.
[22] G. Schotta,et al. Histone H4K20 tri‐methylation at late‐firing origins ensures timely heterochromatin replication , 2017, The EMBO journal.
[23] Juan Carlos Rivera-Mulia,et al. Replication Domains: Genome Compartmentalization into Functional Replication Units. , 2017, Advances in experimental medicine and biology.
[24] Stefan Gräf,et al. Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq) , 2016, Nucleic acids research.
[25] O. Hyrien. How MCM loading and spreading specify eukaryotic DNA replication initiation sites , 2016, F1000Research.
[26] D. MacAlpine,et al. DNA replication origins—where do we begin? , 2016, Genes & development.
[27] K. Struhl,et al. Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers , 2016, Proceedings of the National Academy of Sciences.
[28] F. Fauchereau,et al. Characterization of the replication timing program of 6 human model cell lines , 2016, Genomics data.
[29] Juan Carlos Rivera-Mulia,et al. Replicating Large Genomes: Divide and Conquer. , 2016, Molecular cell.
[30] D. Gilbert,et al. Replication timing and transcriptional control: beyond cause and effect-part III. , 2016, Current opinion in cell biology.
[31] Y. D'Aubenton-Carafa,et al. Replication landscape of the human genome , 2016, Nature Communications.
[32] D. Remus,et al. Post-licensing Specification of Eukaryotic Replication Origins by Facilitated Mcm2-7 Sliding along DNA. , 2015, Molecular cell.
[33] J. van Helden,et al. The chromatin environment shapes DNA replication origin organization and defines origin classes , 2015, Genome research.
[34] Françoise Argoul,et al. Structural organization of human replication timing domains , 2015, FEBS letters.
[35] Scott Cheng‐Hsin Yang,et al. Replication timing is regulated by the number of MCMs loaded at origins , 2015, Genome research.
[36] M. Méchali,et al. DNA replication origin activation in space and time , 2015, Nature Reviews Molecular Cell Biology.
[37] D. MacAlpine,et al. Dynamic loading and redistribution of the Mcm2‐7 helicase complex through the cell cycle , 2015, The EMBO journal.
[38] Yanli Wang,et al. Topologically associating domains are stable units of replication-timing regulation , 2014, Nature.
[39] Mirit I Aladjem,et al. Chromatin structure and replication origins: determinants of chromosome replication and nuclear organization. , 2014, Journal of molecular biology.
[40] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[41] Fidel Ramírez,et al. deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..
[42] Franck Picard,et al. The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells , 2014, PLoS genetics.
[43] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[44] 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.
[45] N. Rhind,et al. DNA replication timing. , 2013, Cold Spring Harbor perspectives in biology.
[46] S. Bell,et al. Helicase loading at chromosomal origins of replication. , 2013, Cold Spring Harbor perspectives in biology.
[47] Duncan J. Smith,et al. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination. , 2013, Molecular cell.
[48] G. Schotta,et al. Histone H4 Lysine 20 methylation: key player in epigenetic regulation of genomic integrity , 2013, Nucleic acids research.
[49] Alain Arneodo,et al. Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm , 2012, Nature Protocols.
[50] Davide Cittaro,et al. Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing , 2012, Genome research.
[51] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[52] Nathan C. Sheffield,et al. The accessible chromatin landscape of the human genome , 2012, Nature.
[53] Yong Zhang,et al. Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.
[54] J. M. Arteaga-Salas,et al. Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus , 2012, The Journal of cell biology.
[55] Günter P. Wagner,et al. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples , 2012, Theory in Biosciences.
[56] Jean-Michel Marin,et al. Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs , 2012, Nature Structural &Molecular Biology.
[57] John Bechhoefer,et al. Regulation of DNA Replication within the Immunoglobulin Heavy-Chain Locus During B Cell Commitment , 2012, PLoS biology.
[58] 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..
[59] Duncan J. Smith,et al. Intrinsic coupling of lagging-strand synthesis to chromatin assembly , 2012, Nature.
[60] Danny Reinberg,et al. PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. , 2012, Genes & development.
[61] 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..
[62] William C Reinhold,et al. Genome-wide depletion of replication initiation events in highly transcribed regions. , 2011, Genome research.
[63] Eric Rivals,et al. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. , 2011, Genome research.
[64] Claude Sardet,et al. The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells , 2010, Nature Cell Biology.
[65] John Bechhoefer,et al. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing , 2010, Molecular systems biology.
[66] S. Dalton,et al. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. , 2010, Genome research.
[67] R. Gordân,et al. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. , 2010, Genome research.
[68] Jingchuan Sun,et al. A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication , 2009, Proceedings of the National Academy of Sciences.
[69] J. Diffley,et al. Eukaryotic DNA replication control: lock and load, then fire. , 2009, Current opinion in cell biology.
[70] M. Eisen,et al. Impact of Chromatin Structures on DNA Processing for Genomic Analyses , 2009, PloS one.
[71] O. Aparicio,et al. To promote and protect: Coordinating DNA replication and transcription for genome stability , 2009, Epigenetics.
[72] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[73] E. Rampakakis. Regulation of the initiation of DNA replication: Interplay between DNA topology and chromatin structure , 2009 .
[74] P. Dijkwel,et al. A winding road to origin discovery , 2009, Chromosome Research.
[75] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[76] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[77] G. Schotta,et al. PR-SET7 and SUV4-20H regulate H4 lysine-20 methylation at imprinting control regions in the mouse , 2008, EMBO Reports.
[78] H. Taubert,et al. Supplementary Figure 6 , 2008 .
[79] P. Klatt,et al. Suv4-20h deficiency results in telomere elongation and derepression of telomere recombination , 2007, The Journal of cell biology.
[80] J. Weissenbach,et al. DNA replication origin interference increases the spacing between initiation events in human cells. , 2006, Molecular biology of the cell.
[81] D. Gilbert,et al. The Chinese Hamster Dihydrofolate Reductase Replication Origin Decision Point Follows Activation of Transcription and Suppresses Initiation of Replication within Transcription Units , 2006, Molecular and Cellular Biology.
[82] D. Wigley,et al. Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase. , 2005, Trends in biochemical sciences.
[83] Vincenzo Pirrotta,et al. Characteristic Low Density and Shear Sensitivity of Cross-Linked Chromatin Containing Polycomb Complexes , 2005, Molecular and Cellular Biology.
[84] C. Schildkraut,et al. Plasticity of DNA Replication Initiation in Epstein-Barr Virus Episomes , 2004, PLoS biology.
[85] E. Kremmer,et al. Complex protein-DNA dynamics at the latent origin of DNA replication of Epstein-Barr virus , 2003, Journal of Cell Science.
[86] S. Forsburg,et al. Regulation of DNA replication , 2003 .
[87] Tom H. Pringle,et al. The human genome browser at UCSC. , 2002, Genome research.
[88] C. Schildkraut,et al. Visualization of DNA Replication on Individual Epstein-Barr Virus Episomes , 2001, Science.
[89] E. Kremmer,et al. Human origin recognition complex binds to the region of the latent origin of DNA replication of Epstein–Barr virus , 2001, The EMBO journal.
[90] M. Méchali,et al. Transition in Specification of Embryonic Metazoan DNA Replication Origins , 1995, Science.
[91] B. Stillman,et al. A yeast chromosomal origin of DNA replication defined by multiple functional elements. , 1992, Science.
[92] M. Gefter,et al. DNA Replication , 2019, Advances in Experimental Medicine and Biology.
[93] G. Klein,et al. Linear association between cellular DNA and Epstein-Barr virus DNA in a human lymphoblastoid cell line. , 1973, Proceedings of the National Academy of Sciences of the United States of America.