XB-ART-42277
Nat Rev Mol Cell Biol
2010 Oct 01;1110:728-38. doi: 10.1038/nrm2976.
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Eukaryotic DNA replication origins: many choices for appropriate answers.
Méchali M
.
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At each cell division in humans, 30,000-50,000 DNA replication origins are activated, and it remains unclear how they are selected and recognized by replication factors. DNA replication in multicellular organisms must accommodate variations in growth conditions and DNA damage. It must also adapt to changes in chromatin organization associated with cell differentiation and development. The selection of replication origins in metazoans seems to involve multiple choices, with the appropriate answers depending on the identity of the cell or the conditions of growth. This suggests that during evolution, the use of replication origins became more controlled by epigenetic mechanisms affecting chromosome dynamics and expression than by DNA synthesis per se.
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References [+] :
Abdurashidova,
Functional interactions of DNA topoisomerases with a human replication origin.
2007, Pubmed
Abdurashidova, Functional interactions of DNA topoisomerases with a human replication origin. 2007, Pubmed
Abraham, Cell cycle checkpoint signaling through the ATM and ATR kinases. 2001, Pubmed
Adachi, Study of the cell cycle-dependent assembly of the DNA pre-replication centres in Xenopus egg extracts. 1994, Pubmed , Xenbase
Aggarwal, Chromatin regulates origin activity in Drosophila follicle cells. 2004, Pubmed
Aparicio, The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. 2004, Pubmed
Aparicio, Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication. 1999, Pubmed
Balestrini, GEMC1 is a TopBP1-interacting protein required for chromosomal DNA replication. 2010, Pubmed , Xenbase
Beall, Role for a Drosophila Myb-containing protein complex in site-specific DNA replication. , Pubmed
Bell, ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. 1992, Pubmed
Berezney, Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. 2000, Pubmed
Blumenthal, The units of DNA replication in Drosophila melanogaster chromosomes. 1974, Pubmed
Bosco, DNA replication control through interaction of E2F-RB and the origin recognition complex. 2001, Pubmed
Branzei, The DNA damage response during DNA replication. 2005, Pubmed
Brewer, Initiation at closely spaced replication origins in a yeast chromosome. 1993, Pubmed
Buongiorno-Nardelli, A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. 1982, Pubmed , Xenbase
Cadoret, Genome-wide studies highlight indirect links between human replication origins and gene regulation. 2008, Pubmed
Caro, A chromatin link that couples cell division to root epidermis patterning in Arabidopsis. 2007, Pubmed
Christov, Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. 2006, Pubmed
Chuang, The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks. 1999, Pubmed
Clarey, Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. 2006, Pubmed
Cohen, Same origins of DNA replication function on the active and inactive human X chromosomes. 2003, Pubmed
Collins, An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. 2002, Pubmed
Comelli, The homeotic protein HOXC13 is a member of human DNA replication complexes. 2009, Pubmed
Costanzo, Reconstitution of an ATM-dependent checkpoint that inhibits chromosomal DNA replication following DNA damage. 2000, Pubmed , Xenbase
Courbet, Replication fork movement sets chromatin loop size and origin choice in mammalian cells. 2008, Pubmed
Crampton, An ARS element inhibits DNA replication through a SIR2-dependent mechanism. 2008, Pubmed
Dai, DNA replication origins in the Schizosaccharomyces pombe genome. 2005, Pubmed
Danis, Specification of a DNA replication origin by a transcription complex. 2004, Pubmed , Xenbase
Dazy, Broadening of DNA replication origin usage during metazoan cell differentiation. 2006, Pubmed
DePamphilis, Eukaryotic DNA replication: anatomy of an origin. 1993, Pubmed
DePamphilis, Regulating the licensing of DNA replication origins in metazoa. 2006, Pubmed
Del Bene, Direct interaction of geminin and Six3 in eye development. 2004, Pubmed , Xenbase
Delgado, Initiation of DNA replication at CpG islands in mammalian chromosomes. 1998, Pubmed
Demeret, Expression of ISWI and its binding to chromatin during the cell cycle and early development. 2002, Pubmed , Xenbase
Desprat, Predictable dynamic program of timing of DNA replication in human cells. 2009, Pubmed
Dimitrova, The spatial position and replication timing of chromosomal domains are both established in early G1 phase. 1999, Pubmed , Xenbase
Doksani, Replicon dynamics, dormant origin firing, and terminal fork integrity after double-strand break formation. 2009, Pubmed
Donaldson, Shaping time: chromatin structure and the DNA replication programme. 2005, Pubmed
Donti, Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins. 2009, Pubmed
Doyon, ING tumor suppressor proteins are critical regulators of chromatin acetylation required for genome expression and perpetuation. 2006, Pubmed
Duncker, The origin recognition complex protein family. 2009, Pubmed
Eaton, Conserved nucleosome positioning defines replication origins. 2010, Pubmed
Egli, Developmental reprogramming after chromosome transfer into mitotic mouse zygotes. 2007, Pubmed
Erzberger, Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. 2006, Pubmed
Field, Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. 2008, Pubmed
Foss, Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. 1993, Pubmed
Fox, A transcriptional silencer as a specialized origin of replication that establishes functional domains of chromatin. 1993, Pubmed
Françon, A hypophosphorylated form of RPA34 is a specific component of pre-replication centers. 2004, Pubmed , Xenbase
Friedman, Multiple determinants controlling activation of yeast replication origins late in S phase. 1996, Pubmed
Friedman, Replication profile of Saccharomyces cerevisiae chromosome VI. 1997, Pubmed
Gavin, Conserved initiator proteins in eukaryotes. 1995, Pubmed
Ge, Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress. 2007, Pubmed
Ghosh, Transcription factor binding and induced transcription alter chromosomal c-myc replicator activity. 2004, Pubmed
Gilbert, Replication origin plasticity, Taylor-made: inhibition vs recruitment of origins under conditions of replication stress. 2007, Pubmed
Gilbert, Replication timing and transcriptional control: beyond cause and effect. 2002, Pubmed
Grégoire, HoxB domain induction silences DNA replication origins in the locus and specifies a single origin at its boundary. 2006, Pubmed
Gómez, Overreplication of short DNA regions during S phase in human cells. 2008, Pubmed
Gómez, Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage. 2004, Pubmed
Haase, Transcription inhibits the replication of autonomously replicating plasmids in human cells. 1994, Pubmed
Hamlin, A revisionist replicon model for higher eukaryotic genomes. 2008, Pubmed
Hashimoto, Xenopus Cut5 is essential for a CDK-dependent process in the initiation of DNA replication. 2003, Pubmed , Xenbase
Hayashi, Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. 2007, Pubmed
Hayashi, The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus. 2009, Pubmed
Heichinger, Genome-wide characterization of fission yeast DNA replication origins. 2006, Pubmed
Heun, The positioning and dynamics of origins of replication in the budding yeast nucleus. 2001, Pubmed
Hiratani, Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. 2010, Pubmed
Hiratani, Global reorganization of replication domains during embryonic stem cell differentiation. 2008, Pubmed
Huberman, Autoradiography of chromosomal DNA fibers from Chinese hamster cells. 1966, Pubmed
Hyrien, Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. 1993, Pubmed , Xenbase
Hyrien, Transition in specification of embryonic metazoan DNA replication origins. 1995, Pubmed , Xenbase
Ibarra, Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication. 2008, Pubmed
Iizuka, Regulation of replication licensing by acetyltransferase Hbo1. 2006, Pubmed , Xenbase
Ilves, Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins. 2010, Pubmed
Jackson, 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, Pubmed
Kalejta, Distal sequences, but not ori-beta/OBR-1, are essential for initiation of DNA replication in the Chinese hamster DHFR origin. 1998, Pubmed
Knott, Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae. 2009, Pubmed
Kohzaki, Transcription factors and DNA replication origin selection. 2005, Pubmed
Kong, Xenopus origin recognition complex (ORC) initiates DNA replication preferentially at sequences targeted by Schizosaccharomyces pombe ORC. 2003, Pubmed , Xenbase
Krasinska, Cdk1 and Cdk2 activity levels determine the efficiency of replication origin firing in Xenopus. 2008, Pubmed , Xenbase
Kubota, A novel ring-like complex of Xenopus proteins essential for the initiation of DNA replication. 2003, Pubmed , Xenbase
Kumagai, TopBP1 activates the ATR-ATRIP complex. 2006, Pubmed , Xenbase
Kumagai, Treslin collaborates with TopBP1 in triggering the initiation of DNA replication. 2010, Pubmed , Xenbase
Kunst, The complete genome sequence of the gram-positive bacterium Bacillus subtilis. 1997, Pubmed
Labit, DNA replication timing is deterministic at the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts. 2008, Pubmed , Xenbase
Laskey, Replication origins in the eucaryotic chromosome. 1981, Pubmed
Lebofsky, DNA replication origin interference increases the spacing between initiation events in human cells. 2006, Pubmed
Li, Spatial distribution and specification of mammalian replication origins during G1 phase. 2003, Pubmed , Xenbase
Lipford, Nucleosomes positioned by ORC facilitate the initiation of DNA replication. 2001, Pubmed
Liu, The Chk1-mediated S-phase checkpoint targets initiation factor Cdc45 via a Cdc25A/Cdk2-independent mechanism. 2006, Pubmed
Lunyak, Developmental changes in the Sciara II/9A initiation zone for DNA replication. 2002, Pubmed
Luo, The cell-cycle regulator geminin inhibits Hox function through direct and polycomb-mediated interactions. 2004, Pubmed
Lutzmann, A Cdt1-geminin complex licenses chromatin for DNA replication and prevents rereplication during S phase in Xenopus. 2006, Pubmed , Xenbase
Lutzmann, MCM9 binds Cdt1 and is required for the assembly of prereplication complexes. 2008, Pubmed , Xenbase
Ma, Spatial and temporal dynamics of DNA replication sites in mammalian cells. 1998, Pubmed
MacAlpine, Coordination of replication and transcription along a Drosophila chromosome. 2004, Pubmed
MacAlpine, Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. 2010, Pubmed
Marheineke, Control of replication origin density and firing time in Xenopus egg extracts: role of a caffeine-sensitive, ATR-dependent checkpoint. 2004, Pubmed , Xenbase
Maric, Developmentally regulated usage of Physarum DNA replication origins. 2003, Pubmed
Maya-Mendoza, Chk1 regulates the density of active replication origins during the vertebrate S phase. 2007, Pubmed
Mesner, Specific signals at the 3' end of the DHFR gene define one boundary of the downstream origin of replication. 2005, Pubmed
Mesner, The dihydrofolate reductase origin of replication does not contain any nonredundant genetic elements required for origin activity. 2003, Pubmed
Miotto, HBO1 histone acetylase activity is essential for DNA replication licensing and inhibited by Geminin. 2010, Pubmed
Mohammad, Tetrahymena ORC contains a ribosomal RNA fragment that participates in rDNA origin recognition. 2007, Pubmed
Mordes, TopBP1 activates ATR through ATRIP and a PIKK regulatory domain. 2008, Pubmed
Mott, DNA replication initiation: mechanisms and regulation in bacteria. 2007, Pubmed
Méchali, DNA replication origins: from sequence specificity to epigenetics. 2001, Pubmed
Méchali, Lack of specific sequence requirement for DNA replication in Xenopus eggs compared with high sequence specificity in yeast. 1984, Pubmed , Xenbase
Nakamura, Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. 1986, Pubmed
Necsulea, The relationship between DNA replication and human genome organization. 2009, Pubmed
Nieduszynski, Genome-wide identification of replication origins in yeast by comparative genomics. 2006, Pubmed
Nishiyama, rac p21 is involved in insulin-induced membrane ruffling and rho p21 is involved in hepatocyte growth factor- and 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced membrane ruffling in KB cells. 1994, Pubmed
Norio, Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. 2005, Pubmed
Norseen, RNA-dependent recruitment of the origin recognition complex. 2008, Pubmed
Okuno, Clustered adenine/thymine stretches are essential for function of a fission yeast replication origin. 1999, Pubmed
Pacek, Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication. 2006, Pubmed , Xenbase
Paixão, Modular structure of the human lamin B2 replicator. 2004, Pubmed
Pak, Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes. 1997, Pubmed , Xenbase
Pasero, Single-molecule analysis reveals clustering and epigenetic regulation of replication origins at the yeast rDNA locus. 2002, Pubmed
Patel, The Hsk1(Cdc7) replication kinase regulates origin efficiency. 2008, Pubmed
Petermann, Chk1 requirement for high global rates of replication fork progression during normal vertebrate S phase. 2006, Pubmed
Pinto, latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant. 1999, Pubmed
Raghuraman, Replication dynamics of the yeast genome. 2001, Pubmed
Remus, DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. 2004, Pubmed
Remus, Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. 2009, Pubmed
Remus, Eukaryotic DNA replication control: lock and load, then fire. 2009, Pubmed
Saha, The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. 2004, Pubmed
Sansam, A vertebrate gene, ticrr, is an essential checkpoint and replication regulator. 2010, Pubmed
Santocanale, A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. 1998, Pubmed
Sasaki, The Chinese hamster dihydrofolate reductase replication origin decision point follows activation of transcription and suppresses initiation of replication within transcription units. 2006, Pubmed , Xenbase
Sasaki, Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolalpha-dE2F locus of Drosophila melanogaster. 1999, Pubmed
Schepers, Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches. 2010, Pubmed
Schwaiger, Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. 2009, Pubmed
Schwaiger, A question of timing: emerging links between transcription and replication. 2006, Pubmed
Segurado, Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. 2003, Pubmed
Seiler, The intra-S-phase checkpoint affects both DNA replication initiation and elongation: single-cell and -DNA fiber analyses. 2007, Pubmed
Seo, Geminin regulates neuronal differentiation by antagonizing Brg1 activity. 2005, Pubmed , Xenbase
Sequeira-Mendes, Transcription initiation activity sets replication origin efficiency in mammalian cells. 2009, Pubmed
Shaw, S-phase progression in mammalian cells: modelling the influence of nuclear organization. 2010, Pubmed
Shechter, ATR and ATM regulate the timing of DNA replication origin firing. 2004, Pubmed , Xenbase
Shima, A viable allele of Mcm4 causes chromosome instability and mammary adenocarcinomas in mice. 2007, Pubmed
Shimada, The origin recognition complex functions in sister-chromatid cohesion in Saccharomyces cerevisiae. 2007, Pubmed
Shirahige, Regulation of DNA-replication origins during cell-cycle progression. 1998, Pubmed
Simpson, Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. 1990, Pubmed
Stanojcic, In Xenopus egg extracts, DNA replication initiates preferentially at or near asymmetric AT sequences. 2008, Pubmed , Xenbase
Stinchcomb, Isolation and characterisation of a yeast chromosomal replicator. 1979, Pubmed
Takahashi, Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex. 2004, Pubmed , Xenbase
Takebayashi, Mapping sites where replication initiates in mammalian cells using DNA fibers. 2001, Pubmed
Touchon, Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. 2005, Pubmed
Triolo, Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing. 1996, Pubmed
Unnikrishnan, Dynamic changes in histone acetylation regulate origins of DNA replication. 2010, Pubmed
Vashee, Sequence-independent DNA binding and replication initiation by the human origin recognition complex. 2003, Pubmed , Xenbase
Vogelauer, Histone acetylation regulates the time of replication origin firing. 2002, Pubmed
Wang, Cooperative sequence modules determine replication initiation sites at the human beta-globin locus. 2006, Pubmed
White, DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. 2004, Pubmed
Wu, A distinct G1 step required to specify the Chinese hamster DHFR replication origin. 1996, Pubmed , Xenbase
Wu, Establishing the program of origin firing during S phase in fission Yeast. 2009, Pubmed
Wyrick, Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. 2001, Pubmed
Xu, Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. 2006, Pubmed
Zegerman, DNA replication as a target of the DNA damage checkpoint. 2009, Pubmed