메뉴 건너뛰기




Volumn 44, Issue 21, 2016, Pages 10230-10247

Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; DNA; OKAZAKI FRAGMENTS;

EID: 85016153135     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw760     Document Type: Article
Times cited : (79)

References (62)
  • 1
    • 0014413470 scopus 로고
    • On the mechanism of DNA replication in mammalian chromosomes
    • Huberman, J.A. and Riggs, A.D. (1968) On the mechanism of DNA replication in mammalian chromosomes. J. Mol. Biol., 32, 327-341.
    • (1968) J. Mol. Biol , vol.32 , pp. 327-341
    • Huberman, J.A.1    Riggs, A.D.2
  • 2
    • 0034008103 scopus 로고    scopus 로고
    • Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci
    • Berezney, R., Dubey, D.D. and Huberman, J.A. (2000) Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma, 108, 471-484.
    • (2000) Chromosoma , vol.108 , pp. 471-484
    • Berezney, R.1    Dubey, D.D.2    Huberman, J.A.3
  • 3
    • 84921799659 scopus 로고    scopus 로고
    • Peaks cloaked in the mist: The landscape of mammalian replication origins
    • Hyrien, O. (2015) Peaks cloaked in the mist: The landscape of mammalian replication origins. J. Cell Biol., 208, 147-160.
    • (2015) J. Cell Biol , vol.208 , pp. 147-160
    • Hyrien, O.1
  • 4
    • 0025147957 scopus 로고
    • An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells
    • Vassilev, L. and Johnson, E.M. (1990) An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Mol. Cell. Biol., 10, 4899-4904.
    • (1990) Mol. Cell. Biol , vol.10 , pp. 4899-4904
    • Vassilev, L.1    Johnson, E.M.2
  • 5
    • 0027749608 scopus 로고
    • Replication structure of the human beta-globin gene domain
    • Kitsberg, D., Selig, S., Keshet, I. and Cedar, H. (1993) Replication structure of the human beta-globin gene domain. Nature, 366, 588-590.
    • (1993) Nature , vol.366 , pp. 588-590
    • Kitsberg, D.1    Selig, S.2    Keshet, I.3    Cedar, H.4
  • 6
    • 0037199945 scopus 로고    scopus 로고
    • The origin recognition complex marks a replication origin in the human TOP1 gene promoter
    • Keller, C., Ladenburger, E.M., Kremer, M. and Knippers, R. (2002) The origin recognition complex marks a replication origin in the human TOP1 gene promoter. J. Biol. Chem., 277, 31430-31440.
    • (2002) J. Biol. Chem , vol.277 , pp. 31430-31440
    • Keller, C.1    Ladenburger, E.M.2    Kremer, M.3    Knippers, R.4
  • 7
    • 0036148206 scopus 로고    scopus 로고
    • Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication
    • Ladenburger, E.M., Keller, C. and Knippers, R. (2002) 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., 22, 1036-1048.
    • (2002) Mol. Cell. Biol , vol.22 , pp. 1036-1048
    • Ladenburger, E.M.1    Keller, C.2    Knippers, R.3
  • 10
    • 0025253541 scopus 로고
    • Autonomous replication of a DNA fragment containing the chromosomal replication origin of the human c-myc gene
    • McWhinney, C. and Leffak, M. (1990) Autonomous replication of a DNA fragment containing the chromosomal replication origin of the human c-myc gene. Nucleic Acids Res., 18, 1233-1242.
    • (1990) Nucleic Acids Res , vol.18 , pp. 1233-1242
    • McWhinney, C.1    Leffak, M.2
  • 11
    • 0032516695 scopus 로고    scopus 로고
    • Genetic dissection of a mammalian replicator in the human beta-globin locus
    • Aladjem, M.I., Rodewald, L.W., Kolman, J.L. and Wahl, G.M. (1998) Genetic dissection of a mammalian replicator in the human beta-globin locus. Science, 281, 1005-1009.
    • (1998) Science , vol.281 , pp. 1005-1009
    • Aladjem, M.I.1    Rodewald, L.W.2    Kolman, J.L.3    Wahl, G.M.4
  • 12
    • 0032807981 scopus 로고    scopus 로고
    • Activity of the c-myc replicator at an ectopic chromosomal location
    • Malott, M. and Leffak, M. (1999) Activity of the c-myc replicator at an ectopic chromosomal location. Mol. Cell. Biol., 19, 5685-5695.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 5685-5695
    • Malott, M.1    Leffak, M.2
  • 14
    • 0024458475 scopus 로고
    • Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments
    • Vassilev, L. and Johnson, E.M. (1989) Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments. Nucleic Acids Res., 17, 7693-7705.
    • (1989) Nucleic Acids Res , vol.17 , pp. 7693-7705
    • Vassilev, L.1    Johnson, E.M.2
  • 15
    • 0032472223 scopus 로고    scopus 로고
    • Discrete start sites for DNA synthesis in the yeast ARS1 origin
    • Bielinsky, A.K. and Gerbi, S.A. (1998) Discrete start sites for DNA synthesis in the yeast ARS1 origin. Science, 279, 95-98.
    • (1998) Science , vol.279 , pp. 95-98
    • Bielinsky, A.K.1    Gerbi, S.A.2
  • 16
    • 84864690009 scopus 로고    scopus 로고
    • Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs
    • Besnard, E., Babled, A., Lapasset, L., Milhavet, O., Parrinello, H., Dantec, C., Marin, J.M. and Lemaitre, J.M. (2012) Unraveling cell type-specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs. Nat. Struct. Mol. Biol., 19, 837-844.
    • (2012) Nat. Struct. Mol. Biol , vol.19 , pp. 837-844
    • Besnard, E.1    Babled, A.2    Lapasset, L.3    Milhavet, O.4    Parrinello, H.5    Dantec, C.6    Marin, J.M.7    Lemaitre, J.M.8
  • 19
    • 84901599268 scopus 로고    scopus 로고
    • The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells
    • Picard, F., Cadoret, J.C., Audit, B., Arneodo, A., Alberti, A., Battail, C., Duret, L. and Prioleau, M.N. (2014) The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells. PLoS Genet., 10, e1004282.
    • (2014) PLoS Genet , vol.10 , pp. e1004282
    • Picard, F.1    Cadoret, J.C.2    Audit, B.3    Arneodo, A.4    Alberti, A.5    Battail, C.6    Duret, L.7    Prioleau, M.N.8
  • 23
    • 84887404285 scopus 로고    scopus 로고
    • Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early-And late-firing origins
    • Mesner, L.D., Valsakumar, V., Cieslik, M., Pickin, R., Hamlin, J.L. and Bekiranov, S. (2013) Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early-And late-firing origins. Genome Res., 23, 1774-1788.
    • (2013) Genome Res , vol.23 , pp. 1774-1788
    • Mesner, L.D.1    Valsakumar, V.2    Cieslik, M.3    Pickin, R.4    Hamlin, J.L.5    Bekiranov, S.6
  • 24
    • 79952270733 scopus 로고    scopus 로고
    • Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription
    • Mesner, L.D., Valsakumar, V., Karnani, N., Dutta, A., Hamlin, J.L. and Bekiranov, S. (2011) Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription. Genome Res., 21, 377-389.
    • (2011) Genome Res , vol.21 , pp. 377-389
    • Mesner, L.D.1    Valsakumar, V.2    Karnani, N.3    Dutta, A.4    Hamlin, J.L.5    Bekiranov, S.6
  • 26
    • 33749670708 scopus 로고    scopus 로고
    • Initiation of chromosomal DNA replication in mammalian cell-free systems
    • Krude, T. (2006) Initiation of chromosomal DNA replication in mammalian cell-free systems. Cell Cycle, 5, 2115-2122.
    • (2006) Cell Cycle , vol.5 , pp. 2115-2122
    • Krude, T.1
  • 27
    • 0034607917 scopus 로고    scopus 로고
    • Initiation of human DNA replication in vitro using nuclei from cells arrested at an initiation-competent state
    • Krude, T. (2000) Initiation of human DNA replication in vitro using nuclei from cells arrested at an initiation-competent state. J. Biol. Chem., 275, 13699-13707.
    • (2000) J. Biol. Chem , vol.275 , pp. 13699-13707
    • Krude, T.1
  • 28
    • 0030887999 scopus 로고    scopus 로고
    • Cyclin/Cdk-dependent initiation of DNA replication in a human cell-free system
    • Krude, T., Jackman, M., Pines, J. and Laskey, R.A. (1997) Cyclin/Cdk-dependent initiation of DNA replication in a human cell-free system. Cell, 88, 109-119.
    • (1997) Cell , vol.88 , pp. 109-119
    • Krude, T.1    Jackman, M.2    Pines, J.3    Laskey, R.A.4
  • 29
    • 0033602015 scopus 로고    scopus 로고
    • Mimosine arrests proliferating human cells before onset of DNA replication in a dose-dependent manner
    • Krude, T. (1999) Mimosine arrests proliferating human cells before onset of DNA replication in a dose-dependent manner. Exp. Cell Res., 247, 148-159.
    • (1999) Exp. Cell Res , vol.247 , pp. 148-159
    • Krude, T.1
  • 30
    • 84896836573 scopus 로고    scopus 로고
    • Activation of the prereplication complex is blocked by mimosine through reactive oxygen species-Activated ataxia telangiectasia mutated (ATM) protein without DNA damage
    • Kubota, S., Fukumoto, Y., Ishibashi, K., Soeda, S., Kubota, S., Yuki, R., Nakayama, Y., Aoyama, K., Yamaguchi, N. and Yamaguchi, N. (2014) Activation of the prereplication complex is blocked by mimosine through reactive oxygen species-Activated ataxia telangiectasia mutated (ATM) protein without DNA damage. J. Biol. Chem., 289, 5730-5746.
    • (2014) J. Biol. Chem , vol.289 , pp. 5730-5746
    • Kubota, S.1    Fukumoto, Y.2    Ishibashi, K.3    Soeda, S.4    Kubota, S.5    Yuki, R.6    Nakayama, Y.7    Aoyama, K.8    Yamaguchi, N.9    Yamaguchi, N.10
  • 31
    • 27744545729 scopus 로고    scopus 로고
    • Distinct populations of human PCNA are required for initiation of chromosomal DNA replication and concurrent DNA repair
    • Szüts, D., Christov, C., Kitching, L. and Krude, T. (2005) Distinct populations of human PCNA are required for initiation of chromosomal DNA replication and concurrent DNA repair. Exp. Cell Res., 311, 240-250.
    • (2005) Exp. Cell Res , vol.311 , pp. 240-250
    • Szüts, D.1    Christov, C.2    Kitching, L.3    Krude, T.4
  • 32
    • 8744313842 scopus 로고    scopus 로고
    • Cell cycle arrest at the initiation step of human chromosomal DNA replication causes DNA damage
    • Szüts, D. and Krude, T. (2004) Cell cycle arrest at the initiation step of human chromosomal DNA replication causes DNA damage. J. Cell Sci., 117, 4897-4908.
    • (2004) J. Cell Sci , vol.117 , pp. 4897-4908
    • Szüts, D.1    Krude, T.2
  • 33
    • 29244469071 scopus 로고    scopus 로고
    • Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system
    • Marheineke, K., Hyrien, O. and Krude, T. (2005) Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system. Nucleic Acids Res., 33, 6931-6941.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6931-6941
    • Marheineke, K.1    Hyrien, O.2    Krude, T.3
  • 38
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
    • Thorvaldsdottir, H., Robinson, J.T. and Mesirov, J.P. (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform., 14, 178-192.
    • (2013) Brief. Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 39
    • 0037052966 scopus 로고    scopus 로고
    • Site-specific and temporally controlled initiation of DNA replication in a human cell-free system
    • Keller, C., Hyrien, O., Knippers, R. and Krude, T. (2002) Site-specific and temporally controlled initiation of DNA replication in a human cell-free system. Nucleic Acids Res., 30, 2114-2123.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2114-2123
    • Keller, C.1    Hyrien, O.2    Knippers, R.3    Krude, T.4
  • 40
    • 0029931399 scopus 로고    scopus 로고
    • DNA replication initiates non-randomly at multiple sites near the c-myc gene in HeLa cells
    • Waltz, S.E., Trivedi, A.A. and Leffak, M. (1996) DNA replication initiates non-randomly at multiple sites near the c-myc gene in HeLa cells. Nucleic Acids Res., 24, 1887-1894.
    • (1996) Nucleic Acids Res , vol.24 , pp. 1887-1894
    • Waltz, S.E.1    Trivedi, A.A.2    Leffak, M.3
  • 41
    • 84921425052 scopus 로고    scopus 로고
    • Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells
    • Xu, S., Grullon, S., Ge, K. and Peng, W. (2014) Spatial clustering for identification of ChIP-enriched regions (SICER) to map regions of histone methylation patterns in embryonic stem cells. Methods Mol. Biol., 1150, 97-111.
    • (2014) Methods Mol. Biol , vol.1150 , pp. 97-111
    • Xu, S.1    Grullon, S.2    Ge, K.3    Peng, W.4
  • 42
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • Zang, C., Schones, D.E., Zeng, C., Cui, K., Zhao, K. and Peng, W. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 25, 1952-1958.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3    Cui, K.4    Zhao, K.5    Peng, W.6
  • 43
    • 0019513002 scopus 로고
    • Chromosome pattern, growth in agar and tumorigenicity in nude mice of four human bladder carcinoma cell lines
    • Hastings, R.J. and Franks, L.M. (1981) Chromosome pattern, growth in agar and tumorigenicity in nude mice of four human bladder carcinoma cell lines. Int. J. Cancer, 27, 15-21.
    • (1981) Int. J. Cancer , vol.27 , pp. 15-21
    • Hastings, R.J.1    Franks, L.M.2
  • 44
    • 77956879643 scopus 로고    scopus 로고
    • Evaluating genome-scale approaches to eukaryotic DNA replication
    • Gilbert, D.M. (2010) Evaluating genome-scale approaches to eukaryotic DNA replication. Nat. Rev. Genet., 11, 673-684.
    • (2010) Nat. Rev. Genet , vol.11 , pp. 673-684
    • Gilbert, D.M.1
  • 48
    • 20144364292 scopus 로고    scopus 로고
    • Prevalence of quadruplexes in the human genome
    • Huppert, J.L. and Balasubramanian, S. (2005) Prevalence of quadruplexes in the human genome. Nucleic Acids Res., 33, 2908-2916.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2908-2916
    • Huppert, J.L.1    Balasubramanian, S.2
  • 51
    • 77649231570 scopus 로고    scopus 로고
    • Defining replication origin efficiency using DNA fiber assays
    • Tuduri, S., Tourriere, H. and Pasero, P. (2010) Defining replication origin efficiency using DNA fiber assays. Chromosome Res., 18, 91-102.
    • (2010) Chromosome Res , vol.18 , pp. 91-102
    • Tuduri, S.1    Tourriere, H.2    Pasero, P.3
  • 54
    • 0025340970 scopus 로고
    • Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain
    • Vaughn, J.P., Dijkwel, P.A. and Hamlin, J.L. (1990) Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell, 61, 1075-1087.
    • (1990) Cell , vol.61 , pp. 1075-1087
    • Vaughn, J.P.1    Dijkwel, P.A.2    Hamlin, J.L.3
  • 55
    • 0036232401 scopus 로고    scopus 로고
    • Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies
    • Dijkwel, P.A., Wang, S. and Hamlin, J.L. (2002) Initiation sites are distributed at frequent intervals in the Chinese hamster dihydrofolate reductase origin of replication but are used with very different efficiencies. Mol. Cell. Biol., 22, 3053-3065.
    • (2002) Mol. Cell. Biol , vol.22 , pp. 3053-3065
    • Dijkwel, P.A.1    Wang, S.2    Hamlin, J.L.3
  • 56
    • 0028829358 scopus 로고
    • Transition in specification of embryonic metazoan DNA replication origins
    • Hyrien, O., Maric, C. and Mechali, M. (1995) Transition in specification of embryonic metazoan DNA replication origins. Science, 270, 994-997.
    • (1995) Science , vol.270 , pp. 994-997
    • Hyrien, O.1    Maric, C.2    Mechali, M.3
  • 57
    • 84924634587 scopus 로고    scopus 로고
    • 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
    • Foulk, M.S., Urban, J.M., Casella, C. and Gerbi, S.A. (2015) 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., 25, 725-735.
    • (2015) Genome Res , vol.25 , pp. 725-735
    • Foulk, M.S.1    Urban, J.M.2    Casella, C.3    Gerbi, S.A.4
  • 59
    • 80052523848 scopus 로고    scopus 로고
    • Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
    • Cayrou, C., Coulombe, P., Vigneron, A., Stanojcic, S., Ganier, O., Peiffer, I., Rivals, E., Puy, A., Laurent-Chabalier, S., Desprat, R. et al. (2011) Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res., 21, 1438-1449.
    • (2011) Genome Res , vol.21 , pp. 1438-1449
    • Cayrou, C.1    Coulombe, P.2    Vigneron, A.3    Stanojcic, S.4    Ganier, O.5    Peiffer, I.6    Rivals, E.7    Puy, A.8    Laurent-Chabalier, S.9    Desprat, R.10
  • 61
    • 33748667563 scopus 로고    scopus 로고
    • Functional requirement of noncoding y RNAs for human chromosomal DNA replication
    • Christov, C.P., Gardiner, T.J., Szüts, D. and Krude, T. (2006) Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol. Cell. Biol., 26, 6993-7004.
    • (2006) Mol. Cell. Biol , vol.26 , pp. 6993-7004
    • Christov, C.P.1    Gardiner, T.J.2    Szüts, D.3    Krude, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.