메뉴 건너뛰기




Volumn 10, Issue 5, 2014, Pages

The Spatiotemporal Program of DNA Replication Is Associated with Specific Combinations of Chromatin Marks in Human Cells

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BUBBLE TRAPPING; CELL CYCLE S PHASE; CELL DIFFERENTIATION; CELL DIVISION; CELL LINE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; CPG ISLAND; DNA RECOMBINATION; DNA REPLICATION; DNA STRAND; EMBRYO; ENRICHMENT CULTURE; EPIGENETICS; GENETIC ASSOCIATION; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; RELIABILITY; SHORT NASCENT STRAND; SPATIOTEMPORAL ANALYSIS; CHROMATIN; GENETICS;

EID: 84901599268     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004282     Document Type: Article
Times cited : (115)

References (47)
  • 1
    • 57349149434 scopus 로고    scopus 로고
    • Genome-wide studies highlight indirect links between human replication origins and gene regulation
    • Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, et al. (2008) Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci USA 105: 15837-15842.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 15837-15842
    • Cadoret, J.C.1    Meisch, F.2    Hassan-Zadeh, V.3    Luyten, I.4    Guillet, C.5
  • 2
    • 84865553042 scopus 로고    scopus 로고
    • Genome-scale identification of active DNA replication origins
    • Cayrou C, Gregoire D, Coulombe P, Danis E, Mechali M, (2012) Genome-scale identification of active DNA replication origins. Methods 57: 158-164.
    • (2012) Methods , vol.57 , pp. 158-164
    • Cayrou, C.1    Gregoire, D.2    Coulombe, P.3    Danis, E.4    Mechali, M.5
  • 3
    • 0031278995 scopus 로고    scopus 로고
    • Replication initiation point mapping
    • Gerbi SA, Bielinsky AK, (1997) Replication initiation point mapping. Methods 13: 271-280.
    • (1997) Methods , vol.13 , pp. 271-280
    • Gerbi, S.A.1    Bielinsky, A.K.2
  • 4
    • 34547637896 scopus 로고    scopus 로고
    • High-throughput mapping of origins of replication in human cells
    • Lucas I, Palakodeti A, Jiang Y, Young DJ, Jiang N, et al. (2007) High-throughput mapping of origins of replication in human cells. EMBO Rep 8: 770-777.
    • (2007) EMBO Rep , vol.8 , pp. 770-777
    • Lucas, I.1    Palakodeti, A.2    Jiang, Y.3    Young, D.J.4    Jiang, N.5
  • 5
    • 77649231877 scopus 로고    scopus 로고
    • Genome-wide approaches to determining origin distribution
    • Cadoret JC, Prioleau MN, (2010) Genome-wide approaches to determining origin distribution. Chromosome Res 18: 79-89.
    • (2010) Chromosome Res , vol.18 , pp. 79-89
    • Cadoret, J.C.1    Prioleau, M.N.2
  • 6
    • 76049105950 scopus 로고    scopus 로고
    • Genomic study of replication initiation in human chromosomes reveals the inuence of transcription regulation and chromatin structure on origin selection
    • Karnani N, Taylor CM, Malhotra A, Dutta A, (2010) Genomic study of replication initiation in human chromosomes reveals the inuence of transcription regulation and chromatin structure on origin selection. Mol Biol Cell 21: 393-404.
    • (2010) Mol Biol Cell , vol.21 , pp. 393-404
    • Karnani, N.1    Taylor, C.M.2    Malhotra, A.3    Dutta, A.4
  • 7
    • 84871992012 scopus 로고    scopus 로고
    • Genome-wide mapping of hu-man DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing
    • Dellino GI, Cittaro D, Piccioni R, Luzi L, Banfi S, et al. (2013) Genome-wide mapping of hu-man DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res 23: 1-11.
    • (2013) Genome Res , vol.23 , pp. 1-11
    • Dellino, G.I.1    Cittaro, D.2    Piccioni, R.3    Luzi, L.4    Banfi, S.5
  • 8
    • 84864684316 scopus 로고    scopus 로고
    • Replication origins run (ultra) deep
    • Gilbert DM, (2012) Replication origins run (ultra) deep. Nat Struct Mol Biol 19: 740-742.
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 740-742
    • Gilbert, D.M.1
  • 9
    • 77951230100 scopus 로고    scopus 로고
    • Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data
    • Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, et al. (2010) Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 38: e13.
    • (2010) Nucleic Acids Res , vol.38
    • Blahnik, K.R.1    Dou, L.2    O'Geen, H.3    McPhillips, T.4    Xu, X.5
  • 10
    • 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, et al. (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
  • 11
    • 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 LD, Valsakumar V, Cieslik M, Pickin R, Hamlin JL, et al. (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
  • 12
    • 77952994784 scopus 로고    scopus 로고
    • Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
    • Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, et al. (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20: 761-770.
    • (2010) Genome Res , vol.20 , pp. 761-770
    • Ryba, T.1    Hiratani, I.2    Lu, J.3    Itoh, M.4    Kulik, M.5
  • 13
    • 34250376064 scopus 로고    scopus 로고
    • Identification of higher-order functional domains in the human ENCODE regions
    • Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA, (2007) Identification of higher-order functional domains in the human ENCODE regions. Genome Res 17: 917-927.
    • (2007) Genome Res , vol.17 , pp. 917-927
    • Thurman, R.E.1    Day, N.2    Noble, W.S.3    Stamatoyannopoulos, J.A.4
  • 14
    • 84864297655 scopus 로고    scopus 로고
    • Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation
    • Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, et al. (2012) Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell 47: 203-214.
    • (2012) Mol Cell , vol.47 , pp. 203-214
    • Chandra, T.1    Kirschner, K.2    Thuret, J.Y.3    Pope, B.D.4    Ryba, T.5
  • 16
    • 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, 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
  • 18
    • 84857472898 scopus 로고    scopus 로고
    • New insights into replication origin characteristics in metazoans
    • Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, et al. (2012) New insights into replication origin characteristics in metazoans. Cell Cycle 11: 658-667.
    • (2012) Cell Cycle , vol.11 , pp. 658-667
    • Cayrou, C.1    Coulombe, P.2    Puy, A.3    Rialle, S.4    Kaplan, N.5
  • 19
    • 77950661675 scopus 로고    scopus 로고
    • Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
    • Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, et al. (2010) Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 20: 447-457.
    • (2010) Genome Res , vol.20 , pp. 447-457
    • Chen, C.L.1    Rappailles, A.2    Duquenne, L.3    Huvet, M.4    Guilbaud, G.5
  • 20
    • 84855272663 scopus 로고    scopus 로고
    • Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome
    • Guilbaud G, Rappailles A, Baker A, Chen CL, Arneodo A, et al. (2011) Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput Biol 7: e1002322.
    • (2011) PLoS Comput Biol , vol.7
    • Guilbaud, G.1    Rappailles, A.2    Baker, A.3    Chen, C.L.4    Arneodo, A.5
  • 21
    • 76349123622 scopus 로고    scopus 로고
    • Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
    • Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, et al. (2010) Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 107: 139-144.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 139-144
    • Hansen, R.S.1    Thomas, S.2    Sandstrom, R.3    Canfield, T.K.4    Thurman, R.E.5
  • 22
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1    Kheradpour, P.2    Mikkelsen, T.S.3    Shoresh, N.4    Ward, L.D.5
  • 24
    • 37249025795 scopus 로고    scopus 로고
    • Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress
    • Ge XQ, Jackson DA, Blow JJ, (2007) Dormant origins licensed by excess Mcm2-7 are required for human cells to survive replicative stress. Genes Dev 21: 3331-3341.
    • (2007) Genes Dev , vol.21 , pp. 3331-3341
    • Ge, X.Q.1    Jackson, D.A.2    Blow, J.J.3
  • 25
    • 48249084972 scopus 로고    scopus 로고
    • Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication
    • Ibarra A, Schwob E, Mendez J, (2008) Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication. Proc Natl Acad Sci USA 105: 8956-8961.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 8956-8961
    • Ibarra, A.1    Schwob, E.2    Mendez, J.3
  • 26
    • 84898649803 scopus 로고    scopus 로고
    • G4 motifs affect origin positioning and efficiency in two vertebrate replicators
    • Valton AL, Hassan-Zadeh V, Lema I, Boggetto N, Alberti P, et al. (2014) G4 motifs affect origin positioning and efficiency in two vertebrate replicators. EMBO J in press.
    • (2014) EMBO J
    • Valton, A.L.1    Hassan-Zadeh, V.2    Lema, I.3    Boggetto, N.4    Alberti, P.5
  • 27
    • 84872038628 scopus 로고    scopus 로고
    • Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm
    • Audit B, Baker A, Chen CL, Rappailles A, Guilbaud G, et al. (2013) Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm. Nat Protoc 8: 98-110.
    • (2013) Nat Protoc , vol.8 , pp. 98-110
    • Audit, B.1    Baker, A.2    Chen, C.L.3    Rappailles, A.4    Guilbaud, G.5
  • 28
    • 70350669746 scopus 로고    scopus 로고
    • Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells
    • Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton Carafa Y, et al. (2009) Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. Nucleic Acids Res 37: 6064-6075.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6064-6075
    • Audit, B.1    Zaghloul, L.2    Vaillant, C.3    Chevereau, G.4    d'Aubenton Carafa, Y.5
  • 30
    • 0038505671 scopus 로고    scopus 로고
    • Epigenomic replication: linking epigenetics to DNA replication
    • McNairn AJ, Gilbert DM, (2003) Epigenomic replication: linking epigenetics to DNA replication. Bioessays 25: 647-656.
    • (2003) Bioessays , vol.25 , pp. 647-656
    • McNairn, A.J.1    Gilbert, D.M.2
  • 31
    • 77956225395 scopus 로고    scopus 로고
    • Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions
    • Gay S, Lachages AM, Millot GA, Courbet S, Letessier A, et al. (2010) Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions. EMBO Rep 11: 698-704.
    • (2010) EMBO Rep , vol.11 , pp. 698-704
    • Gay, S.1    Lachages, A.M.2    Millot, G.A.3    Courbet, S.4    Letessier, A.5
  • 32
    • 0038302923 scopus 로고    scopus 로고
    • Replication of the chicken beta-globin locus: early- firing origins at the 5′ HS4 insulator and the rho- and betaA-globin genes show opposite epigenetic modifications
    • Prioleau MN, Gendron MC, Hyrien O, (2003) Replication of the chicken beta-globin locus: early- firing origins at the 5′ HS4 insulator and the rho- and betaA-globin genes show opposite epigenetic modifications. Mol Cell Biol 23: 3536-3549.
    • (2003) Mol Cell Biol , vol.23 , pp. 3536-3549
    • Prioleau, M.N.1    Gendron, M.C.2    Hyrien, O.3
  • 33
    • 54949085778 scopus 로고    scopus 로고
    • Global reorganization of repli-cation domains during embryonic stem cell differentiation
    • Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, et al. (2008) Global reorganization of repli-cation domains during embryonic stem cell differentiation. PLoS Biol 6: e245.
    • (2008) PLoS Biol , vol.6
    • Hiratani, I.1    Ryba, T.2    Itoh, M.3    Yokochi, T.4    Schwaiger, M.5
  • 34
    • 78149281634 scopus 로고    scopus 로고
    • The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells
    • Tardat M, Brustel J, Kirsh O, Lefevbre C, Callanan M, et al. (2010) The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells. Nat Cell Biol 12: 1086-1093.
    • (2010) Nat Cell Biol , vol.12 , pp. 1086-1093
    • Tardat, M.1    Brustel, J.2    Kirsh, O.3    Lefevbre, C.4    Callanan, M.5
  • 36
    • 44149084708 scopus 로고    scopus 로고
    • DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin
    • Goren A, Tabib A, Hecht M, Cedar H, (2008) DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. Genes Dev 22: 1319-1324.
    • (2008) Genes Dev , vol.22 , pp. 1319-1324
    • Goren, A.1    Tabib, A.2    Hecht, M.3    Cedar, H.4
  • 37
    • 84858972800 scopus 로고    scopus 로고
    • USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator
    • Hassan-Zadeh V, Chilaka S, Cadoret JC, Ma MK, Boggetto N, et al. (2012) USF binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator. PLoS Biol 10: e1001277.
    • (2012) PLoS Biol , vol.10
    • Hassan-Zadeh, V.1    Chilaka, S.2    Cadoret, J.C.3    Ma, M.K.4    Boggetto, N.5
  • 39
    • 84874778180 scopus 로고    scopus 로고
    • PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C
    • Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, et al. (2013) PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 9: e1003283.
    • (2013) PLoS Genet , vol.9
    • Lo Sardo, F.1    Lanzuolo, C.2    Comoglio, F.3    De Bardi, M.4    Paro, R.5
  • 40
    • 49649099991 scopus 로고    scopus 로고
    • Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression
    • Aoto T, Saitoh N, Sakamoto Y, Watanabe S, Nakao M, (2008) Polycomb group protein-associated chromatin is reproduced in post-mitotic G1 phase and is required for S phase progression. J Biol Chem 283: 18905-18915.
    • (2008) J Biol Chem , vol.283 , pp. 18905-18915
    • Aoto, T.1    Saitoh, N.2    Sakamoto, Y.3    Watanabe, S.4    Nakao, M.5
  • 41
    • 84860504565 scopus 로고    scopus 로고
    • Polycomb function during oogenesis is required for mouse embryonic development
    • Posfai E, Kunzmann R, Brochard V, Salvaing J, Cabuy E, et al. (2012) Polycomb function during oogenesis is required for mouse embryonic development. Genes Dev 26: 920-932.
    • (2012) Genes Dev , vol.26 , pp. 920-932
    • Posfai, E.1    Kunzmann, R.2    Brochard, V.3    Salvaing, J.4    Cabuy, E.5
  • 43
    • 20144364292 scopus 로고    scopus 로고
    • Prevalence of quadruplexes in the human genome
    • Huppert JL, 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
  • 44
    • 84861147700 scopus 로고    scopus 로고
    • Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines
    • Baker A, Audit B, Chen CL, Moindrot B, Leleu A, et al. (2012) Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput Biol 8: e1002443.
    • (2012) PLoS Comput Biol , vol.8
    • Baker, A.1    Audit, B.2    Chen, C.L.3    Moindrot, B.4    Leleu, A.5
  • 45
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • Abecasis GR, (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1
  • 46
    • 79959258968 scopus 로고    scopus 로고
    • Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems
    • Le Cao KA, Boitard S, Besse P, (2011) Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinformatics 12: 253.
    • (2011) BMC Bioinformatics , vol.12 , pp. 253
    • Le Cao, K.A.1    Boitard, S.2    Besse, P.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.