메뉴 건너뛰기




Volumn 23, Issue 11, 2013, Pages 1774-1788

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; TRANSCRIPTOME;

EID: 84887404285     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.155218.113     Document Type: Article
Times cited : (70)

References (54)
  • 1
    • 33444460639 scopus 로고    scopus 로고
    • The mammalian b-globin origin of DNA replication
    • Aladjem MI. 2004. The mammalian b-globin origin of DNA replication. Front Biosci 9: 2540-2547.
    • (2004) Front Biosci , vol.9 , pp. 2540-2547
    • Aladjem, M.I.1
  • 2
    • 34447565003 scopus 로고    scopus 로고
    • Replication in context: Dynamic regulation of DNA replication patterns in metazoans
    • Aladjem MI. 2007. Replication in context: Dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 8: 588-600.
    • (2007) Nat Rev Genet , vol.8 , pp. 588-600
    • Aladjem, M.I.1
  • 3
    • 84866377745 scopus 로고    scopus 로고
    • Rif1 choreographs DNA replication timing
    • Aladjem MI. 2012. Rif1 choreographs DNA replication timing. EMBO J 31: 3650-3652.
    • (2012) EMBO J , vol.31 , pp. 3650-3652
    • Aladjem, M.I.1
  • 4
    • 4444384150 scopus 로고    scopus 로고
    • The replicon revisited: An old model learns new tricks in metazoan chromosomes
    • Aladjem MI, Fanning E. 2004. The replicon revisited: An old model learns new tricks in metazoan chromosomes. EMBO Rep 5: 686-691.
    • (2004) EMBO Rep , vol.5 , pp. 686-691
    • Aladjem, M.I.1    Fanning, E.2
  • 5
    • 79953207705 scopus 로고    scopus 로고
    • Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity
    • Balakrishnan L, Bambara RA. 2011. Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity. J Biol Chem 286: 6865-6870.
    • (2011) J Biol Chem , vol.286 , pp. 6865-6870
    • Balakrishnan, L.1    Bambara, R.A.2
  • 7
    • 0026607331 scopus 로고
    • ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex
    • Bell SP, Stillman B. 1992. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature 357: 128-134.
    • (1992) Nature , vol.357 , pp. 128-134
    • Bell, S.P.1    Stillman, B.2
  • 10
    • 0032472223 scopus 로고    scopus 로고
    • Discrete start sites for DNA synthesis in the yeast ARS1 origin
    • Bielinsky AK, Gerbi SA. 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
  • 11
    • 84867744921 scopus 로고    scopus 로고
    • DNA secondary structures: Stability and function of G-quadruplex structures
    • Bochman ML, Paeschke K, Zakian VA. 2012. DNA secondary structures: Stability and function of G-quadruplex structures. Nat Rev Genet 13: 770-780.
    • (2012) Nat Rev Genet , vol.13 , pp. 770-780
    • Bochman, M.L.1    Paeschke, K.2    Zakian, V.A.3
  • 12
    • 0023646792 scopus 로고
    • The localization of replication origins on ARS plasmids in S. Cerevisiae
    • Brewer BJ, Fangman WL. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463-471.
    • (1987) Cell , vol.51 , pp. 463-471
    • Brewer, B.J.1    Fangman, W.L.2
  • 15
    • 84857472898 scopus 로고    scopus 로고
    • MéchaliM. 2012a. New insights into replication origin characteristics in metazoans
    • Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, MéchaliM. 2012a. New insights into replication origin characteristics in metazoans. Cell Cycle 1: 658-667.
    • Cell Cycle , vol.1 , pp. 658-667
    • Cayrou, C.1    Coulombe, P.2    Puy, A.3    Rialle, S.4    Kaplan, N.5    Segal, E.6
  • 17
    • 0023277545 scopus 로고
    • Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
    • Chomczynski P, Sacchi N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156-159.
    • (1987) Anal Biochem , vol.162 , pp. 156-159
    • Chomczynski, P.1    Sacchi, N.2
  • 18
    • 36348988518 scopus 로고    scopus 로고
    • DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI
    • Czajkowsky DM, Liu J, Hamlin JL, Shao Z. 2008. DNA combing reveals intrinsic temporal disorder in the replication of yeast chromosome VI. J Mol Biol 375: 12-19.
    • (2008) J Mol Biol , vol.375 , pp. 12-19
    • Czajkowsky, D.M.1    Liu, J.2    Hamlin, J.L.3    Shao, Z.4
  • 19
    • 0025916653 scopus 로고
    • Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: Stabilization and enrichment of replication intermediates by isolation on the nuclear matrix
    • Dijkwel PA, Vaughn JP, Hamlin JL. 1991. Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: Stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol Cell Biol 11: 3850-3859.
    • (1991) Mol Cell Biol , vol.11 , pp. 3850-3859
    • Dijkwel, P.A.1    Vaughn, J.P.2    Hamlin, J.L.3
  • 20
    • 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 PA, Wang S, Hamlin JL. 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
  • 21
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
    • (2007) Nature , vol.447 , pp. 799-816
  • 22
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 23
    • 77956879643 scopus 로고    scopus 로고
    • Evaluating genome-scale approaches to eukaryotic DNA replication
    • Gilbert DM. 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
  • 26
    • 0026871077 scopus 로고
    • Transcription factors and the control of DNA replication
    • Heintz NH. 1992. Transcription factors and the control of DNA replication. Curr Opin Cell Biol 4: 459-467.
    • (1992) Curr Opin Cell Biol , vol.4 , pp. 459-467
    • Heintz, N.H.1
  • 27
    • 0014413470 scopus 로고
    • On the mechanism of DNA replication in mammalian chromosomes
    • Huberman JA, Riggs AD. 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
  • 28
    • 20144364292 scopus 로고    scopus 로고
    • Prevalence of quadruplexes in the human genome
    • Huppert JL, Balasubramanian S. 2005. Prevalence of quadruplexes in the human genome. Nucl Acids Res 33: 2908-2916.
    • (2005) Nucl Acids Res , vol.33 , pp. 2908-2916
    • Huppert, J.L.1    Balasubramanian, S.2
  • 30
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji H, Jiang H, MaW, Johnson DS, Myers RM,Wong WH. 2008. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
    • (2008) Nat Biotechnol , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Maw Johnson, D.S.3    Myers Rmwong, W.H.4
  • 31
    • 0029742239 scopus 로고    scopus 로고
    • Composite patterns in neutral/neutral twodimensional gels demonstrate inefficient replication origin usage
    • Kalejta RF, Hamlin JL. 1996. Composite patterns in neutral/neutral twodimensional gels demonstrate inefficient replication origin usage. Mol Cell Biol 16: 4915-4922.
    • (1996) Mol Cell Biol , vol.16 , pp. 4915-4922
    • Kalejta, R.F.1    Hamlin, J.L.2
  • 32
    • 0029740659 scopus 로고    scopus 로고
    • Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques
    • Kalejta RF, Lin HB, Dijkwel PA, Hamlin JL. 1996. Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques. Mol Cell Biol 16: 4923-4931.
    • (1996) Mol Cell Biol , vol.16 , pp. 4923-4931
    • Kalejta, R.F.1    Lin, H.B.2    Dijkwel, P.A.3    Hamlin, J.L.4
  • 33
    • 34250327950 scopus 로고    scopus 로고
    • Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
    • Karnani N, Taylor C, Malhotra A, Dutta A. 2007. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 17: 865-876.
    • (2007) Genome Res , vol.17 , pp. 865-876
    • Karnani, N.1    Taylor, C.2    Malhotra, A.3    Dutta, A.4
  • 34
    • 76049105950 scopus 로고    scopus 로고
    • Genomic study of replication initiation in human chromosomes reveals the influence 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 influence 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
  • 35
    • 0024564516 scopus 로고
    • Isolation of human sequences that replicate autonomously in human cells
    • Krysan PJ, Haase SB, Calos MP. 1989. Isolation of human sequences that replicate autonomously in human cells.Mol Cell Biol 9: 1026-1033.
    • (1989) Mol Cell Biol , vol.9 , pp. 1026-1033
    • Krysan, P.J.1    Haase, S.B.2    Calos, M.P.3
  • 37
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 38
    • 79955564639 scopus 로고    scopus 로고
    • Measuring reproducibility of highthroughput experiments
    • Li Q, Brown JB, Huang H, Bickel PJ. 2011. Measuring reproducibility of highthroughput experiments. Ann Appl Stat 5: 1752-1779.
    • (2011) Ann Appl Stat , vol.5 , pp. 1752-1779
    • Li, Q.1    Brown, J.B.2    Huang, H.3    Bickel, P.J.4
  • 40
    • 22144465137 scopus 로고    scopus 로고
    • Promiscuous initiation on mammalian chromosomal DNA templates and its possible suppression by transcription
    • Lin HB, Dijkwel PA, Hamlin JL. 2005. Promiscuous initiation on mammalian chromosomal DNA templates and its possible suppression by transcription. Exp Cell Res 308: 53-64.
    • (2005) Exp Cell Res , vol.308 , pp. 53-64
    • Lin, H.B.1    Dijkwel, P.A.2    Hamlin, J.L.3
  • 41
    • 0025218485 scopus 로고
    • Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant Chinese hamster cell line
    • Ma C, Leu TH, Hamlin JL. 1990. Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant Chinese hamster cell line. Mol Cell Biol 10: 1338-1346.
    • (1990) Mol Cell Biol , vol.10 , pp. 1338-1346
    • Ma, C.1    Leu, T.H.2    Hamlin, J.L.3
  • 43
    • 68349125910 scopus 로고    scopus 로고
    • Isolation of restriction fragments containing origins of replication from complex genomes
    • Mesner LD, Hamlin JL. 2009. Isolation of restriction fragments containing origins of replication from complex genomes. Methods Mol Biol 521: 315-328.
    • (2009) Methods Mol Biol , vol.521 , pp. 315-328
    • Mesner, L.D.1    Hamlin, J.L.2
  • 44
    • 33344470620 scopus 로고    scopus 로고
    • Isolating apparently pure libraries of replication origins from complex genomes
    • Mesner LD, Crawford EL, Hamlin JL. 2006. Isolating apparently pure libraries of replication origins from complex genomes. Mol Cell 21: 719-726.
    • (2006) Mol Cell , vol.21 , pp. 719-726
    • Mesner, L.D.1    Crawford, E.L.2    Hamlin, J.L.3
  • 45
    • 68349148701 scopus 로고    scopus 로고
    • Purification of restriction fragments containing replication intermediates from complex genomes for 2-D gel analysis
    • Mesner LD, Dijkwel PA, Hamlin JL. 2009. Purification of restriction fragments containing replication intermediates from complex genomes for 2-D gel analysis. Methods Mol Biol 521: 121-137.
    • (2009) Methods Mol Biol , vol.521 , pp. 121-137
    • Mesner, L.D.1    Dijkwel, P.A.2    Hamlin, J.L.3
  • 46
    • 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 LD, Valsakumar V, Karnani N, Dutta A, Hamlin JL, 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
  • 47
    • 16644394727 scopus 로고    scopus 로고
    • Plasticity of DNA replication initiation in Epstein-Barr virus episomes
    • Norio P, Schildkraut CL. 2004. Plasticity of DNA replication initiation in Epstein-Barr virus episomes. PLoS Biol 2: e152.
    • (2004) PLoS Biol , vol.2
    • Norio, P.1    Schildkraut, C.L.2
  • 49
    • 77957011803 scopus 로고    scopus 로고
    • Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization
    • Prasanth SG, Shen Z, Prasanth KV, Stillman B. 2010. Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. Proc Natl Acad Sci 107: 15093-15098.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 15093-15098
    • Prasanth, S.G.1    Shen, Z.2    Prasanth, K.V.3    Stillman, B.4
  • 50
    • 0035158109 scopus 로고    scopus 로고
    • Drosophila heterochromatin protein 1 (HP1)/origin recognition complex (ORC) protein is associated with HP1 and ORC and functions in heterochromatin-induced silencing
    • Shareef MM, King C, Damaj M, Badagu R, Huang DW, Kellum R. 2001. Drosophila heterochromatin protein 1 (HP1)/origin recognition complex (ORC) protein is associated with HP1 and ORC and functions in heterochromatin-induced silencing. Mol Biol Cell 12: 1671-1685.
    • (2001) Mol Biol Cell , vol.12 , pp. 1671-1685
    • Shareef, M.M.1    King, C.2    Damaj, M.3    Badagu, R.4    Huang, D.W.5    Kellum, R.6
  • 52
    • 0001792766 scopus 로고    scopus 로고
    • Roles of transcription factors in DNA replication
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • van der Vliet PC. 1996. Roles of transcription factors in DNA replication. In DNA replication in eukaryotic cells (ed.MDePamphilis), pp. 87-118. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1996) DNA Replication in Eukaryotic Cells (Ed.MDePamphilis) , pp. 87-118
    • Van Der Vliet, P.C.1
  • 53
    • 0024458475 scopus 로고
    • Mapping initiation sites of DNA replication in vivo using polymerase chain reaction amplification of nascent strand segments
    • Vassilev LT, Johnson EM. 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.T.1    Johnson, E.M.2
  • 54
    • 77956253770 scopus 로고    scopus 로고
    • Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing
    • Yang SC, Rhind N, Bechhoefer J. 2010. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol 6: 404.
    • (2010) Mol Syst Biol , vol.6 , pp. 404
    • Yang, S.C.1    Rhind, N.2    Bechhoefer, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.