Epigenetic control of DNA replication dynamics in mammals

Nucleus

Volumn 2, Issue 5, 2011, Pages

  Casas Delucchi, Corella S ^a   Cristina Cardoso, M ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Chromatin; DNA methylation; DNA replication; Epigenetics; Histone modifications; Pre replication complexes; Replication foci; Replication origin; Replicon; Replisome

Indexed keywords

CELL CYCLE PROTEIN 6; CPG OLIGODEOXYNUCLEOTIDE; DNA POLYMERASE; HISTONE ACETYLTRANSFERASE; ORIGIN RECOGNITION COMPLEX; REPLICATION FACTOR A; REPLICATION LICENSING FACTOR CDT1; TRICHOSTATIN A;

CELL CYCLE S PHASE; CHROMATIN; CPG ISLAND; DNA METHYLATION; DNA REPLICATION; EPIGENETICS; GENOME; HETEROCHROMATIN; MAMMAL; MATRIX ATTACHMENT REGION; MOLECULAR DYNAMICS; NONHUMAN; REVIEW; SACCHAROMYCES CEREVISIAE;

MAMMALIA; PROKARYOTA;

EID: 80054715963     PISSN: 19491034     EISSN: 19491042     Source Type: Journal    
DOI: 10.4161/nucl.2.5.17861     Document Type: Review

References (161)

1. Huberman JA, Riggs AD. Autoradiography of chromosomal DNA fibers from Chinese hamster cells. Proc Natl Acad Sci USA 1966; 55:599-606; PMID:5221245; DOI:10.1073/pnas.55.3.599.
2. Gilbert DM. Making sense of eukaryotic DNA replication origins. Science 2001; 294:96-100; PMID:11588251; DOI:10.1126/science.1061724.
3. Schwaiger M, Schubeler D. A question of timing: emerging links between transcription and replication. Curr Opin Genet Dev 2006; 16:177-83; PMID:16503127; DOI:10.1016/j.gde.2006.02.007.
4. Taylor JH. Asynchronous duplication of chromosomes in cultured cells of Chinese hamster. J Biophys Biochem Cytol 1960; 7:455-63; PMID:13837165; DOI:10.1083/jcb.7.3.455.
5. Nakamura H, Morita T, Sato C. Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp Cell Res 1986; 165:291-7; PMID:3720850; DOI:10.1016/0014-4827(86)90583-5.
6. Patel PK, Arcangioli B, Baker SP, Bensimon A, Rhind N. DNA replication origins fire stochastically in fission yeast. Mol Biol Cell 2005; 17:308-16; PMID:16251353; DOI:10.1091/mbc.E05-07-0657.
7. Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, et al. Replication dynamics of the yeast genome. Science 2001; 294:115-21; PMID:11588253; DOI:10.1126/science.294.5540.115.
8. Weinreich M, Palacios DeBeer MA, Fox CA. The activities of eukaryotic replication origins in chromatin. Biochim Biophys Acta 2004; 1677:142-57.
9. Calvi BR, Lilly MA, Spradling AC. Cell cycle control of chorion gene amplification. Genes Dev 1998; 12:734-44; PMID:9499407; DOI:10.1101/gad.12.5.734.
10. Hatton KS, Dhar V, Brown EH, Iqbal MA, Stuart S, Didamo VT, et al. Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol 1988; 8:2149-58; PMID:3386634.
11. Hiratani I, Gilbert DM. Replication timing as an epigenetic mark. Epigenetics 2009; 4:93-7; PMID:19242104; DOI:10.4161/epi.4.2.7772.
12. Hyrien O, Maric C, Mechali M. Transition in specification of embryonic metazoan DNA replication origins. Science 1995; 270:994-7; PMID:7481806; DOI:10.1126/science.270.5238.994.
13. Norio P, Kosiyatrakul S, Yang Q, Guan Z, Brown NM, Thomas S, et al. Progressive activation of DNA replication initiation in large domains of the immunoglobulin heavy chain locus during B cell development. Mol Cell 2005; 20:575-87; PMID:16307921; DOI:10.1016/j. molcel.2005.10.029.
14. Aran D, Toperoff G, Rosenberg M, Hellman A. Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 2011; 20:670-80; PMID:21112978; DOI:10.1093/ hmg/ddq513.
15. Eaton ML, Prinz JA, Macalpine HK, Tretyakov G, Kharchenko PV, Macalpine DM. Chromatin signatures of the Drosophila replication program. Genome Res 2011; 21:164-74; PMID:21177973; DOI:10.1101/ gr.116038.110.
16. Karnani N, Taylor C, Malhotra A, Dutta A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 2007; 17:865-76; PMID:17568004; DOI:10.1101/gr.5427007.
17. Lucas I, Palakodeti A, Jiang Y, Young DJ, Jiang N, Fernald AA, et al. High-throughput mapping of origins of replication in human cells. EMBO Rep 2007; 8:770-7; PMID:17668008; DOI:10.1038/sj.embor.7401026.
18. Li JJ, Kelly TJ. Simian virus 40 DNA replication in vitro. Proc Natl Acad Sci USA 1984; 81:6973-7; PMID:6095264; DOI:10.1073/pnas.81.22.6973.
19. Nossal NG. Protein-protein interactions at a DNA replication fork: bacteriophage T4 as a model. FASEB J 1992; 6:871-8; PMID:1310946.
20. Bell SP, Dutta A. DNA replication in eukaryotic cells. Annu Rev Biochem 2002; 71:333-74; PMID:12045100; DOI:10.1146/annurev.biochem.71.110601.135425.
21. Dutta A, Bell SP. Initiation of DNA replication in eukaryotic cells. Annu Rev Cell Dev Biol 1997; 13:293-332; PMID:9442876; DOI:10.1146/annurev. cellbio.13.1.293.
22. DePamphilis ML. Cell cycle dependent regulation of the origin recognition complex. Cell Cycle 2005; 4:70-9; PMID:15611627; DOI:10.4161/cc.4.1.1333.
23. Ohta S, Tatsumi Y, Fujita M, Tsurimoto T, Obuse C. The ORC1 cycle in human cells: II. Dynamic changes in the human ORC complex during the cell cycle. J Biol Chem 2003; 278:41535-40; PMID:12909626; DOI:10.1074/jbc.M307535200.
24. Wu PY, Nurse P. Establishing the program of origin firing during S phase in fission Yeast. Cell 2009; 136:852-64; PMID:19269364; DOI:10.1016/j. cell.2009.01.017.
25. Harvey KJ, Newport J. Metazoan origin selection: origin recognition complex chromatin binding is regulated by CDC6 recruitment and ATP hydrolysis. J Biol Chem 2003; 278:48524-8; PMID:14506278; DOI:10.1074/jbc.M307661200.
26. Mizushima T, Takahashi N, Stillman B. Cdc6p modulates the structure and DNA binding activity of the origin recognition complex in vitro. Genes Dev 2000; 14:1631-41; PMID:10887157.
27. Donovan S, Harwood J, Drury LS, Diffley JF. Cdc6p-dependent loading of Mcm proteins onto prereplicative chromatin in budding yeast. Proc Natl Acad Sci USA 1997; 94:5611-6; PMID:9159120; DOI:10.1073/pnas.94.11.5611.
28. Maiorano D, Lemaitre JM, Mechali M. Stepwise regulated chromatin assembly of MCM2-7 proteins. J Biol Chem 2000; 275:8426-31; PMID:10722676; DOI:10.1074/jbc.275.12.8426.
29. Shin JH, Grabowski B, Kasiviswanathan R, Bell SD, Kelman Z. Regulation of minichromosome maintenance helicase activity by Cdc6. J Biol Chem 2003; 278:38059-67; PMID:12837750; DOI:10.1074/jbc. M305477200.
30. Miotto B, Struhl K. HBO1 histone acetylase activity is essential for DNA replication licensing and inhibited by Geminin. Mol Cell 2010; 37:57-66; PMID:20129055; DOI:10.1016/j.molcel.2009.12.012.
31. McGarry TJ, Kirschner MW. Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell 1998; 93:1043-53; PMID:9635433; DOI:10.1016/ S0092-8674(00)81209-X.
32. Forsburg SL. Eukaryotic MCM proteins: beyond replication initiation. Microbiol Mol Biol Rev 2004; 68:109-31; PMID:15007098; DOI:10.1128/ MMBR.68.1.109-31.2004.
33. Labib K, Diffley JF. Is the MCM2-7 complex the eukaryotic DNA replication fork helicase? Curr Opin Genet Dev 2001; 11:64-70; PMID:11163153; DOI:10.1016/S0959-437X(00)00158-1.
34. Walter J, Newport J. Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA and DNA polymerase alpha. Mol Cell 2000; 5:617-27; PMID:10882098; DOI:10.1016/S1097-2765(00)80241-5.
35. Aparicio OM, Weinstein DM, Bell SP. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 1997; 91:59-69; PMID:9335335; DOI:10.1016/S0092-8674(01)80009-X.
36. Hyrien O, Marheineke K, Goldar A. Paradoxes of eukaryotic DNA replication: MCM proteins and the random completion problem. Bioessays 2003; 25:116-25; PMID:12539237; DOI:10.1002/bies.10208.
37. Laskey RA, Madine MA. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks. EMBO Rep 2003; 4:26-30; PMID:12524516; DOI:10.1038/sj.embor.embor706.
38. Masata M, Juda P, Raska O, Cardoso MC, Raska I. A fraction of MCM 2 proteins remain associated with replication foci during a major part of S phase. Folia Biol (Praha) 2011; 57:3-11.
39. Bousset K, Diffley JF. The Cdc7 protein kinase is required for origin firing during S phase. Genes Dev 1998; 12:480-90; PMID:9472017; DOI:10.1101/gad.12.4.480.
40. Donaldson AD, Fangman WL, Brewer BJ. Cdc7 is required throughout the yeast S phase to activate replication origins. Genes Dev 1998; 12:491-501; PMID:9472018; DOI:10.1101/gad.12.4.491.
41. Pasero P, Duncker BP, Schwob E, Gasser SM. A role for the Cdc7 kinase regulatory subunit Dbf4p in the formation of initiation-competent origins of replication. Genes Dev 1999; 13:2159-76; PMID:10465792; DOI:10.1101/gad.13.16.2159.
42. Sheu YJ, Stillman B. The Dbf4-Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4. Nature 2010; 463:113-7; PMID:20054399; DOI:10.1038/nature08647.
43. Gambus A, Jones RC, Sanchez-Diaz A, Kanemaki M, van Deursen F, Edmondson RD, et al. GINS maintains association of Cdc45 with MCM in replisome progression complexes at eukaryotic DNA replication forks. Nat Cell Biol 2006; 8:358-66; PMID:16531994; DOI:10.1038/ncb1382.
44. Kamimura Y, Tak YS, Sugino A, Araki H. Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. EMBO J 2001; 20:2097-107; PMID:11296242; DOI:10.1093/emboj/20.8.2097.
45. Kanemaki M, Labib K. Distinct roles for Sld3 and GINS during establishment and progression of eukaryotic DNA replication forks. EMBO J 2006; 25:1753-63; PMID:16601689; DOI:10.1038/sj.emboj.7601063.
46. Homesley L, Lei M, Kawasaki Y, Sawyer S, Christensen T, Tye BK. Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins. Genes Dev 2000; 14:913-26; PMID:10783164.
47. Merchant AM, Kawasaki Y, Chen Y, Lei M, Tye BK. A lesion in the DNA replication initiation factor Mcm10 induces pausing of elongation forks through chromosomal replication origins in Saccharomyces cerevisiae. Mol Cell Biol 1997; 17:3261-71; PMID:9154825.
48. Aparicio OM, Stout AM, Bell SP. Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication. Proc Natl Acad Sci USA 1999; 96:9130-5; PMID:10430907; DOI:10.1073/pnas.96.16.9130.
49. Pacek M, Tutter AV, Kubota Y, Takisawa H, Walter JC. Localization of MCM2-7, Cdc45 and GINS to the site of DNA unwinding during eukaryotic DNA replication. Mol Cell 2006; 21:581-7; PMID:16483939; DOI:10.1016/j.molcel.2006.01.030.
50. Zou L, Stillman B. Assembly of a complex containing Cdc45p, replication protein A and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase. Mol Cell Biol 2000; 20:3086-96; PMID:10757793; DOI:10.1128/MCB.20.9.3086-96.2000.
51. Masumoto H, Sugino A, Araki H. Dpb11 controls the association between DNA polymerases alpha and epsilon and the autonomously replicating sequence region of budding yeast. Mol Cell Biol 2000; 20:2809-17; PMID:10733584; DOI:10.1128/MCB.20.8.2809-17.2000.
52. Hübscher U, Maga G, Spadari S. Eukaryotic DNA polymerases. Annu Rev Biochem 2002; 71:133-63; PMID:12045093; DOI:10.1146/annurev.biochem.71.090501.150041.
53. Görisch SM, Cardoso MC. PCNA and DNA Replication (I). In: Lee H, Szyf M, Eds. In Profilerating Cell Nuclear Antigen: Research SignPost 2006; 51-70.
54. Campbell JL. Eukaryotic DNA replication. Annu Rev Biochem 1986; 55:733-71; PMID:3017196; DOI:10.1146/annurev.bi.55.070186.003505.
55. Lebofsky R, Heilig R, Sonnleitner M, Weissenbach J, Bensimon A. DNA replication origin interference increases the spacing between initiation events in human cells. Mol Biol Cell 2006; 17:5337-45; PMID:17005913; DOI:10.1091/mbc.E06-04-0298.
56. Sporbert A, Gahl A, Ankerhold R, Leonhardt H, Cardoso MC. DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters. Mol Cell 2002; 10:1355-65; PMID:12504011; DOI:10.1016/S1097-2765(02)00729-3.
57. Leonhardt H, Rahn HP, Weinzierl P, Sporbert A, Cremer T, Zink D, et al. Dynamics of DNA replication factories in living cells. J Cell Biol 2000; 149:271-80; PMID:10769021; DOI:10.1083/jcb.149.2.271.
58. Maya-Mendoza A, Olivares-Chauvet P, Shaw A, Jackson DA. S phase progression in human cells is dictated by the genetic continuity of DNA foci. PLoS Genet 2010; 6:1000900; PMID:20386742; DOI:10.1371/journal.pgen.1000900.
59. Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, et al. Replication timing of the human genome. Hum Mol Genet 2004; 13:191-202; PMID:14645202; DOI:10.1093/hmg/ddh016.
60. Braunstein JD, Schulze D, DelGiudice T, Furst A, Schildkraut CL. The temporal order of replication of murine immunoglobulin heavy chain constant region sequences corresponds to their linear order in the genome. Nucleic Acids Res 1982; 10:6887-902; PMID:6294619; DOI:10.1093/nar/10.21.6887.
61. O'Keefe RT, Henderson SC, Spector DL. Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences. J Cell Biol 1992; 116:1095-110; PMID:1740468; DOI:10.1083/jcb.116.5.1095.
62. Baddeley D, Chagin VO, Schermelleh L, Martin S, Pombo A, Carlton PM, et al. Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res 2010; 38:8; PMID:19864256; DOI:10.1093/nar/gkp901.
63. Maison C, Almouzni G. HP1 and the dynamics of heterochromatin maintenance. Nat Rev Mol Cell Biol 2004; 5:296-304; PMID:15071554; DOI:10.1038/nrm1355.
64. Alexandrova O, Solovei I, Cremer T, David CN. Replication labeling patterns and chromosome territories typical of mammalian nuclei are conserved in the early metazoan Hydra. Chromosoma 2003; 112:190-200; PMID:14615892; DOI:10.1007/s00412-003-0259-z.
65. Pope BD, Hiratani I, Gilbert DM. Domain-wide regulation of DNA replication timing during mammalian development. Chromosome Res 2010; 18:127-36; PMID:20013151; DOI:10.1007/s10577-009-9100-8.
66. Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2001; 2:292-301; PMID:11283701; DOI:10.1038/35066075.
67. Sadoni N, Cardoso MC, Stelzer EH, Leonhardt H, Zink D. Stable chromosomal units determine the spatial and temporal organization of DNA replication. J Cell Sci 2004; 117:5353-65; PMID:15466893; DOI:10.1242/jcs.01412.
68. Craig JM, Bickmore WA. Chromosome bands-flavours to savour. Bioessays 1993; 15:349-54; PMID:8343145; DOI:10.1002/bies.950150510.
69. Stinchcomb DT, Struhl K, Davis RW. Isolation and characterisation of a yeast chromosomal replicator. Nature 1979; 282:39-43; PMID:388229; DOI:10.1038/282039a0.
70. Theis JF, Dershowitz A, Irene C, Maciariello C, Tobin ML, Liberi G, et al. Identification of mutations that decrease the stability of a fragment of Saccharomyces cerevisiae chromosome III lacking efficient replicators. Genetics 2007; 177:1445-58; PMID:17720931; DOI:10.1534/genetics.107.074690.
71. Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. Conserved nucleosome positioning defines replication origins. Genes Dev 2010; 24:748-53; PMID:20351051; DOI:10.1101/gad.1913210.
72. Diffley JF, Stillman B. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 1989; 246:1034-8; PMID:2511628; DOI:10.1126/science.2511628.
73. Rodríguez-Navarro S. Insights into SAGA function during gene expression. EMBO Rep 2009; 10:843-50; PMID:19609321; DOI:10.1038/embor.2009.168.
74. Vogelauer M, Rubbi L, Lucas I, Brewer BJ, Grunstein M. Histone acetylation regulates the time of replication origin firing. Mol Cell 2002; 10:1223-33; PMID:12453428; DOI:10.1016/S1097-2765(02)00702-5.
75. Bernstein HB, Kinter AL, Jackson R, Fauci AS. Neonatal natural killer cells produce chemokines and suppress HIV replication in vitro. AIDS Res Hum Retroviruses 2004; 20:1189-95; PMID:15588341.
76. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005; 309:626-30; PMID:15961632; DOI:10.1126/science.1112178.
77. Crampton A, Chang F, Pappas DL Jr, Frisch RL, Weinreich M. An ARS element inhibits DNA replication through a SIR2-dependent mechanism. Mol Cell 2008; 30:156-66; PMID:18439895; DOI:10.1016/j.molcel.2008.02.019.
78. Simpson RT. Nucleosome positioning can affect the function of a cis-acting DNA element in vivo. Nature 1990; 343:387-9; PMID:2405281; DOI:10.1038/343387a0.
79. Lipford JR, Bell SP. Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol Cell 2001; 7:21-30; PMID:11172708; DOI:10.1016/S1097-2765(01)00151-4.
80. Méchali M. Eukaryotic DNA replication origins: many choices for appropriate answers. Nat Rev Mol Cell Biol 2010; 11:728-38; PMID:20861881; DOI:10.1038/nrm2976.
81. Stanojcic S, Lemaitre JM, Brodolin K, Danis E, Mechali M. In Xenopus egg extracts, DNA replication initiates preferentially at or near asymmetric AT sequences. Mol Cell Biol 2008; 28:5265-74; PMID:18573882; DOI:10.1128/MCB.00181-08.
82. Li F, Chen J, Solessio E, Gilbert DM. Spatial distribution and specification of mammalian replication origins during G1 phase. J Cell Biol 2003; 161:257-66; PMID:12707307; DOI:10.1083/jcb.200211127.
83. Hyrien O, Mechali M. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J 1993; 12:4511-20; PMID:8223461.
84. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 2008; 6:245; PMID:18842067; DOI:10.1371/journal.pbio.0060245.
85. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, et al. Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci USA 2008; 105:15837-42; PMID:18838675; DOI:10.1073/pnas.0805208105.
86. Buongiorno-Nardelli M, Micheli G, Carri MT, Marilley M. A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 1982; 298:100-2; PMID:7088157; DOI:10.1038/298100a0.
87. Girard-Reydet C, Gregoire D, Vassetzky Y, Mechali M. DNA replication initiates at domains overlapping with nuclear matrix attachment regions in the xenopus and mouse c-myc promoter. Gene 2004; 332:129-38; PMID:15145062; DOI:10.1016/j.gene.2004.02.031.
88. Jackson DA. The organization of replication centres in higher eukaryotes. Bioessays 1990; 12:87-9; PMID:2188654; DOI:10.1002/bies.950120207.
89. Glazko GV, Koonin EV, Rogozin IB, Shabalina SA. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 2003; 19:119-24; PMID:12615002; DOI:10.1016/S0168-9525(03)00016-7.
90. Razin SV, Petrov P, Hancock R. Precise localization of the alpha-globin gene cluster within one of the 20-to 300-kilobase DNA fragments released by cleavage of chicken chromosomal DNA at topoisomerase II sites in vivo: evidence that the fragments are DNA loops or domains. Proc Natl Acad Sci USA 1991; 88:8515-9; PMID:1656447; DOI:10.1073/pnas.88.19.8515.
91. Dijkwel PA, Vaughn JP, Hamlin JL. 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 1991; 11:3850-9; PMID:2072896.
92. Jenke AC, Stehle IM, Herrmann F, Eisenberger T, Baiker A, Bode J, et al. Nuclear scaffold/matrix attached region modules linked to a transcription unit are sufficient for replication and maintenance of a mammalian episome. Proc Natl Acad Sci USA 2004; 101:11322-7; PMID:15272077; DOI:10.1073/pnas.0401355101.
93. Papapetrou EP, Ziros PG, Micheva ID, Zoumbos NC, Athanassiadou A. Gene transfer into human hematopoietic progenitor cells with an episomal vector carrying an S/MAR element. Gene Ther 2006; 13:40-51; PMID:16094410; DOI:10.1038/sj.gt.3302593.
94. Mirkovitch J, Mirault ME, Laemmli UK. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 1984; 39:223-32; PMID:6091913; DOI:10.1016/0092-8674(84)90208-3.
95. Eivazova ER, Gavrilov A, Pirozhkova I, Petrov A, Iarovaia OV, Razin SV, et al. Interaction in vivo between the two matrix attachment regions flanking a single chromatin loop. J Mol Biol 2009; 386:929-37; PMID:19118562; DOI:10.1016/j.jmb.2008.12.022.
96. Courbet S, Gay S, Arnoult N, Wronka G, Anglana M, Brison O, et al. Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 2008; 455:557-60; PMID:18716622; DOI:10.1038/nature07233.
97. Lemaitre JM, Danis E, Pasero P, Vassetzky Y, Mechali M. Mitotic remodeling of the replicon and chromosome structure. Cell 2005; 123:787-801; PMID:16325575; DOI:10.1016/j.cell.2005.08.045.
98. Cheng LZ, Workman JL, Kingston RE, Kelly TJ. Regulation of DNA replication in vitro by the transcriptional activation domain of GAL4-VP16. Proc Natl Acad Sci USA 1992; 89:589-93; PMID:1309949; DOI:10.1073/pnas.89.2.589.
99. Danis E, Brodolin K, Menut S, Maiorano D, Girard-Reydet C, Mechali M. Specification of a DNA replication origin by a transcription complex. Nat Cell Biol 2004; 6:721-30; PMID:15247921; DOI:10.1038/ncb1149.
100. Ghosh D. Nonparametric methods for analyzing replication origins in genomewide data. Funct Integr Genomics 2005; 5:28-31; PMID:15599787; DOI:10.1007/s10142-004-0122-1.
101. Maric C, Benard M, Pierron G. Developmentally regulated usage of Physarum DNA replication origins. EMBO Rep 2003; 4:474-8; PMID:12776736; DOI:10.1038/sj.embor.embor822.
102. Minami H, Takahashi J, Suto A, Saitoh Y, Tsutsumi K. Binding of AlF-C, an Orc1-binding transcriptional regulator, enhances replicator activity of the rat aldolase B origin. Mol Cell Biol 2006; 26:8770-80; PMID:16982680; DOI:10.1128/MCB.00949-06.
103. Kohzaki H, Murakami Y. Transcription factors and DNA replication origin selection. Bioessays 2005; 27:1107-16; PMID:16237674; DOI:10.1002/bies.20316.
104. MacAlpine DM, Rodriguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 2004; 18:3094-105; PMID:15601823; DOI:10.1101/gad.1246404.
105. Haase SB, Heinzel SS, Calos MP. Transcription inhibits the replication of autonomously replicating plasmids in human cells. Mol Cell Biol 1994; 14:2516-24; PMID:8139554.
106. Mesner LD, Hamlin JL. Specific signals at the 3' end of the DHFR gene define one boundary of the downstream origin of replication. Genes Dev 2005; 19:1053-66; PMID:15879555; DOI:10.1101/gad.1307105.
107. Sasaki T, Ramanathan S, Okuno Y, Kumagai C, Shaikh SS, Gilbert DM. The Chinese hamster dihydrofolate reductase replication origin decision point follows activation of transcription and suppresses initiation of replication within transcription units. Mol Cell Biol 2006; 26:1051-62; PMID:16428457; DOI:10.1128/MCB.26.3.1051-62.2006.
108. Lunyak VV, Ezrokhi M, Smith HS, Gerbi SA. Developmental changes in the Sciara II/9A initiation zone for DNA replication. Mol Cell Biol 2002; 22:8426-37; PMID:12446763; DOI:10.1128/MCB.22.24.8426-37.2002.
109. Saha S, Shan Y, Mesner LD, Hamlin JL. The promoter of the Chinese hamster ovary dihydrofolate reductase gene regulates the activity of the local origin and helps define its boundaries. Genes Dev 2004; 18:397-410; PMID:14977920; DOI:10.1101/gad.1171404.
110. Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gomez M. Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet 2009; 5:1000446; PMID:19360092; DOI:10.1371/journal.pgen.1000446.
111. Schwaiger M, Stadler MB, Bell O, Kohler H, Oakeley EJ, Schubeler D. Chromatin state marks cell-type-and gender-specific replication of the Drosophila genome. Genes Dev 2009; 23:589-601; PMID:19270159; DOI:10.1101/gad.511809.
112. Wei X, Samarabandu J, Devdhar RS, Siegel AJ, Acharya R, Berezney R. Segregation of transcription and replication sites into higher order domains. Science 1998; 281:1502-6; PMID:9727975; DOI:10.1126/science.281.5382.1502.
113. Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton-Carafa Y, Thermes C, et al. Open chromatin encoded in DNA sequence is the signature of 'master' replication origins in human cells. Nucleic Acids Res 2009; 37:6064-75; PMID:19671527; DOI:10.1093/nar/gkp631.
114. Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, et al. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLOS Comput Biol 2008; 4:1000216; PMID:18989395; DOI:10.1371/journal.pcbi.1000216.
115. Zhou J, Chau CM, Deng Z, Shiekhattar R, Spindler MP, Schepers A, et al. Cell cycle regulation of chromatin at an origin of DNA replication. EMBO J 2005; 24:1406-17; PMID:15775975; DOI:10.1038/sj.emboj.7600609.
116. Berger SL. The complex language of chromatin regulation during transcription. Nature 2007; 447:407-12; PMID:17522673; DOI:10.1038/nature05915.
117. Lu ZH, Sittman DB, Romanowski P, Leno GH. Histone H1 reduces the frequency of initiation in Xenopus egg extract by limiting the assembly of prereplication complexes on sperm chromatin. Mol Biol Cell 1998; 9:1163-76; PMID:9571247.
118. Tardat M, Brustel J, Kirsh O, Lefevbre C, Callanan M, Sardet C, et al. The histone H4 Lys 20 methyltransferase PR-Set7 regulates replication origins in mammalian cells. Nat Cell Biol 2010; 12:1086-93; PMID:20953199; DOI:10.1038/ncb2113.
119. Aggarwal BD, Calvi BR. Chromatin regulates origin activity in Drosophila follicle cells. Nature 2004; 430:372-6; PMID:15254542; DOI:10.1038/nature02694.
120. Wong PG, Glozak MA, Cao TV, Vaziri C, Seto E, Alexandrow M. Chromatin unfolding by Cdt1 regulates MCM loading via opposing functions of HBO1 and HDAC11-geminin. Cell Cycle 2010; 9:4351-63; PMID:20980834; DOI:10.4161/cc.9.21.13596.
121. Iizuka M, Matsui T, Takisawa H, Smith MM. Regulation of replication licensing by acetyltransferase Hbo1. Mol Cell Biol 2006; 26:1098-108; PMID:16428461; DOI:10.1128/MCB.26.3.1098-108.2006.
122. Donaldson AD. Shaping time: chromatin structure and the DNA replication programme. Trends Genet 2005; 21:444-9; PMID:15951049; DOI:10.1016/j.tig.2005.05.012.
123. Gilbert DM. Replication timing and transcriptional control: beyond cause and effect. Curr Opin Cell Biol 2002; 14:377-83; PMID:12067662; DOI:10.1016/S0955-0674(02)00326-5.
124. Ferguson BM, Fangman WL. A position effect on the time of replication origin activation in yeast. Cell 1992; 68:333-9; PMID:1733502; DOI:10.1016/0092-8674(92)90474-Q.
125. Friedman KL, Diller JD, Ferguson BM, Nyland SV, Brewer BJ, Fangman WL. Multiple determinants controlling activation of yeast replication origins late in S phase. Genes Dev 1996; 10:1595-607; PMID:8682291; DOI:10.1101/gad.10.13.1595.
126. Yompakdee C, Huberman JA. Enforcement of late replication origin firing by clusters of short G-rich DNA sequences. J Biol Chem 2004; 279:42337-44; PMID:15294892; DOI:10.1074/jbc.M407552200.
127. Hayashi M, Katou Y, Itoh T, Tazumi A, Yamada Y, Takahashi T, et al. Genome-wide localization of pre-RC sites and identification of replication origins in fission yeast. EMBO J 2007; 26:1327-39; PMID:17304213; DOI:10.1038/sj.emboj.7601585.
128. Grégoire D, Brodolin K, Mechali M. HoxB domain induction silences DNA replication origins in the locus and specifies a single origin at its boundary. EMBO Rep 2006; 7:812-6; PMID:16845368.
129. Zhou J, Ermakova OV, Riblet R, Birshtein BK, Schildkraut CL. Replication and subnuclear location dynamics of the immunoglobulin heavy-chain locus in B-lineage cells. Mol Cell Biol 2002; 22:4876-89; PMID:12052893; DOI:10.1128/MCB.22.13.4876-89.2002.
130. Drouin R, Lemieux N, Richer CL. Analysis of DNA replication during S-phase by means of dynamic chromosome banding at high resolution. Chromosoma 1990; 99:273-80; PMID:2209226; DOI:10.1007/BF01731703.
131. McNairn AJ, Gilbert DM. Epigenomic replication: linking epigenetics to DNA replication. Bioessays 2003; 25:647-56; PMID:12815720; DOI:10.1002/bies.10305.
132. Goren A, Tabib A, Hecht M, Cedar H. DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. Genes Dev 2008; 22:1319-24; PMID:18443145; DOI:10.1101/gad.468308.
133. Bickmore WA, Carothers AD. Factors affecting the timing and imprinting of replication on a mammalian chromosome. J Cell Sci 1995; 108:2801-9; PMID:7593321.
134. Gribnau J, Hochedlinger K, Hata K, Li E, Jaenisch R. Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization. Genes Dev 2003; 17:759-73; PMID:12651894; DOI:10.1101/gad.1059603.
135. Schübeler D, Lorincz MC, Cimbora DM, Telling A, Feng YQ, Bouhassira EE, et al. Genomic targeting of methylated DNA: influence of methylation on transcription, replication, chromatin structure and histone acetylation. Mol Cell Biol 2000; 20:9103-12; PMID:11094062; DOI:10.1128/MCB.20.24.9103-12.2000.
136. Selig S, Ariel M, Goitein R, Marcus M, Cedar H. Regulation of mouse satellite DNA replication time. EMBO J 1988; 7:419-26; PMID:3366119.
137. Gómez M, Brockdorff N. Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage. Proc Natl Acad Sci USA 2004; 101:6923-8; PMID:15105447; DOI:10.1073/pnas.0401854101.
138. Csankovszki G, Nagy A, Jaenisch R. Synergism of Xist RNA, DNA methylation and histone hypoacetylation in maintaining X chromosome inactivation. J Cell Biol 2001; 153:773-84; PMID:11352938; DOI:10.1083/jcb.153.4.773.
139. Casas-Delucchi CS, van Bemmel JG, Haase S, Herce HD, Nowak D, Meilinger D, et al. Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin. Nucleic Acids Res 2011; PMID:21908399; DOI:10.1093/nar/gkr723.
140. Li J, Santoro R, Koberna K, Grummt I. The chromatin remodeling complex NoRC controls replication timing of rRNA genes. EMBO J 2005; 24:120-7; PMID:15577942; DOI:10.1038/sj.emboj.7600492.
141. Santoro R, Li J, Grummt I. The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nat Genet 2002; 32:393-6; PMID:12368916; DOI:10.1038/ng1010.
142. Lyon MF. Gene action in the X-chromosome of the mouse (Mus musculus L.). Nature 1961; 190:372-3; PMID:13764598; DOI:10.1038/190372a0.
143. Lee JT, Lu N, Han Y. Genetic analysis of the mouse X inactivation center defines an 80-kb multifunction domain. Proc Natl Acad Sci USA 1999; 96:3836-41; PMID:10097124; DOI:10.1073/pnas.96.7.3836.
144. Fang J, Chen T, Chadwick B, Li E, Zhang Y. Ring1b-mediated H2A ubiquitination associates with inactive X chromosomes and is involved in initiation of X inactivation. J Biol Chem 2004; 279:52812-5; PMID:15509584; DOI:10.1074/jbc.C400493200.
145. Heard E, Rougeulle C, Arnaud D, Avner P, Allis CD, Spector DL. Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation. Cell 2001; 107:727-38; PMID:11747809; DOI:10.1016/S0092-8674(01)00598-0.
146. Kohlmaier A, Savarese F, Lachner M, Martens J, Jenuwein T, Wutz A. A chromosomal memory triggered by Xist regulates histone methylation in X inactivation. PLoS Biol 2004; 2:171; PMID:15252442; DOI:10.1371/journal.pbio.0020171.
147. Takagi N, Sugawara O, Sasaki M. Regional and temporal changes in the pattern of X-chromosome replication during the early post-implantation development of the female mouse. Chromosoma 1982; 85:275-86; PMID:6180866; DOI:10.1007/BF00294971.
148. German JL, 3rd, Bearn AG, Mc GJ. Chromosomal studies of three hermaphrodites. Am J Med 1962; 33:83-7; PMID:13897994.
149. Casas-Delucchi CS, Brero A, Rahn HP, Solovei I, Wutz A, Cremer T, et al. Histone acetylation controls the inactive X chromosome replication dynamics. Nat Commun 2011; 2:222; DOI:10.1038/ncomms1218; PMID:21364561.
150. Blumenthal AB, Kriegstein HJ, Hogness DS. The units of DNA replication in Drosophila melanogaster chromosomes. Cold Spring Harb Symp Quant Biol 1974; 38:205-23; PMID:4208784.
151. Schepers A, Papior P. Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches. Chromosome Res 2010; 18:63-77; PMID:19904620; DOI:10.1007/s10577-009-9087-1.
152. Watanabe Y, Fujiyama A, Ichiba Y, Hattori M, Yada T, Sakaki Y, et al. Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet 2002; 11:13-21; PMID:11772995; DOI:10.1093/hmg/11.1.13.
153. Cohen SM, Chastain PD, 2nd, Cordeiro-Stone M, Kaufman DG. DNA replication and the GINS complex: localization on extended chromatin fibers. Epigenetics Chromatin 2009; 2:6; PMID:19442263; DOI:10.1186/1756-8935-2-6.
154. Schwob E, de Renty C, Coulon V, Gostan T, Boyer C, Camet-Gabut L, et al. Use of DNA combing for studying DNA replication in vivo in yeast and mammalian cells. Methods Mol Biol 2009; 521:673-87; PMID:19563133; DOI:10.1007/978-1-60327-815-7_36.
155. Raghuraman MK, Brewer BJ. Molecular analysis of the replication program in unicellular model organisms. Chromosome Res 2010; 18:19-34; PMID:20012185; DOI:10.1007/s10577-009-9099-x.
156. Görisch SM, Sporbert A, Stear JH, Grunewald I, Nowak D, Warbrick E, et al. Uncoupling the replication machinery: replication fork progression in the absence of processive DNA synthesis. Cell Cycle 2008; 7:1983-90; PMID:18604168; DOI:10.4161/cc.7.13.6094.
157. Zappulla DC, Sternglanz R, Leatherwood J. Control of replication timing by a transcriptional silencer. Curr Biol 2002; 12:869-75; PMID:12062049; DOI:10.1016/S0960-9822(02)00871-0.
158. Knott SR, Viggiani CJ, Tavare S, Aparicio OM. 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. Genes Dev 2009; 23:1077-90; PMID:19417103; DOI:10.1101/gad.1784309.
159. Unnikrishnan A, Gafken PR, Tsukiyama T. Dynamic changes in histone acetylation regulate origins of DNA replication. Nat Struct Mol Biol 2010; 17:430-7; PMID:20228802; DOI:10.1038/nsmb.1780.
160. Pryde F, Jain D, Kerr A, Curley R, Mariotti FR, Vogelauer M. H3 k36 methylation helps determine the timing of cdc45 association with replication origins. PLoS ONE 2009; 4:5882; PMID:19521516; DOI:10.1371/journal.pone.0005882.
161. Schwaiger M, Kohler H, Oakeley EJ, Stadler MB, Schubeler D. Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome. Genome Res 2010; 20:771-80; PMID:20435908; DOI:10.1101/gr.101790.109.