The temporal program of DNA replication: new insights into old questions (original) (raw)
Alexandrova O, Solovei I, Cremer T, David CN (2003) Replication labeling patterns and chromosome territories typical of mammalian nuclei are conserved in the early metazoan Hydra. Chromosoma 112:190–200 ArticlePubMedCAS Google Scholar
Azuara V, Brown KE, Williams RRE, Webb N, Dillon N, Festenstein R, Buckle V, Merkenschlager M, Fisher AG (2003) Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication. Nat Cell Biol 5:668–674 ArticlePubMedCAS Google Scholar
Berezney R, Mortillaro MJ, Ma H, Wei X, Samarabandu J, (1995) The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol 162A:1–65 ArticlePubMedCAS Google Scholar
Berezney R, Dubey DD, Huberman JA (2000) Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108:471–484 ArticlePubMedCAS Google Scholar
Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol (in press)
Brown KE, Amoils S, Horn JM, Buckle V, Higgs DR, Merkenschlager M, Fisher AG (2001) Expression of α- and β-globin genes occurs within different nuclear domains in haemopoietic cells. Nat Cell Biol 3:602–606 ArticlePubMedCAS Google Scholar
Camargo M, Cervenka J (1982) Patterns of DNA replication of human chromosomes: II. Replication map and replication model. Am J Hum Genet 34:757–780 PubMedCAS Google Scholar
Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291:1289–1292 ArticlePubMedCAS Google Scholar
Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18:1119–1130 ArticlePubMedCAS Google Scholar
Chambeyron S, Da Silva NR, Lawson KA, Bickmore WA (2005) Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 132:2215–2223 ArticlePubMedCAS Google Scholar
Chaumeil J, Okamoto I, Guggiari M, Heard E (2002) Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells. Cytogenet Genome Res 99:75–84 ArticlePubMedCAS Google Scholar
Christen R, Braconnot J-C (1998) The biology of pelagic tunicates. Oxford University Press, New York Google Scholar
Chubb JR, Boyle S, Perry P, Bickmore WA (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. J Cell Biol 12:439–445 CAS Google Scholar
Cimbora DM, Groudine M (2001) The control of mammalian DNA replication: a brief history of space and timing. Cell 104:643–646 PubMedCAS Google Scholar
Cimbora DM, Schubeler D, Reik A, Hamilton J, Francastel C, Epner EM, Groudine M (2000) Long-distance control of origin choice and replication timing in the human beta-globin locus are independent of the locus control region. Mol Cell Biol 20:5581–5591 ArticlePubMedCAS Google Scholar
Craig JM, Bickmore WA (1994) The distribution of CpG islands in mammalian chromosomes. Nat Genet 7:376–382 ArticlePubMedCAS Google Scholar
Dimitrova D, Berezney R (2002) The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J Cell Sci 115:4037–4051 ArticlePubMedCAS Google Scholar
Dimitrova DS, Gilbert DM (1999) The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol Cell 4:983–993 ArticlePubMedCAS Google Scholar
Donaldson AD (2005) Shaping time: chromatin structure and the DNA replication programme. Trends Genet 21:444–449 ArticlePubMedCAS Google Scholar
Drouin R, Lemieux N, Richer CL (1990) Analysis of DNA replication during S phase by means of dynamic chromosome banding at high resolution. Chromosoma 99:272–280 Article Google Scholar
Dutrillaux B, Couturier J, Richer C-L, Viegas-Peguinot E (1976) Sequence of DNA replication in 277 R- and Q-bands of human chromosomes using a BrdU treatment. Chromosoma 58:51–61 ArticlePubMedCAS Google Scholar
Englmann A, Clarke LA, Christan S, Amaral MD, Schindelhauer D, Zink D (2005) The replication timing of CFTR and adjacent genes. Chromosome Res 13:183–194 ArticlePubMedCAS Google Scholar
Ermakova OV, Nguyen LH, Little RD, Chevillard C, Riblet R, Ashouian N, Birshtein BK, Schildkraut CL (1999) Evidence that a single replication fork proceeds from early to late replicating domains in the IgH locus in a non-B cell line. Mol Cell 3:321–330 ArticlePubMedCAS Google Scholar
Ferreira J, Paolella G, Ramos C, Lamond AI (1997) Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol 139:1597–1610 ArticlePubMedCAS Google Scholar
Furey TS, Haussler D (2003) Integration of the cytogenetic map with the draft human genome sequence. Hum Mol Genet 12:1037–1044 ArticlePubMedCAS Google Scholar
Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A (1984) Replication timing of genes and middle repetitive sequences. Science 224:686–692 ArticlePubMedCAS Google Scholar
Habermann FA, Cremer M, Walter J, Kreth G, von Hase J, Bauer K, Wienberg J, Cremer C, Cremer T, Solovei I (2001) Arrangements of macro- and microchromosomes in chicken cells. Chromosome Res 9:569–584 ArticlePubMedCAS Google Scholar
Hatton KS, Dhar V, Brown EH, Iqbal MA, Stuart S, Didamo VT, Schildkraut CL (1988) Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol 8:2149–2158 PubMedCAS Google Scholar
Hiratani I, Leskovar A, Gilbert DM (2004) Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores. Proc Natl Acad Sci U S A 101:16861–16866 ArticlePubMedCAS Google Scholar
Huberman JA, Riggs AD (1966) Autoradiography of chromosomal DNA fibers from Chinese hamster cells. Proc Natl Acad Sci U S A 55:599–606 ArticlePubMedCAS Google Scholar
ISCN (1995) An international system for human cytogenetic nomenclature. S. Karger, New York Google Scholar
Jackson DA, Pombo A (1998) 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. J Cell Biol 140:1285–1295 ArticlePubMedCAS Google Scholar
Jacob F, Brenner S, Cuzin F (1964) On the regulation of DNA replication in bacteria. Cold Spring Harb Symp Quant Biol 28:329–348 Google Scholar
Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A (2005) Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A 102:6419–6424 ArticlePubMedCAS Google Scholar
Jeppesen P, Turner BM (1993) The inactive X chromosome in female mammals is distinguished by a lack of histone H4 acetylation, a cytogenetic marker for gene expression. Cell 74:281–289 ArticlePubMedCAS Google Scholar
Kennedy BK, Barbie DA, Classon M, Dyson N, Harlow E (2000) Nuclear organization of DNA replication in primary mammalian cells. Genes Dev 14:2855–2868 ArticlePubMedCAS Google Scholar
Kim MA, Johannsmann R, Grzeschik K-H (1975) Giemsa staining of the sites replicating DNA early in human lymphocyte chromosomes. Cytogenet Cell Genet 15:363–371 ArticlePubMedCAS Google Scholar
Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921 ArticlePubMedCAS Google Scholar
Leonhardt H, Rahn H-P, Weinzierl P, Sporbert A, Cremer T, Zink D, Cardoso MC (2000a) Dynamics of DNA replication factories in living cells. J Cell Biol 149:271–279 ArticlePubMedCAS Google Scholar
Leonhardt H, Sporbert A, Cardoso MC (2000b) Targeting regulatory factors to intranuclear replication sites. Crit Rev Eukaryot Gene Expr 12:127–133 Google Scholar
Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31:180–183 ArticlePubMedCAS Google Scholar
Li F, Chen J, Izumi M, Butler MC, Keezer SM, Gilbert DM (2001) The replication timing program of the Chinese hamster beta-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase. J Cell Biol 154:283–292 ArticlePubMedCAS Google Scholar
Li F, Chen J, Solessio E, Gilbert DM (2003) Spatial distribution and specification of mammalian replication origins during G1 phase. J Cell Biol 161:257–266 ArticlePubMedCAS Google Scholar
Lin CM, Fu H, Martinovsky M, Bouhassira E, Aladjem MI (2003) Dynamic alterations of replication timing in mammalian cells. Curr Biol 13:1019–1028 ArticlePubMedCAS Google Scholar
Ma H, Samarabandu J, Devdhar RS, Acharya R, Cheng P-C, Meng C, Berezney R (1998) Spatial and temporal dynamics of DNA replication sites in mammalian cells. J Cell Biol 143:1415–1425 ArticlePubMedCAS Google Scholar
MacAlpine DM, Rodriguez HK, Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18:3094–3105 ArticlePubMedCAS Google Scholar
Mahy NL, Perry PE, Bickmore WA (2002a) Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J Cell Biol 159:753–763 ArticlePubMedCAS Google Scholar
Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA (2002b) Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 157:579–589 ArticlePubMedCAS Google Scholar
Manders EMM, Stap J, Brakenhoff GJ, van Driel R, Aten JA (1992) Dynamics of three-dimensional replication patterns during S-phase, analysed by double labelling of DNA and confocal microscopy. J Cell Sci 103:857–862 PubMedCAS Google Scholar
Manders EMM, Kimura H, Cook PR (1999) Direct imaging of DNA in living cells reveals the dynamics of chromosome formation. J Cell Biol 144:813–821 ArticlePubMedCAS Google Scholar
Mayr C, Jasencakova Z, Meister A, Schubert I, Zink D (2003) Comparative analysis of the functional genome architecture of animal and plant cell nuclei. Chromosome Res 11:471–484 ArticlePubMedCAS Google Scholar
Nakamura H, Morita T, Sato C (1986) Structural organizations of replicon domains during DNA synthetic phase in the mammalian nucleus. Exp Cell Res 165:291–297 ArticlePubMedCAS Google Scholar
Nakayasu H, Berezney R (1989) Mapping replicational sites in the eucaryotic cell nucleus. J Cell Biol 108:1–11 ArticlePubMedCAS Google Scholar
Newlon CS, Theis JF (1993) The structure and function of yeast ARS elements. Curr Opin Genet Dev 3:752–758 ArticlePubMedCAS Google Scholar
O’Keefe RT, Henderson SC, Spector DL (1992) Dynamic organization of DNA replication in mammalian cell nuclei: spatially and temporally defined replication of chromosome-specific α-satellite DNA sequences. J Cell Biol 116:1095–1110 ArticlePubMedCAS Google Scholar
Panning MM, Gilbert DM (2005) Spatio-temporal organization of DNA replication in murine embryonic stem, primary, and immortalized cells. J Cell Biochem 95:74–82 ArticlePubMedCAS Google Scholar
Pepperkok R, Ansorge W (1995) Direct visualization of DNA replication sites in living cells by microinjection of fluorescein-conjugated dUTPs. Methods Mol Cell Biol 5:112–117 Google Scholar
Perry P, Sauer S, Billon N, Richardson WD, Spivakov M, Warnes G, Livesey FJ, Merkenschlager M, Fisher AG, Azuara V (2004) A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle 3:1645–1650 PubMedCAS Google Scholar
Postberg J, Alexandrova O, Cremer T, Lipps HJ (2005) Exploiting nuclear duality of ciliates to analyse topological requirements for DNA replication and transcription. J Cell Sci 118:3973–3983 ArticlePubMedCAS Google Scholar
Raghuraman MK, Winzeler EA, Collingwood D, Hunt S, Wodicka L, Conway A, Lockhart DJ, Davis RW, Brewer BJ, Fangman WL (2001) Replication dynamics of the yeast genome. Science 294:115–121 ArticlePubMedCAS Google Scholar
Rountree MR, Bachman KE, Baylin SB (2000) DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nat Genet 25:269–277 ArticlePubMedCAS Google Scholar
Saccone S, De Sario A, Wiegant J, Raap AK, Della Valle G, Bernardi G (1993) Correlations between isochores and chromosomal bands in the human genome. Proc Natl Acad Sci U S A 90:11929–11933 ArticlePubMedCAS Google Scholar
Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, Turner BM, Zink D (1999) Nuclear organization of mammalian genomes: polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 146:1211–1226 ArticlePubMedCAS Google Scholar
Sadoni N, Cardoso MC, Stelzer EH, Leonhardt H, Zink D (2004) Stable chromosomal units determine the spatial and temporal organization of DNA replication. J Cell Sci 117:5353–5365 ArticlePubMedCAS Google Scholar
Schermelleh L (2003) Dynamic organization of chromosomes in the mammalian cell nucleus. PhD Thesis at the Ludwig-Maximilians-Universität München: 1–121
Schübeler D, Francastel C, Cimbora DM, Reik A, Martin DIK, Groudine M (2000) Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus. Genes Dev 14:940–950 PubMed Google Scholar
Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet 32:438–442 ArticlePubMedCAS Google Scholar
Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O’Neill LP, Turner BM, Delrow J, Bell SP, Groudine M (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18:1263–1271 ArticlePubMed Google Scholar
Selig S, Okumura K, Ward DC, Cedar H (1992) Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J 11:1217–1225 PubMedCAS Google Scholar
Smith ZE, Higgs DR (1999) The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum Mol Genet 8:1373–1386 ArticlePubMedCAS Google Scholar
Spada F, Chioda M, Thompson EM (2005) Histone H4 post-translational modifications in chordate mitotic and endoreduplicative cell cycles. J Cell Biochem 95:885–901 ArticlePubMedCAS Google Scholar
Sparvoli E, Levi M, Rossi E (1994) Replication clusters may form structurally stable complexes of chromatin and chromosomes. J Cell Sci 107:3097–3103 PubMedCAS Google Scholar
Sporbert A, Gahl A, Ankerhold R, Leonhardt H, Cardoso MC (2002) DNA polymerase clamp shows little turnover at established replication sites but sequential do novo assembly at adjacent origin clusters. Mol Cell 10:1355–1365 ArticlePubMedCAS Google Scholar
Thomson I, Gilchrist S, Bickmore WA, Chubb JR (2004) The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 14:166–172 ArticlePubMedCAS Google Scholar
Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AHC (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res 13:1998–2004 ArticlePubMedCAS Google Scholar
Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J et al (2000) Large-scale chromatin organisation of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 113:1565–1576 PubMedCAS Google Scholar
Walter J, Schermelleh L, Cremer M, Tashiro S, Cremer T (2003) Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J Cell Biol 160:685–697 ArticlePubMedCAS Google Scholar
Watanabe Y, Fujiyama A, Ichiba Y, Hattori M, Yada T, Sakaki Y, Ikemura T (2002) Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions. Hum Mol Genet 11:13–21 ArticlePubMedCAS Google Scholar
White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schubeler D (2004) DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A 101:17771–17776 ArticlePubMedCAS Google Scholar
Williams RRE, Azuara V, Perry P, Sauer S, Dvorkina M, Jorgensen H, Roix J, McQueen P, Misteli T, Merkenschlager M, Fisher AG (2006) Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci 119:132–140 ArticlePubMedCAS Google Scholar
Woodfine K, Fiegler H, Beare DM, Collins JE, McCann OT, Young BD, Debernardi S, Mott R, Dunham I, Carter NP (2004) Replication timing of the human genome. Hum Mol Genet 13:191–202 ArticlePubMedCAS Google Scholar
Wyman C, Botchan M (1995) DNA replication. A familiar ring to DNA polymerase processivity. Curr Biol 5:334–337 ArticlePubMedCAS Google Scholar
Yunis JJ (1981) Mid-prophase human chromosomes. The attainment of 2000 bands. Hum Genet 56:293–298 ArticlePubMedCAS Google Scholar
Yurov YB, Liapunova NA (1977) The units of DNA replication in the mammalian chromosomes: evidence for a large size of replication units. Chromosoma 60:253–267 ArticlePubMedCAS Google Scholar
Zhang J, Xu F, Hashimshony T, Keshet I, Cedar H (2002) Establishment of transcriptional competence in early and late S phase. Nature 420:198–202 ArticlePubMedCAS Google Scholar
Zhou J, Ermakova OV, Riblet R, Birshtein BK, Schildkraut CL (2002) Replication and subnuclear location dynamics of the immunoglobulin heavy-chain locus in B-lineage cells. Mol Cell Biol 22:4876–4889 ArticlePubMedCAS Google Scholar
Zink D, Cremer T, Saffrich R, Fischer R, Trendelenburg MF, Ansorge W, Stelzer EHK (1998) Structure and dynamics of human interphase chromosome territories in vivo. Hum Genet 102:241–251 ArticlePubMedCAS Google Scholar
Zink D, Bornfleth H, Visser A, Cremer C, Cremer T (1999) Organization of early and late replicating DNA in human chromosome territories. Exp Cell Res 247:176–188 ArticlePubMedCAS Google Scholar
Zink D, Sadoni N, Stelzer E (2003) Visualizing chromatin and chromosomes in living cells. Methods 29:42–50 ArticlePubMedCAS Google Scholar
Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, Rudolph C, Alt F, Luther K, Braz N, Sadoni N, Rosenecker J, Schindelhauer D (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166:815–825 ArticlePubMedCAS Google Scholar