Megabase replication domains along the human genome: Relation to chromatin structure and genome organisation

Sub-Cellular Biochemistry

Volumn 61, Issue , 2013, Pages 57-80

  Audit, Benjamin ^a,b   Zaghloul, Lamia ^a,c   Baker, Antoine ^a,c   Arneodo, Alain ^a,b   Chen, Chun Long ^d   d’Aubenton Carafa, Yves ^d   Thermes, Claude ^d  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ DE LYON   (France)

^c Laboratoire Joliot Curie   (France)

^d CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

DNA; HISTONE;

BIOLOGICAL MODEL; BIOSYNTHESIS; CHEMISTRY; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONFORMATION; DNA REPLICATION; DNA REPLICATION ORIGIN; GENE EXPRESSION REGULATION; HUMAN; HUMAN GENOME; METABOLISM; PROTEIN CONFORMATION; REGULATORY SEQUENCE; REVIEW; STRUCTURE ACTIVITY RELATION;

CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA; DNA REPLICATION; GENE EXPRESSION REGULATION; GENOME, HUMAN; HISTONES; HUMANS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; REGULATORY SEQUENCES, NUCLEIC ACID; REPLICATION ORIGIN; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84894258661     PISSN: 03060225     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-94-007-4525-4_3     Document Type: Article

References (92)

1. Antequera F, Bird A (1999) CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 9: R661-R667.
2. Arneodo A, Audit B, Decoster N, Muzy JF, Vaillant C (2002) Wavelet based multifractal formalism: application to DNA sequences, satellite images of the cloud structure and stock market data. In: Bunde A, Kropp J, Schellnhuber HJ (eds) The science of disasters: climate disruptions, heart attacks, and market crashes. Springer, Berlin, pp 26-102.
3. Arneodo A, Bacry E, Muzy JF (1995) The thermodynamics of fractals revisited with wavelets. Physica A 213: 232-275.
4. Arneodo A, d'Aubenton-Carafa Y, Audit B, Brodie of Brodie EB, Nicolay S, St-Jean P, Thermes C, Touchon M, Vaillant C (2007) DNA in chromatin: from genome-wide sequence analysis to the modeling of replication in mammals. Adv Chem Phys 135: 203-252.
5. Arneodo A, Vaillant C, Audit B, Argoul F, d'Aubenton Carafa Y, Thermes C (2011) Multi-scale coding of genomic information: from DNA sequence to genome structure and function. Phys Rep 498: 45-188.
6. Audit B, Nicolay S, Huvet M, Touchon M, d'Aubenton-Carafa Y, Thermes C, Arneodo A (2007) DNA replication timing data corroborate in silico human replication origin predictions. Phys Rev Lett 99: 248102.
7. Audit B, Zaghloul L, Vaillant C, Chevereau G, d'Aubenton-Carafa Y, Thermes C, Arneodo A (2009) Open chromatin encoded in DNA sequence is the signature of "master" replication origins in human cells. Nucleic Acids Res 37: 6064-6075.
8. Baker A, Audit B, Chen CL, Moindrot B, Leleu A, Guilbaud G, Rappailles A, Vaillant C, Goldar A, Mongelard F et al (2012) Replication fork polarity gradients revealed by megabase-sized U-shape replication timing domains in human cell lines. PLOS Comput Biol 8: e1002443.
9. Baker A, Nicolay S, Zaghloul L, d'Aubenton-Carafa Y, Thermes C, Audit B, Arneodo A (2010) Wavelet-based method to disentangle transcription-and replication-associated strand asymmetries in mammalian genomes. Appl Comput Harmon Anal 28: 150-170.
10. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
11. Bell SP, Dutta A (2002) DNA replication in eukaryotic cells. Annu Rev Biochem 71: 333-374.
12. Bernardi G (2001) Misunderstandings about isochores. Part 1. Gene 276: 3-13.
13. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
14. Bird AP, Wolffe AP (1999) Methylation-induced repression-belts, braces, and chromatin. Cell 99: 451-454.
15. Bogan JA, Natale DA, Depamphilis ML (2000) Initiation of eukaryotic DNA replication: conservative or liberal? J Cell Physiol 184: 139-150.
16. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
17. Brodie of Brodie EB, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A (2005) From DNA sequence analysis to modeling replication in the human genome. Phys Rev Lett 94: 248103.
18. Bulmer M (1991) Strand symmetry of mutation rates in the beta-globin region. J Mol Evol 33: 305-310.
19. Cadoret JC, Meisch F, Hassan-Zadeh V, Luyten I, Guillet C, Duret L, Quesneville H, Prioleau MN (2008) Genome-wide studies highlight indirect links between human replication origins and gene regulation. Proc Natl Acad Sci USA 105: 15837-15842.
20. Chen CL, Duquenne L, Audit B, Guilbaud G, Rappailles A, Baker A, Huvet M, d'Aubenton Carafa Y, Hyrien O, Arneodo A et al (2011) Replication-associated mutational asymmetry in the human genome. Mol Biol Evol 28: 2327-2337.
21. Chen CL, Rappailles A, Duquenne L, Huvet M, Guilbaud G, Farinelli L, Audit B, d'Aubenton Carafa Y, Arneodo A, Hyrien O et al (2010) Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes. Genome Res 4: 447-457.
22. Chevereau G, Palmeira L, Thermes C, Arneodo A, Vaillant C (2009) Thermodynamics of intragenic nucleosome ordering. Phys Rev Lett 103: 188103.
23. Conti C, Sacca B, Herrick J, Lalou C, Pommier Y, Bensimon A (2007) Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. Mol Biol Cell 18: 3059-3067.
24. Courbet S, Gay S, Arnoult N, Wronka G, Anglana M, Brison O, Debatisse M (2008) Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455: 557-560.
25. Coverley D, Laskey RA (1994) Regulation of eukaryotic DNA replication. Annu Rev Biochem 63: 745-776.
26. Danis E, Brodolin K, Menut S, Maiorano D, Girard-Reydet C, Méchali M (2004) Specification of a DNA replication origin by a transcription complex. Nat Cell Biol 6: 721-730.
27. Demeret C, Vassetzky Y, Méchali M (2001) Chromatin remodelling and DNA replication: from nucleosomes to loop domains. Oncogene 20: 3086-3093.
28. Desprat R, Thierry-Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J, Bouhassira EE (2009) Predictable dynamic program of timing of DNA replication in human cells. Genome Res 19: 2288-2299.
29. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378-1385.
30. Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z, Simon I (2008) Global organization of replication time zones of the mouse genome. Genome Res 18: 1562-1570.
31. Francino MP, Ochman H (2000) Strand symmetry around the beta-globin origin of replication in primates. Mol Biol Evol 17: 416-422.
32. Frank AC, Lobry JR (1999) Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238: 65-77.
33. Gerbi SA, Bielinsky AK (1997) Replication initiation point mapping. Methods 13: 271-280.
34. Gerbi SA, Bielinsky AK (2002) DNA replication and chromatin. Curr Opin Genet Dev 12: 243-248.
35. Gierlik A, Kowalczuk M, Mackiewicz P, Dudek MR, Cebrat S (2000) Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J Theor Biol 202: 305-314.
36. Gilbert DM (2001) Making sense of eukaryotic DNA replication origins. Science 294: 96-100.
37. Gilbert DM (2004) In search of the holy replicator. Nat Rev Mol Cell Biol 5: 848-855.
38. Goldman MA, Holmquist GP, Gray MC, Caston LA, Nag A (1984) Replication timing of genes and middle repetitive sequences. Science 224: 686-692.
39. Hamlin JL, Mesner LD, Lar O, Torres R, Chodaparambil SV, Wang L (2008) A revisionist replicon model for higher eukaryotic genomes. J Cell Biochem 105: 321-329.
40. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA (2010) Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 107: 139-144.
41. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Calcar SV, Qu C, Ching KA et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
42. Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S et al (2010) Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Genome Res 20: 155-169.
43. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schubeler D, Gilbert DM (2008) Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245.
44. Huvet M, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Arneodo A, Thermes C (2007) Human gene organization driven by the coordination of replication and transcription. Genome Res 17: 1278-1285.
45. Hyrien O, Goldar A (2010) Mathematical modelling of eukaryotic DNA replication. Chromosome Res 18: 147-161.
46. Hyrien O, Méchali M (1993) Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos. EMBO J 12: 4511-4520.
47. Jacob F, Brenner S, Cuzin F (1963) On the regulation of DNA replication in bacteria. Cold Spring Harb Symp Quant Biol 28: 329-342.
48. 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.
49. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ et al (2003) The UCSC genome browser database. Nucleic Acids Res 31: 51-54.
50. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
51. Lemaitre JM, Danis E, Pasero P, Vassetzky Y, Mechali M (2005) Mitotic remodeling of the replicon and chromosome structure. Cell 123: 787-801.
52. Lemaitre C, Tannier E, Gautier C, Sagot MF (2008) Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinformatics 9: 286.
53. Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A, Tannier E, Audit B (2009) Analysis offine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation. BMC Genomics 10: 335.
54. Lobry JR (1995) Properties of a general model of DNA evolution under no-strand-bias conditions. J Mol Evol 40: 326-330.
55. Lobry JR (1996) Aymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13: 660-665.
56. MacAlpine DM, Rodriguez HK, Bell SP (2004) Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18: 3094-3105.
57. Macleod D, Ali RR, Bird A (1998) An alternative promoter in the mouse major histocompatibility complex class II I-Abeta gene: implications for the origin of CpG islands. Mol Cell Biol 18: 4433-4443.
58. Mallat S (1998) A wavelet tour of signal processing. Academic, New York.
59. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
60. McNairn AJ, Gilbert DM (2003) Epigenomic replication: linking epigenetics to DNA replication. Bioessays 25: 647-656.
61. Méchali M (2001) DNA replication origins: from sequence specificity to epigenetics. Nat Rev Genet 2: 640-645.
62. Mesner LD, Crawford EL, Hamlin JL (2006) Isolating apparently pure libraries of replication origins from complex genomes. Mol Cell 21: 719-726.
63. Miele V, Vaillant C, d'Aubenton-Carafa Y, Thermes C, Grange T (2008) DNA physical properties determine nucleosome occupancy from yeast tofly. Nucleic Acids Res 36: 3746-3756.
64. Mrázek J, Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 95: 3720-3725.
65. Muzy JF, Bacry E, Arneodo A (1994) The multifractal formalism revisited with wavelets. Int J Bifurc Chaos 4: 245-302.
66. Nicolay S, Brodie of Brodie EB, Touchon M, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A (2007) Bifractality of human DNA strand-asymmetry profiles results from transcription. Phys Rev E 75: 032902.
67. Ozsolak F, Song JS, Liu XS, Fisher DE (2007) High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 25: 244-248.
68. Ponger L, Duret L, Mouchiroud D (2001) Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res 11: 1854-1860.
69. Remus D, Beall EL, Botchan MR (2004) DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. EMBO J 23: 897-907.
70. Rocha EP, Danchin A, Viari A (1999) Universal replication biases in bacteria. Mol Microbiol 32: 11-16.
71. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20: 761-770.
72. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A et al (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3: 511-518.
73. Sasaki T, Sawado T, Yamaguchi M, Shinomiya T (1999) Specification of regions of DNA replication initiation during embryogenesis in the 65-kilobase DNApolalpha-dE2F locus of Drosophila melanogaster. Mol Cell Biol 19: 547-555.
74. Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103: 1412-1417.
75. Schepers A, Ritzi M, Bousset K, Kremmer E, Yates JL, Harwood J, Diffley JF, Hammerschmidt W (2001) Human origin recognition complex binds to the region of the latent origin of DNA replication of epstein-barr virus. EMBO J 20: 4588-4602.
76. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898.
77. Schübeler D, Scalzo D, Kooperberg C, van Steensel B, Delrow J, Groudine M (2002) Genomewide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing. Nat Genet 32: 438-442.
78. Schwaiger M, Schubeler D (2006) A question of timing: emerging links between transcription and replication. Curr Opin Genet Dev 16: 177-183.
79. Sequeira-Mendes J, Diaz-Uriarte R, Apedaile A, Huntley D, Brockdorff N, Gomez M (2009) Transcription initiation activity sets replication origin efficiency in mammalian cells. PLoS Genet 5: e1000446.
80. St-Jean P, Vaillant C, Audit B, Arneodo A (2008) Spontaneous emergence of sequence-dependent rosettelike folding of chromatinfiber. Phys Rev E 77: 061923.
81. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
82. 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.
83. Tillier ER, Collins RA 2000 The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 50: 249-257.
84. Touchon M, Arneodo A, d'Aubenton-Carafa Y, Thermes C (2004) Transcription-coupled and splicingcoupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res 32: 4969-4978.
85. Touchon M, Nicolay S, Arneodo A, d'Aubenton-Carafa Y, Thermes C (2003) Transcriptioncoupled TA and GC strand asymmetries in the human genome. FEBS Lett 555: 579-582.
86. Touchon M, Nicolay S, Audit B, Brodie of Brodie EB, d'Aubenton-Carafa Y, Arneodo A, Thermes C (2005) Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci USA 102: 9836-9841.
87. Vaillant C, Audit B, Arneodo A (2007) Experiments confirm the influence of genome long-range correlations on nucleosome positioning. Phys Rev Lett 99: 218103.
88. Vaillant C, Palmeira L, Chevereau G, Audit B, d'Aubenton-Carafa Y, Thermes C, Arneodo A (2010) A novel strategy of transcription regulation by intra-genic nucleosome ordering. Genome Res 20: 59-67.
89. Vashee S, Cvetic C, Lu W, Simancek P, Kelly TJ, Walter JC (2003) Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes Dev 17: 1894-1908.
90. Woodfine K, Beare DM, Ichimura K, Debernardi S, Mungall AJ, Fiegler H, Collins VP, Carter NP, Dunham I (2005) Replication timing of human chromosome 6. Cell Cycle 4: 172-176.
91. Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I (2010) Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet 6: e1001011.
92. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.