DNA in chromatin: From genome-wide sequence analysis to the modeling of replication in mammals

Advances in Chemical Physics

Volumn 135, Issue , 2007, Pages 203-252

  Arneodo, A ^a   Audit, B ^a   Brodie of Brodie, E B ^a   Nicolay, S ^a   St Jean, P ^a   d'Aubenton Carafa, Y ^b   Thermes, C ^b   Touchon, M ^b   Vaillant, C ^c  

^a Laboratoire Joliot Curie   (France)

^b CNRS   (France)

^c University of Paris 5   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34247348278     PISSN: 00652385     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (161)

1. K. E. van Holde, Chromatin, Springer-Verlag, New York, 1988.
2. A. P. Wolffe, Chromatin Structure and Function, 3rd ed., Academic Press, London, 1998.
3. C. R. Calladine, and H. R. Drew, Understanding DNA, Academic Press, San Diego, 1999.
4. B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson. Molecular Biology of the Cell, 3rd ed., Garland Publishing, New York, 1994.
5. J. Widom, Structure, dynamics and function of chromatin in vitro. Annu. Rev. Biophys. Biomol. Struct. 27, 285-327 (1998).
6. K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, and T. J. Richmond, Crystal structure of the nucleosome core particle at 2.8 å resolution. Nature 389, 251-260 (1997).
7. L. Chantalat, J. M. Nicholson, S. J. Lambert, A. J. Reid, M. J. Donovan, C. D. Reynolds, C. M. Wood, and J. P. Baldwin, Structure of the histone-core octamer in KCl/phosphate crystals at 2.15 Å resolution. Acta Crystallogr D Biol. Crystallogr. 59, 1395-1407 (2003).
8. T. J. Richmond, and C. A. Davey, The structure of DNA in the nucleosome core. Nature 423, 145-150 (2003).
9. I. Ioshikhes, A. Bolshoy, K. Derenshteyn, M. Borodovsky, and E. N. Trifonov, Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. J. Mol. Biol. 262, 129-139 (1996).
10. H. Herzel, O. Weiss, and E. N. Trifonov, 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. Bioinformatics 15, 187-193 (1999).
11. B. Audit, C. Thermes, C. Vaillant, Y. d'Aubenton-Carafa, J.-F. Muzy, and A. Arneodo, Long-range correlations in genomic DNA: A signature of the nucleosomal structure. Phys. Rev. Lett. 86, 2471-2474 (2001).
12. B. Audit, C. Vaillant, A. Arneodo, Y. d'Aubenton-Carafa, and C. Thermes, Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes. J. Mol. Biol. 316, 903-918 (2002).
13. A. Arneodo, B. Audit, N. Decoster, J.-F. Muzy, and C. Vaillant, Wavelet based multifractal formalism: Application to DNA sequences, satellite images of the cloud structure and stock market data, in The Science of Disasters: Climate Disruptions, Heart Attacks, and Market Crashes, Springer-Verlag, Berlin, 2002, pp. 26-102.
14. U. K. Laemmli, E. Käs, L. Poljak, and Y. Adachi, Scaffold-associated regions: Cis-acting determinants of chromatin structural loops and functional domains. Curr. Opin. Genet. Dev. 2, 275-285 (1992).
15. Y. Saitoh, and U. K. Laemmli, From the chromosomal loops and the scaffold to the classic bands of metaphase chromosomes. Cold Spring Harb. Symp. Quant. Biol. 58, 755-765 (1993).
16. A. S. Belmont, and K. Bruce, Visualization of G1 chromosomes: A folded, twisted, supercoiled chromonema model of interphase chromatid structure. J. Mol. Biol. 127, 287-302 (1994).
17. A. S. Belmont, S. Dietzel, A. C. Nye, Y. G. Strukov, and T. Tumbar, Large-scale chromatin structure and function. Curr. Opin. Cell Biol. 11, 307-311 (1999).
18. P. J. Horn, and C. L. Peterson, Molecular biology. Chromatin higher order folding - wrapping up transcription. Science 297, 1824-1827 (2002).
19. R. K. Sachs, G. van den Engh, B. Trask, H. Yokota, and J. E. Hearst, A random-walk/giant-loop model for interphase chromosomes. Proc. Natl. Acad. Sci. USA 92, 2710-2714 (1995).
20. J. Ostashevsky, A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. Mol. Biol. Cell 9, 3031-3040 (1998).
21. C. Münkel, R. Eils, S. Dietzel, D. Zink, C. Mehring, G. Wedemann, T. Cremer, and J. Langowski, Compartmentalization of interphase chromosomes observed in simulation and experiment. J. Mol. Biol. 285, 1053-1065 (1999).
22. P. R. Cook, A chromomeric model for nuclear and chromosome structure. J. Cell. Sci. 108, 2927-2935 (1995).
23. P. R. Cook, Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32, 347-352 (2002).
24. N. L. Mahy, P. E. Perry, and W. A. Bickmore, Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J. Cell Biol. 159, 753-763 (2002).
25. G. Felsenfeld, and M. Groudine, Controlling the double helix. Nature 421, 448-453 (2003).
26. A. Arneodo, E. Bacry, P. V. Graves, and J.-F Muzy, Characterizing long-range correlations in DNA sequences from wavelet analysis. Phys. Rev. Lett. 74, 3293-3296 (1995).
27. A. Arneodo, Y. d'Aubenton-Carafa, E. Bacry, P. V. Graves, J.-F. Muzy, and C. Thermes, Wavelet based fractal analysis of DNA sequences. Physica D 96, 291-320 (1996).
28. Y. Meyer, ed. Wavelets and Their Applications, Springer, Berlin, 1992.
29. S. Mallat, A Wavelet Tour of Signal Processing, Academic Press, New York, 1998.
30. C. Vaillant, B. Audit, and A. Arneodo, Thermodynamics of DNA loops with long-range correlated structural disorder. Phys. Rev. Lett. 95, 068101 (2005).
31. C. Vaillant, B. Audit, C. Thermes, and A. Arneodo, Formation and positioning of nucleosomes: effect of sequence dependent long-range correlated structural disorder. Eur. Phys. J. E, 19, 263-277 (2006).
32. C. Vaillant, B. Audit and A. Arneodo, First experimental evidence of nucleosome positioning by genomic long-range correlations. Preprint. (2006).
33. G.-C. Yuan, Y.-J. Liu, M. F. Dion, M. D. Slack, L. F. Wu, S. J. Altschuler, and O. J. Rando, Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309, 626-630 (2005).
34. S. Nicolay, F. Argoul, M. Touchon, Y. d'Aubenton-Carafa. C. Thermes, and A. Arneodo, Low frequency rhythms in human DNA sequences: A key to the organization of gene location and orientation? Phys. Rev. Lett. 93, 108101 (2004).
35. S. Nicolay, E.-B. Brodie of Brodie, M. Touchon, Y. d'Aubenton-Carafa, C. Thermes, and A. Arneodo, From scale invariance to deterministic chaos in DNA sequences: towards a deterministic description of gene organization in the human genome. Physica A 342, 270-280 (2004).
36. M. Touchon, S. Nicolay, A. Arneodo, Y. d'Aubenton-Carafa, and C. Thermes, Transcription-coupled TA and GC strand asymmetries in the human genome. FEBS Lett. 555, 579-582 (2003).
37. M. Touchon, A. Arneodo, Y. d'Aubenton-Carafa, and C. Thermes, Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucl. Acids Res. 32, 4969-4978 (2004).
38. M. Touchon, S. Nicolay, B. Audit, E.-B. Brodie of Brodie, Y. d'Aubenton-Carafa, A. Arneodo, and C. Thermes, Replication-associated strand asymmetries in mammalian genomes: Towards detection of replication origins. Proc. Natl. Acad. Sci. USA 102, 9836-9841 (2005).
39. E.-B. Brodie of Brodie, S. Nicolay, M. Touchon, B. Audit, Y. d'Aubenton-Carafa, C. Thermes, and A. Arneodo, From DNA sequence analysis to modelling replication in the human genome. Phys. Rev. Lett. 94, 248103 (2005).
40. A. F. A. Smit, R. Hubley, and P. Green, RepeatMasker Open 3.0, http://www.repeatmasker.org. (1996-2004).
41. E.-M. Ladenburger, C. Keller, and R. Knippers, Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication. Mol. Cell. Biol. 22, 1036-1048 (2002).
42. T. Taira, S. M. Iguchi-Ariga, and H. Ariga, A novel DNA replication origin identified in the human heat shock protein 70 gene promoter. Mol. Cell. Biol. 14, 6386-6397 (1994).
43. C. Keller, E.-M. Ladenburger, M. Kremer, and R. Knippers, The origin recognition complex marks a replication origin in the human TOP1 gene promoter. J. Biol. Chem. 277. 31430-31440 (2002).
44. L. Vassilev, and E. M. Johnson, An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Mol. Cell. Biol. 10, 4899-4904 (1990).
45. T. Nenguke, M. I. Aladjem, J. F. Gusella, N. S. Wexler, and N. Arnheim, Candidate DNA replication initiation regions at human trinucleotide repeat disease loci. Hum Mol. Genet. 12, 1021-1028 (2003).
46. F. D. Araujo, J. D. Knox, S. Ramchandani, R. Pelletier, P. Bigey, G. Price, M. Szyf, and M. Zannis-Hadjopoulos, Identification of initiation sites for DNA replication in the human dnmt1 (DNA-methyltransferase) locus. J. Biol. Chem. 274, 9335-9341 (1999).
47. M. Giacca, L. Zentilin, P. Norio, S. Diviacco, D. Dimitrova, G. Contreas, G. Biamonti, G. Perini, F. Weighardt, et al. Fine mapping of a replication origin of human DNA. Proc. Natl. Acad. Sci. USA 91, 7119-7123 (1994).
48. D. Kitsberg, S. Selig, I. Keshet, and H. Cedar, Replication structure of the human beta-globin gene domain. Nature 366, 588-590 (1993).
49. S. Schwartz, Z. Zhang, K. A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller, PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10, 577-586 (2000).
50. A. Arneodo, F. Argoul, E. Bacry, J. Elezgaray, and J.-F. Muzy, Ondelettes Multifractales et Turbulences: de l'ADN aux Croissances Cristallines, Diderot Editeur, Arts et Sciences, Paris, (1995).
51. E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
52. G. Bernardi, The isochore organization of the human genome. Annu. Rev. Genet. 23, 637-661 (1989).
53. G. Bernardi, The human genome: Organization and evolutionary history. Annu. Rev. Genet. 29, 445-476 (1995).
54. A. Nekrurenko, and W. H. Li, Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10, 1986-1995 (2000).
55. D. Häring, and J. Kypr, No isochores in the human chromosomes 21 and 22? Biochem. Biophys. Res. Commun. 280, 567-573 (2001).
56. G. Bernardi, Misunderstandings about isochores. Part 1. Gene 276, 3-13 (2001).
57. A. Eyre-Walker, and L. D. Hurst, The evolution of isochores. Nat. Rev. Genet. 2, 549-555 (2001).
58. W. Li, Are isochore sequences homogeneous? Gene 300, 129-139 (2002).
59. N. Cohen, T. Dagan, L. Stone, and D. Graur, GC composition of the human genome: in search of isochores. Mol. Biol. Evol. 22, 1260-1272 (2005).
60. A. Pavlícek, J. Paces, O. Clay, and G. Bernardi, A compact view of isochores in the draft human genome sequence. FEBS Lett. 511, 165-169 (2002).
61. H. Hori, and S. Osawa, Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species. Biosystems 19, 163-172 (1986).
62. G. D'Onofrio, D. Mouchiroud, B. Aïissani, C. Gautier, and G. Bernardi, Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol. 32, 504-510 (1991).
63. D. Graur, and W. H. Li, Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, MA, 1999.
64. J. R. Paulson, and U. K. Laemmli, The structure of histone-depleted metaphase chromosomes. Cell 12, 817-828 (1977).
65. S. M. Gasser, and U. K. Laemmli, A glimpse at chromosomal order. Trends Genet. 3, 16-22 (1987).
66. J. B. Rattner, and C. C. Lin, Radial loops and helical coils coexist in metaphase chromosomes. Cell 42, 291-296 (1985).
67. E. Boy de la Tour, and U. K. Laemmli, The metaphase scaffold is helically folded: Sister chromatids have predominantly opposite helical handedness. Cell 55, 937-944 (1988).
68. M. G. Poirier, A. Nemani, P. Gupta, S. Eroglu, and J. F. Marko, Probing chromosome structure with dynamic force relaxation. Phys. Rev. Lett. 86, 360-363 (2001).
69. J. M. Bridger, and W. A. Bickmore, Putting the genome on the map. Trends Genet. 14, 403-409 (1998).
70. T. Cremer, and C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292-301 (2001).
71. A. S. Belmont, Visualizing chromosome dynamics with GFP. Trends Cell Biol. 11, 250-257 (2001).
72. S. M. Gasser, Visualizing chromatin dynamics in interphase nuclei. Science 296, 1412-1416 (2002).
73. D. Zink, T. Cremer, R. Saffrich, R. Fischer, M. F. Trendelenburg, W. Ansorge, and E. H. Stelzer, Structure and dynamics of human interphase chromosome territories in vivo. Hum. Genet. 102, 241-251 (1998).
74. C. Münkel, and J. Langowski, Chromosome structure predicted by a polymer model. Phys. Rev. E 57, 5888-5896 (1998).
75. L. Manuelidis. A view of interphase chromosomes. Science 250, 1533-1540 (1990).
76. L. Manuelidis, and T. L. Chen, A unified model of eukaryotic chromosomes. Cytometry 11, 8-25 (1990).
77. C. L. Woodcock, H. Woodcock, and R. A. Horowitz, Ultrastructure of chromatin. I. Negative staining of isolated fibers. J. Cell Sci. 99, 99-106 (1991).
78. C. L. Woodcock, Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J. Cell Biol. 125, 11-19 (1994).
79. A. S. Belmont, Large-scale chromatin organization, in Genome Structure and Function, Kluwer Academic Publishers, Dordrecht, 1997, p. 261.
80. W. G. Müller, D. Rieder, G. Kreth, C. Cremer, Z. Trajanoski, and J. G. McNally, Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol. Cell. Biol. 24, 9359-9370 (2004).
81. D. A. Jackson, and A. Pombo, 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 (1998).
82. H. Ma, J. Samarabandu, R. S. Devdhar, R. Acharya, P. C. Cheng, C. Meng, and R. Berezney, Spatial and temporal dynamics of DNA replication sites in mammalian cells. J. Cell Biol. 143, 1415-1425 (1998).
83. R. Berezney, D. D. Dubey, and J. A. Huberman, Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 108, 471-484 (2000).
84. H. J. Edenberg, and J. A. Huberman, Eukaryotic chromosome replication. Annu. Rev. Genet. 9, 245-284 (1975).
85. R. Hand, Eucaryotic DNA: Organization of the genome for replication. Cell 15, 317-325 (1978).
86. Y. B. Yurov, and N. A. Liapunova, The units of DNA replication in the mammalian chromosomes: evidence for a large size of replication units. Chromosoma 60, 253-267 (1977).
87. N. A. Liapunova, Organization of replication units and DNA replication in mammalian cells as studied by DNA fiber radioautography. Int. Rev. Cytol. 154, 261-308 (1994).
88. E. Chargaff, Structure and function of nucleic acids as cell constituents. Fed. Proc. 10, 654-659 (1951).
89. R. Rudner, J. D. Karkas, and E. Chargaff, Separation of B. subtilis DNA into complementary strands. 3. Direct analysis. Proc. Natl. Acad. Sci. USA 60, 921-922 (1968).
90. J. W. Fickett, D. C. Torney, and D. R. Wolf, Base compositional structure of genomes. Genomics 13, 1056-1064 (1992).
91. J. R. Lobry, Properties of a general model of DNA evolution under no-strand-bias conditions. J. Mol. Evol. 40, 326-330 (1995).
92. J. Mrázek, and S. Karlin, Strand compositional asymmetry in bacterial and large viral genomes. Proc. Natl. Acad. Sci. USA 95, 3720-3725 (1998).
93. A. C. Frank, and J. R. Lobry, Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms. Gene 238, 65-77 (1999).
94. E. P. Rocha, A. Danchin, and A. Viari, Universal replication biases in bacteria. Mol. Microbiol. 32, 11-16 (1999).
95. E. R. M. Tillier, and R. A. Collins, The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J. Mol. Evol. 50, 249-257 (2000).
96. E.-B. Brodie of Brodie, De l'analyse des séquences d'ADN à la modélisation de la réplication chez les mammiferes. Ph.D. thesis, ENS de Lyon, France, 2005.
97. S. Nicolay, Analyse des séquences d'ADN par la transformée en ondelettes: Fxtraction d'informations structurelles, dynamiques et fonctionnelles. Ph.D. thesis, University of Lieg̀e, Belgium, 2006.
98. T. Gojobori, W. H. Li, and D. Graur, Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18, 360-369 (1982).
99. W. H. Li, C. I. Wu, and C. C. Luo, Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J. Mol. Evol. 21, 58-71 (1984).
100. D.A. Petrov, and D. L. Hartl, Patterns of nucleotide substitution in Drosophila and mammalian genomes. Proc. Natl. Acad. Sci. USA 96, 1475-1479 (1999).
101. Z. Zhang, and M. Gerstein, Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31, 5338-5348 (2003).
102. J. M. Freeman, T. N. Plasterer, T. F. Smith, and S. C. Mohr, Patterns of genome organization in bacteria. Science 279, 1827 (1998).
103. A. Beletskii, A. Grigoriev, S. Joyce, and A. S. Bhagwat, Mutations induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome. J. Mol. Biol. 300, 1057-1065 (2000).
104. M. P. Francino, and H. Ochman, Deamination as the basis of strand-asymmetric evolution in transcribed Escherichia coli sequences. Mol. Biol. Evol. 18, 1147-1150 (2001).
105. L. Duret, Evolution of synonymous codon usage in metazoans. Curr Opin. Genet. Dev. 12, 640-649 (2002).
106. C. Shioiri, and N. Takahata, Skew of mononucleotide frequencies, relative abundance of dinucleotides, and DNA strand asymmetry. J. Mol. Evol. 53, 364-376 (2001).
107. P. Green, B. Ewing, W. Miller, P. J. Thomas, and E. D. Green, Transcription-associated mutational asymmetry in mammalian evolution. Nat. Genet. 33, 514-517 (2003).
108. J. Q. Svejstrup, Mechanisms of transcription-coupled DNA repair. Nat. Rev. Mol. Cell Biol. 3, 21-29 (2002).
109. M. Touchon, Biais de composition chez les mammiferes.: Rôle de la transcription et de la réplication. Ph.D. thesis, University Denis Diderot, Paris VII, France, 2005.
110. F. Jacob, S. Brenner, and F. Cuzin, On the regulation of DNA replication in bacteria. Cold Spring Harb. Symp. Quant. Biol. 28, 329-342 (1963).
111. S. P. Bell, and A. Dutta, DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71, 333-374 (2002).
112. O. Hyrien, and M. Méchali, 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 (1993).
113. S. A. Gerbi, and A. K. Bielinsky, DNA replication and chromatin. Curr Opin. Genet. Dev. 12, 243-248 (2002).
114. D. Schübeler, D. Scalzo, C. Kooperberg, B. van Steensel, J. Delrow, and M. Groudine, Genome-wide DNA replication profile for Drosophila melanogaster. A link between transcription and replication timing. Nat. Genet. 32, 438-442 (2002).
115. D. Fisher, and M. Méchali, Vertebrate HoxB gene expression requires DNA replication. EMBO J. 22, 3737-3748 (2003).
116. M. Anglana, F. Apiou, A. Bensimon, and M. Debatisse, Dynamics of DNA replication in mammalian somatic cells: Nucleotide pool modulates origin choice and interorigin spacing. Cell 114, 385-394 (2003).
117. D. M. Gilbert, Making sense of eukaryotic DNA replication origins. Science 294, 96-100 (2001).
118. D. Coverley, and R. A. Laskey, Regulation of eukaryotic DNA replication. Annu. Rev. Biochem. 63, 745-776 (1994).
119. T. Sasaki, T. Sawado, M. Yamaguchi, and T. Shinomiya, 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 (1999).
120. J. A. Bogan, D. A. Natale, and M. L. Depamphilis, Initiation of eukaryotic DNA replication: conservative or liberal? J. Cell. Physiol. 184, 139-150 (2000).
121. D. M. Gilbert, In search of the holy replicator. Nat. Rev. Mol. Cell Biol. 5, 848-855 (2004).
122. M. Méchali, DNA replication origins: from sequence specificity to epigenetics. Nat. Rev. Genet. 2, 640-645 (2001).
123. C. Demeret, Y. Vassetzky, and M. Méchali, Chromatin remodelling and DNA replication: From nucleosomes to loop domains. Oncogene 20, 3086-3093 (2001).
124. A. J. McNairn, and D. M. Gilbert, Epigenomic replication: Linking epigenetics to DNA replication. Bioessays 25, 647-656 (2003).
125. B. J. Brewer, When polymerases collide: Replication and the transcriptional organization of the E. coli chromosome. Cell 53, 679-686 (1988).
126. E. P. C. Rocha, P. Guerdoux-Jamet, I. Moszer, A. Viari, and A. Danchin, Implication of gene distribution in the bacterial chromosome for the bacterial cell factory. J. Biotech. 78, 209-219 (2000).
127. P. Lopez, and H. Philippe, Composition strand asymmetries in prokaryotic genomes: mutational bias and biased gene orientation. C. R. Acad. Sci. III 324, 201-208 (2001).
128. E. P. C. Rocha, Is there a role for replication fork asymmetry in the distribution of genes in bacterial genomes. Trends Microbiol. 10, 393-395 (2002).
129. M. Bulmer, Strand symmetry of mutation rates in the beta-globin region. J. Mol. Evol. 33, 305-310 (1991).
130. M. P. Francino, and H. Ochman, Strand symmetry around the beta-globin origin of replication in primates. Mol. Biol. Evol. 17, 416-422 (2000).
131. A. Gierlik, M. Kowalczuk, R Mackiewicz, M. R. Dudek, and S. Cebrat, Is there replication-associated mutational pressure in the Saccharomyces cerevisiae genome? J. Theor Biol. 202, 305-314 (2000).
132. E. Louie, J. Ott, and J. Majewski, Nucleotide frequency variation across human genes. Genome Res. 13, 2594-2601 (2003).
133. P. Kapranov, S. E. Cawley, J. Drenkow, S. Bekiranov, R. L. Strausberg, S. P. A. Fodor, and T. R. Gingeras, Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916-919 (2002).
134. J. Chen, M. Sun, S. Lee, G. Zhou, J. D. Rowley, and S. M. Wang, Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl. Acad. Sci. USA, 99, 12257-12262 (2002).
135. J. L. Rinn, G. Euskirchen, P. Bertone, R. Martone, N. M. Luscombe, S. Hartman, P. M. Harrison, F. K. Nelson, P. Miller, et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17, 529-540 (2003).
136. D. Kampa, J. Cheng, P. Kapranov, M. Yamanaka, S. Brubaker, S. Cawley, J. Drenkow, A. Piccolboni, S. Bekiranov, et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331-342 (2004).
137. T. Imanishi, T. Itoh, Y. Suzuki, C.O' Donovan, S. Fukuchi, K. O. Koyanagi, R. A. Barrero, T. Tamura, Y. Yamaguchi-Kabata, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, e162 (2004).
138. C. Girard-Reydet, D. Grégoire, Y. Vassetzky, and M. Méchali, DNA replication initiates at domains overlapping with nuclear matrix attachment regions in the Xenopus and mouse c-myc promoter. Gene 332, 129-138 (2004).
139. L. T. Vassilev, W. C. Burhans, and M. L. DePamphilis, Mapping an origin of DNA replication at a single-copy locus in exponentially proliferating mammalian cells. Mol. Cell. Biol. 10, 4685-4689 (1990).
140. S. Codlin, and J. Z. Dalgaard, Complex mechanism of site-specific DNA replication termination in fission yeast. EMBO J. 22, 3431-3440 (2003).
141. D. Santamaria, E. Viguera, M. L. Martinez-Robles, O. Hyrien, P. Hernandez, D. B. Krimer, and J. B. Schvartzman, Bi-directional replication and random termination. Nucleic Acids Res. 28, 2099-2107 (2000).
142. R. D. Little, T. H. Platt, and C. L. Schildkraut, Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 13, 6600-6613 (1993).
143. E. J. White, O. Emanuelsson, D. Scalzo, T. Royce, S. Kosak, E. J. Oakeley, S. Weissman, M. Gerstein, M. Groudine, et al. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc. Natl. Acad. ScL USA 101, 17771-17776 (2004).
144. H. G. Callan, Replication of DNA in the chromosomes of eukaryotes. Proc. R. Soc. Lond. B Biol. Sci. 181, 19-41 (1972).
145. S. Asakura, and F. Oosawa, On interaction between two bodies immersed in a solution of macromolecules. J. Chem. Phys. 22, 1255-1256 (1954).
146. Y. Snir, and R. D. Kamien, Entropically driven helix formation. Science 307, 1067 (2005).
147. K. van Holde, and J. Zlatanova, What determines the folding of the chromatin fiber? Proc. Natl. Acad. Sci. USA 93, 10548-10555 (1996).
148. B. Mergell, R. Everaers, and H. Schiessel, Nucleosome interactions in chromatin: Fiber stiffening and hairpin formation. Phys. Rev. E 70, 011915 (2004).
149. A. Lesne, and J. M. Victor, Chromatin fiber functional organization: Some plausible models. Eur. Phys. J. E, 19, 279-290 (2005).
150. C. L. Woodcock, S. A. Grigoryev, R. A. Horowitz, and N. Whitaker, A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc. Natl. Acad Sci. USA 90, 9021-9025 (1993).
151. A. Y. Grossberg, and A. R. Khoklov, in Statistical Physics of Macromolecules, AIP Series in Polymers and Complex Materials, R. Larson and P. A. Pincus, eds., AIP Press, Woodbury, 1994.
152. S. Jun, J. Bechhoefer, and B.-Y Ha, Diffusion-limited loop formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing. Europhys. Lett. 64, 420-426 (2003).
153. H. Yamakawa, and W. H. Stockmayer, Statistical mechanics of wormlike chains. II. Excluded volume effects. J. Chem. Phys. 57, 2843-2854 (1972).
154. St. P. Jean, C. Vaillant, B. Audit, and A. Arneodo, Spontaneous emergence of rosette like folding of chromatin: A keystone to replication and transcription regulation. Preprint, 2006.
155. H. Reiss, H. L. Frisch, and J. L. Lebowitz, Statistical mechanics of rigid spheres. J. Chem. Phys. 31, 369-380 (1959).
156. A. D. Dinsmore, A. G. Yodh, and D. J. Pine, Phase diagrams of nearly-hard-sphere binary colloids. Phys. Rev. E 52, 4045-4057 (1995).
157. N. F. Carnahan, and K. E. Starling, Equation of state for nonattracting rigid spheres. J. Chem. Phys. 51, 635-636 (1969).
158. A. P. Minton, The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276, 10577-10580 (2001).
159. J. Herrick, P. Stanislawski, O. Hyrien, and A. Bensimon, Replication fork density increases during DNA synthesis in X. laevis egg extracts. J. Mol. Biol. 300, 1133-1142 (2000).
160. J. Zlatanova, and S. H. Leuba, Chromatin fibers, one-at-a-time. J. Mol. Biol. 331, 1-19 (2003).
161. C. Tassius, C. Moskalenko, P, Minard, M. Desmadril, J. Elezgaray, and F. Argoul, Probing the dynamics of a confined enzyme by surface plasmon resonance. Physica A 342, 402-409 (2004).