D. Santis, P. Palleschi, A. Morosetti, S. Savino, and M. , Structure and superstructures in periodical polynucleotides Structures and dynamics of nucleic acids, proteins and membranes, pp.3-49, 1986.

D. Santis, P. Palleschi, A. Savino, M. Scipioni, and A. , A theoretical model of DNA curvature, Biophysical Chemistry, vol.32, issue.2-3, pp.305-322, 1988.
DOI : 10.1016/0301-4622(88)87016-9

D. Santis, P. Palleschi, A. Savino, M. Scipioni, and A. , Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature, Biochemistry, vol.29, issue.39, pp.9269-73, 1990.
DOI : 10.1021/bi00491a023

A. Scipioni, S. Pisano, A. Bergia, M. Savino, B. Samorì et al., Recognition on the Nanoscale of a DNA Sequence by an Inorganic Crystal Surface, ChemBioChem, vol.34, issue.11, pp.1645-1653, 2006.
DOI : 10.1002/cbic.200600079

E. Trifonov and J. Sussman, The pitch of chromatin DNA is reflected in its nucleotide sequence., Proceedings of the National Academy of Sciences, vol.77, issue.7, pp.3816-3836, 1980.
DOI : 10.1073/pnas.77.7.3816

E. Trifonov, Sequence-dependent deformational anisotropy of chromatin DNA, Nucleic Acids Research, vol.8, issue.17, pp.4041-53, 1980.
DOI : 10.1093/nar/8.17.4041

G. Mengeritsky and E. Trifonov, Nucleotide sequence-directed mapping of the nucleosomes, Nucleic Acids Research, vol.11, issue.11, pp.3833-51, 1983.
DOI : 10.1093/nar/11.11.3833

P. Hagerman, Sequence dependence of the curvature of DNA: a test of the phasing hypothesis, Biochemistry, vol.24, issue.25, pp.7033-7039, 1985.
DOI : 10.1021/bi00346a001

H. Koo, H. Wu, and D. Crothers, DNA bending at adenine ?? thymine tracts, Nature, vol.24, issue.6062, pp.501-507, 1986.
DOI : 10.1038/320501a0

P. Hagerman, Sequence-Directed Curvature of DNA, Annual Review of Biochemistry, vol.59, issue.1, pp.449-50, 1986.
DOI : 10.1146/annurev.bi.59.070190.003543

A. Bolshoy, P. Mcnamara, R. Harrington, and E. Trifonov, Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles., Proceedings of the National Academy of Sciences, vol.88, issue.6, pp.2312-2318, 1991.
DOI : 10.1073/pnas.88.6.2312

A. Gorin, V. Zhurkin, and W. Olson, B-DNA Twisting Correlates with Base-pair Morphology, Journal of Molecular Biology, vol.247, issue.1, pp.34-48, 1995.
DOI : 10.1006/jmbi.1994.0120

W. Olson, A. Gorin, X. Lu, L. Hock, and V. Zhurkin, DNA sequence-dependent deformability deduced from protein-DNA crystal complexes, Proceedings of the National Academy of Sciences, vol.95, issue.19, pp.11163-11171, 1998.
DOI : 10.1073/pnas.95.19.11163
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC21613

C. Anselmi, D. Santis, P. Paparcone, R. Savino, M. Scipioni et al., From the sequence to the superstructural properties of DNAs, Biophysical Chemistry, vol.95, issue.1, pp.23-47, 2002.
DOI : 10.1016/S0301-4622(01)00246-0

D. Santis, P. Fuà, M. Savino, M. Anselmi, C. Bocchinfuso et al., Sequence Dependent Circularization of DNAs:?? A Physical Model to Predict the DNA Sequence Dependent Propensity to Circularization and Its Changes in the Presence of Protein-Induced Bending, The Journal of Physical Chemistry, vol.100, issue.23, pp.9968-76, 1996.
DOI : 10.1021/jp9526096

C. Anselmi, G. Bocchinfuso, D. Santis, P. Fuà, M. Scipioni et al., Statistical Thermodynamic Approach for Evaluating the Writhe Transformations in Circular DNAs, The Journal of Physical Chemistry B, vol.102, issue.29, pp.5704-5718, 1998.
DOI : 10.1021/jp981552v

C. Anselmi, G. Bocchinfuso, D. Santis, P. Savino, M. Scipioni et al., Dual role of DNA intrinsic curvature and flexibility in determining nucleosome stability, Journal of Molecular Biology, vol.286, issue.5, pp.1293-301, 1999.
DOI : 10.1006/jmbi.1998.2575

C. Anselmi, G. Bocchinfuso, D. Santis, P. Savino, M. Scipioni et al., A Theoretical Model for the Prediction of Sequence-Dependent Nucleosome Thermodynamic Stability, Biophysical Journal, vol.79, issue.2, pp.601-614, 2000.
DOI : 10.1016/S0006-3495(00)76319-3

A. Scipioni, S. Pisano, C. Anselmi, M. Savino, D. Santis et al., Dual role of sequence-dependent DNA curvature in nucleosome stability: the critical test of highly bent Crithidia fasciculata DNA tract, Biophysical Chemistry, vol.107, issue.1, pp.7-17, 2004.
DOI : 10.1016/S0301-4622(03)00214-X

A. Scipioni, S. Morosetti, D. Santis, and P. , A statistical thermodynamic approach for predicting the sequence-dependent nucleosome positioning along genomes, Biopolymers, vol.7, issue.12, pp.1143-53, 2009.
DOI : 10.1002/bip.21276

B. Sampaolese, A. Bergia, and A. Scipioni, Recognition of the DNA sequence by an inorganic crystal surface, Proceedings of the National Academy of Sciences, vol.99, issue.21, pp.13566-70, 2002.
DOI : 10.1073/pnas.202471699

L. Landau and E. Lifshitz, Theory of elasticity, 1970.

A. Morozov, K. Fortney, D. Gaykalova, V. Studitsky, J. Widom et al., Using DNA mechanics to predict in vitro nucleosome positions and formation energies, Nucleic Acids Research, vol.37, issue.14, pp.4707-4729, 2009.
DOI : 10.1093/nar/gkp475

M. Packer, M. Dauncey, and C. Hunter, Sequence-dependent DNA structure: tetranucleotide conformational maps, Journal of Molecular Biology, vol.295, issue.1, pp.85-103, 2000.
DOI : 10.1006/jmbi.1999.3237

J. Marini, S. Levene, D. Crothers, and P. Englund, Bent helical structure in kinetoplast DNA, Proceedings of the National Academy of Sciences, vol.79, issue.24, pp.7664-7672, 1982.
DOI : 10.1073/pnas.79.24.7664

H. Wu and D. Crothers, The locus of sequence-directed and protein-induced DNA bending, Nature, vol.1, issue.5959, pp.509-522, 1984.
DOI : 10.1038/308509a0

C. Anselmi, D. Santis, P. Paparcone, R. Savino, M. Scipioni et al., From the sequence to the superstructural properties of DNAs, Biophysical Chemistry, vol.95, issue.1, pp.23-47, 2002.
DOI : 10.1016/S0301-4622(01)00246-0

D. Gennes and P. , Reptation of a Polymer Chain in the Presence of Fixed Obstacles, The Journal of Chemical Physics, vol.55, issue.2, pp.572-581, 1971.
DOI : 10.1063/1.1675789

O. Lumpkin, P. Dejardin, and B. Zimm, Theory of gel electrophoresis of DNA, Biopolymers, vol.81, issue.8, pp.1573-93, 1985.
DOI : 10.1002/bip.360240812

S. Diekmann, DNA methylation can enhance or induce DNA curvature, EMBO J, vol.6, pp.4213-4220, 1987.

D. Milton, M. Casper, and R. Gesteland, Saturation mutagenesis of a DNA region of bend, Journal of Molecular Biology, vol.213, issue.1, pp.135-175, 1990.
DOI : 10.1016/S0022-2836(05)80126-3

P. Chastain, E. Eichler, S. Kang, D. Nelson, S. Levene et al., Anomalous Rapid Electrophoretic Mobility of DNA Containing Triplet Repeats Associated with Human Disease Genes, Biochemistry, vol.34, issue.49, pp.16125-16156, 1995.
DOI : 10.1021/bi00049a027

P. Chastain and R. Sinden, CTG repeats associated with human genetic disease are inherently flexible, Journal of Molecular Biology, vol.275, issue.3, pp.405-416, 1998.
DOI : 10.1006/jmbi.1997.1502

C. Bustamante, S. Smith, J. Liphardt, and D. Smith, Single-molecule studies of DNA mechanics, Current Opinion in Structural Biology, vol.10, issue.3, pp.279-85, 2000.
DOI : 10.1016/S0959-440X(00)00085-3

C. Rivetti, M. Guthold, and C. Bustamante, Scanning Force Microscopy of DNA Deposited onto Mica: EquilibrationversusKinetic Trapping Studied by Statistical Polymer Chain Analysis, Journal of Molecular Biology, vol.264, issue.5, pp.919-951, 1996.
DOI : 10.1006/jmbi.1996.0687

C. Rivetti, C. Walker, and C. Bustamante, Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility, Journal of Molecular Biology, vol.280, issue.1, pp.41-59, 1998.
DOI : 10.1006/jmbi.1998.1830

G. Zuccheri, A. Scipioni, V. Cavaliere, G. Gargiulo, D. Santis et al., Mapping the intrinsic curvature and flexibility along the DNA chain, Proceedings of the National Academy of Sciences, vol.98, issue.6, pp.3074-3083, 2001.
DOI : 10.1073/pnas.051631198
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC30609

A. Scipioni, C. Anselmi, G. Zuccheri, B. Samorì, D. Santis et al., Sequence-Dependent DNA Curvature and Flexibility from Scanning Force Microscopy Images, Biophysical Journal, vol.83, issue.5, pp.2408-2426, 2002.
DOI : 10.1016/S0006-3495(02)75254-5
URL : http://doi.org/10.1016/s0006-3495(02)75254-5

A. Scipioni, G. Zuccheri, C. Anselmi, A. Bergia, B. Samorì et al., Sequence-Dependent DNA Dynamics by Scanning Force Microscopy Time-Resolved Imaging, Chemistry & Biology, vol.9, issue.12, pp.1315-1336, 2002.
DOI : 10.1016/S1074-5521(02)00282-X
URL : http://doi.org/10.1016/s1074-5521(02)00282-x

J. Sponer, J. Leszczynski, and P. Hobza, Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases, Biopolymers, vol.123, issue.1, pp.3-31, 2002.
DOI : 10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4

J. Griffith, M. Bleyman, C. Rauch, P. Kitchin, and P. Englund, Visualization of the bent helix in kinetoplast DNA by electron microscopy, Cell, vol.46, issue.5, pp.717-741, 1986.
DOI : 10.1016/0092-8674(86)90347-8

D. Rhodes and A. Klug, Sequence-dependent helical periodicity of DNA, Nature, vol.11, issue.5821, pp.378-80, 1981.
DOI : 10.1038/292378a0

K. Holde, The origin of life and evolution, pp.31-46, 1980.

R. Saladino, C. Crestini, V. Neri, J. Brucato, L. Colangeli et al., Synthesis and Degradation of Nucleic Acid Components by Formamide and Cosmic Dust Analogues, ChemBioChem, vol.47, issue.8, pp.1368-74, 2005.
DOI : 10.1002/cbic.200500035

R. Saladino, C. Crestini, S. Pino, G. Costanzo, D. Mauro et al., Formamide and the origin of life, Physics of Life Reviews, vol.9, issue.1, pp.84-104, 2012.
DOI : 10.1016/j.plrev.2011.12.002
URL : https://hal.archives-ouvertes.fr/pasteur-00961566

C. Anselmi, D. Santis, P. Paparcone, R. Savino, M. Scipioni et al., A Possible Role of DNA Superstructures in Genome Evolution, Origins of Life and Evolution of the Biosphere, vol.34, issue.1/2, pp.143-152, 2004.
DOI : 10.1023/B:ORIG.0000009835.26904.50

T. Richmond, J. Finch, B. Rushton, D. Rhodes, and A. Klug, Structure of the nucleosome core particle at 7 ??? resolution, Nature, vol.14, issue.5986, pp.29-36, 1984.
DOI : 10.1038/311532a0

K. Luger, A. Mader, R. Richmond, D. Sargent, and T. Richmond, Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, vol.389, pp.251-60, 1997.

C. Davey, D. Sargent, K. Luger, A. Maeder, and T. Richmond, Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9?? Resolution, Journal of Molecular Biology, vol.319, issue.5, pp.1097-113, 2002.
DOI : 10.1016/S0022-2836(02)00386-8

K. Luger and J. Hansen, Nucleosome and chromatin fiber dynamics, Current Opinion in Structural Biology, vol.15, issue.2, pp.188-96, 2005.
DOI : 10.1016/j.sbi.2005.03.006

S. Satchwell, H. Drew, and A. Travers, Sequence periodicities in chicken nucleosome core DNA, Journal of Molecular Biology, vol.191, issue.4, pp.659-75, 1986.
DOI : 10.1016/0022-2836(86)90452-3

T. Shrader and D. Crothers, Artificial nucleosome positioning sequences., Proceedings of the National Academy of Sciences, vol.86, issue.19, pp.7418-7440, 1989.
DOI : 10.1073/pnas.86.19.7418
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC298075/pdf

T. Shrader and D. Crothers, Effects of DNA sequence and histone-histone interactions on nucleosome placement, Journal of Molecular Biology, vol.216, issue.1, pp.69-84, 1990.
DOI : 10.1016/S0022-2836(05)80061-0

P. Lowary and J. Widom, Nucleosome packaging and nucleosome positioning of genomic DNA, Proceedings of the National Academy of Sciences, vol.94, issue.4, pp.1183-1191, 1997.
DOI : 10.1073/pnas.94.4.1183

P. Lowary and J. Widom, New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning, Journal of Molecular Biology, vol.276, issue.1, pp.19-42, 1998.
DOI : 10.1006/jmbi.1997.1494

T. Bishop, Geometry of the Nucleosomal DNA Superhelix, Biophysical Journal, vol.95, issue.3, pp.1007-1024, 2008.
DOI : 10.1529/biophysj.107.122853

Y. Moshkin, G. Chalkley, T. Kan, B. Reddy, Z. Ozgur et al., Remodelers Organize Cellular Chromatin by Counteracting Intrinsic Histone-DNA Sequence Preferences in a Class-Specific Manner, Molecular and Cellular Biology, vol.32, issue.3, pp.675-88, 2012.
DOI : 10.1128/MCB.06365-11

C. Wu and A. Travers, Relative Affinities of DNA Sequences for the Histone Octamer Depend Strongly upon Both the Temperature and Octamer Concentration, Biochemistry, vol.44, issue.43, pp.14329-14363, 2005.
DOI : 10.1021/bi050915w

S. Godde and A. Wolffe, Nucleosome assembly on CTG triplet repeats, J Biol Chem, vol.271, pp.15222-15231, 1996.

S. Godde, S. Kass, M. Hirst, and A. Wolffe, Nucleosome Assembly on Methylated CGG Triplet Repeats in the Fragile X Mental Retardation Gene 1 Promoter, Journal of Biological Chemistry, vol.271, issue.40, pp.24325-24333, 1996.
DOI : 10.1074/jbc.271.40.24325

Y. Wang, R. Gellibolian, M. Shimizu, R. Wells, and J. Griffith, Long CCG Triplet Repeat Blocks Exclude Nucleosomes: A Possible Mechanism for the Nature of Fragile Sites in Chromosomes, Journal of Molecular Biology, vol.263, issue.4, pp.511-517, 1996.
DOI : 10.1006/jmbi.1996.0593

H. Widlund, H. Cao, S. Simonsson, E. Magnusson, T. Simonsson et al., Identification and characterization of genomic nucleosome-positioning sequences, Journal of Molecular Biology, vol.267, issue.4, pp.807-824, 1997.
DOI : 10.1006/jmbi.1997.0916

S. Cacchione, A. Cerone, and M. Savino, In vitro low propensity to form nucleosomes of four telomeric sequences, FEBS Letters, vol.400, issue.1, pp.37-41, 1997.
DOI : 10.1016/S0014-5793(96)01318-X

H. Cao, H. Widlund, T. Simonsson, and M. Kubista, TGGA repeats impair nucleosome formation, Journal of Molecular Biology, vol.281, issue.2, pp.253-60, 1998.
DOI : 10.1006/jmbi.1998.1925

D. Fitzgerald and J. Anderson, Unique translational positioning of nucleosomes on synthetic DNAs, Nucleic Acids Research, vol.26, issue.11, pp.2526-2561, 1998.
DOI : 10.1093/nar/26.11.2526

D. Fitzgerald and J. Anderson, DNA distortion as a factor in nucleosome positioning, Journal of Molecular Biology, vol.293, issue.3, pp.477-91, 1999.
DOI : 10.1006/jmbi.1999.3171

C. S. Filesi, D. Santis, P. Rossetti, L. Savino, and M. , The main role of the sequence-dependent DNA elasticity in determining the free energy of nucleosome formation on telomeric DNAs, Biophysical Chemistry, vol.83, issue.3, pp.223-260, 1999.
DOI : 10.1016/S0301-4622(99)00143-X

S. Mattei, B. Sampaolese, D. Santis, P. Savino, and M. , Nucleosome organization on Kluyveromyces lactis centromeric DNAs, Biophysical Chemistry, vol.97, issue.2-3, pp.173-87, 2002.
DOI : 10.1016/S0301-4622(02)00066-2

S. Cacchione, J. Rodriguez, R. Mechelli, L. Franco, and M. Savino, Acetylated nucleosome assembly on telomeric DNAs, Biophysical Chemistry, vol.104, issue.2, pp.381-92, 2003.
DOI : 10.1016/S0301-4622(03)00028-0

J. Virstedt, T. Berge, R. Henderson, M. Waring, and A. Travers, The influence of DNA stiffness upon nucleosome formation, Journal of Structural Biology, vol.148, issue.1, pp.2408-2426, 2004.
DOI : 10.1016/j.jsb.2004.03.007

M. Spiegel, Fourier analysis, 1974.

M. Tolstorukov, A. Colasanti, D. Mccandlish, W. Olson, and V. Zhurkin, A Novel Roll-and-Slide Mechanism of DNA Folding in Chromatin: Implications for Nucleosome Positioning, Journal of Molecular Biology, vol.371, issue.3, pp.725-763, 2007.
DOI : 10.1016/j.jmb.2007.05.048

O. Gotoh and Y. Tagashira, Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles, Biopolymers, vol.277, issue.5, pp.1033-1075, 1981.
DOI : 10.1002/bip.1981.360200513

J. Santalucia, A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics, Proceedings of the National Academy of Sciences, vol.95, issue.4, pp.1460-1465, 1998.
DOI : 10.1073/pnas.95.4.1460

A. Travers, The structural basis of DNA flexibility, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.362, issue.1820, pp.1423-1461, 2004.
DOI : 10.1098/rsta.2004.1390

H. Drew and R. Dickerson, Structure of a B-DNA dodecamer, Journal of Molecular Biology, vol.151, issue.3, pp.535-56, 1981.
DOI : 10.1016/0022-2836(81)90009-7

E. Liepnish, G. Otting, and K. Wuthrich, NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution, Nucleic Acids Res, vol.20, pp.4549-53, 1992.
DOI : 10.1142/9789812795830_0059

H. Berman, Hydration of DNA: take 2, Current Opinion in Structural Biology, vol.4, issue.3, pp.345-50, 1994.
DOI : 10.1016/S0959-440X(94)90102-3

L. Mcfail-isom, C. Sines, and L. William, DNA structure: cations in charge?, Current Opinion in Structural Biology, vol.9, issue.3, pp.298-308, 1999.
DOI : 10.1016/S0959-440X(99)80040-2

N. Hud, V. Sklenar, and J. Feigon, Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending, Journal of Molecular Biology, vol.286, issue.3, pp.651-60, 1999.
DOI : 10.1006/jmbi.1998.2513

B. Bernstein, C. Liu, E. Humphrey, E. Perlstein, and S. Schreiber, Global nucleosome occupancy in yeast, Genome Biology, vol.5, issue.9, p.62, 2004.
DOI : 10.1186/gb-2004-5-9-r62

C. Lee, Y. Shibata, B. Rao, B. Strahl, and J. Lieb, Evidence for nucleosome depletion at active regulatory regions genome-wide, Nature Genetics, vol.12, issue.8, pp.900-905, 2004.
DOI : 10.1093/nar/30.4.e15

G. Yuan, Y. Liu, M. Dion, M. Slack, L. Wu et al., Genome-Scale Identification of Nucleosome Positions in S. cerevisiae, Science, vol.309, issue.5734, pp.626-656, 2005.
DOI : 10.1126/science.1112178

E. Sekinger, Z. Moqtaderi, and K. Struhl, Intrinsic Histone-DNA Interactions and Low Nucleosome Density Are Important for Preferential Accessibility of Promoter Regions in Yeast, Molecular Cell, vol.18, issue.6, pp.735-783, 2005.
DOI : 10.1016/j.molcel.2005.05.003

W. Lee, D. Tillo, N. Bray, R. Morse, R. Davis et al., A high-resolution atlas of nucleosome occupancy in yeast, Nature Genetics, vol.32, issue.10, pp.1235-1279, 2007.
DOI : 10.1038/ng2117

T. Mavrich, I. Ioshikhes, B. Venters, C. Jiang, L. Tomsho et al., A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome, Genome Research, vol.18, issue.7, pp.1073-83, 2008.
DOI : 10.1101/gr.078261.108

Y. Field, N. Kaplan, Y. Fondufe-mittendorf, I. Moore, E. Sharon et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Computational Biology, vol.77, issue.11, p.1000216, 2008.
DOI : 10.1371/journal.pcbi.1000216.s007

N. Kaplan, I. Moore, Y. Fondufe-mittendorf, A. Gossett, D. Tillo et al., The DNA-encoded nucleosome organization of a eukaryotic genome, Nature, vol.12, issue.7236, pp.362-368, 2009.
DOI : 10.1038/nature07667

C. Jiang and B. Pugh, A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome, Genome Biology, vol.10, issue.10, p.109, 2009.
DOI : 10.1186/gb-2009-10-10-r109

Y. Zhang, Z. Moqtaderi, B. Rattner, G. Euskirchen, M. Snyder et al., Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo, Nature Structural & Molecular Biology, vol.371, issue.8, pp.847-53, 2009.
DOI : 10.1038/nsmb.1636

O. Rando, Genome-Wide Mapping of Nucleosomes in Yeast, Methods Enzymol, vol.470, pp.105-123, 2010.
DOI : 10.1016/S0076-6879(10)70005-7

A. Stein, T. Takasuka, and C. Collings, Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences?, Nucleic Acids Research, vol.38, issue.3, pp.709-728, 2009.
DOI : 10.1093/nar/gkp1043

N. Kaplan, I. Moore, Y. Fondufe-mittendorf, A. Gossett, D. Tillo et al., Nucleosome sequence preferences influence in vivo nucleosome organization, Nature Structural & Molecular Biology, vol.14, issue.8, pp.918-938, 2010.
DOI : 10.1101/gr.076463.108

Y. Zhang, Z. Moqtaderi, B. Rattner, G. Euskirchen, M. Snyder et al., Reply to ???Evidence against a genomic code for nucleosome positioning???, Nature Structural & Molecular Biology, vol.1, issue.8, pp.920-923, 2010.
DOI : 10.1016/0022-2836(88)90603-1
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742340

B. Pugh, A preoccupied position on nucleosomes, Nature Structural & Molecular Biology, vol.17, issue.8, p.923, 2010.
DOI : 10.1038/nsmb.1636

D. Boffelli, D. Santis, P. Palleschi, A. Savino, and M. , The curvature vector in nucleosomal DNAs and theoretical prediction of nucleosome positioning, Biophysical Chemistry, vol.39, issue.2, pp.127-163, 1991.
DOI : 10.1016/0301-4622(91)85014-H

D. Santis, P. Fuà, M. Palleschi, A. Savino, and M. , Relationships between intrinsic and induced curvature in DNAs: Theoretical prediction of nucleosome positioning, Biophysical Chemistry, vol.46, issue.2, pp.193-204, 1993.
DOI : 10.1016/0301-4622(93)85027-F

I. Ioshikhes, A. Bolshoy, K. Derenshteyn, M. Borodovsky, and E. Trifonov, Nucleosome DNA Sequence Pattern Revealed by Multiple Alignment of Experimentally Mapped Sequences, Journal of Molecular Biology, vol.262, issue.2, pp.129-168, 1996.
DOI : 10.1006/jmbi.1996.0503

G. Mengeritsky and E. Trifonov, Nucleotide sequence-directed mapping of the nucleosomes, Nucleic Acids Research, vol.11, issue.11, pp.3833-51, 1983.
DOI : 10.1093/nar/11.11.3833

I. Gabdank, D. Barash, and E. Trifonov, Single-base Resolution Nucleosome Mapping on DNA Sequences, Journal of Biomolecular Structure and Dynamics, vol.8, issue.6, pp.107-129, 2010.
DOI : 10.1080/07391102.2010.10507347

T. Bettecken, Z. Frenkel, and E. Trifonov, Nucleosome DNA sequence structure of isochores, BMC Genomics, vol.21, p.203, 2011.

T. Bettecken, Z. Frenkel, and E. Trifonov, Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes, BMC Genomics, vol.263, issue.1, p.273, 2011.
DOI : 10.1016/j.jtbi.2009.11.020

A. Rapoport, Z. Frenkel, and E. Trifonov, Nucleosome Positioning Pattern Derived from Oligonucleotide Compositions of Genomic Sequences, Journal of Biomolecular Structure and Dynamics, vol.332, issue.4, pp.567-74, 2011.
DOI : 10.1080/07391102.2011.10531243

E. Segal, Y. Fondufe-mittendorf, L. Chen, A. Thåström, Y. Field et al., A genomic code for nucleosome positioning, Nature, vol.11, issue.7104, pp.772-780, 2006.
DOI : 10.1016/j.jmb.2004.03.032

D. Tillo, N. Kaplan, I. Moore, Y. Fondufe-mittendorf, A. Gossett et al., High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences, PLoS ONE, vol.5, issue.2, p.9129, 2010.
DOI : 10.1371/journal.pone.0009129.g002
URL : http://doi.org/10.1371/journal.pone.0009129

H. Peckham, R. Thurman, Y. Fu, J. Stamatoyannopoulos, W. Noble et al., Nucleosome positioning signals in genomic DNA, Genome Research, vol.17, issue.8, pp.1170-1177, 2007.
DOI : 10.1101/gr.6101007
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933512

A. Scipioni, S. Morosetti, D. Santis, and P. , Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches, J Biomol Struct Dyn, vol.27, pp.747-64, 2010.

V. Iyer and K. Struhl, Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure, EMBO J, vol.14, pp.2570-2579, 1995.

V. Miele, C. Vaillant, Y. Aubenton-carafa, C. Thermes, and T. Grange, DNA physical properties determine nucleosome occupancy from yeast to fly, Nucleic Acids Research, vol.36, issue.11, pp.3746-56, 2008.
DOI : 10.1093/nar/gkn262
URL : https://hal.archives-ouvertes.fr/hal-00428131

C. Vaillant, B. Audit, and A. Arneodo, Experiments Confirm the Influence of Genome Long-Range Correlations on Nucleosome Positioning, Physical Review Letters, vol.99, issue.21, p.218103, 2007.
DOI : 10.1103/PhysRevLett.99.218103
URL : https://hal.archives-ouvertes.fr/hal-00337710

F. Battistini, C. Hunter, I. Moore, and J. Widom, Structure-Based Identification of New High-Affinity Nucleosome Binding Sequences, Journal of Molecular Biology, vol.420, issue.1-2, pp.8-16, 2012.
DOI : 10.1016/j.jmb.2012.03.026

T. Van-der-heijden, J. Van-vugt, C. Logie, and J. Van-noort, Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy, Proceedings of the National Academy of Sciences, vol.109, issue.38, pp.2514-2536, 2012.
DOI : 10.1073/pnas.1205659109

M. Caserta, E. Agricola, M. Churcher, E. Hiriart, L. Verdone et al., A translational signature for nucleosome positioning in vivo, Nucleic Acids Research, vol.37, issue.16, pp.5309-5330, 2009.
DOI : 10.1093/nar/gkp574

C. Stockdale, A. Flaus, H. Ferreira, and T. Owen-hughes, Analysis of Nucleosome Repositioning by Yeast ISWI and Chd1 Chromatin Remodeling Complexes, Journal of Biological Chemistry, vol.281, issue.24, pp.16279-88, 2006.
DOI : 10.1074/jbc.M600682200

L. Verdone, G. Camilloni, D. Mauro, E. Caserta, and M. , Chromatin remodeling during Saccharomyces cerevisiae ADH2 gene activation., Molecular and Cellular Biology, vol.16, issue.5, pp.1978-88, 1996.
DOI : 10.1128/MCB.16.5.1978
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC231185

H. Cole, B. Howard, and D. Clark, Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes, Nucleic Acids Research, vol.39, issue.22, pp.9521-9556, 2011.
DOI : 10.1093/nar/gkr643

J. Widom, A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells., Proceedings of the National Academy of Sciences, vol.89, issue.3, pp.1095-1104, 1992.
DOI : 10.1073/pnas.89.3.1095

A. Scipioni, G. Turchetti, S. Morosetti, D. Santis, and P. , Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin, Biophysical Chemistry, vol.148, issue.1-3, pp.56-67, 2010.
DOI : 10.1016/j.bpc.2010.02.010

K. Brogaard, L. Xi, J. Wang, and J. Widom, A map of nucleosome positions in yeast at base-pair resolution, Nature, vol.7, pp.496-501, 2012.
DOI : 10.1038/nature11142