M. Beato and K. Eisfeld, Transcription factor access to chromatin, Nucleic Acids Research, vol.25, issue.18, pp.3559-3563, 1997.
DOI : 10.1093/nar/25.18.3559

P. B. Becker, NEW EMBO MEMBER'S REVIEW: Nucleosome sliding: facts and fiction, The EMBO Journal, vol.21, issue.18, pp.4749-4753, 2002.
DOI : 10.1093/emboj/cdf486

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC126283

S. Henikoff and K. Ahmad, ASSEMBLY OF VARIANT HISTONES INTO CHROMATIN, Annual Review of Cell and Developmental Biology, vol.21, issue.1, pp.133-153, 2005.
DOI : 10.1146/annurev.cellbio.21.012704.133518

S. Henikoff, T. Furuyama, and K. Ahmad, Histone variants, nucleosome assembly and epigenetic inheritance, Trends in Genetics, vol.20, issue.7, pp.320-326, 2004.
DOI : 10.1016/j.tig.2004.05.004

B. D. Strahl and C. D. Allis, The language of covalent histone modifications, Nature, vol.96, issue.6765, pp.41-45, 2000.
DOI : 10.1038/47412

C. L. Peterson and J. L. Workman, Promoter targeting and chromatin remodeling by the SWI/SNF complex. Current opinion in genetics & development, pp.187-192, 2000.

A. Travers, An Engine for Nucleosome Remodeling, Cell, vol.96, issue.3, pp.311-314, 1999.
DOI : 10.1016/S0092-8674(00)80543-7

T. Tsukiyama and C. Wu, Chromatin remodeling and transcription. Current opinion in genetics & development, pp.182-191, 1997.

A. Hamiche, J. G. Kang, C. Dennis, H. Xiao, and C. Wu, Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF, Proceedings of the National Academy of Sciences, vol.7, issue.1, pp.14316-14321, 2001.
DOI : 10.1016/S1097-2765(01)00158-7

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC64679

G. Langst, E. J. Bonte, D. F. Corona, P. B. Becker, Y. et al., Nucleosome Movement by CHRAC and ISWI without Disruption or trans-Displacement of the Histone Octamer, Cell, vol.97, issue.7, pp.843-852389, 1999.
DOI : 10.1016/S0092-8674(00)80797-7

I. Whitehouse, A. Flaus, B. R. Cairns, M. F. White, J. L. Workman et al., Nucleosome mobilization catalysed by the yeast SWI/SNF complex, Nature, vol.400, pp.784-787, 1999.

D. W. Abbott, V. S. Ivanova, X. Wang, W. M. Bonner, and J. Ausio, Characterization of the Stability and Folding of H2A.Z Chromatin Particles. IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION, Journal of Biological Chemistry, vol.276, issue.45, pp.41945-41949, 2001.
DOI : 10.1074/jbc.M108217200

D. Angelov, A. Molla, P. Y. Perche, F. Hans, J. Cote et al., The Histone Variant MacroH2A Interferes with Transcription Factor Binding and SWI/SNF Nucleosome Remodeling, Molecular Cell, vol.11, issue.4, pp.1033-1041, 2003.
DOI : 10.1016/S1097-2765(03)00100-X

URL : https://hal.archives-ouvertes.fr/hal-00023762

Y. Bao, K. Konesky, Y. J. Park, S. Rosu, P. N. Dyer et al., Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA, Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA, pp.3314-3324, 2004.
DOI : 10.1016/0168-9525(96)81401-6

S. Chakravarthy, Y. Bao, V. A. Roberts, D. Tremethick, and K. Luger, Structural Characterization of Histone H2A Variants, Cold Spring Harbor Symposia on Quantitative Biology, vol.3, issue.0, pp.227-234, 2004.
DOI : 10.1002/(SICI)1520-6408(1998)22:1<1::AID-DVG1>3.0.CO;2-A

J. Y. Fan, D. Rangasamy, K. Luger, and D. J. Tremethick, H2A.Z Alters the Nucleosome Surface to Promote HP1??-Mediated Chromatin Fiber Folding, Molecular Cell, vol.16, issue.4, pp.655-661, 2004.
DOI : 10.1016/j.molcel.2004.10.023

R. K. Suto, M. J. Clarkson, D. J. Tremethick, and K. Luger, Crystal structure of a nucleosome core particle containing the variant histone H2A, Z. Nature structural biology, vol.7, pp.1121-1124, 2000.

K. Ahmad and S. Henikoff, Epigenetic Consequences of Nucleosome Dynamics, Cell, vol.111, issue.3, pp.281-284, 2002.
DOI : 10.1016/S0092-8674(02)01081-4

J. Ausio, D. W. Abbott-kamakaka, R. T. , and S. Biggins, The many tales of a tail: carboxyl-terminal tail heterogeneity specializes histone H2A variants for defined chromatin function Histone variants: deviants?, Biochemistry Genes & development, vol.41, issue.19, pp.5945-5949295, 2002.

K. Sarma and D. Reinberg, Histone variants meet their match, Nature Reviews Molecular Cell Biology, vol.119, issue.2, pp.139-149, 2005.
DOI : 10.1038/nrm1567

B. P. Chadwick and H. F. Willard, A Novel Chromatin Protein, Distantly Related to Histone H2a, Is Largely Excluded from the Inactive X Chromosome, The Journal of Cell Biology, vol.10, issue.2, pp.375-384, 2001.
DOI : 10.1093/nar/27.3.711

A. Angelov, J. Hamiche, C. Bednar, P. Faivre-moskalenko, S. Bouvet et al., Dissection of the unusual structural and functional properties of the variant H2A, pp.4234-4244, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00335077

K. Luger, A. W. Mader, R. K. Richmond, D. F. Sargent, T. J. Richmond-polach et al., Crystal structure of the nucleosome core particle at 2.8 A resolution Restriction enzymes as probes of nucleosome stability and dynamics, Nature Methods in enzymology, vol.389, issue.304, pp.251-260278, 1997.

C. Wu and A. Travers, A 'one-pot' assay for the accessibility of DNA in a nucleosome core particle, Nucleic Acids Research, vol.32, issue.15, p.122, 2004.
DOI : 10.1093/nar/gnh121

M. Tomschik, H. Zheng, K. Van-holde, J. Zlatanova, and S. H. Leuba, Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer, Proceedings of the National Academy of Sciences, vol.52, issue.1, pp.3278-3283, 2005.
DOI : 10.1146/annurev.physchem.52.1.233

K. Toth, N. Brun, and J. Langowski, Trajectory of Nucleosomal Linker DNA Studied by Fluorescence Resonance Energy Transfer, Biochemistry, vol.40, issue.23, pp.6921-6928, 2001.
DOI : 10.1021/bi002695m

H. Schiessel, The physics of chromatin, Journal of Physics: Condensed Matter, vol.15, issue.19, pp.699-774, 2003.
DOI : 10.1088/0953-8984/15/19/203

T. C. Bishop, Molecular Dynamics Simulations of a Nucleosome and Free DNA, Journal of Biomolecular Structure and Dynamics, vol.362, issue.6, pp.673-686, 2005.
DOI : 10.1080/07391102.2005.10507034

S. Sharma, F. Ding, and N. V. Dokholyan, Multiscale Modeling of Nucleosome Dynamics, Biophysical Journal, vol.92, issue.5, pp.1457-1470, 2007.
DOI : 10.1529/biophysj.106.094805

G. Wedemann and J. Langowski, Computer Simulation of the 30-Nanometer Chromatin Fiber, Biophysical Journal, vol.82, issue.6, pp.2847-2859, 2002.
DOI : 10.1016/S0006-3495(02)75627-0

J. Z. Ruscio and A. Onufriev, A Computational Study of Nucleosomal DNA Flexibility, Biophysical Journal, vol.91, issue.11, pp.4121-4132, 2006.
DOI : 10.1529/biophysj.106.082099

G. Binnig, C. F. Quate, and C. Gerber, Atomic Force Microscope, Physical Review Letters, vol.56, issue.9, pp.930-933, 1986.
DOI : 10.1103/PhysRevLett.56.930

J. Zlatanova and S. H. Leuba, Chromatin Fibers, One-at-a-time, Journal of Molecular Biology, vol.331, issue.1, pp.1-19, 2003.
DOI : 10.1016/S0022-2836(03)00691-0

M. Ji, P. Hou, Z. Lu, and N. He, Covalent Immobilization of DNA onto Functionalized Mica for Atomic Force Microscopy, Journal of Nanoscience and Nanotechnology, vol.4, issue.6, pp.580-584, 2004.
DOI : 10.1166/jnn.2004.005

Y. Lyubchenko, L. Shlyakhtenko, R. Harrington, P. Oden, and S. Lindsay, Atomic force microscopy of long DNA: imaging in air and under water., Proceedings of the National Academy of Sciences, vol.90, issue.6, pp.2137-2140, 1993.
DOI : 10.1073/pnas.90.6.2137

Y. L. Lyubchenko, P. I. Oden, D. Lampner, S. M. Lindsay, and K. A. Dunker, Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces, Nucleic Acids Research, vol.21, issue.5, pp.1117-1123, 1993.
DOI : 10.1093/nar/21.5.1117

A. Podesta, L. Imperadori, W. Colnaghi, L. Finzi, P. Milani et al., Atomic force microscopy study of DNA deposited on poly l-ornithine-coated mica, Journal of Microscopy, vol.215, issue.3, pp.236-240, 2004.
DOI : 10.1111/j.0022-2720.2004.01372.x

A. Podesta, M. Indrieri, D. Brogioli, G. S. Manning, P. Milani et al., Positively Charged Surfaces Increase the Flexibility of DNA, Biophysical Journal, vol.89, issue.4, pp.2558-2563, 2005.
DOI : 10.1529/biophysj.105.064667

K. Umemura, J. Komatsu, T. Uchihashi, N. Choi, S. Ikawa et al., Atomic Force Microscopy of RecA???DNA Complexes Using a Carbon Nanotube Tip, Biochemical and Biophysical Research Communications, vol.281, issue.2, pp.390-395, 2001.
DOI : 10.1006/bbrc.2001.4333

H. Wang, R. Bash, J. G. Yodh, G. L. Hager, D. Lohr et al., Glutaraldehyde Modified Mica: A New Surface for Atomic Force Microscopy of Chromatin, Biophysical Journal, vol.83, issue.6, pp.3619-3625, 2002.
DOI : 10.1016/S0006-3495(02)75362-9

J. F. Kepert, J. Mazurkiewicz, G. L. Heuvelman, K. F. Toth, and K. Rippe, NAP1 Modulates Binding of Linker Histone H1 to Chromatin and Induces an Extended Chromatin Fiber Conformation, Journal of Biological Chemistry, vol.280, issue.40, pp.34063-34072, 2005.
DOI : 10.1074/jbc.M507322200

J. F. Kepert, K. F. Toth, M. Caudron, N. Mucke, J. Langowski et al., Conformation of Reconstituted Mononucleosomes and Effect of Linker Histone H1 Binding Studied by Scanning Force Microscopy, Biophysical Journal, vol.85, issue.6, pp.4012-40224464, 1999.
DOI : 10.1016/S0006-3495(03)74815-2

S. Aoyagi, P. A. Wade, and J. J. Hayes, Nucleosome Sliding Induced by the xMi-2 Complex Does Not Occur Exclusively via a Simple Twist-diffusion Mechanism, Journal of Biological Chemistry, vol.278, issue.33, pp.30562-30568, 2003.
DOI : 10.1074/jbc.M304148200

C. N. Johnson, N. L. Adkins, and P. Georgel, Chromatin remodeling complexes: ATP-dependent machines in action, Biochemistry and Cell Biology, vol.83, issue.4, pp.405-417, 2005.
DOI : 10.1139/o05-115

O. Donohue, M. F. , I. Duband-goulet, A. Hamiche, and A. Prunell, Octamer displacement and redistribution in transcription of single nucleosomes, Nucleic Acids Research, vol.22, issue.6, pp.937-945, 1994.
DOI : 10.1093/nar/22.6.937

P. Furrer, J. Bednar, J. Dubochet, A. Hamiche, and A. Prunell, DNA at the Entry-Exit of the Nucleosome Observed by Cryoelectron Microscopy, Journal of Structural Biology, vol.114, issue.3, pp.177-183, 1995.
DOI : 10.1006/jsbi.1995.1017

G. Li, M. Levitus, C. Bustamante, J. Widom-lowary, P. T. et al., Rapid spontaneous accessibility of nucleosomal DNA, Nature Structural & Molecular Biology, vol.255, issue.1, pp.46-53, 1998.
DOI : 10.1016/0076-6879(94)44022-0

K. Luger, T. J. Rechsteiner, and T. J. Richmond, Expression and Purification of Recombinant Histones and Nucleosome Reconstitution, Methods in molecular biology, vol.119, pp.1-16, 1999.
DOI : 10.1385/1-59259-681-9:1

D. Angelov, A. Verdel, W. An, V. Bondarenko, F. Hans et al., SWI/SNF remodeling and p300-dependent transcription of histone variant H2ABbd nucleosomal arrays, The EMBO Journal, vol.276, issue.19, pp.3815-3824, 2004.
DOI : 10.1074/jbc.273.33.21352

URL : https://hal.archives-ouvertes.fr/inserm-00444420

J. Cote, J. Quinn, J. L. Workman, and C. L. Peterson, Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex, Science, vol.265, issue.5168, pp.53-60, 1994.
DOI : 10.1126/science.8016655

V. Mutskov, D. Gerber, D. Angelov, J. Ausio, J. Workman et al., Persistent Interactions of Core Histone Tails with Nucleosomal DNA following Acetylation and Transcription Factor Binding, Molecular and Cellular Biology, vol.18, issue.11, pp.6293-6304, 1998.
DOI : 10.1128/MCB.18.11.6293

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.919-932, 1996.
DOI : 10.1006/jmbi.1996.0687

F. Valle, M. Favre, P. De-los-rios, A. Rosa, and G. Dietler, Scaling Exponents and Probability Distributions of DNA End-to-End Distance, Physical Review Letters, vol.95, issue.15, p.158105, 2005.
DOI : 10.1103/PhysRevLett.95.158105

J. Y. Ye, K. Umemura, M. Ishikawa, and R. Kuroda, Atomic Force Microscopy of DNA Molecules Stretched by Spin-Coating Technique, Analytical Biochemistry, vol.281, issue.1, pp.21-25, 2000.
DOI : 10.1006/abio.2000.4544

W. Gonzalez, Digital Image Processing 2nd Edition, 2002.

D. J. Rigotti, B. Kokona, T. Horne, E. K. Acton, C. D. Lederman et al., Quantitative atomic force microscopy image analysis of unusual filaments formed by the Acanthamoeba castellanii myosin II rod domain, Analytical Biochemistry, vol.346, issue.2, pp.189-200, 2005.
DOI : 10.1016/j.ab.2005.08.026

C. Rivetti and S. Codeluppi, Accurate length determination of DNA molecules visualized by atomic force microscopy: evidence for a partial B- to A-form transition on mica, Ultramicroscopy, vol.87, issue.1-2, pp.55-66, 2001.
DOI : 10.1016/S0304-3991(00)00064-4

T. S. Spisz, Y. Fang, R. H. Reeves, C. K. Seymour, I. N. Bankman et al., Automated sizing of DNA fragments in atomic force microscope images, Medical & Biological Engineering & Computing, vol.27, issue.3, pp.667-672, 1998.
DOI : 10.1007/BF02518867

J. Canny, A computational approach to edge detection, pp.679-698, 1986.

G. Varadhan, W. Robinett, D. Erie, and R. M. Ii, <title>Fast simulation of atomic-force-microscope imaging of atomic and polygonal surfaces using graphics hardware</title>, Visualization and Data Analysis 2002, 2003.
DOI : 10.1117/12.458778

J. S. Villarrubia, Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation, Journal of Research of the National Institute of Standards and Technology, vol.102, issue.4, pp.425-453, 1997.
DOI : 10.6028/jres.102.030

URL : http://doi.org/10.6028/jres.102.030

K. J. Polach, J. Widom-polach, K. J. , and J. Widom, A Model for the Cooperative Binding of Eukaryotic Regulatory Proteins to Nucleosomal Target Sites, Journal of Molecular Biology, vol.258, issue.5, pp.800-812130, 1995.
DOI : 10.1006/jmbi.1996.0288

J. D. Anderson and J. Widom, Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites, Journal of Molecular Biology, vol.296, issue.4, pp.979-987, 2000.
DOI : 10.1006/jmbi.2000.3531

C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, and T. J. 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.1097-1113, 2002.
DOI : 10.1016/S0022-2836(02)00386-8

D. N. Nikova, L. H. Pope, M. L. Bennink, K. A. Van-leijenhorst-groener, K. Van-der-werf et al., Unexpected Binding Motifs for Subnucleosomal Particles Revealed by Atomic Force Microscopy, Biophysical Journal, vol.87, issue.6, pp.4135-4145, 2004.
DOI : 10.1529/biophysj.104.048983

URL : http://doi.org/10.1529/biophysj.104.048983

T. Gautier, D. W. Abbott, A. Molla, A. Verdel, J. Ausio et al., Histone variant H2ABbd confers lower stability to the nucleosome, Histone variant H2ABbd confers lower stability to the nucleosome, pp.715-720, 2004.
DOI : 10.1038/81971

URL : https://hal.archives-ouvertes.fr/inserm-00335082

S. R. Kassabov, N. M. Henry, M. Zofall, T. Tsukiyama, and B. Bartholomew, High-Resolution Mapping of Changes in Histone-DNA Contacts of Nucleosomes Remodeled by ISW2, Molecular and Cellular Biology, vol.22, issue.21, pp.7524-7534, 2002.
DOI : 10.1128/MCB.22.21.7524-7534.2002

A. Shundrovsky, C. L. Smith, J. T. Lis, C. L. Peterson, and M. D. Wang, Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules, Nature Structural & Molecular Biology, vol.58, issue.6, pp.549-554, 2006.
DOI : 10.1038/nsmb1102

Y. Zhang, C. L. Smith, S. W. Saha, S. Grill, S. B. Mihardja et al., DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC, Molecular Cell, vol.24, issue.4, pp.559-568, 2006.
DOI : 10.1016/j.molcel.2006.10.025

M. Zofall, J. Persinger, S. R. Kassabov, and B. Bartholomew, Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome, Nature Structural & Molecular Biology, vol.276, issue.4, pp.339-346, 2006.
DOI : 10.1006/meth.1999.0880