The influence of the cylindrical shape of the nucleosomes and H1 defects on properties of chromatin.

We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes, and the distance d between the in and outgoing DNA strands orthogonal to the axis of the corresponding nucleosome cylinder. Factoring these chromatin features in, one gets essential changes in the chromatin phase diagram: Not only the shape of the excluded-volume borderline changes but also the orthogonal distance d has a dramatic influence on the forbidden area. Furthermore, we examined the influence of H1 defects on the properties of the chromatin fiber. Thus, we present two possible strategies for chromatin compaction: The use of very dense states in the phase diagram in the gaps in the excluded-volume, borderline, or missing H1 histones can lead to very compact fibers. The chromatin fiber might use both of these mechanisms to compact itself at least locally. Line densities computed within the model coincident with the experimental values.

[1]  T. Richmond,et al.  X-ray structure of a tetranucleosome and its implications for the chromatin fibre , 2005, Nature.

[2]  A J Koster,et al.  Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  T. Richmond,et al.  Nucleosome Arrays Reveal the Two-Start Organization of the Chromatin Fiber , 2004, Science.

[4]  T. Richmond,et al.  Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.

[5]  K. Luger,et al.  Structure and dynamic properties of nucleosome core particles , 2005, FEBS letters.

[6]  A. Stein,et al.  Histone H1 Depletion in Mammals Alters Global Chromatin Structure but Causes Specific Changes in Gene Regulation , 2005, Cell.

[7]  P. Gennes.  Scaling Concepts in Polymer Physics , 1979 .

[8]  A. Klug,et al.  Structure of the 3000Å chromatin filament: X-ray diffraction from oriented samples , 1985, Cell.

[9]  J. Mozziconacci,et al.  How the chromatin fiber deals with topological constraints. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[10]  A Klug,et al.  Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin , 1979, The Journal of cell biology.

[11]  A Klug,et al.  Solenoidal model for superstructure in chromatin. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[12]  J. Widom.  Physicochemical studies of the folding of the 100 A nucleosome filament into the 300 A filament. Cation dependence. , 1986, Journal of molecular biology.

[13]  Minoru Toda,et al.  Springer Series in Solid-State Sciences , 1989 .

[14]  J. Dubochet,et al.  Chromatin conformation and salt-induced compaction: three-dimensional structural information from cryoelectron microscopy , 1995, The Journal of cell biology.

[15]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[16]  Dieter W Heermann,et al.  Two-angle model and phase diagram for chromatin. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[17]  Dieter W Heermann,et al.  Dynamic Simulation of Active/Inactive Chromatin Domains , 2005, Journal of biological physics.

[18]  D. Dunlap,et al.  Direct observation of DNA distortion by the RSC complex. , 2006, Molecular cell.

[19]  K. V. van Holde,et al.  Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Grigoryev,et al.  A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Helmut Schiessel,et al.  Nucleosome interactions in chromatin: fiber stiffening and hairpin formation. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[22]  Patrick Heun,et al.  Long-range compaction and flexibility of interphase chromatin in budding yeast analyzed by high-resolution imaging techniques. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[23]  K. V. van Holde,et al.  Chromatin fiber structure: morphology, molecular determinants, structural transitions. , 1998, Biophysical journal.

[24]  V. Ramakrishnan,et al.  Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[25]  K. V. van Holde,et al.  Chromatin Higher Order Structure: Chasing a Mirage?(*) , 1995, The Journal of Biological Chemistry.

[26]  W. Gelbart,et al.  DNA folding: structural and mechanical properties of the two-angle model for chromatin. , 2001, Biophysical journal.

[27]  Claudio Nicolini,et al.  Chromatin Structure and Function , 1979, NATO Advanced Study Institutes Series.

[28]  K. V. van Holde,et al.  What determines the folding of the chromatin fiber? , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[29]  N. Metropolis,et al.  The Monte Carlo method. , 1949 .