The effect of the internucleosomal interaction on the folding of the chromatin fiber Export

@article{citeulike:3056714, abstract = {The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by post-translational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo (MC) computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the MC simulation, the nucleosome shape was described as an oblate spherocylinder and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber. 10.1529/biophysj.107.120543}, author = {Stehr, Rene and Kepper, Nick and Rippe, Karsten and Wedemann, Gero}, citeulike-article-id = {3056714}, citeulike-linkout-0 = {http://dx.doi.org/10.1529/biophysj.107.120543}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18658212}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18658212}, day = {25}, doi = {10.1529/biophysj.107.120543}, journal = {Biophys. J.}, keywords = {biophysics, chromatin, epigenetics, modeling}, month = {July}, pages = {biophysj.107.120543+}, posted-at = {2008-07-29 14:01:49}, priority = {4}, title = {The effect of the internucleosomal interaction on the folding of the chromatin fiber}, url = {http://dx.doi.org/10.1529/biophysj.107.120543}, year = {2008} }

TY - JOUR ID - citeulike:3056714 L3 - citeulike-article-id:3056714 N2 - The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by post-translational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo (MC) computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the MC simulation, the nucleosome shape was described as an oblate spherocylinder and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber. 10.1529/biophysj.107.120543 JF - Biophys. J. TI - The effect of the internucleosomal interaction on the folding of the chromatin fiber SP - biophysj.107.120543 KW - biophysics KW - chromatin KW - epigenetics KW - modeling AU - Stehr, Rene AU - Kepper, Nick AU - Rippe, Karsten AU - Wedemann, Gero PY - 2008/07/25/ UR - http://dx.doi.org/10.1529/biophysj.107.120543 ER -