Geometrical, conformational and topological restraints in regular nucleosome compaction in chromatin

The folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the e...

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Bibliographic Details
Published in:	Biophysical chemistry Vol. 148; no. 1; pp. 56 - 67
Main Authors:	Scipioni, Anita, Turchetti, Giulia, Morosetti, Stefano, De Santis, Pasquale
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 01-05-2010
Subjects:	Conformational equivalence DNA - chemistry Histones - chemistry Models, Molecular Nucleosome packing in chromatin Nucleosomes - chemistry Protein Conformation Protein Folding Topological conditions Torsional energy of linkers Torsional energy of linkers Nucleosome packing in chromatin Topological conditions Conformational equivalence
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Summary:	The folding of the nucleosome array into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The statistical analysis of the nucleosome repeat length in chromatin fibers reveals the presence of a ten-fold periodicity suggesting the existence of orientational constraints of the nucleosome units that provide the geometrical conditions of helical conformations. Recently, the elucidation of the x-ray crystal structure of a nucleosome tetramer array and the interpretation of electron microscopy images of reconstituted nucleosome arrays suggested two different architectures of the chromatin fiber. We approached the problem by integrating the experimental findings with geometrical, conformational and topological restraints, under the hypothesis of the minimum distortion of the nucleosome and linker DNA structures. We show that the excluded volume at linker crossing and the torsional energy limit the possible close packing of the nucleosomes in the chromatin fiber. In particular, the torsional energy of the chromatin fiber appears crucial in determining the kind of nucleosome packing for short nucleosome repeat lengths as in telomeres and yeast chromatin.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0301-4622 1873-4200
DOI:	10.1016/j.bpc.2010.02.010