Sequence-dependent DNA helical rise and nucleosome stability.

BMC Molecular Biology
Francesco Pedone, Daniele Santoni

Abstract

Nucleosomes are the basic structural units of eukaryotic chromatin and play a key role in regulation of gene expression. After resolution of the nucleosome structure, the bipartite nature of this particle has revealed itself and has disclosed the presence, on the histone surface, of a symmetric distribution of positive charges, able to interact with their negative DNA phosphate counterpart. We analyzed helical steps in known nucleosomal DNA sequences, observing a significant relationship between their symmetric distribution and nucleosome stability. Synthetic DNA sequences able to form stable nucleosomes were used to compare distances on the left and on the right side of the nucleosomal dyad axis, where DNA phosphates and charged residues of the (H3H4)2-tetramer interact. We observed a linear relationship between coincidence of distances and nucleosome stability, i. e., the more symmetric these distances the more stable the nucleosome. Curves related to this symmetric distribution along the DNA sequence identify preferential sites for positioning of the dyad axis, which we termed palinstases. The comparison of our data with known nucleosome positions in archaeal and eukaryotic sequences shows many coincidences of location. Sequ...Continue Reading

References

Oct 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·T E Shrader, D M Crothers
May 5, 1987·Journal of Molecular Biology·H R Drew, C R Calladine
Jan 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·R T Simpson, D W Stafford
May 21, 1998·Nucleic Acids Research·D J Fitzgerald, J N Anderson
Aug 12, 1998·Journal of Molecular Biology·H CaoM Kubista
Jan 7, 2000·Journal of Molecular Biology·M J PackerC A Hunter
Jun 25, 2002·Journal of Molecular Biology·Curt A DaveyTimothy J Richmond
May 9, 2003·Nature·Timothy J Richmond, Curt A Davey
Sep 23, 2003·Journal of Molecular Biology·Eleanor J GardinerPeter Willett
Jun 18, 2005·Science·Guo-Cheng YuanOliver J Rando
Aug 27, 2005·Cell·Dmitry K PokholokRichard A Young
May 10, 2006·PLoS Genetics·Pär G EngströmLeonard Lipovich
Jul 25, 2006·Nature·Eran SegalJonathan Widom
Sep 12, 2006·Nature Genetics·Ilya P IoshikhesB Franklin Pugh
Jan 16, 2007·Nature Biotechnology·Fatih OzsolakDavid E Fisher
Jun 26, 2007·Journal of Molecular Biology·Michael Y TolstorukovVictor B Zhurkin
Jul 11, 2007·Genome Research·Heather E PeckhamZhiping Weng
Sep 18, 2007·Nature Genetics·William LeeCorey Nislow
Jan 9, 2008·PLoS Computational Biology·Clinton H HansenNed S Wingreen
Jan 30, 2008·PLoS Computational Biology·Guo-Cheng Yuan, Jun S Liu
Mar 11, 2008·Cell·Dustin E SchonesKeji Zhao
Apr 15, 2008·Nature·Travis N MavrichB Franklin Pugh
May 20, 2008·Nucleic Acids Research·Vincent MieleThierry Grange
Aug 30, 2008·PLoS Computational Biology·Shobhit GuptaWilliam Stafford Noble

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Citations

Jan 12, 2012·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Francesco Pedone, Daniele Santoni
Dec 18, 2015·Nucleic Acids Research·Kevin HauserCarlos Simmerling
Dec 3, 2016·PloS One·Davide Vergni, Daniele Santoni
Jul 6, 2019·Scientific Reports·Reinhard HeckelRobert N Grass
Nov 20, 2018·Genomics·Francesco PedoneDaniele Santoni

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Methods Mentioned

BETA
PCR
X-ray
NMR

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