Genomic studies and computational predictions of nucleosome positions and formation energies.

Advances in Protein Chemistry and Structural Biology
Denis Tolkunov, Alexandre V Morozov

Abstract

Chromatin is a complex of DNA, RNA, and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around which 147 base pairs of DNA are wound in almost two turns of a left-handed superhelix. Chromatin is a dynamic structure that exerts profound influence on regulation of gene expression and other cellular functions. These chromatin-directed processes are facilitated by optimizing nucleosome positions throughout the genome and by remodeling nucleosomes in response to various external and internal signals such as environmental perturbations. Here we discuss the large-scale maps of nucleosome positions made available through recent advances in parallel high-throughput sequencing and microarray technologies. We show that these maps reveal common features of nucleosome organization in eukaryotic genomes. We also survey the computational models designed to predict nucleosome formation scores or energies and demonstrate how these predictions can be used to position multiple nucleosomes on the genome without steric overlap.

Citations

Nov 11, 2015·Nucleic Acids Research·Jyotsana J ParmarRanjith Padinhateeri
Feb 7, 2013·Journal of Biomolecular Structure & Dynamics·Victor G LevitskyAlexander V Vershinin
Jan 31, 2017·Biophysical Journal·Marco TompitakHelmut Schiessel
Jul 7, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Răzvan V CherejiAlexandre V Morozov
May 31, 2012·Molekuliarnaia biologiia·V B TeĭfV I Krot
Dec 19, 2012·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Jian-Ying WangGuoqing Liu
Oct 3, 2014·Briefings in Functional Genomics·Răzvan V Chereji, Alexandre V Morozov
Aug 23, 2011·Journal of Statistical Physics·Răzvan V Chereji, Alexandre V Morozov
Sep 19, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Michael Sheinman, Ho-Ryun Chung
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Guénola DrillonAlain Arneodo
Sep 14, 2010·Trends in Genetics : TIG·Lu Bai, Alexandre V Morozov

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