Genomic studies and computational predictions of nucleosome positions and formation energies

Denis Tolkunov, Alexandre Morozov

Research output: Contribution to journalArticle

18 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1-57
Number of pages57
JournalAdvances in Protein Chemistry and Structural Biology
Volume79
Issue numberC
DOIs
StatePublished - Dec 20 2010

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry

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