  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 which 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 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 computational models designed to predict
nucleosome formation scores or energies, and demonstrate how these predictions
can be used to position multiple nucleosome on the genome without steric
overlap.
