Nucleosome positioning and energetics: Recent advances in genomic and computational studies

TL;DR

This paper reviews recent advances in understanding nucleosome positioning and energetics through genomic mapping and computational modeling, highlighting how these insights influence gene regulation and chromatin dynamics.

Contribution

It provides a comprehensive overview of recent high-throughput mapping techniques and computational models for nucleosome positioning and energetics.

Findings

Large-scale nucleosome maps reveal common organizational features.

Computational models can predict nucleosome formation and positioning.

Predictions enable placement of multiple nucleosomes without overlap.

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 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.