Analysis of the primary structure of chromatin with next-generation sequencing

The recent development of next-generation sequencing technology has enabled significant progress in chromatin structure analysis. Here, we review the experimental and bioinformatic approaches to studying nucleosome positioning and histone modification profiles on a genome-wide scale using this technology. These studies advanced our knowledge of the nucleosome positioning patterns of both epigenetically modified and bulk nucleosomes, and elucidated the role of such patterns in the regulation of gene expression. The identification and analysis of large sets of nucleosome-bound DNA sequences allowed a better understanding of the rules that govern nucleosome positioning in organisms of varying complexity. We also discuss the existing challenges and prospects of using next-generation sequencing for nucleosome positioning analysis and outline the importance of such studies for the entire chromatin structure field.