Patterns of Nucleosome and Chromatin Modifications and Their Effects on Chromatin States

Abstract

Chromatin packages eukaryotic DNA, it can affect accessibility of DNA, thus chromatin has important roles in gene transcription regulation, DNA replication, DNA repair, and so on. The basic unit of chromatin is nucleosome consisting of ~147 DNA which sharply bends and tightly wraps on surface of octamer of histones. Between two nucleosomes is linker DNA. Histones can be modified by methylation and acetylation. Chromatin state(euchromatin and heterochromatin) is determined by the combinatorial effects of nucleosome positioning, histone modifications, and chromatin-binding proteins. Recently, by virtue of high throughput sequencing technique, the distributions of the chromatin marks were genome-widely determined in various cells. Results indicated that the distribution mode is specific at key sites of genome and is dynamically changed with both cell types and environment stimulus, showing a complex plot. In this paper, we detailedly reviewed the distribution modes of chromatin marks, biological meanings of the modes, interactions of the chromatin marks(nucleosome, DNA and histone modifications, histone variants, chromatin-binding proteins), techniques that were used to determine the marks, and the computational analysis for chromatin states. This work is important in understanding epigenetic regulation mechanism.