We studied the structure of nucleosomes, the assembly of nucleosomes and how these properties are altered by DNA methylation and histone acetylation based on single molecule and ensemble fluorescence measurements. Our study revealed that a compact and rigid nucleosome structure is induced by CpG methylation in both internal and terminal regions of nucleosomal DNA. Real-time monitoring of nucleosome assembly with NAP1 revealed that there are at least 3 stable intermediate states during the assembly. The kinetic stabilities of the intermediate states are significantly elevated upon CpG methylation. These results suggest that CpG methylation stabilizes the nucleosome structure and inhibits the disassembly by destabilizing the transition states. We also characterized effects of histone acetylation by Piccolo NuA4 on the structure of a nucleosome and dinucleosomes. Upon the acetylation, we observed directional unwrapping of nucleosomal DNA that accompanies a topology change. We proposed a structural model for a dinucleosome in chromatin based on the structure of a dinucleosome spontaneously formed by two mononucleosomes in solution, which depends strongly on Mg2+ concentration and histone acetylation state. Mainly rendered by single molecule observations, these results suggest that structural changes of nucleosomes induced upon DNA methylation and histone acetylation may contribute to the regulation of genome activities.