ABSTRACT: Nucleosomes are the fundamental packing units of the eukaryotic genome. The structure and structural dynamics of nucleosomes are at the core of gene regulation mechanisms. We studied the structure and assembly of nucleosomes and how they are altered by DNA methylation or histone acetylation based on single molecule fluorescence measurements. Our study revealed that these chromatin modifications induce changes in the structure and assembly of nucleosomes that may directly contribute to the formation of repressive or open chromatin conformations. Our study demonstrates how single molecule methods can be utilized to complement ensemble-averaged or static structures observed with the conventional structural biology tools.