The Effect of a DNA Methylation Pattern On the Nucleosome Array Self Assembly

DNA in eukaryotic cells is folded into an organized array facilitated by a protein complex, i.e. a histone octamer. This compact protein-DNA complex, known as a nucleosome array, regulates the gene expression in eukaryotic cells by limiting the accessibility of genomic sequences. A nucleosome array is formed through a self-assembly process and assumes a highly regular structure dictated by the genetic, i.e. DNA sequences, as well as epigenetic contexts, i.e. DNA methylation and histone post-translational modifications. This paper focuses on the effect of DNA methylation pattern on the nucleosome array conformation and stability. We will specifically evaluate: (i) the effect of DNA methylation pattern on the nucleosome binding affinity and the nucleosome array positioning pattern; and (2) the effect of DNA methylation pattern on the dynamics of a nucleosome array. These effects will be discussed in terms of the inter- and intra-nucleosome interactions that mediate the self assembly process of a nucleosome array. Their implications for the epigenetic regulation of eukaryotic chromatin will also be discussed.