One of the major mechanisms of regulation of gene expression in eukaryotes is by chemical modifications of nucleosomal histones, genomic DNA, and other gene regulatory proteins. Chromatin in eukaryotes is highly condensed and inaccessible to many regulatory proteins. Chemical modifications of histones and DNA alter the structure and dynamics of the chromatin. Through selective modifications, the reshaped structure of chromatin segments may allow selective access of transcription machinery and transcriptional regulators to segments that otherwise would not have been accessible. This mechanism of transcriptional regulation is widespread in the eukaryotic domain. Three principal modifications are acetylation and phosphorylation of histone, and methylation of histones and DNA. We describe the effect of these modifications on the structure and dynamics of nucleosomes and higher-order chromatin structure and how these marks recruit other important proteins in site-specific ways. We also describe the writers and erasers of these marks.