All cells of a multicellular eukaryotic organism carry almost the same genome, still they obviously demonstrate phenotypes of very divergent kinds. The most probable explanation of the divergence is that different groups of genes are expressed in cells of different types. Expression is regulated at all steps between DNA and a protein, but transcription regulation is the most common regulatory mechanism. Transcription factors, which bind to specific areas of chromatin, can mediate the regulation. Their binding depends on the chromatin structure, which drastically differs among cell types. The key role in the structural organization is played by covalent histone modifications in chromatin. A combination of particular modifications in a chromatin region determines its structure and, consequently, its accessibility for enzymes. The best studied histone modifications are described in the review. Each modification has its specific mechanism that the cell uses to establish or to eliminate it. Activity of various Polycomb complexes is a key mechanism that represses chromatin and plays a central role, for example, in cell differentiation. The compositions and functionality of Polycomb complexes in various species are considered. Owing to modern experimental techniques, ample data are currently available for histone modifications and other epigenomic features of chromatin in various tissues and organisms, allowing bioinformatic investigation of the epigenome. Many computational and visualization methods have been developed for such studies, and the main of them are covered in the review.