Epigenetic changes also include modification of the DNA and proteins bound to it through methylation, acylation or bonding through other reaction groups based on nucleic acids or on the aminoacids of chromosome proteins. Some of these changes are also transferred to further cellular generations. For example, cells may contain specialized enzymes that search for places in the DNA where one of the chains is methylated. They then methylate the second chain from these hemimethylated sites. If replication occurs in a certain DNA section, then these enzymes methylate the newly synthesized chain and thus renew the relevant methylation signal. Methylation of the regulation areas of some DNA sections can negatively or positively affect their transcription and the relevant regulation changes are transferred to further generations in the given cellular line.
Functional and morphological differentiation of the individual cellular lines is of fundamental importance in formation of the bodies of multi-cellular organisms. The individual animal and plant tissues consist of specialized cells, where division of these cells or their more or less specialized precursors again yields the specialized cells of the relevant tissues. It is highly probable that most differentiation changes occur through covalent and noncovalent modifications of regulation areas of the individual components of chromatin. Obviously, other cellular structures can also become the carriers of epigenetic information. Especially the receptor apparatus of the external cell membrane decides to a substantial degree which signals the given cell can receive and to which it can react. Synthesis of receptors, which enable receiving of the given signal, can also be part of the response to a particular signal. This means that the relevant differentiated state of the cells of a certain line is spontaneously maintained over time without requiring any modification of the actual cellular DNA. According to some authors, the formation of specialized mechanisms of epigenetic inheritance permitted the formation of complicated multicellular organisms.
In a number of organisms, mechanisms of epigenetic inheritance are also involved in the transfer of phenotype plasticity traits from one generation to the next. The greatest numbers of examples of epigenetically inherited phenotype modifications are known for plants. For example, the morphology of individual flax plants differs very substantially according to the amount of nutrients in the soil, where the particular trait, gained during a single generation, is passed on through the seeds to the next generation. However, examples of similar phenotype modifications, which can be inherited even after a number of generations, are also encountered in some animals, especially those that reproduce asexually. Methylation and suppression of the cycloidea gene in the flax Linaria vulgaris, which demonstrably occurred at least 250 years ago and has been maintained by artificial selection to the present day, is probably the longest transferred (known) epigenetic modification. It is quite possible that many other known mutations actually correspond to epimutation – epigenetic changes inherited for a long time.