Messenger RNA is the bridge between the genetic code and the resulting proteins, as it is what carries the necessary information that gets translated into proteins. Modifications to the actual, physical genetic code are likely to be deleterious; therefore, minor modifications, such as methylation, done to mRNA are preferable (nevertheless, modifications are still seen throughout the genome). The four major types of modifications done to mRNA are N7-methylguanine (at the 5′ cap), N-methyladenosine, 5-methylcytosine, and 2′-O-methylation. The modification seen at the 5 cap perfectly demonstrates how modifications to mRNA can impact its function, as the 5 cap is necessary to initiate translation. Therefore, modifications, such as N7-methylguanine during RNA processing, to the 5' cap may effect the ability of the ribosome to initiate translation. It is important to note that not all modifications happening to the mRNA are epigenetic, some, like the N7-methylguanosine cap, are RNA editing.
mRNA molecules demonstrate something known as "modification stoichiometry". Modification stoichiometry is when only a portion of transcripts have a specific modification at a particular modification site. Typically, under normal cell conditions, the modification stoichiometry is very low, there are a very few number of transcripts that have specific modifications. However, as cell conditions change, the fraction of modified transcripts can change as well. As with other types of RNA, modifications impact the overall structure of the mRNA. Altering its structure may cause the mRNA to take different paths. For example, a normal transcript might be fated to be translated; however, the introduction of a modified base can disrupt its structure and send it down a different path, and that particular transcript may now be targeted for degradation.