The correlation between DNA methylation and chromatin structure, as it relates to transcriptional activity, is demonstrated by the observation that there are several proteins, that bind to methylated CpGs but not to unmethylated CpGs, whose functions are integrated into transcriptional regulation. There are currently 15 genes in the human genome that encode proteins that bind to methyl-CpG in DNA. These 15 proteins are divided into 3 subfamilies identified by structural similarities. These sub-families are the methyl binding domain (MBD) proteins, the methyl-CpG-binding zinc finger proteins (also called the Kaiso family), and the SRA domain ( S ET and R ING finger domain A ssociated) containing proteins. The SET domain is so-called because it was first identified in three Drosophila proteins called S uppressor of variegation variant 3-9 [Su(var)3-9], E nhancer of zeste, and T rithorax. The RING domain is a zinc-finger-like domain which gets its name from the term R eally I nteresting N ew G ene.
The translation of mRNA can also be controlled by a number of mechanisms, mostly at the level of initiation. Recruitment of the small ribosomal subunit can indeed be modulated by mRNA secondary structure, antisense RNA binding, or protein binding. In both prokaryotes and eukaryotes, a large number of RNA binding proteins exist, which often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer). Some transcripts act as ribozymes and self-regulate their expression.