Final answer:
In vertebrates, the base that is most frequently methylated is cytosine, particularly within CpG islands of DNA, which influences gene expression and is essential for development.
Step-by-step explanation:
The most frequently methylated base in vertebrates is cytosine, especially within the specific regions of DNA known as CpG islands. These regions have a high frequency of cytosine and guanine dinucleotide DNA pairs (CG), and it is the cytosine in the CG pair that is typically subject to methylation. This methylation process is crucial since it changes how DNA interacts with various proteins, including the histone proteins that are essential for controlling access to genetic regions. As a result, methylated genes are usually silenced, which means they are not transcribed into RNA and thus not expressed as proteins. This mechanism is a form of epigenetic regulation and plays a significant role in gene expression and development.