Evolutionary evidence suggests that CpG island-associated Alus are frequently unmethylated in human germline

Most Alu elements are considered to belong to the methylated fraction of the genome that has undergone CpG depletion, whereas CpG islands are characteristically unmethylated. By analysing the CpG content of >12,000 autosomal CpG island-Alu Sx pairs we wanted to study what happens when an Alu is situated close to a CpG island. We have found that many Alus located close to CpG islands have retained a high proportion of CpG sites, which is consistent with these Alus being unmethylated in the human germline.