Striking bimodal methylation of the repeat unit of the tandem array encoding human U2 snRNA (the RNU2 locus)

The genes encoding human U2 small nuclear RNA are arrayed in tandem (the RNU2 locus) and have undergone concerted evolution for >35 Myr. Tandem organization of repetitive sequences may facilitate recombination that underlies concerted evolution, but could risk instability. Since DNA methylation plays a crucial role in genome stability, we investigated the methylation status of the RNU2 locus to understand the forces maintaining array stability and homogeneity. We found that a region of approximately 1.5 kb spanning the U2 promoter, U2 gene sequence, and CT microsatellite is completely unmethylated, whereas the rest of the repeat is heavily methylated. Since the U2 transcription enhancer DSE and CT microsatellite mark the boundaries between methylated and unmethylated domains, they might function as cis-acting elements for establishing and maintaining proper methylation at the RNU2 locus. Interestingly, the RNU2 locus in human fibrosarcoma line HT1080 is hypomethylated, and de novo methylation did not occur in an artificial U2 tandem array introduced by stable transfection. The observed bimodal methylation pattern may be important for both efficient transcription of U2 gene and maintenance of nearly perfect tandem arrays in somatic cells.