Fine structure of ribosomal RNA. II. Distribution of methylated sequences within Xenopus laevis rRNA

The distribution of methyl groups in rRNA from Xenopus laevis was analyzed by hybridization of rRNA to subfragments of either of two cloned rDNA fragments, X1r11 and X1r12, which together constitute a complete rDNA repeat unit. Using a mixture of 3H-methyl plus 32P-labelled rRNA as probe, the molar yield of methyl groups per rRNA region in hybrid could be calculated. For this calculation the length of the rRNA coding region in each DNA subfragment is needed, which was determined for X1r11 subfragments by the nuclease S1 mapping method of Berk and Sharp. The results show that both in 18S and 28S rRNA the methyl groups are nonrandomly distributed. For 18S rRNA, clustering was found within a 3' terminal fragment of 310 nucleotides. For 28S rRNA, clustering of methyl groups was found within a region of 750 nucleotides in length, which ends 500 nucleotides from the 3' end. In contrast, the 28S rRNA 5' terminal region of 900 nucleotides is clearly undermethylated. The general position of methyl groups in 28S rRNA correlates with the location of evolutionarily conserved sequences in this molecule, as recently determined in our laboratory.