Base pairing between U3 and the pre‐ribosomal RNA is required for 18S rRNA synthesis.

The nucleolus, the site of pre‐ribosomal RNA (pre‐rRNA) synthesis and processing in eukaryotic cells, contains a number of small nucleolar RNAs (snoRNAs). Yeast U3 snoRNA is required for the processing of 18S rRNA from larger precursors and contains a region complementary to the pre‐rRNA. Substitution mutations in the pre‐rRNA which disrupt this base pairing potential are lethal and prevent synthesis of 18S rRNA. These mutant pre‐rRNAs show defects in processing which closely resemble the effects of genetic depletion of components of the U3 snoRNP. Co‐expression of U3 snoRNAs which carry compensatory mutations allows the mutant pre‐rRNAs to support viability and synthesize 18S rRNA at high levels. Pre‐rRNA processing steps which are blocked by the external transcribed spacer region mutations are largely restored by expression of the compensatory U3 mutants. Pre‐rRNA processing therefore requires direct base pairing between snoRNA and the substrate. Base pairing with the substrate is thus a common feature of small RNAs involved in mRNA and rRNA maturation.

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