U3 small nucleolar RNA is essential for cleavage at sites 1, 2 and 3 in pre-rRNA and determines which rRNA processing pathway is taken in Xenopus oocytes.

A molecular dissection of U3 small nucleolar RNA (snoRNA) was performed in vivo in Xenopus oocytes and the effects on rRNA processing were analyzed. Oocyte injection of antisense oligonucleotides against parts of U3 snoRNA resulted in specific fragmentation of U3 by endogenous RNase H. Fragmentation of U3 domain II correlated with a decrease in 20 S pre-rRNA and a concomitant increase in 36 S pre-rRNA, indicating reduced cleavage at site 3. Conversely, fragmentation of U3 domain I completely blocked 18 S rRNA formation, increased the 20 S rRNA precursor, and decreased 36 S pre-rRNA, indicating inhibition of cleavage at sites 1+2. rRNA processing defects at sites 1+2 or 3 after destruction of intact endogenous U3 snoRNA were rescued by injection of in vitro transcripts of U3 snoRNA or certain U3 fragments. Thus, cleavage at sites 1+2 and 3 is U3 snoRNA dependent. Moreover, U3 snoRNA has two functional modules: domain I for sites 1+2 cleavage and domain II for site 3 cleavage. The data suggest that whichever of these U3 domains acts first determines which rRNA processing pathway will be taken: cleavage first at site 3 of pre-rRNA leads to pathway A, whereas cleavage first at sites 1+2 leads to pathway B for rRNA processing. Predictions of this model were validated by rescue of site 3 cleavage by injection of just domain II after U3 depletion. Rescue of sites 1+2 cleavage required covalent continuity of domain I with the hinge region and non-covalent association with domain II. We could experimentally shift which rRNA processing pathway was taken by injecting fragments of U3 to compete with endogenous U3 snoRNA.