Functionality and substrate specificity of human box H/ACA guide RNAs

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Abstract
A large number of box H/ACA RNAs have been identified in human cells, and have been predicted to account for nearly all pseudouridylation sites in human rRNAs. However, the function of these mammalian H/ACA RNAs in directing pseudouridylation has been verified experimentally in only two cases. In this study, we used three in vitro reconstitution systems, including yeast and mammalian systems, to test the function of seven H/ACA RNAs guiding16 pseudouridylation sites. Our results verified 12 of these sites; four predictions were incorrect. Further analyses indicated that three components, including the stability of the hairpin structure harboring the pseudouridylation pocket, the stability of guide sequence–target RNA base-pairing interaction, and the distance between the target uridine and the box H or ACA, were critical for the guide function, as changes in these components were sufficient to alter the functionality and specificity of the pseudouridylation pocket. The dynamic functional changes in response to changes in these three important components were further tested in vivo, and the results were completely consistent with the in vitro results. Finally, we compared our results with predictions made by two computer programs, as well as predictions made by human experts using visual inspection. We found that the predictions of one program (snoGPS) agreed with our experimental results with 100% sensitivity (12/12) and 75% specificity (3/4).