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Nucleic Acids Research 2005 33(15):4995-5005; doi:10.1093/nar/gki815
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Published online 6 September 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA

Anton V. Borovjagin and Susan A. Gerbi*

Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Division of Biology and Medicine Providence, RI 02912, USA

*To whom correspondence should be addressed. Tel: +1 401 863 2359; Fax: +1 401 863 1348; Email: Susan_Gerbi{at}Brown.edu

Received May 17, 2005. Revised July 15, 2005. Accepted August 18, 2005.

Correct docking of U3 small nucleolar RNA (snoRNA) on pre-ribosomal RNA (pre-rRNA) is essential for rRNA processing to produce 18S rRNA. In this report, we have used Xenopus oocytes to characterize the structural requirements of the U3 snoRNA 3'-hinge interaction with region E1 of the external transcribed spacer (ETS) of pre-rRNA. This interaction is crucial for docking to initiate rRNA processing. 18S rRNA production was inhibited when fewer than 6 of the 8 bp of the U3 3'–hinge complex with the ETS could form; moreover, base pairing involving the right side of the 3'-hinge was more important than the left. Increasing the length of the U3 hinge–ETS interaction by 9 bp impaired rRNA processing. Formation of 18S rRNA was also inhibited by swapping the U3 5'- and 3'-hinge interactions with the ETS or by shifting the base pairing of the U3 3'-hinge to the sequence directly adjacent to ETS region E1. However, 18S rRNA production was partially restored by a compensatory shift that allowed the sequence adjacent to the U3 3'-hinge to pair with the eight bases directly adjacent to ETS region E1. The results suggest that the geometry of the U3 snoRNA interaction with the ETS is critical for rRNA processing.


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