New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
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↵1 These authors contributed equally to this work.
Abstract
This report presents a valuable new bioinformatics package for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service, which is not available elsewhere, enables a user to visualize the positions of pseudouridines, 2′-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. Our tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of new tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database available publicly at http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.
Keywords
Footnotes
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Reprint requests to: Maurille J. Fournier, Department of Biochemistry and Molecular Biology, Lederle Graduate Research Tower, University of Massachusetts, Amherst, MA 01003, USA; e-mail: 4nier{at}biochem.umass.edu; fax: (413) 545-3291.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.373107.
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- Received November 3, 2006.
- Accepted December 4, 2006.
- Copyright © 2007 RNA Society
