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Dr. Maurille J. Fournier Molecular Biology of the Small Nucleolar RNPs (snoRNPs): A Major Frontier in Eukaryotic RNA Research and New Tools for Biotechnology |
| Background and Training | |
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Ph.D.: Dartmouth Medical School |
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| Research Area | |
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The focus of our research is the small nucleolar RNAs (snoRNAs) and the snoRNA:protein complexes (snoRNPs) that exist in eukaryotic cells. We are interested in several aspects of snoRNA and snoRNP synthesis and function. The snoRNPs play direct roles in the synthesis of ribosomal RNA and, surprisingly, a growing number of other RNAs that are transcribed in the nucleoplasm and localize in different, non-nucleolar locations in the cell (e.g., splicing snRNAs). Most of the known snoRNPs synthesize two types of modified nucleotides in rRNA; a few others are involved in the processing (cleavage) of precursor rRNA transcripts. There are two main families of snoRNPs and these are classified by the snoRNA component. One family, called the box C/D snoRNPs, mediates the formation of large numbers of 2’-O-methylated nucleotides (Nm) in rRNA. The second family, called the box H/ACA snoRNPs, is responsible for the synthesis of large numbers of pseudouridines (psi), by isomerization of uridine. The rRNAs from yeast and humans contain about 50 and 100 modifications of each type, respectively. The nucleotides to be modified are targeted by the snoRNA component (guide function), through complementary base pairing, and the modification reaction is catalyzed by a protein component in the snoRNP particle. A few snoRNPs in each major family are required for cleavage of pre-rRNA, and are thought to help fold and organize the transcript for the cleavage reactions (possible chaperone function). The snoRNP complexes contain an unknown number of proteins. Thus far, a few core proteins have been identified in each major snoRNP family, and these are highly conserved among eukaryotes. Strikingly, Archaeal organisms also contain such RNA and protein components, indicating the snoRNP machinery is of ancient evolutionary origin. |
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| Contributions to snoRNP research from our laboratory | |
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Major contributions to the snoRNA/snoRNP field from our group include: 1) early identification of over 30 snoRNAs in yeast, showing that snoRNA populations are much larger than previously thought; 2) discovery of one of the two major families of snoRNAs (the H/ACA family) and establishing the accepted system for classifying snoRNAs and snoRNPs; 3) co-discovery of the guide functions of the snoRNAs; 4) determining that the simple box C/D motif in the C/D snoRNAs is the localization signal for targeting snoRNAs to the nucleolus, 5) demonstrating that a snoRNA can deliver a powerful RNA-cutting ribozyme to the nucleolus, where it cleaved a target RNA with near-perfect efficiency - covered by Science and Nature Biotechnology; 6) determining that snoRNPs that create modifications in the peptidyl transferase center are needed for normal protein synthesis activity, suggesting that the modifications (and snoRNPs?) influence ribosome structure or function, and; 7) showing that the guide function of the C/D snoRNAs can be manipulated to introduce methylation point mutations into novel RNA sites in vivo, for functional mapping of rRNA, In principle, the new genetically engineered ribozyme and nucleotide modification functions can be used to selectively inhibit RNA activity in vivo, and kill abnormal cells and pathogens. |
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| Prognosis for the future and current work | |
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The snoRNP field is still in its infancy and many important discoveries remain to be made. Examples of key issues to be resolved include: 1) defining the steps involved in snoRNP biogenesis and where these occur in the nucleus; 2) learning the precise mechanisms by which snoRNPs mediate the modification and processing functions, and; 3) discovering the effects of nucleotide modification on rRNA and ribosome function. This last question is one of the oldest in RNA science, and can now be examined by disrupting pre-selected modifications genetically, at individual sites or in particular domains. Current work in our laboratory is devoted to understanding how the modifying and processing snoRNPs carry out their functions, describing snoRNA and snoRNP biosynthesis, and exploring the potential for using snoRNPs as tools in basic research and biotechnology applications. In this last regard, three U.S. patents have been awarded to the University of Massachusetts for strategies that feature snoRNAs as tools for biotechnology and medicine. |
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| Components of the major types of snoRNP complexes. Consensus structures are shown for the two major types of guide snoRNAs, and the core proteins known for each snoRNP family are listed. Most C/D snoRNPs (left) are involved in 2’-O-methylation, and most H/ACA snoRNPs (right) mediate the formation of pseudouridine. The snoRNP particles base-pair with pre-ribosomal RNA, through the snoRNA guide sequences, and the modification reaction is catalyzed by a snoRNP protein. | |
| Representative Publications | |
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Liang, XH., Liu, Q. and Fournier, M.J. Loss of a hypermodified nucleotide in the ribosome small subunit Liang, XH., Liu, B., Piekna-Przybylska D. Liu, Q. and Fournier, M.J. 2008. Mis-targeted methylation in rRNA can severely impair ribosome synthesis and activity. RNA Biol. 5: 1-6. Piekna-Przybylska D., Przybylska, P., Baudin-Baillieu, A., Rousset, J-P. and Fournier M.J. 2008. Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit. J. Biol. Chem. 283: 26026-26036. Piekna-Przybylska, D., Decatur, W. A. and Fournier, M.J. 2008. The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res.36:D178-83. Liang, XH, Liu, Q. and Fournier, M.J. 2007. rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. Mol. Cell. 28: 965-977. Decatur, W.A., Liang, X.H., Piekna-Przybylska, D. and Fournier, M.J. 2007. Identifying effects of snoRNA guided modifications on the synthesis and function of the yeast ribosome. Methods Enzymol.:RNA Modification, J. Gott, Ed., Academic Press, New York. 425: 283-316 Piekna-Przybylska, D., Liu, B. and Fournier, M.J. 2007. The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes. Methods Enzymol.:RNA Modification, J. Gott, Ed., Academic Press, New York. 425: 317-353. Saikia, M., Dai, Q., Decatur, W.A., Fournier, M.J., Piccirilli, J.A. and Pan, T. 2006. A systematic, ligation-based approach to study RNA modifications. RNA 12:2025-2033. Liang, X. and Fournier, M.J. 2006. The helicase Has1p is required for snoRNA release from pre-rRNA. Mol. Cell Biol. 26:7437-7450. Liu, B. and Fournier, M.J. 2004. Interference Probing of rRNA with snoRNPs: A Novel Approach for Functional Mapping of RNA In Vivo. RNA 2004: 1130-1141. Schattner, P., Decatur, W. A., Davis, C. A., Ares, M. Jr., Fournier, M. J., and Lowe, T.M. 2004. Genome-Wide Searching for Pseudouridylation Guide snoRNAs: Analysis of the Saccharomyces cerevisiae Genome. Nucleic Acids Res. 2004 32:4281-4296. Bertrand, E. and Fournier, M.J. 2004. The snoRNPs and Related Machines: Ancient Devices That Mediate Maturation of rRNA and Other RNAs. pp. 225-261. The Nucleolus (M.O.J. Olson, ed.). Landes Bioscience Publishing/ www.Eurekah.com. Omer, A.D., Zeische, S., Decatur, W.A., Fournier, M.J., and Dennis, P.P. 2003. RNA-Modifying Machines in Archaea. Mol. Microbiol. 48: 617-629. King, T.H., Liu, B., McCully, R.R., and Fournier, M.J. 2003. Ribosome Structure and Activity are Altered in Cells Lacking snoRNPs That Form Pseudouridines in the Peptidyl Transferase Center. Mol. Cell 11: 425-435. Decatur, W.A. and Fournier, M.J. 2003. RNA-Guided Nucleotide Modification of Ribosomal and Other RNAs. A Minireview. J. Biol. Chem. 278: 695-698. Decatur, W.A. and Fournier, M.J. 2002. rRNA Modifications and Ribosome Function. Trends Biochem. Sci. 27: 344-351. King, T., Decatur, W., Bertrand, E., Maxwell, E.S. and Fournier, M.J. 2001. A Well-Connected and Conserved Nucleoplasmic Helicase is Required for Production of Box C/D and H/ACA snoRNAs and Localization of snoRNP Proteins. Mol. Cell Biol. 21:7731-7746. Liu, B., Ni, J. and Fournier, M.J. 2001. Probing RNA In Vivo with Methylation Guide snoRNAs. Methods 23, 276-286. Zebarjadian, Y., King T., Fournier, M.J., Clarke, L. and Carbon, J. 1999. Point Mutations in Yeast CBF5 can Abolish In Vivo Pseudouridylation of Ribosomal RNA. Mol. Cell. Biol. 19: 7461-7472. |
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| Patents | |
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‘Hybrid Ribozymes and Methods of Use’ (M.J. Fournier, D.A. Samarsky, G. Ferbeyre and R. Cedergren). Application filed May 9, 1997. U.S. patent awarded Aug. 24, 1999 (5,942,395). ‘Sequence-Specific Methylation of Ribonucleic Acid’ (M.J. Fournier and J.Ni). Provisional application filed June 28, 1996. U.S. patent awarded Oct. 26, 1999 (5,972,705). ‘Site-Specific Synthesis of Pseudouridine in RNA’ (M.J. Fournier and J. Ni). Provisional application submitted May 9, 1997; U.S. patent awarded Nov. 23, 1999 (5,989,911). |
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| Useful sites for yeast snoRNA work | |
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UMass Yeast snoRNA Database - Major properties of the S. cerevisiae snoRNAs are available in a database developed in our laboratory, by Dmitry A. Samarsky. Eddy lab snoRNA database - Another valuable database, created by Todd Lowe and Sean Eddy at Washington University, contains detailed information about the C/D guide snoRNAs in yeast and the Archaea. UMass 3D Modification Maps of the Ribosome - In this resource developed in our lab by Wayne Decatur, sites of modified nucleotides in yeast and E. coli are highlighted using available atomic resolution structures of the ribosome. UMASS Online Interactive Tour of the Large Ribosomal Subunit - For the general public. This was constructed by Wayne Decatur in the Fournier laboratory using Protein Explorer by Eric Martz. Saccharomyces Genome Database at Stanford University. Guttell Lab Comparative rRNA Website at Texas University. MSDS sheets online for UMASS - Chemical reagent safety data, for research personnel. |