Genomes and Genes
Wayne A Decatur
Affiliation: University of Massachusetts
- RNA-modifying machines in archaeaArina D Omer
Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
Mol Microbiol 48:617-29. 2003..This article summarizes our current knowledge about small-non-coding RNAs in Archaea, their roles in ribosome biogenesis and their relationships to the complexes that have been identified in eukaryotic cells...
- RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genesHenri Grosjean
Department of Microbiology, University of Florida, Gainsville, FL 32611, Florida, USA
BMC Genomics 9:470. 2008....
- Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAsWayne A Decatur
Department of Biochemistry and Molecular Biology, 903 Lederle Graduate Research Tower, University of Massachusetts, Amherst, MA 01003, USA
Mol Cell Biol 28:3089-100. 2008..8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis...
- The 3D rRNA modification maps database: with interactive tools for ribosome analysisDorota Piekna-Przybylska
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
Nucleic Acids Res 36:D178-83. 2008..The database can be accessed at http://people.biochem.umass.edu/fournierlab/3dmodmap/..
- Identifying effects of snoRNA-guided modifications on the synthesis and function of the yeast ribosomeWayne A Decatur
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
Methods Enzymol 425:283-316. 2007..Methods are also included for characterizing modification effects on cell growth, antibiotic sensitivity, rRNA processing, formation of various rRNP complexes, translation activity, and rRNA structure within the ribosome...
- New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNADorota Piekna Przybylska
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
RNA 13:305-12. 2007....
- Fine-tuning of translation termination efficiency in Saccharomyces cerevisiae involves two factors in close proximity to the exit tunnel of the ribosomeIsabelle Hatin
IGM, Universite Paris Sud, UMR 8621, F91405 Orsay, France
Genetics 177:1527-37. 2007..Among them, SSB1 and snR18, two factors close to the exit tunnel of the ribosome, directed the strongest antisuppression effects when overexpressed, showing that they may be involved in fine-tuning of the translation termination level...
- Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genomePeter Schattner
Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
Nucleic Acids Res 32:4281-96. 2004..With this work, 41 of the 44 known pseudouridine modifications in S.cerevisiae rRNA have been linked with a verified snoRNA, providing the most complete accounting of the H/ACA snoRNAs that guide pseudouridylation in any species...
- rRNA modifications and ribosome functionWayne A Decatur
Trends Biochem Sci 27:344-51. 2002..The correlations suggest that many ribosome functions benefit from nucleotide modification...
- A systematic, ligation-based approach to study RNA modificationsMridusmita Saikia
Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
RNA 12:2025-33. 2006..Multiple modification sites can be examined in the same ligation reaction. The feasibility of this method is demonstrated for three 2'O-methyl modification sites in yeast rRNA...