RNA Processing


	J. Scott Butler, Ph.D. The biogenesis of mature eukaryotic RNAs requires post-transcriptional processing reactions that provide targets for the regulation of gene expression. Little is known about how RNA processing pathways are co-regulated to produce balanced levels of mature RNAs in response to changes in the cell's intracellular and extra-cellular environment. The research in my laboratory focuses on the roles of nuclear proteins implicated in the post-transcriptional regulation of mRNA and rRNA levels in S. cerevisiae. We are specifically interested in a recently identified complex of nucleases, called the exosome, which plays a critical role in the 3' end processing and degradation of nuclear RNAs.

	Clara Kielkopf, Ph.D. Noncoding sequences interrupt almost all human genes, and must be removed from pre-mRNAs by splicing before translation into proteins. Our laboratory seeks to understand the structural, thermodynamic, and kinetic characteristics driving protein-RNA and protein-protein interactions during identification and pairing of the the appropriate pre-mRNA splice sites. Given that errors in pre-mRNA splice site identification account for more than 50% of human genetic diseases, and are frequently associated with cancers and leukemias, biophysical maps of the key molecular interactions provide foundations for new therapeutic approaches.

	Lynne E. Maquat, Ph.D. In numerous inherited diseases, frameshift and nonsense mutations result in mRNA degradation. Degradation provides a means to protect cells from the potentially deleterious effects of routine mistakes in gene expression and, remarkably, depends on proteins that bind mRNA as a consequence of pre-mRNA splicing. We are currently investigating the mechanistic links between nuclear splicing and cytoplasmic translation in order to gain insight into disease therapies.

	Eric M. Phizicky, Ph.D. Functional genomics is an approach to rapidly link biochemical activities with genes. Using an ordered array of yeast strains and proteins, we have used this approach to rapidly screen thousands of gene products and identified 16 associated with different biochemical activities. We are also studying tRNA splicing mechanisms in yeast and mammals, and why some bacteria have a functional tRNA splicing enzyme, but no apparent corresponding splicing requirement. Our future directions are to improve arrays and extend the functional genomic approach to different classes of activities.

	Terry Platt, Ph.D. Termination of transcription and its degree of coupling to mRNA 3'-end processing is an important aspect of gene expression in both prokaryotic and eukaryotic organisms. We are studying E. coli and yeast as paradigms for these classes, to elucidate the molecular mechanisms governing the formation of mature messenger RNA 3' ends by the transcriptional and processing machinery. Our approaches combine genetic and biochemical techniques to examine the nature of the termination sites in the DNA or RNA, and the proteins and activities that regulate their function.

	Fred Sherman, Ph.D. Yeast is an ideal model system to study many aspects of gene expression in eukaryotic cells. By using iso-1-cytochrome c as a model gene, we have identified many general principles involved in transcription, translation, co-translational and post-translational modification, mitochondrial import, heme attachment, enzymatic functions and protein degradation. Currently, our efforts have been directed toward understanding the relationships between protein structure, protein modifications and degradation in vivo, and in uncovering new degradation systems in mitochondria.

	Harold C. Smith, Ph.D. mRNA is not only spliced, but also edited to produce a final processed message. mRNA editing is regulated developmentally in a tissue-specific manner and can be significantly altered by diet, hormonal changes, and toxins such as ethanol. We are studying the regulation of editing at the level of cell signaling and trafficking of the editing factors between the cytoplasm and the nucleus (ultimately the intracellular site where mRNA editing takes place). Animal model systems and whole cell microinjections analyses are being used to determine the molecules and mechanisms involved in apoB mRNA editing.

	Joseph E. Wedekind, Ph.D. The hairpin ribozyme is a naturally occurring RNA enzyme that cleaves a cognate substrate in the absence of protein. Among ribozymes the hairpin is unique in that specific ions do not participate in the chemical step, but rather the nucleotide bases function as acid/base catalysts. To elucidate the mechanism of hairpin ribozyme catalysis we employ X-ray crystallography and enzymology to identify chemical groups that contribute to activity, and substrate selectivity. This information is beneficial in the design of ribozyme-based therapeutics that target disease-causing RNA messages.

	Yi-Tao Yu, Ph.D. Pre-mRNA splicing is essential for the appropriate excision of introns and expression of mature gene products. The splicing reaction occurs in the spliceosome, a massive complex containing five small nuclear RNAs (snRNAs) and a large number of proteins. Interestingly, the five snRNAs are all post-transcriptionally modified. Our research focuses on spliceosomal snRNA modifications and their roles in pre-mRNA splicing. Furthermore, we use a combined approach of molecular biology and cell biology to determine how and where within the cell the spliceosomal snRNAs are modified.