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David Engelke

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Primary Appointment:
PubMed Name: Engelke DR
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  We study the biosynthesis of small RNAs in eukaryotes. Most experiments are carried out in yeast to take advantage of genetic and molecular experimental tools, but experiments in human and mouse cells have also addressed potential clinical uses of small nucleic acids.

Organization of Nuclear Genes - One area of investigation is the chromatin structure of actively transcribed genes and the mechanism by which transcription factors control that structure. RNA polymerase III transcription units influence the structure and transcriptional activity of the surrounding chromatin in the yeast genome, and can act as negative regulatory elements (silencers) of neighboring genes. Silencing involves subnuclear localization of tRNA genes and is not related to other forms of transcriptional silencing in yeast. Further evidence suggests that spatial organization of genes in response to transcriptional programming is widespread in yeast and other eukaryotes, and that pol III units play a major role in this organization. We are investigating the mechanism of this three-dimensional organization using genetic, biochemical, and cytological approaches.

Small RNA Biosynthetic Pathway - One of the earliest and most interesting enzymes in the tRNA biosynthetic pathway is RNase P, an ancient enzyme composed of both a catalytic RNA subunit and protein “cofactors”. The bacterial enzymes have only a single small, dispensable protein subunit, but the nuclear enzyme has twenty times as much protein, split into nine essential subunits. Multiple lines of evidence suggest that the early tRNA biosynthetic pathway, including RNase P and the early pre-tRNA processing pathway are nucleolar, and there is evidence that RNase P is also involved in ribosomal RNA and messenger RNA pathways. We are investigating the functions of the RNase P subunits in carrying out these multiple tasks, as well as creating a three-dimensional structural model of the interaction of this complex enzyme with RNA substrates.

Selection of Diagnostic RNA Aptamers - Nucleic acid “aptamers” are ligands selected from a random sequence library. With sufficient selective pressure, it is possible to derive aptamers that bind to virtually any molecule or surface – far exceeding the limits of antibody selection. In addition, nucleic acids can easily be labeled with fluorescent dyes, radionuclides, or affinity tags, making aptamer ligands an attractive potential source of diagnostic and affinity reagents. The laboratory is interested in selecting and testing a number of such reagents as diagnostics and as tools in the characterization of RNP complexes.