David Engelke, Ph.D.

Interim Chair
Professor, Biological Chemistry

3200D MSRB3, Box 5606


Administrative Contact

Amanda Howard


Biological Chemistry, Medical School

Areas of Interest

The main research interest of the Engelke lab has been the biosynthesis of small RNAs in eukaryotes, and we have an increasing focus on the spatial organization of genes and RNA processing pathways. Most investigations have been carried out in yeast to take advantage of genetic and molecular tools, but we have also addressed problems in both small RNA expression and genome organization in mammalian cells.

Recent research projects Spatial organization of genes in nuclei. One area of investigation is the chromatin structure of actively transcribed genes and the mechanism by which transcription factors control that structure. We have primarily examined genes transcribed by RNA polymerase III and have helped establish a model for stable activation of genes in chromatin. We have also found that these small 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. This "silencing" involves subnuclear localization of tRNA genes and is not related to other forms of transcriptional silencing in yeast. We are investigating the mechanism of this regulation and gene localization using genetic, biochemical, and cytological approaches. This research has shown that genetic organization and retrieval mechanisms are subject to three-dimensional organization in the nucleus, and since the hundreds of tRNA genes are distributed throughout the chromosomes, this affects spatial organization of most of the genome. We investigate the mechanism of this localization and its overall consequences for information storage in both yeast and mammals.

tRNA Biosynthetic Pathway. Pre-tRNA primary transcripts undergo extensive processing before being useful in translation. The early processing pathway in the nucleus includes several nucleolytic cleavages to remove leader, trailing, and intronic sequences, and several different types of nucleoside modifications. One of the earliest and most interesting enzymes in this pathway, RNase P, is composed of both a catalytic RNA subunit and protein. The highly ordered tertiary structures of the enzyme and substrate RNAs provide the active site recognition and cleavage events without the need for a protein superstructure, and do so without any apparent Watson-Crick base pairing between the two RNAs. The bacterial enzymes have only a single small, dispensable protein subunit, but the eukaryotic nuclear holoenzyme has nine essential protein subunits, in addition to the large RNA subunit. Multiple lines of evidence show that the early pre-tRNA biosynthetic pathway, including RNase P, may be localized to the nucleoli, where it is coordinated with ribosomal RNA processing. We are investigating the interaction of the RNase P subunits with this pathway, as well as attempting to create a three-dimensional structural model of the interaction of this complex enzyme with pre-tRNA substrates. We are also investigating the possible role of RNase P in additional RNA biosynthetic pathways.

Selection of Diagnostic RNA Aptamers. Nucleic acid "aptamersâ" 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, affinity tags, or PCR detection sites, making aptamer ligands an attractive potential source of diagnostic and affinity reagents. The laboratory has developed a number of such tools for characterization of RNP complexes, and we are continuing with the development of diagnostic applications.

Laboratory Members:

Phil Smaldino, Postdoctoral Fellow
Mirjana Persaud, Post Baccalaureate Student
David Read, Undergraduate Student
Brian Carrick, Undergraduate Student
May Tsoi, Research Assistant

Honors & Awards

1980-1982 National Research Service Award in Genetics
1993-1994 Faculty Recognition Award, University of Michigan
1999-2000 Board of Directors, the RNA Society
2003 Distinguished Faculty Achievement Award, University of Michigan
2004 Distinguished Faculty Lectureship, University of Michigan Medical School
2005-2009 Senior Fellow, Michigan Society of Fellows
2007 Rackham Graduate School Distinguished Faculty Mentor Award
2008 AAAS Fellow

Published Articles or Reviews

Thompson, M, Haeusler, RA, Good, PD, and Engelke, DR. Nucleolar clustering of dispersed tRNA genes. Science 302: 139-1401, 2003

Paul, CP, Good, PD, Li, SXL, Kleihauer, A, Rossi, JJ, and Engelke, DR. Localized expression of small RNA inhibitors in human cells. Mol. Therapy 7:
237-247. 2003

Coughlin, DJ and Engelke, DR. RNA interference. in RNA Interference: Nuts & Bolts, (D. Engelke, ed.) DNA Press (Eagleville, PA),pp. 13-20, 2003

Scott, FH and Engelke, DR. Identification and characterization of RNA-binding proteins through three-hybrid analysis. in press in “Handbook of RNA Biochemistry” (A.Bindereif, R. Hartmann, A. Schon, E. Westhof, eds.), Wiley-VHF, Weinheim, Germany (2004)

Haeusler, RA and Engelke, DR. (2004) Gene organization in three dimensions: Thinking outside the line. Cell Cycle 3: 273-275 (2004)

Engelke, DR and Rossi, JJ (eds.) Methods in Enzymology, 392 (2005)
Engelke, DR and Hopper, AK. Modified view of tRNA: stability amid sequence diversity. Mol. Cell 21: 144-145. (preview) 2006

Leontis, NB, Altman, R, Berman, HM, Brenner, SE, Brown, J, Engelke, D, Harvey, SC, Holbrook, SR, Jossinet, F, Lewis, SE, Major, F, Mathews, DH, Richardson, J, Williamson, JR, and Westhof, E. The RNA Ontology Consortium: An open invitation to the RNA community. RNA 12: 533-541 2006

Walker, SC and Engelke, DR. Ribonuclease P: The evolution of an ancient RNA enzyme. Crit. Rev. Biochem. Mol. Biol. 41: 77-102. 2006

Xiao, S, Hsieh, J, Nugent, RL, Coughlin, DJ, Fierke, CA, and Engelke, DR. Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP. RNA, 12: 1023-1037 2006

Pratt-Hyatt, MJ, Kapadia KM, Wilson TE, and Engelke DR. Increased recombination between active tRNA genes. DNA and Cell Biol. 25: 359-364. 2006
Haeusler, RA and Engelke, DR. Spatial organization of transcription by RNA polymerase III. Nucl. Acids Res. 34: 4826-4836 (2006)

Moir, RD, Lee, JH, Haeusler, RA, Desai, N, Engelke, DR, and Willis, IM. Protein kinase A regulates RNA polymerase III transcription through the nuclear localization of Maf1. Proc. Natl. Acad. Sci. USA 103: 15044-15049 (2006)

Haeusler, RA and Engelke, DR. Spatial organization by RNA polymerase III. Nucl. Acids Res. 34: 4826-4836, 2006

Xiao, S, Hsieh, J, Nugent, RL, Coughlin, DJ, Fierke, CA, and Engelke, DR. Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP. RNA, 12:1023-1037. 2006

Aspinall, TV, Gordon, JMB, Bennett, HJ, Karahalios, P, Bukowski, J-P, Walker, SC, Engelke, DR, and Avis, JM. Interactions between subunits of Saccharomyces cerevisiae RNase MRP support a conserved eukaryotic RNaseP/MRP architecture. Nucl. Acids Res. 35: 6439-6450. 2007

Haeusler, RA, Pratt-Hyatt, M, Good, PD, and Engelke, DR. Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes. Genes & Devel. 22: 2204-2214, 2008http://genesdev.cshlp.org/content/22/16/2204

Coughlin, DJ, Pleiss, JA, Walker, SC, Guthrie, C, and Engelke, DR. Genome-wide search for RNase P substrates reveals nuclear RNase P is involved in maturation of intron-encoded box C/D small nucleolar RNAs. Proc. Natl. Acad. Sci. USA, 105: 12218-12223, 2008 http://www.pnas.org/content/105/34/12218

Walker, SC, Houser-Scott, F, Srisawat, C. and Engelke, DR. RNA Affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol Biol. (488) 23-40, 2008http://www.springerlink.com/content/m62r26481l027238/

Walker, SC and Engelke, DR. A protein-only RNase P in human mitochondria. Cell 135: 412-414 2008 http://www.cell.com/retrieve/pii/S0092867408013007

*Hsieh, J, *Walker, SC, Fierke, CA, and Engelke, DR. Pre-tRNA cleavage by the yeast nuclear RNase P holoenzyme is rate-limited by slow product release. RNA, e-pub ahead of print, 2008 [*= authors contributed equally] http://rnajournal.cshlp.org/content/early/2008/12/17/rna.1309409

Marvin, MC and Engelke, DR. RNase P: increased versatility through protein complexity. RNA Biology, 6: 40-42, 2009 PMID: 19106627.

Coughlin, DJ, Babak, T, Nihranz, C, Hughes, TR, and Engelke, DR. Prediction and verification of mouse tRNA gene families. RNA Biology 6: 195-202, 2009 PMID: 19246989, NIHMSID #109486, PMC2783191. http://www.landesbioscience.com/journals/rnabiology/article/8050

Marvin, MC and Engelke, DR. Broadening the mission of an RNA enzyme. J. Cell. Biochem. 108: 1244-1251, 2009 PMID: 19844921. http://www3.interscience.wiley.com/journal/122654735/abstract

Pai, DA and Engelke, DR. Spatial organization of genes as a component of regulated expression. Chromosoma epub 8/30/2009, PMID: 19727792. http://www.springerlink.com/content/9685562762225472/

Hopper, AK, Pai, DA and Engelke, DR. Cellular dynamics of tRNAs and their genes. FEBS Lett. (epub) 2009, PMID19931532. http://www.febsletters.org/article/S0014-5793%2809%2900966-1/abstract

Walker, S.C., Marvin, M.C. and Engelke, D.R. Eukaryote RNase P and RNase MRP. in "Ribonuclease P", pp.173-202 (F. Liu, ed.) Springer. 2009

Srisawat, C and Engelke, DR. Selection of RNA aptamers that bind HIV-1 LTR DNA: strand invaders. Nucl. Acids. Res. 38: 8306-8315. 2010, PMC3001068

Walker, SC, Good, PD, Gipson, TA and Engelke, DR. The dual use of RNA aptamer sequences for affinity purification and localization studies of RNAs and RNA-protein complexes. Methods in Molecular Biology 714: 423-444, 2011 PMID 21431756

Marvin, MC, Walker, SC, Fierke, CA and Engelke, DR. Binding and cleavage of unstructured RNA by nuclear RNase P. RNA 17: 1429-1440, 2011, PMC3153968

Marvin, MC, Clauder-Münster, S, Walker, SC, Sarkeshik, A, Yates III, JR, Steinmetz, LM, and Engelke, DR. Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. RNA 17, 2011, PMC3153968

Rodley*, CDM, Pai*, DA, Mills, TA, Engelke, DR, and O’Sullivan, JM. tRNA gene identity affects nuclear positioning. PLoS ONE, 2011;6(12):e29267, 2011. (* = equal contribution). PMC3242769

Pratt-Hyatt, M., Haeusler, RA, Wozniak, GG, Pai, DA, McLeod, IX, Yates III, JR, Hopper, AK, and Engelke, DR. Mod5, a tRNA modifying enzyme, binds to tRNA gene complexes and affects local transcriptional silencing. Proc. Natl. Acad. Sci. USA110: doi: 10.1073/pnas.1219946110. PMC3746885, 2013

Good, PD, Kendall, A, Ignatz-Hoover, J, Miller, EL, Pai, DA, Rivera, SR, Carrick, B, and Engelke, DR. Silencing near tRNA genes is nucleosome
-mediated and distinct from boundary element function. Gene 526: 7-15 PMC3745993, 2013

O’Sullivan*, JM, Pai*, DA, Cridge, AG, Engelke, DR and Ganley, ARD. The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure? Biomolecular Concepts 4: 277-286 DOI10.1515/bmc-2012-0043, 2013 (* equal contribution)

Howard, MJ, Liu, X., Lim, WH, Klemm, B, Fierke, CA, Koutmous, M, and Engelke, DR. RNase P enzymes: divergent scaffolds for a conserved biological reaction. RNA Biol. 10: 909-914 PMC3904588, 2013

Pai, DA, Kaplan, CD, Kweon, HK, Murakami, Kl Andrews, PC, and Engelke, DR. RNAs inhibit transcription by yeast RNA polymerase II by preventing binding of the DNA template. RNA, 20: 644-655, PMC3988566 2014

Inswasti, C, Cridge, AG, Engelke, DR, Ganley, ARD, and O’Sullivan, JM. A sequence specific interaction between the Saccharomyces cerevisiae ribosomal RNA gene repeats and a locus encoding an RNA polymerase I subunit affects rDNA copy number. Mol Cell Biol., in
review. 2014

Smaldino, PJ, and Engelke, DR. The cytoplasmic and nuclear populations of the eukaryote tRNA-isopentenyl transferase have distinct functions with implications in human cancer. Gene, in review, 2014