- Assistant Professor, University of Notre Dame
- Postdoctoral Fellow, Yale University and Howard Hughes Medical Institute
- Ph.D. in Biochemistry, The Ohio State University
- B.S. in Chemistry and Biological Sciences, Wright State University
- NIH Pathway to Independence Award (K99/R00)
- American Cancer Society Postdoctoral Fellowship
- OSU Presidential Fellowship
- American Heart Association Predoctoral Fellowship
Structural, Biochemical & Cellular Roles of RNA Triple Helices
RNA structure is largely viewed as being single stranded or double stranded, although triple-stranded RNA structures were deduced to form in test tubes almost 60 years ago. Despite this early discovery, only four examples of RNA triple helices have been validated in eukaryotic cellular RNAs. The long-term goal of the Brown laboratory is to understand the structural, biochemical, and cellular roles of RNA triple helices using the MALAT1 triple helix as a model. This triple helix forms at the 3' end of the long noncoding RNA, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1). This triple helix forms when a U-rich internal loop of a stem-loop structure binds and sequesters a downstream 3-terminal A-rich tract. This unique triple-helical structure, composed of nine U•A-U triples separated by a C+•G-C triple and C-G doublet, protects MALAT1 from an uncharacterized rapid nuclear RNA pathway.
The fundamental structural and biochemical properties of RNA triple helices remain to be rigorously characterized. The Brown laboratory is interested in several key questions. Do proteins bind specifically to the MALAT1 triple helix? Is there an undiscovered class of triple-stranded RNA binding proteins? How does the cell degrade a highly stable triple-helical RNA structure? What is the relative stability of canonical (U•A-U and C•G-C) versus non-canonical base triples? Can successive non-canonical base triples form a stable triple helix? What are the structural parameters of an ideal RNA triple helix? What is the folding pathway of an RNA triple helix? What other RNA triple helices exist in mammalian cells? To investigate these questions, we are currently using a variety of approaches, including X-ray crystallography, cell-based assays, molecular biology, classical biochemistry and high-throughput methods.
Studying the MALAT1 triple helix will advance our understanding of cancer. MALAT1 is upregulated in multiple types of cancer and promotes tumor growth by affecting proliferation, invasion, and metastasis. Importantly, the region of MALAT1 that is sufficient to induce oncogenic activities includes the triple helix. Our work shows that the MALAT1 triple helix is required for MALAT1 accumulation; therefore, we are currently exploring whether the triple helix plays a direct role in mediating oncogenic activities beyond its function as an RNA stability element.
- Kunkler, C. N., Hulewicz, J. P., Hickman, S. C., Wang, M. C., McCown, P. J., Brown, J. A. "Stability of an RNA•DNA-DNA triple helix depends on base triplet composition and length of the RNA third strand" 2019 Nucleic Acids Research, 47 (14), pp. 7213-7222. DOI:10.1093/nar/gkz573.
- Ruszkowska, A., Ruszkowski, M., Dauter, Z., Brown, J.A. "Structural insights into the RNA methyltransferase domain of METTL16" 2018 Scientific Reports, 8 (1), 5311. DOI: 10.1038/s41598-018-23608-8
- Brown, J.A., Kinzig, C.G., Degregorio, S.J., Steitz, J.A. "Methyltransferase-like protein 16 binds the 3'-terminal triple helix of MALAT1 long noncoding RNA" 2016 Proceedings of the National Academy of Sciences of the United States of America, 113 (49), pp. 14013-14018. DOI: 10.1073/pnas.1614759113
- Brown, J.A., Kinzig, C.G., Degregorio, S.J., Steitz, J.A. "Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix" 2016 RNA, 22 (5), pp. 743-749. DOI: 10.1261/rna.055707.115
- Brown, J.A., Steitz, J.A. "Intronless β-globin reporter: A tool for studying nuclear RNA stability elements" 2016 Methods in Molecular Biology, 1428, pp. 77-92. DOI: 10.1007/978-1-4939-3625-0_5
- Brown, J.A., Bulkley, D., Wang, J., Valenstein, M.L., Yario, T.A., Steitz, T.A., Steitz, J.A. "Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix" 2014 Nature Structural and Molecular Biology, 21 (7), pp. 633-640. DOI: 10.1038/nsmb.2844