This research project is centered on the hypothesis that ribonucleic acid (RNA) structure and RNA-chromatin associated protein interactions play crucial roles in maintaining genome stability. Non-coding RNAs (ncRNAs) serve as key regulators of gene expression and are known to physically associate with chromatin-associated proteins to organize changes in gene architecture during specific development stages of the cell. A subset of these RNA-protein interactions are linked to ageing, cancer metastasis, and neuronal development. As genomic approaches begin to identify RNA-protein associations and their links to cancer, there remains limited information about epigenetic-based RNA binding proteins at the molecular level. We seek to understand how RNA functionally interacts with the lysine specific demethylase-1 (LSD1) protein enzyme. LSD1 is an essential histone methylation regulator and has oncogenic properties in several cancers including: prostate, bladder, neuroblastoma, lung, and breast cancer. LSD1 is implicated in cancer through its vast interaction network. LSD1 also interacts with many RNA molecules involved in cell differentiation and can function to regulate conserved RNA-mediated repressor complexes in the cell. An ncRNA, termed TERRA, enables LSD1 to interact with a DNA double strand break repair enzyme at the ends of chromosomes (telomeres), demonstrating that the RNA binding properties of LSD1 are important for gene regulation. TERRA is a regulatory RNA that is transcribed from yeast to humans and can adopt a non-canonical guanine quadruplex (GQ) RNA architecture in vitro and in vivo. TERRA?s abundance in the cell correlates with progressive telomere shortening and the stabilization of telomeric heterochromatin. We hypothesize that RNA-LSD1 assemblies play key roles in gene expression and propose that GQ RNAs serve as crucial regulators of chromatin-associated proteins. The proposed studies will 1) elucidate the biochemical and structural mechanisms of a TERRA RNA-LSD1 interaction and 2) examine how non-canonical structured RNAs contact LSD1 to influence telomeric regulatory pathways. The long-term goal of this project is to understand how RNA structure influences LSD1 regulatory networks. Results from these studies will provide insight into the mechanisms of RNA-based epigenetic regulation and serves as a starting point in the development of ?tailored? probes that target histone methylation regulators in a pathway-specific manner.

Public Health Relevance

Telomeres are tightly regulated in order to maintain chromosomal stability; misregulation of ribonucleic acid (RNA) - protein interactions at telomeres can lead to degenerative disorders and cancer. The goal of this study is to understand how a telomeric non-coding RNA, termed TERRA, interacts with a chromatin associated protein that is essential for development. The results of this study will provide important clues in the development of therapeutics that target human disease and aberrant cellular differentiation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Gaillard, Shawn R
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Marquette University
Schools of Arts and Sciences
United States
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Zeng, Danyun; Brown, Benjamin P; Voehler, Markus W et al. (2018) NMR resonance assignments of RNase P protein from Thermotoga maritima. Biomol NMR Assign 12:183-187
Martin, William J; Reiter, Nicholas J (2017) Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes. Biochemistry 56:3-13
Hirschi, Alexander; Martin, William J; Luka, Zigmund et al. (2016) G-quadruplex RNA binding and recognition by the lysine-specific histone demethylase-1 enzyme. RNA 22:1250-60