RNA Modifications: Understanding Structure and Function at the Molecular Level

Sophisticated tools unlock the epitranscriptome’s role in health and disease

RNA and DNA are nucleic acids which are one of the three major macromolecules essential for all known forms of life. The more scientists have studied RNA, the more we have come to learn the complicated way in which RNA implicates various biological roles in coding, decoding, regulation, and even expression of genes. Dr. Pat Limbach, Professor and Ohio Eminent Scholar of Chemistry at the University of Cincinnati, studies RNA and in particular, how and why the cell “decorates” RNA with various chemical groups. These decorations require the cell to expend significant resources and prior research suggests these decorations play important structural and functional roles. The significance of Dr. Limbach’s research arises from the fundamental role that RNA has within cellular processes. His ongoing research has applications in understanding the human microbiome, cancer, and stress-induced diseases like Parkinson’s and Alzheimer’s.

With an approach that uses high-end technology based on mass spectrometry, Dr. Limbach and his team are able to directly measure the presence and levels of RNA decorations, or modifications. In addition to using such techniques, Dr. Limbach is continually developing technology that is uniquely suited to study decorations on RNA structures. Therefore, as one in only a handful of laboratories in the world that bring such technology to bear on questions related to RNA modifications, his work is necessary for the advancement in understanding these questions. Additionally, under the direction of Dr. Limbach, who was initially trained in a small liberal arts college, the team moves away from a strictly reductionist approach and rather, integrates multiple disciplines with a focus on the big picture. With collaborations spanning the globe and an active team at the University of Cincinnati, Dr. Limbach’s research highlights his unique expertise in using mass spectrometry to study RNA modification.

Current research includes:

  • Health and Disease: Dr. Limbach’s current research is focused on understanding RNA modifications that can be adversely affected during cellular dysfunction, so that his team can elucidate the interplay between protein synthesis and metabolism with various cancers. Dr. Limbach and his team are uniquely positioned to measure how competing populations of microorganisms influence RNA modifications -- both in the microorganism and the human host -- thus his work has applications in understanding the human microbiome, wherein bacteria within our gut interact to promote healthy metabolic functions.

  • Mass Spectrometry: Dr. Limbach’s group seeks to create ever more sensitive and accurate mass spectrometry approaches to identify RNA modifications – including modifications that previously were unknown or uncharacterized. Such projects involve improved front-end sample purification technology and new operating tricks with the mass spectrometer to extract greater information from any single analysis. Dr. Limbach pushes boundaries forward by developing new biochemical reagents that will enable multiplexed analysis of modified RNAs, thereby increasing the throughput of analysis. Furthermore, he is exploring new analytical strategies that allow for global quantitative measurements of specific modifications on RNAs. For example, he and his team are pursuing a new area of characterizing the epitranscriptome. The epitranscriptome involves dynamic changes associated with human RNA modifications – while it had been assumed these decorations were static, research studies suggest that RNA modifications vary with cell type, cellular conditions, and could potentially be regulated as an integral component of cellular metabolism.

  • Non-Natural RNA Modifications: A new area Dr. Limbach is excited to explore is how non-natural RNA modifications adversely impact RNA structure and function. While damage to DNA is well-known and studied, the technology and approaches for studying RNA damage have lagged behind. As researchers begin appreciating the important role of RNA in cellular health, Dr. Limbach’s new research advances provide his team with a unique opportunity to explore how prevalent RNA damage is within cells; to understand which RNAs are susceptible to damage, and to characterize biochemical approaches used by the cell to recognize and possibly eliminate or repair damaged RNA. This research has applications in stress-induced diseases, not only those related to immunological challenges but also oxidative stresses such as occur in the brain. Many of the diseases of interest are those associated with aging. He and his team are bringing a unique viewpoint and scientific expertise to bear on these diseases.

Bio

Dr. Limbach grew up in rural Indiana where he was always exploring wildlife and habitats in old creek beds or checking under rocks to find the perfect fish bait. He describes his early years of curiosity driven experimentation as “more destructive curiosity” as he recalls flipping rocks over to find exotic looking bugs and wondering what their insides were made up of. After completing high school, Dr. Limbach moved to Kentucky where he attended Centre College, a small liberal arts college where he felt he could figure out where his professional goals would lead him. This gave him the opportunity to dabble in all sorts of classes including economics, religion, chemistry, and physics.

Eventually landing on chemistry, Dr. Limbach was offered summer employment as a lab assistant where he was able to spend time developing experiments which was strikingly different from his experiences in lab courses where he was told which experiment to perform. He so enjoyed his time at the lab that he began to alter his postbaccalaureate plans hoping to work for a company as a research assistant. When his professor and mentor learned of his new professional goals, he sat Dr. Limbach down and suggested a career as a research professor. Once exposed to the idea of doing research as a career, he gravitated towards two areas that matched his skills and interests -- mass spectrometry, which is a technology-heavy instrumental method, and biochemistry, which seems to contain some of our ultimate questions on how things work. Since the early days of his undergraduate career, Dr. Limbach has spent his career just as excited as his first encounters experimenting in a lab. His motivation as a faculty member has always arisen from his students -- whether undergraduate, graduate, or postgraduate -- their interest and excitement in what he does in the lab help keep him, “young and engaged.”

In his free time, aside from research, Dr. Limbach enjoys spending time with his friends and family and volunteering at church. Additionally, he loves sports. When not busy with friends and family, you can find him playing softball, swimming, running or golfing.

Website: http://bearcatms.uc.edu

Publications

Functional Role of Methylation of G518 of the 16S rRNA 530 loop by GidB in Mycobacterium tuberculosis

PDF

Systematic identification tRNAome and its dynamics in Lactococcus lactis

PDF

Mass Spectrometry for the Identification and Characterization of Modified Nucleosides and Nucleic Acids

PDF

In vivo X-ray footprinting of pre-30S ribosomes reveals chaperone-dependent remodeling of late assembly intermediates

PDF

The Global Identification of tRNA Isoacceptors by Targeted Tandem Mass Spectrometry

PDF

Awards

2013 Fellow, American Association for the Advancement of Science (AAAS)

2009 Cincinnati Chemist of the Year Award, Cincinnati Section American Chemical Society

2008 Sigma Xi Young Investigator Research Award, University of Cincinnati

2003 Ohio Eminent Scholar in Mass Spectrometry

1999 Award of Excellence in Undergraduate Teaching, College of Basic Sciences, LSU