Ralph Kleiner
Contact:
Associate Professor of Chemistry
[email protected]
Frick Laboratory, 359
609-258-1654
Faculty Assistant:
Angela Dolce
Faculty / Grants Assistant
[email protected]
Frick Laboratory, A87
609-258-5075
Research Focus
The Kleiner lab studies the function and regulation of cellular RNA using the tools of chemical biology. RNA is a central molecule in biology that controls the flow of genetic information, and its behavior is regulated by a diversity of chemical and biochemical mechanisms with important roles in health and disease. Our lab focuses on investigating the post-transcriptional regulation of RNA function by interactions with RNA-binding proteins (RBPs) and chemical “epitranscriptomic” modifications to the canonical nucleotides. Additionally, we have developed broadly applicable chemical tools for measuring cellular RNA synthesis and turnover, localization, and structure. All projects involve a mix of chemical and biological methods and span in vitro and cellular/organismal systems.
RNA-binding proteins (RBPs). The human proteome is estimated to contain >1500 proteins that interact with RNA. These proteins are known as RNA-binding proteins (RBPs) and control all aspects of the RNA lifecycle from synthesis to degradation, but the biochemical and biological functions of many RBPs are poorly understood. A large number of RBPs are implicated in human diseases and emerging therapeutic strategies are targeting RBP-RNA interactions. We are developing and applying enabling strategies for characterizing cellular RNA-protein binding events using chemoproteomics and RNA editing platforms. Our goal is to develop a biochemical framework for the function of diverse RBPs and apply these principles to inform therapeutic targeting and manipulation of RBP-RBA interactions.
RNA modifications. The four canonical nucleotide structures (A, C, G, and U) are diversified through the enzyme-mediated installation of post-transcriptional modifications. Over >150 modified RNA nucleotides have been detected in diverse organisms and many modifications and RNA modifying enzymes are broadly conserved across evolution. Links between RNA modifications and human diseases have also emerged in recent years. Despite their ubiquity, the function of most RNA modifications is not well established in large part due to limitations in available technologies for mapping modifications and characterizing associated regulatory proteins (i.e. enzymes and modification reader proteins). We are developing novel chemical approaches for discoverying RNA modifying enzymes and characterizing their substrates. In parallel, we are pursuing functional studies to establish the role of RNA modification pathways in gene expression regulation.
Honors
International Chemical Biology Society (ICBS) Young Chemical Biologist Award (2023)
Kavli Fellow (2023)
NSF CAREER Award (2019)
Sloan Research Fellowship (2019)
Sidney Kimmel Foundation Scholar Award (2017)
Damon Runyon Dale F. Frey Award for Breakthrough Scientists (2016)
Revson Foundation Fellowship in Biomedical Science (2014)
Damon Runyon Cancer Research Foundation Postdoctoral Fellowship (2012)
Selected Publications
Inhibition of nucleolar transcription by oxaliplatin involves ATM/ATR kinase signaling. Nechay, M.; Wang, D.; Kleiner, R.E. Cell Chem. Biol. 30, 906-919 (2023).
Profiling dynamic RNA-protein interactions using small molecule-induced RNA editing. Seo, K.W.; Kleiner, R.E. Nat. Chem. Biol. 19, 1361-1371 (2023).
Global Discovery of Covalent Modulators of Ribonucleoprotein Granules. Ciancone, A.M.*; Seo, K.W.*; Chen, M.*; Borne, A.L.; Libby, A.H.; Bai, D.L.; Kleiner, R.E.*; and Hsu*, K.L. J. Am. Chem. Soc. 145, 11056-66 (2023).
Chemical Method to Sequence 5-Formylcytosine on RNA. Li, A.; Sun, X.; Arguello, A.E.; Kleiner, R.E. ACS Chem. Biol. 17, 503-508 (2022).
Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases. Arguello, A.E.; Li, A.; Sun, X.; Eggert, T.W.; Mairhofer, E.; Kleiner, R.E. Nat. Commun. 13, 4176 (2022).
Live-cell RNA imaging with metabolically incorporated fluorescent nucleosides. Wang, D.; Shalamberidze, A.; Arguello, A.E.; Purse, B. Kleiner, R.E. J. Am. Chem. Soc. 144, 14647-14656 (2022).
Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation. Dai, W.; Li, A.; Yu, N.J.; Nguyen, T.; Leach, R.W.; Wuhr, M.; Kleiner, R.E. Nat. Chem. Biol. 17, 1178-1187 (2021).
Cell- and Polymerase-Selective Metabolic Labeling of Cellular RNA with 2’-Azidocytidine. Wang, D.; Zhang, Y.; Kleiner, R. E. J. Am. Chem. Soc. 142, 14417-14421 (2020).
YTHDF2 Recognition of N1-methyladenosine (m1A)-modified RNA Is Associated with Transcript Destabilization. Seo, K. W.; Kleiner, R. E. ACS Chem. Biol. 15, 132-139 (2020).
In vitro selection with a site-specifically modified RNA library reveals the binding preferences of N6-methyladenosine (m6A) reader proteins. Arguello, A. E.; Leach, R. W.; Kleiner, R. E. Biochemistry 58, 3386-3395 (2019).
A Metabolic Engineering Approach to Incorporate Modified Pyrimidine Nucleosides into Cellular RNA. Zhang, Y.; Kleiner, R. E. J. Am. Chem. Soc. 141, 3347-3351 (2019).
RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein-RNA Interactome. Arguello, A. E.; DeLiberto, A. N.; Kleiner, R. E. J. Am. Chem. Soc. 139, 17249-17252 (2017).
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