Our long-term goal is to elucidate the mechanisms by which the spliceosome catalyzes pre-mRNA splicing and in particular to define the structural and functional role of RNA and protein in catalysis. Catalysis of pre-mRNA splicing by the spliceosome is a defining feature of eukaryotes. In humans, catalysis is required to excise ten introns on average for nearly every gene, and catalysis at alternative sites expands the proteome and contributes to the complexity of higher eukaryotes. Indeed, mutations in at least 15% of human diseases result from errors in splicing. Despite this importance of pre-mRNA splicing to eukaryotic gene expression, for decades our understanding of splicing catalysis has languished, particularly in comparison to our understanding of catalysis at the two other major stages of gene expression - transcription and translation. We have not even known whether catalysis is mediated by the RNA or protein parts of the spliceosome. However, through our collaborative efforts, we have recently provided definitive evidence that the RNA parts catalyze splicing, positioning two divalent metal ions for interaction with the scissile phosphates. Strikingly, our work also establishes that the spliceosome utilizes a catalytic mechanism indistinguishable from the catalytic mechanism of self-splicing group II RNA introns, extending the parallels with the group II intron to the atomic level at the catalytic core and providing strog support for the hypothesis that these two enzymes share common evolutionary origins. Despite this advance and other achievements in the field, many fundamental questions remain. For example, how are the nucleophiles in either splicing system activated for catalysis, how does the architecture of the spliceosomal catalytic core position the reactive sites for catalysis, and what is the role of protein in mediating RNA-based catalysis? To answer these questions, we aim to test a metal cluster model for catalysis of nuclear pre-mRNA splicing, to define the architecture and dynamics of the catalytic core of the spliceosome, and to define the essential role of protein in assisting RNA-based splicing catalysis. We will accomplish these aims through a continuation of our unique and synergistic collaboration that allows for a combined approach of chemistry, biochemistry and molecular genetics. This work will transform our understanding of the roles of RNA and protein in spliceosomal catalysis, with significant implications for understanding the origins and evolution of the spliceosome.

Public Health Relevance

It has been estimated that at least 15% of human diseases result from defects in splicing. Our ability to treat such diseases will depend, in large part, on ur understanding of the complexities of the splicing machinery. In its attempt to clarify the essentia catalytic components of the spliceosome, this project will provide novel insights into the fundamental mechanisms that must function properly in healthy human cells and thereby illuminate possible mechanisms for disease as well as potential strategies for treatment.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Bender, Michael T
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University of Chicago
Schools of Medicine
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Sundaram, Karthik M; Zhang, Yilin; Mitra, Anirban K et al. (2017) Prolactin Receptor-Mediated Internalization of Imaging Agents Detects Epithelial Ovarian Cancer with Enhanced Sensitivity and Specificity. Cancer Res 77:1684-1696
Piccirilli, Joseph A; Staley, Jonathan P (2016) Reverse transcriptases lend a hand in splicing catalysis. Nat Struct Mol Biol 23:507-9
Lu, Jun; Koo, Selene C; Li, Nan-Sheng et al. (2015) Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. Nucleosides Nucleotides Nucleic Acids 34:114-29
Li, Nan-Sheng; Tuttle, Nicole; Staley, Jonathan P et al. (2014) Synthesis and incorporation of the phosphoramidite derivative of 2'-O-photocaged 3'-s-thioguanosine into oligoribonucleotides: substrate for probing the mechanism of RNA catalysis. J Org Chem 79:3647-52
Fica, Sebastian M; Mefford, Melissa A; Piccirilli, Joseph A et al. (2014) Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol 21:464-471
Keenholtz, Ross A; Mouw, Kent W; Boocock, Martin R et al. (2013) Arginine as a general acid catalyst in serine recombinase-mediated DNA cleavage. J Biol Chem 288:29206-14
Schellenberg, Matthew J; Wu, Tao; Ritchie, Dustin B et al. (2013) A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Nat Struct Mol Biol 20:728-34
Fica, Sebastian M; Tuttle, Nicole; Novak, Thaddeus et al. (2013) RNA catalyses nuclear pre-mRNA splicing. Nature 503:229-34
Sakaguchi, Reiko; Giessing, Anders; Dai, Qing et al. (2012) Recognition of guanosine by dissimilar tRNA methyltransferases. RNA 18:1687-701
Frederiksen, John K; Li, Nan-Sheng; Das, Rhiju et al. (2012) Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. RNA 18:1123-41

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