RNA molecules with structure-dependent functions play important roles throughout molecular biology, and the broad, long-term objective of this grant is to understand these roles. The experiments of this proposal focus on the mechanism, biology, and evolution of RNA interference (RNAi), an example of a structure-dependent function in which double-stranded RNA (dsRNA) triggers the destruction of corresponding cellular mRNAs. Although RNAi has been lost in Saccharomyces cerevisiae, it is present in other budding yeasts, including Saccharomyces castellii (a close relative of S. cerevisiae) and Candida albicans (a common human pathogen). These species use noncanonical Dicer proteins to process long dsRNA into small interfering RNAs (siRNAs), which are loaded into the Argonaute protein to direct silencing. Introducing Dicer and Argonaute of S. castellii restores RNAi in S. cerevisiae, and the reconstituted pathway silences endogenous retrotransposons. The discovery of RNAi in budding yeast opens new opportunities for exploring the mechanism, biology, and evolution of the pathway. The first specific aim of the proposed experiments is to determine the consequences of losing or restoring RNAi. Methods will include phenotypic profiling, small-RNA sequencing, and mRNA sequencing. Endogenous dsRNA elements known as Killer elements also will be monitored, with the expectation that their retention will be compromised in the RNAi-reconstituted S. cerevisiae strain. These experiments will explore how cells cope with the introduction of a new gene-regulatory pathway and provide insight into why RNAi was lost in some species.
The second aim i s to identify additional components of RNAi in budding yeast. Methods will include genetic selections and mass spectrometry of co-immunoprecipitated proteins. Identifying new components and modifiers would be important not only for understanding the yeast pathway but could shed light on RNAi pathways in plants and animals, including humans. Results of both this aim and aim 1 will also be of practical interest for those using RNAi-reconstituted strains to study gene function in S. cerevisiae and those attempting to port RNAi into other RNAi-deficient organisms.
The third aim i s to determine the mechanism of RNAi in budding yeast. To test the hypothesis that silencing is post- transcriptional, RNAi-mutant strains will be monitored for changes in RNA Polymerase II binding, mRNA turnover, and the correspondence between sequenced siRNAs and mRNA degradation fragments. Biochemical and structural experiments will also test a proposed mechanism for how purified budding-yeast Dicer produces 23-nt siRNAs, despite lacking the protein domain that canonical Dicers require for this activity. Experiments of all three aims will leverage, for the first time, the powerful tools of budding yeast for the study of RNAi. A thorough understanding of this recently identified pathway in budding yeast should provide important insights regarding RNAi and related gene-silencing pathways in other eukaryotes and thereby contribute to fundamental knowledge relevant to human health.
The experiments of this proposal focus on the phenomenon known as """"""""RNA interference,"""""""" which protects animals, plants, and fungi from viruses and genomic parasites. The goals are to learn about the biochemical mechanism and biological functions of RNAi in yeast species that are closely related to baker's yeast. Achieving these goals will help researchers design new tools for studying the function of genes in various animal and fungal species (including some that cause human diseases) and will provide insights into how cells normally determine the amount of protein that is produced from each gene.
| Chen, Grace R; Sive, Hazel; Bartel, David P (2017) A Seed Mismatch Enhances Argonaute2-Catalyzed Cleavage and Partially Rescues Severely Impaired Cleavage Found in Fish. Mol Cell 68:1095-1107.e5 |
| Weinberg, David E; Shah, Premal; Eichhorn, Stephen W et al. (2016) Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. Cell Rep 14:1787-1799 |
| Dumesic, Phillip A; Natarajan, Prashanthi; Chen, Changbin et al. (2013) Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 152:957-68 |
| Curtis, Edward A; Bartel, David P (2013) Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme. RNA 19:1116-28 |
| Bernstein, Douglas A; Vyas, Valmik K; Weinberg, David E et al. (2012) Candida albicans Dicer (CaDcr1) is required for efficient ribosomal and spliceosomal RNA maturation. Proc Natl Acad Sci U S A 109:523-8 |
| Nakanishi, Kotaro; Weinberg, David E; Bartel, David P et al. (2012) Structure of yeast Argonaute with guide RNA. Nature 486:368-74 |
| Weinberg, David E; Nakanishi, Kotaro; Patel, Dinshaw J et al. (2011) The inside-out mechanism of Dicers from budding yeasts. Cell 146:262-76 |
| Koldobskaya, Yelena; Duguid, Erica M; Shechner, David M et al. (2011) A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nat Struct Mol Biol 18:100-6 |
| Drinnenberg, Ines A; Fink, Gerald R; Bartel, David P (2011) Compatibility with killer explains the rise of RNAi-deficient fungi. Science 333:1592 |
| Shechner, David M; Bartel, David P (2011) The structural basis of RNA-catalyzed RNA polymerization. Nat Struct Mol Biol 18:1036-42 |
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