Eukaryotic mRNA can be controlled at many different steps. After transcription, a battery of processing steps generate mature mRNAs. Transport, translational activity, mRNA stability, and mRNA localization govern when, where and how much protein a mature mRNA produces. The ultimate objective of our work is to understand the molecular mechanisms that regulate mature mRNAs. In this proposal, we focus on how the region of the mRNA past the termination codon -- the 3' untranslated region (3'UTR) --governs mRNA fate and function. We concentrate on control of translation and stability. To do so, we focus on a paradigmatic network of regulatory proteins characterized during the last grant period. A family of highly conserved 3'UTR binding proteins, the PUF proteins, are critical in this network. Our goals are to understand, in molecular terms, how PUF proteins and their partners control the fate and function of mature mRNAs. The approach taken is first to elucidate in detail how PUF proteins recognize specific RNA sequences, focusing on and exploiting the extraordinary modularity of their interactions with RNA. We determine how RNA sequence specificity is generated in nature, and the limits to which it can be manipulated. We combine molecular genetics and biochemistry to reveal the functions and mechanisms of PUF proteins in S. cerevisiae. We build on the foundations we have laid in C. elegans. Throughout, we combine molecular genetics with in vitro systems, and develop methods that may have broader utility. We focus sharply on PUF proteins to illuminate broadly how 3'UTR controls function, evolve, and coordinate expression of multiple mRNAs.
| Lapointe, Christopher P; Stefely, Jonathan A; Jochem, Adam et al. (2018) Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Syst 6:125-135.e6 |
| Aoki, Scott T; Porter, Douglas F; Prasad, Aman et al. (2018) An RNA-Binding Multimer Specifies Nematode Sperm Fate. Cell Rep 23:3769-3775 |
| Lapointe, Christopher P; Wickens, Marvin (2018) RNA Tagging: Preparation of High-Throughput Sequencing Libraries. Methods Mol Biol 1649:455-471 |
| Wilinski, Daniel; Buter, Natascha; Klocko, Andrew D et al. (2017) Recurrent rewiring and emergence of RNA regulatory networks. Proc Natl Acad Sci U S A 114:E2816-E2825 |
| Lapointe, Christopher P; Preston, Melanie A; Wilinski, Daniel et al. (2017) Architecture and dynamics of overlapped RNA regulatory networks. RNA 23:1636-1647 |
| Shin, Heaji; Haupt, Kimberly A; Kershner, Aaron M et al. (2017) SYGL-1 and LST-1 link niche signaling to PUF RNA repression for stem cell maintenance in Caenorhabditis elegans. PLoS Genet 13:e1007121 |
| Prasad, Aman; Porter, Douglas F; Kroll-Conner, Peggy L et al. (2016) The PUF binding landscape in metazoan germ cells. RNA 22:1026-43 |
| Aoki, Scott T; Kershner, Aaron M; Bingman, Craig A et al. (2016) PGL germ granule assembly protein is a base-specific, single-stranded RNase. Proc Natl Acad Sci U S A 113:1279-84 |
| Wilinski, Daniel; Qiu, Chen; Lapointe, Christopher P et al. (2015) RNA regulatory networks diversified through curvature of the PUF protein scaffold. Nat Commun 6:8213 |
| Waghray, Shruti; Williams, Clay; Coon, Joshua J et al. (2015) Xenopus CAF1 requires NOT1-mediated interaction with 4E-T to repress translation in vivo. RNA 21:1335-45 |
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