I am Jean-Denis, a French Canadian who came to the US to complete his Post-doctoral studies at Yale University and who is now joining the UCONN Health team as an Assistant Professor.
Professionally, I am a very enthusiastic person. I love to share my passion for science with others and discuss about new ideas, experiments, results, recent publications, meetings and more. I completed my B.Sc. in Biotechnology at Université de Sherbrooke (Québec, Canada) and my Ph.D. in Biochemistry in the laboratory of Jean-Pierre Perreault at Université de Sherbrooke (Québec Canada).
My work discovered novel properties and functions of RNA G-quadruplexes, a structure formed by G-rich sequences. First, I characterized their folding properties and dynamics in vitro (Beaudoin JD, et al. 2008; Beaudoin JD, et al. 2013).
Next, I developed an algorithm to locate genomic sequences susceptible to form G-quaruplexes (Beaudoin JD, et al. 2014) and found that, in human cell cultures, 5’-UTR G-quadruplexes act as key translational repressors (Beaudoin JD and Perreault JP, 2010) and 3’-UTR G-quadruplexes can modulate alternative polyadenylation leading to differential expression (Beaudoin JD. and Perreault JP., Nucleic Acids Res. 2013). Together, this work provided mechanistic insights into a previously unrecognized role for RNA G-quadruplexes in gene expression regulation.
Following from this work, we developed an oligonucleotide-based approach to target individual RNA G-quadruplexes and tune gene expression in a desired direction (Rouleau SG, Beaudoin JD, et al. 2015). These findings highlighted the potential to target RNA regulatory elements to control gene expression, opening promising novel therapeutic strategies.
For my postdoctoral work, I extended my expertise in molecular, cellular and RNA biology to study a fundamental process in all animals, the maternal-to-zygotic transition, where post-transcriptional regulation orchestrates a profound change in the embryonic transcriptional landscape. Here, I asked two central questions: what are the RNA structures formed during early embryogenesis and how do they interact with cellular factors to control gene expression during development? To address these questions, I developed innovative genome-wide in vivo RNA probing techniques to gain structural information on the zebrafish transcriptome during embryogenesis. I also expanded my technical repertoire to perform high throughput approaches to measure genome-wide gene expression in vivo, including mRNA abundance (RNA-seq) and translation (Ribo-seq). By integrating this information, I generated a global interaction map between RNA structure, mRNA stability and translation during early embryogenesis (Beaudoin JD*, Novoa EM* et al. 2018.). Our results provide three major insights: (1) Contrary to the current dogma, we found that untranslated mRNAs are more structured in vivo compared to in vitro, (2) globally, translation guides mRNA structures rather than structure guiding translation (Karmer MC and Gregory BD, 2018.), and (3) RNA structures remodeled in 3’-UTRs are enriched for regulatory activity during development.