Publications

2026

Jahangirnejad S, Côté JP, Lafontaine DA. (2026). Importance of riboswitch-regulated genes for Pseudomonas aeruginosa.  J Mol Biol. 438(8):169724.

2025

Jahangirnejad S, Côté JP, Lafontaine DA. (2025). The Thiamin Pyrophosphate Riboswitch is Affected by Lysine-derived Metabolic Conversion Products in Escherichia coli.  J Mol Biol. 437(17):169207.

2024

Vézina Bédard AS, Michaud A, Quenette F, Singh N, de Lemos Martins F, Wade JT, Guillier M, Lafontaine DA. (2024). Regulation of magnesium ion transport in Escherichia coli: insights into the role of the 5' upstream region in corA expression.  RNA Biol. 21(1):94-106.

Grondin JP, Geffroy M, Simoneau-Roy M, Chauvier A, Turcotte P, St-Pierre P, Dubé A, Moreau J, Massé E, Penedo JC, Lafontaine DA. (2024). Insights into the cotranscriptional and translational control mechanisms of the Escherichia coli tbpA thiamin pyrophosphate riboswitch.  Commun Biol. 7(1):1345.

Eschbach SH, Hien EDM, Ghosh T, Lamontagne AM, Lafontaine DA. (2024). The Escherichia coli ribB riboswitch senses flavin mononucleotide within a defined transcriptional window.  RNA. 30(12):1660-1673.

Hien EDM, St-Pierre P, Penedo JC, Lafontaine DA. (2024). Cotranscriptional Folding of a 5' Stem-loop in the Escherichia coli tbpA Riboswitch at Single-nucleotide Resolution.  J Mol Biol. 436(22):168771.

Hien EDM, Chauvier A, St-Pierre P, Lafontaine DA. (2024). Structural Characterization of the Cotranscriptional Folding of the Thiamin Pyrophosphate Sensing thiC Riboswitch in Escherichia coli.  Biochemistry. 63(13):1608-1620.

Michaud A, Garneau D, Côté JP, Lafontaine DA. (2024). Fluorescent riboswitch-controlled biosensors for the genome scale analysis of metabolic pathways.  Sci Rep. 14(1):12555.

Bastet L, Korepanov AP, Jagodnik J, Grondin JP, Lamontagne AM, Guillier M, Lafontaine DA. (2024). Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms.  Nucleic Acids Res. 52(10):5852-5865.

Ghosh T, Jahangirnejad S, Chauvier A, Stringer AM, Korepanov AP, Côté JP, Wade JT, Lafontaine DA. (2024). Direct and indirect control of Rho-dependent transcription termination by the Escherichia coli lysC riboswitch.  RNA. 30(4):381-391.

2022

Jeanneau S, Jacques PÉ, Lafontaine DA. (2022). Investigating the role of RNA structures in transcriptional pausing using in vitro assays and in silico analyses.  RNA Biol. 19(1):916-927.

2021

Zeller MJ, Favorov O, Li K, Nuthanakanti A, Hussein D, Michaud A, Lafontaine DA, Busan S, Serganov A, Aubé J, Weeks KM. (2021). SHAPE-enabled fragment-based ligand discovery for RNA.  Proc Natl Acad Sci U S A. 119(20):e2122660119.

Nadon JF, Epshtein V, Cameron E, Samatov MR, Vasenko AS, Nudler E, Lafontaine DA. (2021). Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems.  Commun Biol. 12;5(1):457.

Chauvier A, St-Pierre P, Nadon JF, Hien EDM, Pérez-González C, Eschbach SH, Lamontagne AM, Penedo JC, Lafontaine DA. (2021). Monitoring RNA dynamics in native transcriptional complexes.  Proc Natl Acad Sci U S A. 118(45):e2106564118.

Smith-Peter E, Séguin DL, St-Pierre É, Sekulovic O, Jeanneau S, Tremblay-Tétreault C, Lamontagne AM, Jacques PÉ, Lafontaine DA, Fortier LC. (2021). Inactivation of the riboswitch-controlled GMP synthase GuaA in Clostridioides difficile is associated with severe growth defects and poor infectivity in a mouse model of infection.  RNA Biol. 18(sup2):699-710.

St-Pierre P, Shaw E, Jacques S, Dalgarno PA, Perez-Gonzalez C, Picard-Jean F, Penedo JC, Lafontaine DA. (2021). A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.  Nucleic Acids Res. 49(10):5891-5904.

2020

Bédard AV, Hien EDM, Lafontaine DA. (2020). Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins.  Biochim Biophys Acta Gene Regul Mech. 1863(3):194501.

2019

Chauvier A, Nadon JF, Grondin JP, Lamontagne AM, Lafontaine DA. (2019). Role of a hairpin-stabilized pause in the Escherichia coli thiC riboswitch function.  RNA Biol. 16(8):1066-1073.

McCluskey K, Boudreault J, St-Pierre P, Perez-Gonzalez C, Chauvier A, Rizzi A, Beauregard PB, Lafontaine DA, Penedo JC. (2019). Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2.  Nucleic Acids Res. 47(12):6478-6487.

2018

Laterreur N, Lemieux B, Neumann H, Berger-Dancause JC, Lafontaine D, Wellinger RJ. (2018). The yeast telomerase module for telomere recruitment requires a specific RNA architecture.  RNA. 24(8):1067-1079.

Bastet L, Turcotte P, Wade JT, Lafontaine DA. (2018). Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay.  RNA Biol. 15(6):679-682.

Yan LH, Le Roux A, Boyapelly K, Lamontagne AM, Archambault MA, Picard-Jean F, Lalonde-Seguin D, St-Pierre E, Najmanovich RJ, Fortier LC, Lafontaine D, Marsault É. (2018). Purine analogs targeting the guanine riboswitch as potential antibiotics against Clostridioides difficile.  Eur J Med Chem. 143:755-768.

2017

Dussault AM, Dubé A, Jacques F, Grondin JP, Lafontaine DA. (2017). Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.  RNA. 23(10):1539-1551.

Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne AM, Prévost K, Massé E, Wade JT, Lafontaine DA. (2017). Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation.  Nucleic Acids Res. 45(12):7474-7486.

Chauvier A, Picard-Jean F, Berger-Dancause JC, Bastet L, Naghdi MR, Dubé A, Turcotte P, Perreault J, Lafontaine DA. (2017). Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.  Nat Commun. 8:13892.

2016

Perez-Gonzalez C, Lafontaine DA, Penedo JC. (2016). Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.  Front Chem. 4:33.

Comeau MA, Lafontaine DA, Abou Elela S. (2016). The catalytic efficiency of yeast ribonuclease III depends on substrate specific product release rate.  Nucleic Acids Res. 44(16):7911-21.

Perez-Gonzalez C, Grondin JP, Lafontaine DA, Carlos Penedo J. (2016). Biophysical Approaches to Bacterial Gene Regulation by Riboswitches.  Adv Exp Med Biol. 915:157-91.

2015

Blouin S, Craggs TD, Lafontaine DA, Penedo JC. (2015). Functional Studies of DNA-Protein Interactions Using FRET Techniques.  Methods Mol Biol. 1334:115-41.

Chauvier A, Lafontaine DA. (2015). Probing of Nascent Riboswitch Transcripts.  Methods Mol Biol. 1334:109-14.

Boudreault J, Perez-Gonzalez DC, Penedo JC, Lafontaine DA. (2015). Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms.  Methods Mol Biol. 1334:101-7.

Smith-Peter E, Lamontagne AM, Lafontaine DA. (2015). Role of lysine binding residues in the global folding of the lysC riboswitch.  RNA Biol. 12(12):1372-82.

Lussier A, Bastet L, Chauvier A, Lafontaine DA. (2015). A kissing loop is important for btuB riboswitch ligand sensing and regulatory control.  J Biol Chem. 290(44):26739-51.

Bordeleau E, Purcell EB, Lafontaine DA, Fortier LC, Tamayo R, Burrus V. (2015). Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile.  J Bacteriol. 197(5):819-32.

2014

Shaw E, St-Pierre P, McCluskey K, Lafontaine DA, Penedo JC. (2014). Using sm-FRET and denaturants to reveal folding landscapes.  Methods Enzymol. 549:313-41.

St-Pierre P, McCluskey K, Shaw E, Penedo JC, Lafontaine DA. (2014). Fluorescence tools to investigate riboswitch structural dynamics.  Biochim Biophys Acta. 1839(10):1005-1019.

Eschbach SH, Lafontaine DA. (2014). RNA conformational changes analyzed by comparative gel electrophoresis.  Methods Mol Biol. 1086:255-64.

2013

Laterreur N, Eschbach SH, Lafontaine DA, Wellinger RJ. (2013). A new telomerase RNA element that is critical for telomere elongation.  Nucleic Acids Res. 41(16):7713-24.

Chinnappan R, Dubé A, Lemay JF, Lafontaine DA. (2013). Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay.  Nucleic Acids Res. 41(10):e106.

Lalaouna D, Simoneau-Roy M, Lafontaine D, Massé E. (2013). Regulatory RNAs and target mRNA decay in prokaryotes.  Biochim Biophys Acta. 1829(6-7):742-7.

Ster C, Allard M, Boulanger S, Lamontagne Boulet M, Mulhbacher J, Lafontaine DA, Marsault E, Lacasse P, Malouin F. (2013). Experimental treatment of Staphylococcus aureus bovine intramammary infection using a guanine riboswitch ligand analog.  J Dairy Sci. 96(2):1000-8.

2012

Caron MP, Bastet L, Lussier A, Simoneau-Roy M, Massé E, Lafontaine DA. (2012). Dual-acting riboswitch control of translation initiation and mRNA decay.  Proc Natl Acad Sci U S A. 109(50):E3444-53.

Eschbach SH, St-Pierre P, Penedo JC, Lafontaine DA. (2012). Folding of the SAM-I riboswitch: a tale with a twist.  RNA Biol. 9(5):535-41.

2011

Tremblay R, Lemay JF, Blouin S, Mulhbacher J, Bonneau É, Legault P, Dupont P, Penedo JC, Lafontaine DA. (2011). Constitutive regulatory activity of an evolutionarily excluded riboswitch variant.  J Biol Chem. 286(31):27406-15.

Heppell B, Blouin S, Dussault AM, Mulhbacher J, Ennifar E, Penedo JC, Lafontaine DA. (2011). Molecular insights into the ligand-controlled organization of the SAM-I riboswitch.  Nat Chem Biol. 7(6):384-92. 

Bastet L, Dubé A, Massé E, Lafontaine DA. (2011). New insights into riboswitch regulation mechanisms.  Mol Microbiol. 80(5):1148-54.

Lemay JF, Desnoyers G, Blouin S, Heppell B, Bastet L, St-Pierre P, Massé E, Lafontaine DA. (2011). Comparative study between transcriptionally- and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms.  PLoS Genet. 7(1):e1001278.

Blouin S, Chinnappan R, Lafontaine DA. (2011). Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation.Nucleic Acids Res. 39(8):3373-87.

2010

Mulhbacher J, St-Pierre P, Lafontaine DA. (2010). Therapeutic applications of ribozymes and riboswitches.  Curr Opin Pharmacol. 10(5):551-6.

Mulhbacher J, Brouillette E, Allard M, Fortier LC, Malouin F, Lafontaine DA. (2010). Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways.  PLoS Pathog. 6(4):e1000865.

Caron MP, Lafontaine DA, Massé E. (2010). Small RNA-mediated regulation at the level of transcript stability.  RNA Biol. 7(2):140-4. 

2009

Lemay JF, Penedo JC, Mulhbacher J, Lafontaine DA. (2009). Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches.  Methods Mol Biol. 540:65-76.

Heppell B, Mulhbacher J, Penedo JC, Lafontaine DA. (2009). Application of fluorescent measurements for characterization of riboswitch-ligand interactions.  Methods Mol Biol. 540:25-37.

 Blouin S, Craggs TD, Lafontaine DA, Penedo JC. (2009). Functional studies of DNA-protein interactions using FRET techniques.  Methods Mol Biol. 543:475-502.
Blouin S, Mulhbacher J, Penedo JC, Lafontaine DA. (2009). Riboswitches: ancient and promising genetic regulators.  Chembiochem. 10(3):400-16.

2008

Heppell B, Lafontaine DA. (2008). Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot.  Biochemistry. 47(6):1490-9.

2007

Mulhbacher J, Lafontaine DA. (2007). Ligand recognition determinants of guanine riboswitches.  Nucleic Acids Res. 35(16):5568-80.

Blouin S, Lafontaine DA. (2007). A loop-loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.  RNA. 13(8):1256-67.

Lemay JF, Lafontaine DA. (2007). Core requirements of the adenine riboswitch aptamer for ligand binding.  RNA. 13(3):339-50.

2006

Lemay JF, Lafontaine DA. (2006). The adenine riboswitch: a new gene regulation mechanism.  Med Sci (Paris). 22(12):1053-9.

Lemay JF, Penedo JC, Tremblay R, Lilley DM, Lafontaine DA. (2006). Folding of the adenine riboswitch.  Chem Biol. 13(8):857-68.