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Lafontaine lab :: Publications


Direct and Indirect Control of Rho-Dependent Transcription Termination by the Escherichia coli lysC Riboswitch.
Ghosh T, Jahangirnejad S, Chauvier A, Stringer AM, Korepanov AP, Cote JP, Wade JT, Lafontaine DA.
RNA, 119(20), In press.


SHAPE-enabled fragment-based ligand discovery for RNA.
Zeller MJ, Favorov O, Li K, Nuthanakanti A, Hussein D, Michaud A, Lafontaine DA, Busan S, Serganov A, Aube J, Weeks KM.
Proc Natl Acad Sci U S A., 119(20), 2022.

Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems.
Nadon JF, Epshtein V, Cameron E, Samatov MR, Vasenko AS, Nudler E, Lafontaine DA.
Commun. Biol., 5(1), 2022.


Monitoring RNA dynamics in native transcriptional complexes.
Chauvier A, St-Pierre P, Nadon JF, Hien E, Perez-Gonzalez C, Eschbach SH, Lamontagne AM, Penedo JC, Lafontaine DA.
Proc Natl Acad Sci U S A., 118(45), 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.
Smith-Peter E, Lalonde Seguin D, St-Pierre E, Sekulovic O, Jeanneau S, Tremblay-Tetreault C, Lamontagne AM, Lafontaine DA, Fortier LC.
RNA Biol, 18, 2021.

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


Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins.
Bedard AV, Hien EDM, Lafontaine DA.
Biochim Biophys Acta Gene Regul Mech., 1863(63), 2020.


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

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


The yeast telomerase recruitment module requires a specific RNA architecture.
Laterreur N, Lemieux B, Neumann H, Berger-Dancause JC, Lafontaine DA, Wellinger RJ.
RNA, May 18, 2018.

Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay.
Bastet L, Turcotte P, Wade JT, Lafontaine DA.
RNA Biol, Apr 3:1-4, 2018.


Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.
Dussault AM, Dube A, Jacques F, Grondin JP, Lafontaine DA.
RNA, 23(10):1539-51, 2017.

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

Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation.
Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne AM, Prevost K, Masse E, Wade JT, Lafontaine DA.
Nucleic Acids Res, 45(12):7474-86, 2017.


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

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

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


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

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

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

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

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

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


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

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

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


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

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

Regulatory RNAs and target mRNA decay in prokaryotes.
Lalaouna D, Simoneau-Roy M, Lafontaine DA, Masse E.
BBA - Gene Regulatory Mechanisms, 1829:742-7, 2013.

Single-molecule denaturation of riboswitches.
Dalgarno P, Bordello J, Morris R, St-Pierre P, Dube A, Samuel I, Lafontaine DA, Penedo JC.
Nucleic Acids Res, 41:4253-65, 2013.

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


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

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


Constitutive regulatory activity of an evolutionary-excluded riboswitch variant.
Tremblay R, Lemay JF, Blouin S, Mulhbacher J, Bonneau E, Legault P, Dupont P, Penedo JC, Lafontaine DA.
The Journal of Biological Chemistry, 286:27406-15, 2011.

New insights into riboswitch regulation mechanisms.
Bastet L, Dub� A, Masse E, Lafontaine DA.
Molecular Microbiology, 80:1148-54, 2011.

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

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

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


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

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

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

Riboswitch structure: an internal residue mimicking the purine ligand.
Delfosse V, Bouchard P, Bonneau E, Dagenais P, Lemay JF, Lafontaine DA, Legault P.
Nucleic Acids Res, 38:32057-68, 2010.


Functional studies of DNA-protein interactions using FRET techniques.
Blouin S, Craggs T, Lafontaine DA, Penedo JC.
Methods Mol Biol, 543:475-502, 2009.

Molecular Basis of RNA-Mediated Gene Regulation on the Adenine Riboswitch by Single-Molecule Approaches.
Lemay JF, Mulhbacher J, Penedo JC, Lafontaine DA.
Methods Mol Biol, 540:65-76, 2009.

Application of Fluorescence Measurements for Characterization of Riboswitch-Ligand Interactions.
Heppell B, Mulhbacher J, Penedo JC, Lafontaine DA.
Methods Mol Biol, 540:25-37, 2009.

Riboswitches: Ancient and Promising Genetic Regulators.
Blouin S, Mulhbacher J, Penedo JC, Lafontaine DA.
ChemBioChem, 10:400-16, 2009.


Natural Functional Nucleic Acids: Ribozymes and Riboswitches.
Tremblay R, Mulhbacher J, Blouin S, Penedo JC, Lafontaine DA.
(2008). Functional Nucleic Acids for Analytical Applications (Li Y. and Yi L., Eds.), Springer, New-York, NY.

Folding of the SAM Aptamer is Determined by the Formation of a K-turn-dependent Pseudoknot.
Heppell B, Lafontaine DA.
Biochemistry, 47:1490-9, 2008.


Ligand recognition determinants of guanine riboswitches.
Mulhbacher J, Lafontaine DA.
Nucleic Acids Research, 35:5568-5580, 2007.

A loop-loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.
Blouin S, Lafontaine DA.
RNA, 13:1256-1267, 2007.

Core requirements of the adenine riboswitch aptamer for ligand binding.
Lemay JF, Lafontaine DA.
RNA, 13:339-350, 2007.


Folding of the adenine riboswitch.
Lemay JF, Penedo C, Tremblay R, Lilley DMJ, Lafontaine DA.
Chemistry & Biology, 13:857-68, 2006.

Le ribor�gulateur ad�nine: Un nouveau mode de r�gulation g�n�tique.
Lemay JF, Lafontaine DA.
M�decine/Sciences, 22:1053-60, 2006.


The global structure of the VS ribozyme.
Lafontaine DA, Norman DG, Lilley DM.
EMBO J., 21:2461-71, 2002.

Functional group requirements in the probable active site of the VS ribozyme
Lafontaine DA, Wilson TJ, Zhao ZY, Lilley DM
J Mol Biol., 323:23-34, 2002.

Folding and catalysis by the VS ribozyme.
Lafontaine DA, Norman DG, Lilley DM.
Biochimie, 84:889-96, 2002.

The structure and active site of the Varkud satellite ribozyme.
Lafontaine DA, Norman DG, Lilley DM.
Biochem Soc Trans., Nov;30(Pt 6):1170-5, 2002.


Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction.
Lafontaine DA, Norman DG, Lilley DM.
EMBO J., 20:1415-24, 2001.

The A730 loop is an important component of the active site of the VS ribozyme.
Lafontaine DA, Wilson TJ, Norman DG, Lilley DM.
J Mol Biol., 312:663-74, 2001.


Nucleotides -1 to -4 of hepatitis delta ribozyme substrate increase the specificity of ribozyme cleavage.
Deschenes P, Lafontaine DA, Charland S, Perreault JP.
Antisense Nucleic Acid Drug Dev., 10:53-61, 2000.


Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme.
Lafontaine DA, Ananvoranich S, Perreault JP.
Nucleic Acids Res., 27:3236-43, 1999.

Mutational analysis of the antigenomic trans-acting delta ribozyme: the alterations of the middle nucleotides located on the P1 stem.
Ananvoranich S, Lafontaine DA, Perreault JP.
Nucleic Acids Res., 27:1473-9, 1999.

The viroid and viroid-like RNA database.
Lafontaine DA, Deschenes P, Bussiere F, Poisson V, Perreault JP.
Nucleic Acids Res., 27(1):186-7, 1999.


Kinetic analysis of delta ribozyme cleavage.
Mercure S, Lafontaine D, Ananvoranich S, Perreault JP.
Biochemistry, 37:16975-82, 1998.

Identification of a Crohn's disease specific transcript with potential as a diagnostic marker.
Lafontaine DA, Mercure S, Perreault JP.
Gut, 42:878-82, 1998.

The viroid and viroid-like RNA database.
Lafontaine DA, Mercure S, Poisson V, Perreault JP.
Nucleic Acids Res., 26(1):190-1, 1998.


Update of the viroid and viroid-like sequence database: addition of a hepatitis delta virus RNA section.
Lafontaine D, Mercure S, Perreault JP.
Nucleic Acids Res., 25(1):123-5, 1997.


Compilation and analysis of viroid and viroid-like RNA sequences.
Mercure S, Lafontaine D, Ananvoranich S, Perreault JP.
Nucleic Acids Res., 24:1793-8, 1996.


Intra- and intermolecular nonenzymatic ligations occur within transcripts derived from the peach latent mosaic viroid.
Lafontaine D, Beaudry D, Marquis P, Perreault JP.
Virology, 212:705-9, 1995.