Sébastien H. Eschbach

Université de Sherbrooke

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Daniel A. Lafontaine

Université de Sherbrooke

Anne-Marie Lamontagne

Université de Sherbrooke

Elsa D. M. Hien

Université de Sherbrooke

Patrick St-Pierre

Université de Sherbrooke

J. Carlos Penedo

University of St Andrews

Jean‐François Nadon

Université de Sherbrooke

Cibran Pérez‐González

Center for Research in Molecular Medicine and Chronic Diseases

M. Metzler

Karlsruhe Institute of Technology

Raymund J. Wellinger

Université de Sherbrooke

Nancy Laterreur

Université de Sherbrooke

Cooperative Institutions

Université de Sherbrooke

University of St Andrews

Laboratoire de Mathématiques d'Orsay

University of Dundee

Cancer Research UK

Universidade de Santiago de Compostela

Scottish Universities Physics Alliance

Karlsruhe Institute of Technology

Karlsruhe University of Education

University of Kaiserslautern

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RNA Conformational Changes Analyzed by Comparative Gel Electrophoresis

Methods in molecular biology (2013)

Sébastien H. Eschbach Daniel A. Lafontaine

Folding (DSP implementation)

Riboswitch

Dihedral angle

10.1007/978-1-62703-667-2_15

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Citations (6)

Folding of the SAM-I riboswitch

RNA Biology (2012)

Sébastien H. Eschbach Patrick St-Pierre J. Carlos Penedo Daniel A. Lafontaine

Riboswitches are ligand-dependent RNA genetic regulators that control gene expression by altering their structures. The elucidation of riboswitch conformational changes before and after ligand recognition is crucial to understand how riboswitches can achieve high ligand binding affinity and discrimination against cellular analogs. The detailed characterization of riboswitch folding pathways suggest that they may use their intrinsic conformational dynamics to sample a large array of structures, some of which being nearly identical to ligand-bound molecules. Some of these structural conformers can be "captured" upon ligand binding, which is crucial for the outcome of gene regulation. Recent studies about the SAM-I riboswitch have revealed unexpected and previously unknown RNA folding mechanisms. For instance, the observed helical twist of the P1 stem upon ligand binding to the SAM-I aptamer adds a new element in the repertoire of RNA strategies for recognition of small metabolites. From an RNA folding perspective, these findings also strongly indicate that the SAM-I riboswitch could achieve ligand recognition by using an optimized combination of conformational capture and induced-fit approaches, a feature that may be shared by other RNA regulatory sequences.

Riboswitch

Aptamer

Folding (DSP implementation)

Nucleic acid structure

10.4161/rna.19648

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Citations (20)

Alternaria toxins: DNA strand-breaking activity in mammalian cellsin vitro

Mycotoxin Research (2007)

Erika Pfeiffer Sébastien H. Eschbach M. Metzler

Alternariol

Chinese hamster

10.1007/bf02951512

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Citations (109)

A new telomerase RNA element that is critical for telomere elongation

Nucleic Acids Research (2013)

Nancy Laterreur Sébastien H. Eschbach Daniel A. Lafontaine Raymund J. Wellinger

The stability of chromosome ends, the telomeres, is dependent on the ribonucleoprotein telomerase. In vitro , telomerase requires at least one RNA molecule and a reverse transcriptase-like protein. However, for telomere homeostasis in vivo , additional proteins are required. Telomerase RNAs of different species vary in size and sequence and only few features common to all telomerases are known. Here we show that stem-loop IVc of the Saccharomyces cerevisiae telomerase RNA contains a structural element that is required for telomerase function in vivo . Indeed, the distal portion of stem-loop IVc stimulates telomerase activity in vitro in a way that is independent of Est1 binding on more proximal portions of this stem-loop. Functional analyses of the RNA in vivo reveal that this distal element we call telomerase-stimulating structure (TeSS) must contain a bulged area in single stranded form and also show that Est1-dependent functions such as telomerase import or recruitment are not affected by TeSS. This study thus uncovers a new structural telomerase RNA element implicated in catalytic activity. Given previous evidence for TeSS elements in ciliate and mammalian RNAs, we speculate that this substructure is a conserved feature that is required for optimal telomerase holoenzyme function.

Telomerase RNA component

10.1093/nar/gkt514

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Citations (16)

The Escherichia coli ribB riboswitch senses flavin mononucleotide within a defined transcriptional window

RNA (2024)

Sébastien H. Eschbach Elsa D. M. Hien Tithi Ghosh Anne-Marie Lamontagne Daniel A. Lafontaine

Riboswitches are metabolite-binding RNA regulators that modulate gene expression at the levels of transcription and translation. One of the hallmarks of riboswitch regulation is that they undergo structural changes upon metabolite binding. While a lot of effort has been put to characterize how the metabolite is recognized by the riboswitch, there is still relatively little information regarding how ligand sensing is performed within a transcriptional context. Here, we study the ligand-dependent cotranscriptional folding of the FMN-sensing ribB riboswitch of Escherichia coli . Using RNase H assays to study nascent ribB riboswitch transcripts, DNA probes targeting the P1 and sequestering stems indicate that FMN binding leads to the protection of these regions from RNase H cleavage, consistent with the riboswitch inhibiting translation initiation when bound to FMN. Our results show that ligand sensing is strongly affected by the position of elongating RNA polymerase, which is defining an FMN-binding transcriptional window that is bordered in its 3′ extremity by a transcriptional pause site. Also, using successively overlapping DNA probes targeting a subdomain of the riboswitch, our data suggest the presence of a previously unsuspected helical region involving the 3′ strand of the P1 stem. Our results show that this helical region is conserved across bacterial species, thus suggesting that this predicted structure, the anti*-P1 stem, is involved in the FMN-free conformation of the ribB riboswitch. Overall, our study further demonstrates that intricate folding strategies may be used by riboswitches to perform metabolite sensing during the transcriptional process.

Flavin mononucleotide

Riboswitch

10.1261/rna.080074.124

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Citations (1)

Monitoring RNA dynamics in native transcriptional complexes

Proceedings of the National Academy of Sciences (2021)

Adrien Chauvier Patrick St-Pierre Jean‐François Nadon Elsa D. M. Hien Cibran Pérez‐González

Significance Transcription of DNA into RNA is crucial to life, and understanding RNA polymerase (RNAP) function has received considerable attention. In contrast, how the nascent RNA folds into structures that impact transcription itself and regulate gene expression remains poorly understood. Here, we combine single-molecule Förster resonance energy transfer and site-specific fluorescent labelling of transcripts within native complexes to enable real-time cotranscriptional folding studies of a metabolite-sensing riboswitch from Escherichia coli . By monitoring the folding of riboswitches stalled at RNAP pausing sites and during active elongation, we reveal a crucial role for RNAP, which directs RNA folding to allow thiamin pyrophosphate sensing within a precise, transcriptional hotspot. Our approach offers a unique opportunity to unveil cotranscriptional processes in eukaryotic and bacterial systems.

Riboswitch

Transcription

Stringent response

10.1073/pnas.2106564118

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Citations (34)