Michael Ryckelynck, PhD. Group leader at UPR 9002 – ARN CNRS
Contact
Michaël Ryckelynck
Phone
E-Mail
Website
UPR 9002 – ARN CNRS
Institut de Biologie Moléculaire et Cellulaire du CNRS
2 allée Konrad Roentgen
67084 Strasbourg Cedex
France
Research topics
- Non-covalent molecular interactions of RNA architectural networks
- Modeling of bacterial regulatory networks involving regulatory RNAs
- Microfluidics and single cell studies of non-coding RNA network dynamics
- Transcriptional and post-transcriptional regulation networks involving Staf
Role in NetRNA
As the coordinator, Eric Westhof is in charge of the overall organization of the network, the follow-up of the finances and the installation of the microfluidic platform so that each of the teams can function efficiently towards our main goals. The team will also assure bioinformatic help, set-up a bioinformatic platform and promote the systems biology analysis of the data gathered in order to quantitate the netwokrs of interactions between non-coding RNAs.
Working Group
Publications
2023
Husser, C.; Vuilleumier, S.; Ryckelynck, M.
FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride Article de journal
Dans: Small, vol. 19, iss. 13, p. e2205232, 2023, ISSN: 1613-6829.
@article{pmid36436882,
title = {FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride},
author = {C. Husser and S. Vuilleumier and M. Ryckelynck},
doi = {10.1002/smll.202205232},
issn = {1613-6829},
year = {2023},
date = {2023-03-29},
urldate = {2023-03-01},
journal = {Small},
volume = {19},
issue = {13},
pages = {e2205232},
abstract = {Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.},
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Husser, C.; Baudrey, S.; Ryckelynck, M.
High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics Article de journal
Dans: Methods Mol Biol, vol. 2570, p. 243–269, 2023, ISSN: 1940-6029.
@article{pmid36156788,
title = {High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics},
author = {C. Husser and S. Baudrey and M. Ryckelynck},
doi = {10.1007/978-1-0716-2695-5_19},
issn = {1940-6029},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Methods Mol Biol},
volume = {2570},
pages = {243--269},
abstract = {Small-molecule sensing is a major issue as they can serve both in fundamental science and as makers of various diseases, contaminations, or even environment pollution. RNA aptamers are single-stranded nucleic acids that can adopt different conformations and specifically recognize a wide range of ligands, making them good candidates to develop biosensors of small molecules. Recently, light-up RNA aptamers have been introduced and used as starting building blocks of RNA-based fluorogenic biosensors. They are typically made of three domains: a reporter domain (a light-up aptamer), connected to a sensor domain (another aptamer) via a communication module. The latter is instrumental as being in charge of information transmission between the sensor and the reporting domains. Here we present an ultrahigh-throughput screening procedure to develop RNA-based fluorogenic biosensors by selecting optimized communication modules through an exhaustive functional exploration of every possible sequence permutation using droplet-based microfluidics and next-generation sequencing.},
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2022
Baudrey, S.; Cubi, R.; Ryckelynck, M.
Droplet-Based Microfluidic Chip Design, Fabrication, and Use for Ultrahigh-Throughput DNA Analysis and Quantification Article de journal
Dans: Adv Exp Med Biol, vol. 1379, p. 445–460, 2022, ISSN: 0065-2598.
@article{pmid35761003,
title = {Droplet-Based Microfluidic Chip Design, Fabrication, and Use for Ultrahigh-Throughput DNA Analysis and Quantification},
author = {S. Baudrey and R. Cubi and M. Ryckelynck},
doi = {10.1007/978-3-031-04039-9_18},
issn = {0065-2598},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Adv Exp Med Biol},
volume = {1379},
pages = {445--460},
abstract = {DNA is widely used as a biomarker of contamination, infection, or disease, which has stimulated the development of a wide palette of detection and quantification methods. Even though several analytical approaches based on isothermal amplification have been proposed, DNA is still mainly detected and quantified by quantitative PCR (qPCR). However, for some analyses (e.g., in cancer research) qPCR may suffer from limitations arising from competitions between highly similar template DNAs, the presence of inhibitors, or suboptimal primer design. Nevertheless, digitalizing the analysis (i.e., individualizing DNA molecules into compartments prior to amplifying them in situ) allows to address most of these issues. By its capacity to generate and manipulate millions of highly similar picoliter volume water-in-oil droplets, microfluidics offers both the required miniaturization and parallelization capacity, and led to the introduction of digital droplet PCR (ddPCR). This chapter aims at introducing the reader to the basic principles behind ddPCR while also providing the key guidelines to fabricate, set up, and use his/her own ddPCR platform. We further provide procedures to detect and quantify DNA either purified in solution or directly from individualized cells. This approach not only gives access to DNA absolute concentration with unrivaled sensitivity, but it may also be the starting point of more complex in vitro analytical pipelines discussed at the end of the chapter.},
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2021
Bouhedda, F.; Ryckelynck, M.
Compartmentalization-based technologies for in vitro selection and evolution of ribozymes and light-up RNA aptamers Chapitre d'ouvrage
Dans: Müller, W. Winkler B. Masquida S. (Ed.): Ribozymes, vol. 28, no. 6, p. 721-738, John Wiley & Sons, Ltd, 2021, (2296-889X (Print) 2296-889X (Linking) Journal Article).
@inbook{nokey,
title = {Compartmentalization-based technologies for in vitro selection and evolution of ribozymes and light-up RNA aptamers},
author = {F. Bouhedda and M. Ryckelynck},
editor = {W. Winkler B. Masquida S. Müller},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527814527.ch28},
doi = {10.1002/9783527814527.ch28},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
booktitle = {Ribozymes},
volume = {28},
number = {6},
issue = {2},
pages = {721-738},
publisher = {John Wiley & Sons, Ltd},
abstract = {Summary Catalytic RNAs, also known as ribozymes, are naturally found in every living cell where they can occupy functions as important as peptide bond formation catalysis or intron splicing just as two examples. Besides, ribozymes are thought to be very ancient molecules that might have been the key actors of the so-called RNA world, but they also hold great promise for plenty of modern applications. These features have stimulated the development of in vitro evolution methodologies aiming at characterizing existing but also isolate new artificial ribozymes. Whereas bulk approaches in which all the RNA sequences of library are assayed in a single reaction mixture may be efficient to select fast, single-turn-over and/or self-modifying catalysts, this format is less adapted to the isolation of multiple turnover trans-acting molecules. Instead, a compartmentalization approach in which each variant is isolated and assayed into an individual compartment is better suited. In this chapter, we review the different strategies available to perform such compartmentalization and that range from hand-made water-in-oil emulsion to more advanced microfluidic-assisted ultrahigh-throughput screening. We finally extend the applications scope of these technologies to other RNAs (i.e., light-up RNA aptamers) for which a functional screening may also reveal more efficient than more conventional bulk in vitro selections.},
note = {2296-889X (Print)
2296-889X (Linking)
Journal Article},
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Cubi, R; Bouhedda, F; Collot, M; Klymchenko, A S; Ryckelynck, M
microIVC-Useq: a microfluidic-assisted high-throughput functionnal screening in tandem with next generation sequencing and artificial neural network to rapidly characterize RNA molecules Article de journal
Dans: Rna, p. in press, 2021, ISBN: 33952671, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
@article{nokey,
title = {microIVC-Useq: a microfluidic-assisted high-throughput functionnal screening in tandem with next generation sequencing and artificial neural network to rapidly characterize RNA molecules},
author = {R Cubi and F Bouhedda and M Collot and A S Klymchenko and M Ryckelynck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33952671},
doi = {10.1261/rna.077586.120},
isbn = {33952671},
year = {2021},
date = {2021-01-01},
journal = {Rna},
pages = {in press},
abstract = {The function of an RNA is intimately linked to its three-dimensional structure. X-ray crystallography or NMR allow the fine structural characterization of small RNA (e.g., aptamers) with a precision down to atomic resolution. Yet, these technics are time consuming, laborious and do not inform on mutational robustness and the extent to which a sequence can be modified without altering RNA function, an important set of information to assist RNA engineering. On another hand, thought powerful, in silico predictions still lack the required accuracy. These limitations can be overcome by using high-throughput microfluidic-assisted functional screening technologies, as they allow exploring large mutant libraries in a rapid and cost-effective manner. Among them, we recently introduced the microfluidic-assisted In Vitro Compartmentalization (microIVC), an efficient screening strategy in which reactions are performed in picoliter droplets at rates of several thousand per second. We later improved microIVC efficiency by using in tandem with high throughput sequencing, thought a laborious bioinformatic step was still required at the end of the process. In the present work, we strongly increased the automation level of the pipeline by implementing an artificial neural network enabling unsupervised bioinformatic analysis. We demonstrate the efficiency of this "microIVC-Useq" technology by rapidly identifying a set of sequences readily accepted by a key domain of the light-up RNA aptamer SRB-2. This work not only shed some new light on the way this aptamer can be engineered, but it also allowed us to easily identify new variants with an up-to 10-fold improved performance.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
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