RNA Sequence, Structure & Function

RNA is perhaps the most fascinating of all biological molecules. It is at the same time a reservoir of genetic information, a catalyst of chemical reactions and a genetic regulator. Its study is of major interest in many fields, from the most fundamental (origins of life) to the most applied (molecular diagnosis, drugs, genome engineering).

Our team, composed mainly of bioinformaticians, works to discover and understand the function of RNAs using sequence and structure data.

Our team, composed mainly of bioinformaticians, works to discover and understand the function of RNAs using sequence and structure data.

Discovery of new RNAs

Claire Toffano-Nioche and Daniel Gautheret are developing bioinformatics tools for the discovery of new RNAs in high-throughput sequence data. Millions of “RNA-seq” sequence sets have accumulated in public databases. We are developing tools combining bioinformatics and artificial intelligence to re-interrogate these data and identify new RNAs such as non-coding RNAs and messenger RNA variants, which we associate with phenotypes to identify RNAs of medical interest.

 

In parallel, Maria Costa is developing new sequencing methods to identify modified nucleotides in RNA. Our team is thus part of a new discipline, epitranscriptomics, which aims to elucidate the repertoire of chemical modifications affecting a given transcriptome and to understand the impact of these modifications in the genetic expression program of the organism.

 

Finally, Christine Pourcel and Gilles Vergnaud seek to identify the repeated sequences of CRISPR structures using a machine learning approach, by analyzing the primary structure and folding of the corresponding small RNAs. This work is done in collaboration with Mélina Gallopin.

RNA structures, interactions and functions

Fabrice Leclerc develops bioinformatics tools for the prediction of RNA-protein contacts in three-dimensional space. These programs also predict the RNA sequences that form the best substrates for a given RNA-binding protein. Such tools have potential applications in the design of new drugs.

 

Maria Costa uses different experimental approaches to study the biology of group II introns, introns that are both ribozymes (catalytic RNAs) and highly abundant mobile genetic elements in bacterial genomes. Group II introns are also of great evolutionary interest as ancestors of fundamental systems in eukaryotes such as nuclear introns, the spliceosome, and retrotransposons. Moreover, these introns are the basis for the development of powerful biotechnological tools for bacterial genome engineering, non-coding RNA mapping or high throughput sequencing. 

Artistic view of a possible RNA world, with the first proto-cells containing RNA carrying genetic information, ribozymes, and proteins and metabolites (Credit: Fabrice Leclerc).

team

Daniel GAUTHERET

Group Leader

Professor

Maria COSTA

Researcher

Claire TOFFANO-NIOCHE

Researcher

Gilles VERGNAUD

Volunteer Researcher

Fabrice LECLERC

Researcher

Christine POURCEL

Volunteer Researcher

Antoine LAINE

Assistant Engineer

Lucie GOMES

Master Intern

Hugues HERRMANN

Master Intern

Haoliang XUE

PhD student

Yunfeng WANG

PhD student

Roy GONZALEZ-ALEMAN

PhD student

Taher YACOUB

PhD student

Coline GARDOU

Intern student

Mehdi ABDELLI

PhD student

Latest publications

González-Alemán,R., Chevrollier,N., Simoes,M., Montero-Cabrera,L. and Leclerc,F. (2021) MCSS-Based Predictions of Binding Mode and Selectivity of Nucleotide Ligands. J Chem Theory Comput, 10.1021/acs.jctc.0c01339.

 

Zygmunt, Michel S, Gilles Vergnaud, Axel Cloeckaert. Whole-Genome Sequence of a Brucella pinnipedialis Sequence Type 54 Strain Isolated from a Hooded Seal (Cystophora cristata) from the North Atlantic Ocean, Norway. Microbiol Resour Announc. 2021;10(18). https://doi.org/10.1128/MRA.00271-21.

 

Wang, Yunfeng, Haoliang Xue, Christine Pourcel, Yang Du, Daniel Gautheret. 2-kupl: mapping-free variant detection from DNA-seq data of matched samples. BMC Bioinformatics. 2021;22(1):304. https://doi.org/10.1186/s12859-021-04185-6.

 

Shevtsov, Vladislav, Alma Kairzhanova, Alexandr Shevtsov, Alexandr Shustov, Ruslan Kalendar, Sarsenbay Abdrakhmanov, Larissa Lukhnova, Uinkul Izbanova, Yerlan Ramankulov, Gilles Vergnaud. Genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan. PLoS Negl Trop Dis. 2021;15(5):e0009419. https://doi.org/10.1371/journal.pntd.0009419.

 

Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, Commes T.  Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets. NAR Genom Bioinform. 2021 Jun 23;3(3):lqab058.  https://10.1093/nargab/lqab058

 

Kuksin M, Morel D, Aglave M, Danlos FX, Marabelle A, Zinovyev A, Gautheret D, Verlingue L. Applications of single-cell and bulk RNA sequencing in onco-immunology. Eur J Cancer. 2021 May;149:193-210. https://doi.org/10.1016/j.ejca.2021.03.005

 

Nguyen HTN, Xue H, Firlej V, Ponty Y, Gallopin M, Gautheret D. Reference-free transcriptome signatures for prostate cancer prognosis. 
BMC Cancer. 2021 Apr 12;21(1):394. https://doi.org/10.1186/s12885-021-08021-1

For all the publications of the Team click on the button below.

External funding

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