Useful Links

NCBI - Litterature

EcoCyc- Genomes and genes

Galaxy - RNAseq data analysis

Target RNA - RNA-RNA interaction preductions

IDT - Oligonucleotides analysis

RNAfold - RNA secondary structure predictions

UCSC - RNAseq data visualisation

sRNATarBase - sRNA database

mFOLD - RNA secondary structure predictions

ExPaSy- Protein prediction and analysis tools

Bacterial functional non-coding RNAs

Bacterial cells have evolved in a way that allows them to adapt to different environmental stresses (e.g. temperature, nutrient starvation, oxidative stress). Underlying this capability is the tight genetic regulation bacteria can demonstrate in stressful conditions. A number of mechanisms can be exploited by the cells to achieve genetic regulation. Our research team mainly focuses on elucidating molecular mechanisms of riboswitches and small regulatory RNA in bacteria cells.

Riboswitches are RNA structures found in the 5’non-coding extremities of different genes. Their response to the presence or absence of a specific metabolite (the ligand) is characterized by major structural modifications. These specific changes result in the regulation of the downstream gene.

Small regulatory RNAs (sRNAs) are generally non-coding RNAs that interact with an mRNA target by imperfectly base-pairing with it. This imperfect interaction allows repression or activation of a pool of mRNA targets using various mechanisms. Even though sRNAs have been discovered over a decade ago, we are only beginning to appreciate the extent of their targetomes. In the aim to elucidate sRNA targetomes, we developed an in vivo capture technology combining MS2 affinity purification and high-throughput RNA sequencing (MAPS). MAPS helped us identify new targets of sRNAs found in Escherichia coli. These new targets were never identified as such by classical analytic methods such as Northern blots or microarrays. MAPS also allowed our group to identify a new type of functional non-coding RNA in bacteria: functional tRNA-derived fragments.

MAPS opens a door to the global study of RNA-RNA interactions. This technic can be applied to E. coli but also to other pathogen agents. This new experimental approach, we aim to identify new targets of sRNA implicated in various metabolisms and in virulence.

 

Research themes

 

MAPS: an overview