References of "Repoila, Francis"
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See detailDynamic insights on transcription initiation and RNA processing during bacterial adaptation
Lacoux, Caroline; Fouquier d'Hérouël, Aymeric UL; Wessner- Le Bohec, Françoise et al

in RNA (2020)

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental ... [more ▼]

Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σE system in E. coli was coupled to our previously-described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5’ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity; i) constant and independent of RNA levels, ii) increased once RNA has accumulated, and iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes, and can serve as blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control. [less ▲]

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See detailWhole genome mapping of 5' ends in bacteria by tagged sequencing: A comprehensive view in Enterococcus faecalis
Innocenti, Nicolas; Golumbeanu, Monica; Fouquier d'Hérouël, Aymeric UL et al

in RNA (2015), 21(5), 1018-1030

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See detailRegulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen Enterococcus faecalis.
Wessner, Francoise; Lacoux, Caroline; Goeders, Nathalie et al

in RNA biology (2015), 12(10), 1099-1108

We discovered a chromosomal locus containing two toxin-antitoxin modules (TAs) with an antisense transcriptional organization in the E. faecalis clinical isolate V583. These TAs are homologous to the type ... [more ▼]

We discovered a chromosomal locus containing two toxin-antitoxin modules (TAs) with an antisense transcriptional organization in the E. faecalis clinical isolate V583. These TAs are homologous to the type I txpA-ratA system and the type II mazEF, respectively. We have shown that the putative MazF is toxic for E. coli and triggers RNA degradation, and its cognate antitoxin MazE counteracts toxicity. The second module, adjacent to mazEF, expresses a toxin predicted to belong to the TxpA type I family found in Firmicutes, and the antisense RNA antidote, RatA. Genomic analysis indicates that the cis-association of mazEF and txpA-ratA modules has been favored during evolution, suggesting a selective advantage for this TA organization in the E. faecalis species. We showed regulatory interplays between the two modules, involving transcription control and RNA stability. Remarkably, our data reveal that MazE and MazEF have a dual transcriptional activity: they act as autorepressors and activate ratA transcription, most likely in a direct manner. RatA controls txpA RNA levels through stability. Our data suggest a pivotal role of MazEF in the coordinated expression of mazEF and txpA-ratA modules in V583. To our knowledge, this is the first report describing a crosstalk between type I and II TAs. [less ▲]

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See detailRNA-mediated Control of Bacterial Gene Expression: Role of Regulatory non-Coding RNAs
Mandin, Pierre; Toledo-Arana, Alejandro; Fouquier d'Hérouël, Aymeric UL et al

in Meyers, Robert (Ed.) Encyclopedia of Cell and Molecular Biology and Molecular Medicine. RNA Regulation (2013)

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See detailA simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis.
Fouquier d'herouël, Aymeric UL; Wessner, Françoise; Halpern, David et al

in Nucleic acids research (2011), 39(7), 46

Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5'RACE-derivative method coined '5'tagRACE', to ... [more ▼]

Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5'RACE-derivative method coined '5'tagRACE', to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5'tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5'tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin-antitoxin modules. [less ▲]

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