Fabien Darfeuille

Fabien Darfeuille
French Institute of Health and Medical Research | Inserm · INSERM U1212

PhD

About

73
Publications
12,070
Reads
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3,518
Citations
Citations since 2016
24 Research Items
1705 Citations
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
2016201720182019202020212022050100150200250
Additional affiliations
January 2011 - October 2016
French Institute of Health and Medical Research
Position
  • STRAMES Group leader, CR1 INSERM
November 2005 - December 2010
INSERM U869 - Université de Bordeaux
Position
  • Small RNA in Helicobacter pylori
March 2003 - November 2005
Uppsala University
Position
  • PostDoc Position
Description
  • Small RNA in Escherichia coli
Education
September 1999 - December 2002
Université Bordeaux Segalen - INSERM U386
Field of study
  • HIV-1 transcritpion and Aptamer

Publications

Publications (73)
Article
Full-text available
Type I toxin–antitoxin systems (T1TAs) are extremely potent bacterial killing systems difficult to characterize using classical approaches. To assess the killing capability of type I toxins and to identify mutations suppressing the toxin expression or activity, we previously developed the FASTBAC-Seq (Functional AnalysiS of Toxin–Antitoxin Systems...
Article
Full-text available
Type I toxin-antitoxin (T1TA) systems constitute a large class of genetic modules with antisense RNA (asRNA)-mediated regulation of gene expression. They are widespread in bacteria and consist of an mRNA coding for a toxic protein and a noncoding asRNA that acts as an antitoxin preventing the synthesis of the toxin by directly basepairing to its co...
Preprint
Full-text available
Type I toxin-antitoxin (T1TA) systems constitute a large class of genetic modules with antisense RNA (asRNA)-mediated regulation of gene expression. They are widespread in bacteria and consist of an mRNA coding for a toxic protein and a noncoding asRNA that acts as an antitoxin preventing the synthesis of the toxin by directly basepairing to its co...
Article
RNA molecules adopt defined structural conformations that are essential to exert their function. During the course of evolution, the structure of a given RNA can be maintained via compensatory base-pair changes that occur among covarying nucleotides in paired regions. Therefore, for comparative, structural, and evolutionary studies of RNA molecules...
Article
Full-text available
Post-transcriptional regulation plays important roles to finely tune gene expression in bacteria. In particular, regulation of type I toxin-antitoxin (TA) systems is achieved through sophisticated mechanisms involving toxin mRNA folding. Here, we set up a genetic approach to decipher the molecular underpinnings behind the regulation of a type I TA...
Article
Background: We previously reported the identification of the aapA1/IsoA1 locus as part of a new family of toxin-antitoxin (TA) systems in the human pathogen Helicobacter pylori. AapA1 belongs to type I TA bacterial toxins, and both its mechanism of action towards the membrane and toxicity features are still unclear. Methods: The biochemical char...
Article
Full-text available
In most bacteria, ribosomal RNA is transcribed as a single polycistronic precursor that is first processed by RNase III. This double-stranded specific RNase cleaves two large stems flanking the 23S and 16S rRNA mature sequences, liberating three 16S, 23S and 5S rRNA precursors, which are further processed by other ribonucleases. Here, we investigat...
Preprint
Full-text available
Post-transcriptional regulation plays important roles to finely tune gene expression in bacteria. In particular, regulation of type I toxin-antitoxin (TA) systems is achieved through sophisticated mechanisms involving toxin mRNA folding. Here, we set up a genetic approach to decipher the molecular underpinnings behind the regulation of a type I TA...
Article
Full-text available
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers, thus being oncogenic. The inhibition of oncogenic miRNAs (defined as the blocking of miRNAs’ production or f...
Article
Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays t...
Article
Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding, Page 1 of 2 Abstract Toxin-antitoxin (TA) systems are, by definition, simple genetic loci composed of two genes: a toxin and an antitoxin that counteracts either the toxin’s action or its expression. Usually, toxin synthesi...
Article
Full-text available
MicroRNAs are key factors in the regulation of gene expression and their deregulation has been directly linked to various pathologies such as cancer. The use of small molecules to tackle the overexpression of oncogenic miRNAs has proved its efficacy and holds the promise for therapeutic applications. Here we describe the screening of a 640-compound...
Chapter
As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin–antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations of in vivo results. To fill this gap, we developed a systematic ap...
Book
As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin-antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations of in vivo results. To fill this gap, we developed a systematic ap...
Article
About 150 participants attended the symposium organised at the Palais de la Bourse in Bordeaux, France on September 22-23, 2017. Thirty speakers from all over the world delivered lectures covering selection processes, aptamer chemistry and innovative applications of these powerful tools that display major advantages over antibodies. Beyond the rema...
Article
Full-text available
The symposium covered the many different aspects of the selection and the characterization of aptamers as well as their application in analytical, diagnostic and therapeutic areas. Natural and artificial riboswitches were discussed. Recent advances for the design of mutated polymerases and of chemically modified nucleic acid bases that provide apta...
Article
Full-text available
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces...
Chapter
The intense study of Helicobacter pylori, one of the most prevalent human pathogens, has contributed much to understanding of bacterial virulence mechanisms. While genome sequencing revealed a high genetic diversity among Helicobacter strains, its transcriptional organization has been less understood. The H. pylori genome encodes for only a small n...
Article
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers and that the inhibition of these oncogenic miRNAs could find application in the therapy of different types of...
Article
Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen Helicobacter pylori, an exo- and endoribonuclease RNase...
Article
Full-text available
MicroRNAs regulate eukaryotic gene expression upon pairing onto target mRNAs. This targeting is influenced by the complementarity between the microRNA "seed" sequence at its 5' end and the seed-matching sequences in the mRNA. Here, we assess the efficiency and specificity of 8-mer locked nucleic acid (LNA)-modified oligonucleotides raised against t...
Article
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers and revealed to be oncogenic and to play a pivotal role in initiation and progression of these pathologies. I...
Article
MicroRNAs, small non-coding RNAs expressed by eukaryotic cells, play pivotal roles in shaping cell differentiation and organism development. Deregulated microRNA expression is associated with several types of diseases including cancers, immune disorders and infection. Acting at the post-transcriptional level, miRNAs have expanded our understanding...
Article
Full-text available
Chronic Helicobacter pylori infection provokes an inflammation of the gastric mucosa, at high risk for ulcer and cancer development. The most virulent strains harbor the cag pathogenicity island (cagPAI) encoding a type 4 secretion system, which allows delivery of bacterial effectors into gastric epithelial cells, inducing pro-inflammatory response...
Data
Post-transcriptional regulation of ZEB1 expression by miR-200b&c. (A) Inverse relationship between miR-200b&c and ZEB1 expressions in human cell lines. Upper panel, endogenous expression of mature miR-200b or-200c determined by RT-qPCR; bars indicate mean ± SD of miRNA expression normalized to U6 snRNA (n = 5). Lower panels, ZEB1 and tubulin immuno...
Data
Up-regulation of miR-200b and miR-200c in MKN-74 and NCI-N87 cells 24 h post infection with cagPAI+ H. pylori (Hp WT) at MOI 100 bacteria/cell. Bars represent mean ± SD of RTqPCR data for miR-200b or miR-200b relative to U6 snRNA and compared to non infected cells (NI); n = 4, *: p-value <0.05; **, p<0.01; ***, p<0.001. (DOCX)
Data
MiR-200b-200a-429 promoter activity. (A) MiR-200b-200a-429 promoter activity in HEK293, AGS or MKN-74 cells measured by the promoter luciferase reporter; upper panel, bars represent mean ± SD of the luciferase activity of the miRNA promoter relative to that of SV40 promoter reporter (n = 2); lower panel, ZEB1 and tubulin immunoblots. (B) SV40 promo...
Data
E-cadherin immunolabeling in NCI-N87 cells in basal conditions (left panel) or upon infection with wild type H. pylori at MOI100 (right panel). Cell were fixed and labeled stepwise with a anti-E-cadherin monoclonal antibody (1/1,600 dilution, Sigma, France), and then with a mixture containing a AlexaFluor 488-labeled anti-mouse secondary antibody (...
Data
NF-κB immunofluorescence in AGS cells transfected with pEGFP (left panels) or pEGFP-IκB (right panels) in basal conditions or upon infection. Cells were seeded in 8-well Labteck™ chambers and transfected with the expression vectors at 100 ng/well. Forty eight hrs post-transfection, cells were infected with wild type H. pylori at MOI 100. Six hrs la...
Data
List of oligonucleotide primers. (DOCX)
Data
Expression of the miR-200 family members in gastric epithelial cell lines. (A) Levels of miR-200 in basal conditions: values represent mean ± SD of RT-qPCR data for each miRNA relative to snoR25 (n = 4). (B) Variations of miR-200a, -429 and -141, 24 h post-infection with cagPAI+ H. pylori (Hp WT) or the isogenic CagA-deficient strain, both at MOI 1...
Data
Cell morphology of AGS, MKN74 or NCI-N87 cells, not infected (NI) or upon 24 h infection with either cagPAI+ wild type H. pylori (Hp WT) or its isogenic mutants deleted either for cagA (Hp ΔCagA) or cagE (Hp ΔCagE), each at MOI 100 bacteria/cell. In Hp WT-infected AGS or NCI-N87 cells, cells with typical mesenchymal phenotype are highlighted. Hp WT...
Article
Full-text available
Regardless of their targets and modes of action, subinhibitory concentrations of antibiotics can have an impact on cell physiology and trigger a large variety of cellular responses in different bacterial species. Subinhibitory concentrations of β-lactam antibiotics cause reactive oxygen species production and induce PolIV-dependent mutagenesis in E...
Data
Full-text available
Supplementary Figures S1-S4, Supplementary Tables S1-S5, Supplementary Methods and Supplementary References
Article
Full-text available
Protein complexes directing messenger RNA (mRNA) degradation are present in all kingdoms of life. In Escherichia coli, mRNA degradation is performed by an RNA degradosome organized by the major ribonuclease RNase E. In bacteria lacking RNase E, the existence of a functional RNA degradosome is still an open question. Here, we report that in the bact...
Article
Full-text available
ABSTRACT: MicroRNAs, post-transcriptional regulators of eukaryotic gene expression, are implicated in host defense against pathogens. Viruses and bacteria have evolved strategies that suppress microRNA functions, resulting in a sustainable infection. In this work we report that Helicobacter pylori, a human stomach-colonizing bacterium responsible f...
Data
Full-text available
Tables S1-4. Table S1: 454 results of the micro RNA (miRNA) content in AGS cells in basal conditions and upon Helicobacter pylori infection (MirBase 14.0). miRNAs studied in this paper are represented in bold. P values are calculated using Fisher's exact test. Table S2: miRNAs listed in regards of their known function. miRNAs counting more than 100...
Data
Full-text available
Figure S1. Large tumor suppressor homolog 2 (LATS2) translation efficiency in AGS (high miR-372 and miR-373) and MKN-74 (low miR-372 and miR-373) cells. AGS or MKN-74 cells were plated at 0.7.105 or 105 cells/well, respectively, in a 24-well plate and transfected the following day with 100 ng/well pGL3, pGL3-LATS2 or pGL3-LATS2mut vectors [36], eac...
Data
Full-text available
Figure S2. Effect of antisense oligonucleotides treatment on micro RNA (miRNA) expression (A,B), large tumor suppressor homolog 2 (LATS2) expression (D) and cell growth rate (C,E). (A) Endogenous expression of miR-372, miR-373 and miR-200b was determined 48 h post transfection by quantitative real time PCR (RT-qPCR) in untreated cells (mock) or cel...
Data
Full-text available
Figure S3. Helicobacter pylori-induced morphological changes (A) and proinflammatory responses (B,C) in AGS cells. (A) Morphology of uninfected AGS cells or cells infected for 24 h with H. pylori 26695 wild-type strain or its isogenic mutants H. pylori ΔCagA and ΔCagE at multiplicity of infection (MOI) 100 was visualized by phase contrast microscop...
Data
Full-text available
Figure S5. Helicobacter pylori strain-specific repression of primary (pri-)miR-371-372-373 and upregulation of the enhanced green fluorescent protein (EGFP)-3' untranslated region (UTR) large tumor suppressor homolog 2 (LATS2) reporter gene. AGS cells were infected with H. pylori type I strains (P12) or type II strain (SS1, X47) at a multiplicity o...
Data
Full-text available
Figure S4. Enhanced green fluorescent protein (EGFP) fluorescence of large tumor suppressor homolog 2 (LATS2) reporter-AGS cells transfected with as372-373 or sc372-373. Cells were transfected twice with 100 nM antisense or scramble oligonucleotides and observed 24 h after the last transfection on an inverted microscope (Zeiss) in phase contrast (r...
Data
Full-text available
Figure S6. CagA-dependent accumulation of Helicobacter pylori-infected AGS cells in G0/G1 phase. Cellular DNA contents of uninfected AGS cells or cells infected for 24 h with wild-type, ΔCagA or ΔCagE H. pylori were stained by iodide propidium and analyzed by flow cytometry.
Article
Full-text available
The replication of the genomic RNA of the hepatitis C virus (HCV) of positive polarity involves the synthesis of a replication intermediate of negative polarity by the viral RNA-dependent RNA polymerase (NS5B). In vitro and likely in vivo, the NS5B initiates RNA synthesis without primers. This de novo mechanism needs specific interactions between t...
Article
Full-text available
Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differenti...
Article
Chronic infection by Helicobacter pylori is a major risk factor for gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma. H. pylori possesses a set of virulence factors, including the CagA effector, which interferes with intracellular signalling pathways and mediates phenotypic alterations, strongly evoking neoplasic transformation...
Article
Regulatory ncRNAs (non-coding RNAs) adjust bacterial physiology in response to environmental cues. ncRNAs can base-pair to mRNAs and change their translation efficiency and/or their stability, or they can bind to proteins and modulate their activity. ncRNAs have been discovered in several species throughout the bacterial kingdom. This review illust...
Article
Full-text available
The interactions of numerous regulatory small RNAs (sRNAs) with target mRNAs have been characterized, but how sRNAs can regulate multiple, structurally unrelated mRNAs is less understood. Here we show that Salmonella GcvB sRNA directly acts on seven target mRNAs that commonly encode periplasmic substrate-binding proteins of ABC uptake systems for a...
Chapter
Full-text available
In recent years, small regulatory RNAs have been discovered at a staggering rate both in prokaryotes and eukaryotes. By now it is clear that post-transcriptional regulation of gene expression mediated by such RNAs is the rule rather than—as previously believed—the exception. In this chapter, we focus on small RNAs (sRNAs) encoded by bacterial chrom...
Article
Most antisense RNAs in bacteria inhibit translation by competing with ribosomes for translation initiation regions (TIRs) on nascent mRNA. We propose a mechanism by which an antisense RNA inhibits translation without binding directly to a TIR. The tisAB locus encodes an SOS-induced toxin, and IstR-1 is the antisense RNA that counteracts toxicity. W...
Article
Aptamers interacting with RNA hairpins through loop-loop (so-called kissing) interactions have been described as an alternative to antisense oligomers for the recognition of RNA hairpins. R06, an RNA aptamer, was previously shown to form a kissing complex with the TAR (trans-activating responsive) hairpin of HIV-1 RNA (Ducongé and Toulmé (1999) RNA...
Chapter
IntroductionTargeting Double-stranded Nucleic AcidsLoop-Loop Interactions RNA-RNA Kissing ComplexesDNA-RNA Kissing ComplexesDouble RNA-RNA Kissing LoopsApical Loop-Internal Loop InteractionsChemically Modified Aptamers Recognizing RNA TargetsBiological Properties of Aptamers Targeted to Nucleic AcidsConclusion AcknowledgmentsReferences RNA-RNA Kiss...
Article
Full-text available
This paper shows that the small RNA MicA (previously SraD) is an antisense regulator of ompA in Escherichia coli. MicA accumulates upon entry into stationary phase and down-regulates the level of ompA mRNA. Regulation of ompA (outer membrane protein A), previously attributed to Hfq/mRNA binding, is lost upon deletion of the micA gene, whereas overe...
Article
One of the major limitations of the use of phosphodiester oligonucleotides in cells is their rapid degradation by nucleases. To date, several chemical modifications have been employed to overcome this issue but insufficient efficacy and/or specificity have limited their in vivo usefulness. In this work conformationally restricted nucleotides, locke...
Article
Full-text available
One of the major limitations of the use of phosphodiester oligonucleotides in cells is their rapid degradation by nucleases. To date, several chemical modifications have been employed to overcome this issue but insufficient efficacy and/or specificity have limited their in vivo usefulness. In this work conformationally restricted nucleotides, locke...
Article
Oligonucleotides exhibiting a strong affinity and a high specificity for RNA hairpins were obtained by in vitro selection. Such oligomers give rise to loop-loop complexes with the target hairpins: the trans-activation responsive (TAR) element of the Human Immunodeficiency virus-1 (HIV-1) or subdomains of the Hepatitis C virus (HCV) mRNA. Chemically...
Article
The interaction of the TAR RNA element of human immunodeficiency virus type 1 (HIV-1) with a 2'-O-methyl analogue of an RNA hairpin aptamer previously identified by in vitro selection [Ducongé, F., and Toulmé, J. J. (1999) RNA 5, 1605-1614] was characterized by UV-monitored thermal denaturation and surface plasmon resonance experiments. The complex...