Publications by authors named "Dilek Imanci"

10 Publications

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ZNRF3 and RNF43 cooperate to safeguard metabolic liver zonation and hepatocyte proliferation.

Cell Stem Cell 2021 Jun 11. Epub 2021 Jun 11.

Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland. Electronic address:

AXIN2 and LGR5 mark intestinal stem cells (ISCs) that require WNT/β-Catenin signaling for constant homeostatic proliferation. In contrast, AXIN2/LGR5+ pericentral hepatocytes show low proliferation rates despite a WNT/β-Catenin activity gradient required for metabolic liver zonation. The mechanisms restricting proliferation in AXIN2+ hepatocytes and metabolic gene expression in AXIN2+ ISCs remained elusive. We now show that restricted chromatin accessibility in ISCs prevents the expression of β-Catenin-regulated metabolic enzymes, whereas fine-tuning of WNT/β-Catenin activity by ZNRF3 and RNF43 restricts proliferation in chromatin-permissive AXIN2+ hepatocytes, while preserving metabolic function. ZNRF3 deletion promotes hepatocyte proliferation, which in turn becomes limited by RNF43 upregulation. Concomitant deletion of RNF43 in ZNRF3 mutant mice results in metabolic reprogramming of periportal hepatocytes and induces clonal expansion in a subset of hepatocytes, ultimately promoting liver tumors. Together, ZNRF3 and RNF43 cooperate to safeguard liver homeostasis by spatially and temporally restricting WNT/β-Catenin activity, balancing metabolic function and hepatocyte proliferation.
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http://dx.doi.org/10.1016/j.stem.2021.05.013DOI Listing
June 2021

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.

Mol Cell 2021 01 7;81(2):255-267.e6. Epub 2020 Dec 7.

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address:

Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements (CREs). Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we present a DNA footprinting method that detects individual molecular interactions of transcription factors and nucleosomes with DNA in vivo. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules at mouse CREs. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that high DNA co-occupancy occurs for most types of transcription factors, in the absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy in binding cooperativity. Our results reveal the interactions regulating CREs at molecular resolution and identify DNA co-occupancy as a widespread cooperativity mechanism used by transcription factors to remodel chromatin.
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http://dx.doi.org/10.1016/j.molcel.2020.11.015DOI Listing
January 2021

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.

Nat Commun 2020 05 29;11(1):2680. Epub 2020 May 29.

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in mouse embryonic stem cells. We find that enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state DNA methylation. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils a genome-scale map of methylation kinetics, revealing highly variable and context-specific activity for the DNA methylation machinery.
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http://dx.doi.org/10.1038/s41467-020-16354-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7260214PMC
May 2020

Long-lasting successful dissemination of resistance to oxazolidinones in MDR Staphylococcus epidermidis clinical isolates in a tertiary care hospital in France.

J Antimicrob Chemother 2018 Jan;73(1):41-51

Department of Bacteriology-Parasitology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France.

Objectives: Patient- and procedure-related changes in modern medicine have turned CoNS into one of the major nosocomial pathogens. Treatments of CoNS infections are challenging owing to the large proportion of MDR strains and oxazolidinones often remain the last active antimicrobial molecules. Here, we have investigated a long-lasting outbreak (2010-13) due to methicillin- and linezolid-resistant (LR) CoNS (n = 168), involving 72 carriers and 49 infected patients.

Methods: Antimicrobial susceptibilities were tested by the disc diffusion method and MICs were determined by broth microdilution or Etest. The clonal relationship of LR Staphylococcus epidermidis (LRSE) was first determined using a semi-automated repetitive element palindromic PCR (rep-PCR) method. Then, WGS was performed on all cfr-positive LRSE (n = 30) and LRSE isolates representative of each rep-PCR-defined clone (n = 17). Self-transferability of cfr-carrying plasmids was analysed by filter-mating experiments.

Results: This outbreak was caused by the dissemination of three clones (ST2, ST5 and ST22) of LRSE. In these clones, linezolid resistance was caused by (i) mutations in the chromosome-located genes encoding the 23S RNA and L3 and L4 ribosomal proteins, but also by (ii) the dissemination of two different self-conjugative plasmids carrying the cfr gene encoding a 23S RNA methylase. By monitoring linezolid prescriptions in two neighbouring hospitals, we highlighted that the spread of LR-CoNS was strongly associated with linezolid use.

Conclusions: Physicians should be aware that plasmid-encoded linezolid resistance has started to disseminate among CoNS and that rational use of oxazolidinones is critical to preserve these molecules as efficient treatment options for MDR Gram-positive pathogens.
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http://dx.doi.org/10.1093/jac/dkx370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890688PMC
January 2018

New MCM8 mutation associated with premature ovarian insufficiency and chromosomal instability in a highly consanguineous Tunisian family.

Fertil Steril 2017 10 30;108(4):694-702. Epub 2017 Aug 30.

Inserm UMRS_1185, Faculté de Médecine Paris Sud, Université Paris-Sud, Université Paris Saclay, Le Kremlin-Bicêtre, France; Service de Génétique Moléculaire, Pharmacogénétique et Hormonologie, Hôpital Bicêtre, Assistance publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.

Objective: To identify the gene(s) involved in the etiology of premature ovarian insufficiency in a highly consanguineous Tunisian family.

Design: Genetic analysis of a large consanguineous family with several affected siblings.

Setting: University hospital-based cytogenetics and molecular genetics laboratories.

Patient(s): A highly consanguineous Tunisian family with several affected siblings born to healthy second-degree cousins.

Intervention(s): None.

Main Outcome Measure(s): Targeted exome sequencing was performed by next-generation sequencing for affected family members. Mutations were validated by Sanger sequencing. Functional experiments were performed to explore the deleterious effects of the identified mutation. DNA damage was induced by increasing mitomycin C (MMC) concentrations on cultured peripheral lymphocytes.

Result(s): Analysis of the next-generation sequencing data revealed a new homozygous missense mutation in the minichromosome maintenance 8 gene (MCM8).This homozygous mutation (c. 482A>C; p.His161Pro) was predicted to be deleterious and segregated with the disease in the family. MCM8 participates in homologous recombination during meiosis and DNA double-stranded break repair by dimerizing with MCM9. Mcm8 knock out results in an early block in follicle development and small gonads. Given this, we tested the chromosomal breakage repair capacity of homozygous and heterozygous MCM8 p.His161Pro mutation on cultured peripheral lymphocytes exposed to increasing MMC concentrations. We found that chromosomal breakage after MMC exposure was significantly higher in cells from homozygously affected individuals than in those from a healthy control.

Conclusion(s): Our findings provide additional support to the view that MCM8 mutations are involved in the primary ovarian insufficiency phenotype.
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http://dx.doi.org/10.1016/j.fertnstert.2017.07.015DOI Listing
October 2017

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters.

Mol Cell 2017 Aug 20;67(3):411-422.e4. Epub 2017 Jul 20.

Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Sciences, Petersplatz 1, 4001 Basel, Switzerland. Electronic address:

Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here, we harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy. Additionally, perturbation of transcriptional initiation reveals an unexpectedly high turnover of polymerases at paused promoters-an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than by stable polymerase stalling. In support of this non-processive model, we observe that induction of the paused heat shock promoter depends on continuous initiation. Our study provides a framework to quantify protein binding at single-molecule resolution and refines concepts of transcriptional pausing.
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http://dx.doi.org/10.1016/j.molcel.2017.06.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548954PMC
August 2017

First Occurrence of OXA-72-Producing Acinetobacter baumannii in Serbia.

Antimicrob Agents Chemother 2016 10 23;60(10):5724-30. Epub 2016 Sep 23.

Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France French National Reference Center for Antibiotic Resistance: Carbapenemase Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France EA7391 (Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases), Faculty of Medicine, University Paris-Sud, University Paris-Saclay, Le Kremlin-Bicêtre, France.

Here, we characterized the first OXA-72-producing Acinetobacter baumannii isolate (designated MAL) recovered from a urine sample from a Serbian patient. Antimicrobial susceptibility testing, plasmid analysis, and whole-genome sequencing (WGS) were performed to fully characterize the resistome of the A. baumannii MAL clinical isolate. The isolate was multidrug resistant and remained susceptible only to colistin and tigecycline. PCR analysis revealed the presence of the carbapenemase OXA-72, an OXA-40 variant. Extraction by the Kieser method revealed the presence of two plasmids, and one of these, a ca. 10-kb plasmid, harbored the blaOXA-72 gene. WGS revealed 206 contigs corresponding to a genome of 3.9 Mbp in size with a G+C content of 38.8%. The isolate belonged to sequence type 492 and to worldwide clone II (WWCII). Naturally occurring β-lactamase-encoding genes (blaADC-25 and blaOXA-66) were also identified. Aminoglycoside resistance genes encoding one aminoglycoside adenyltransferase (aadA2), three aminoglycoside phosphatases (strA, strB, aphA6), and one 16S RNA methylase (armA) conferring resistance to all aminoglycosides were identified. Resistance to fluoroquinolones was likely due to mutations in gyrA, parC, and parE Of note, the resistome matched perfectly with the antibiotic susceptibility testing results.
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http://dx.doi.org/10.1128/AAC.01016-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038319PMC
October 2016

Whole-Genome Sequence of a European Clone II and OXA-72-Producing Acinetobacter baumannii Strain from Serbia.

Genome Announc 2015 Dec 10;3(6). Epub 2015 Dec 10.

Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France EA7391 "Structure, dynamic, function and expression of broad spectrum β-lactamases," Université Paris Sud, Université Paris-Saclay, Faculte de Medecine, Le Kremlin-Bicêtre, France

We report here the draft genome sequence of a carbapenem-resistant Acinetobacter baumannii strain isolated from a patient, a strain which previously stayed in Serbia. This isolate possessed the blaOXA-72 carbapenemase gene. The draft genome sequence consists of a total length of 3.91 Mbp, with an average G+C content of 38.8%.
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http://dx.doi.org/10.1128/genomeA.01390-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675936PMC
December 2015

Draft Genome Sequence of the Serratia rubidaea CIP 103234T Reference Strain, a Human-Opportunistic Pathogen.

Genome Announc 2015 Nov 19;3(6). Epub 2015 Nov 19.

APHP, Bicêtre Hospital, Bactériologie-Hygiene Unit, Le-Kremlin Bicêtre, France EA7361 Structure, dynamic, function and expression of broad spectrum β-lactamases, Paris-Sud University, LabEx Lermit, Faculty of Medecine, Orsay, France French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France

We provide here the first genome sequence of a Serratia rubidaea isolate, a human-opportunistic pathogen. This reference sequence will permit a comparison of this species with others of the Serratia genus.
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http://dx.doi.org/10.1128/genomeA.01340-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653788PMC
November 2015

Fructose 1,6-bisphosphatase deficiency: clinical, biochemical and genetic features in French patients.

J Inherit Metab Dis 2015 Sep 20;38(5):881-7. Epub 2015 Jan 20.

Service de Biochimie, CHU Bicêtre, AP-HP, Le Kremlin-Bicêtre, France.

Fructose-1,6-bisphosphatase (FBPase) deficiency is a very rare autosomal recessive disorder caused by a mutation of the fructose-1,6-bisphosphatase gene(FBP1). Disease is mainly revealed by hypoglycemia and lactic acidosis, both symptoms being characteristic for an enzymatic block in the last steps of the gluconeogenesis. Twelve patients with FBPase deficiency were diagnosed in France in the 2001-2013 period, using a diagnostic system based on a single blood sample which allows simultaneous enzyme activity measurement on mononuclear white blood cells and molecular analysis. Sequencing of exons and intron-exon junctions of FBP1 gene was completed in unsolved cases by a gene dosage assay developed for each exon. For most patients, first metabolic decompensation occurred before two years of age with a similar sequence: the triggering factors were fever, fasting, or decrease of food intake. However, diagnosis was made late at a mean age of 3 years, as mitochondrial defects or glycogen storage diseases were firstly suspected. Enzyme activity in leukocytes was dramatically decreased (<10%). Twelve different mutations were identified in 22 alleles among them seven were novels: one missense mutation c.472C > T, one point deletion c.48del, one point duplication c.865dupA, one deletion-insertion, and two splice mutations (c.427-1del and c.825 + 1G > A). We described the first intragenic deletion in FBP1 (g.97,364,754_97,382,011del) in homozygous state. Our report also confirms that this very rare disease is misdiagnosed, as other energetic defects are firstly suspected.
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http://dx.doi.org/10.1007/s10545-014-9804-6DOI Listing
September 2015
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