Publications by authors named "Sophie Lemoine"

34 Publications

The Tumor Microenvironment Impairs Th1 IFNγ Secretion through Alternative Splicing Modifications of Pre-mRNA.

Cancer Immunol Res 2021 Mar 8;9(3):324-336. Epub 2021 Jan 8.

CRI INSERM UMR1231 "Lipids, Nutrition and Cancer," Team "CAdIR," Dijon, Burgundy, France.

It is clearly established that the immune system can affect cancer response to therapy. However, the influence of the tumor microenvironment (TME) on immune cells is not completely understood. In this respect, alternative splicing is increasingly described to affect the immune system. Here, we showed that the TME, via a TGFβ-dependent mechanism, increased alternative splicing events and induced the expression of an alternative isoform of the IRF1 transcription factor (IRF1Δ7) in Th1 cells. We found that the SFPQ splicing factor (splicing factor, proline- and glutamine-rich) was responsible for the IRF1Δ7 production. We also showed, in both mice and humans, that the IRF1 alternative isoform altered the full-length IRF1 transcriptional activity on the promoter, resulting in decreased IFNγ secretion in Th1 cells. Thus, the IRF1Δ7 isoform was increased in the TME, and inhibiting IRF1Δ7 expression could potentiate Th1 antitumor responses.
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http://dx.doi.org/10.1158/2326-6066.CIR-19-0679DOI Listing
March 2021

Adipocyte Reprogramming by the Transcriptional Coregulator GPS2 Impacts Beta Cell Insulin Secretion.

Cell Rep 2020 09;32(11):108141

Cordeliers Research Centre, INSERM, Immunity and Metabolism in Diabetes Laboratory, Sorbonne Université, Université de Paris, 75006 Paris, France. Electronic address:

Glucose homeostasis is maintained through organ crosstalk that regulates secretion of insulin to keep blood glucose levels within a physiological range. In type 2 diabetes, this coordinated response is altered, leading to a deregulation of beta cell function and inadequate insulin secretion. Reprogramming of white adipose tissue has a central role in this deregulation, but the critical regulatory components remain unclear. Here, we demonstrate that expression of the transcriptional coregulator GPS2 in white adipose tissue is correlated with insulin secretion rate in humans. The causality of this relationship is confirmed using adipocyte-specific GPS2 knockout mice, in which inappropriate secretion of insulin promotes glucose intolerance. This phenotype is driven by adipose-tissue-secreted factors, which cause increased pancreatic islet inflammation and impaired beta cell function. Thus, our study suggests that, in mice and in humans, GPS2 controls the reprogramming of white adipocytes to influence pancreatic islet function and insulin secretion.
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http://dx.doi.org/10.1016/j.celrep.2020.108141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7495095PMC
September 2020

Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection.

Retrovirology 2020 08 17;17(1):25. Epub 2020 Aug 17.

Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France.

Background: Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced pre-messenger RNA (pre-mRNA) and a balanced proportion of unspliced and spliced transcripts is critical for the production of infectious virions. Understanding the mechanisms involved in the regulation of viral RNA is therefore of potential therapeutic interest. However, monitoring the regulation of alternative splicing events at a transcriptome-wide level during cell infection is challenging. Here we used the long-read cDNA sequencing developed by Oxford Nanopore Technologies (ONT) to explore in a quantitative manner the complexity of the HIV-1 transcriptome regulation in infected primary CD4+ T cells.

Results: ONT reads mapping to the viral genome proved sufficiently long to span all possible splice junctions, even distant ones, and to be assigned to a total of 150 exon combinations. Fifty-three viral RNA isoforms, including 14 new ones were further considered for quantification. Relative levels of viral RNAs determined by ONT sequencing showed a high degree of reproducibility, compared favourably to those produced in previous reports and highly correlated with quantitative PCR (qPCR) data. To get further insights into alternative splicing regulation, we then compiled quantifications of splice site (SS) usage and transcript levels to build "splice trees", a quantitative representation of the cascade of events leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2 and its impact on viral isoform levels. Furthermore, we produced the first dynamic picture of the cascade of events occurring between 12 and 24 h of viral infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation.

Conclusion: ONT sequencing is a convenient and reliable strategy that enabled us to grasp the dynamic of the early splicing events modulating the viral RNA landscape in HIV-1 infected cells.
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http://dx.doi.org/10.1186/s12977-020-00533-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7433067PMC
August 2020

Loss of G protein pathway suppressor 2 in human adipocytes triggers lipid remodeling by upregulating ATP binding cassette subfamily G member 1.

Mol Metab 2020 12 13;42:101066. Epub 2020 Aug 13.

Department of Biosciences and Nutrition, Karolinska Institute, 14183 Huddinge, Sweden. Electronic address:

Objective: Adipogenesis is critical for adipose tissue remodeling during the development of obesity. While the role of transcription factors in the orchestration of adipogenic pathways is already established, the involvement of coregulators that transduce regulatory signals into epigenome alterations and transcriptional responses remains poorly understood. The aim of our study was to investigate which pathways are controlled by G protein pathway suppressor 2 (GPS2) during the differentiation of human adipocytes.

Methods: We generated a unique loss-of-function model by RNAi depletion of GPS2 in human multipotent adipose-derived stem (hMADS) cells. We thoroughly characterized the coregulator depletion-dependent pathway alterations during adipocyte differentiation at the level of transcriptome (RNA-seq), epigenome (ChIP-seq H3K27ac), cistrome (ChIP-seq GPS2), and lipidome. We validated the in vivo relevance of the identified pathways in non-diabetic and diabetic obese patients.

Results: The loss of GPS2 triggers the reprogramming of cellular processes related to adipocyte differentiation by increasing the responses to the adipogenic cocktail. In particular, GPS2 depletion increases the expression of BMP4, an important trigger for the commitment of fibroblast-like progenitors toward the adipogenic lineage and increases the expression of inflammatory and metabolic genes. GPS2-depleted human adipocytes are characterized by hypertrophy, triglyceride and phospholipid accumulation, and sphingomyelin depletion. These changes are likely a consequence of the increased expression of ATP-binding cassette subfamily G member 1 (ABCG1) that mediates sphingomyelin efflux from adipocytes and modulates lipoprotein lipase (LPL) activity. We identify ABCG1 as a direct transcriptional target, as GPS2 depletion leads to coordinated changes of transcription and H3K27 acetylation at promoters and enhancers that are occupied by GPS2 in wild-type adipocytes. We find that in omental adipose tissue of obese humans, GPS2 levels correlate with ABCG1 levels, type 2 diabetic status, and lipid metabolic status, supporting the in vivo relevance of the hMADS cell-derived in vitro data.

Conclusion: Our study reveals a dual regulatory role of GPS2 in epigenetically modulating the chromatin landscape and gene expression during human adipocyte differentiation and identifies a hitherto unknown GPS2-ABCG1 pathway potentially linked to adipocyte hypertrophy in humans.
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http://dx.doi.org/10.1016/j.molmet.2020.101066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509237PMC
December 2020

Regulatory T Cells Expressing Tumor Necrosis Factor Receptor Type 2 Play a Major Role in CD4+ T-Cell Impairment During Sepsis.

J Infect Dis 2020 09;222(7):1222-1234

EA3826 Thérapeutiques Anti-Infectieuses, Institut de Recherche en Santé 2 Nantes Biotech, Université de Nantes, Nantes, France.

Sepsis causes inflammation-induced immunosuppression with lymphopenia and alterations of CD4+ T-cell functions that renders the host prone to secondary infections. Whether and how regulatory T cells (Treg) are involved in this postseptic immunosuppression is unknown. We observed in vivo that early activation of Treg during Staphylococcus aureus sepsis induces CD4+ T-cell impairment and increases susceptibility to secondary pneumonia. The tumor necrosis factor receptor 2 positive (TNFR2pos) Treg subset endorsed the majority of effector immunosuppressive functions, and TNRF2 was particularly associated with activation of genes involved in cell cycle and replication in Treg, probably explaining their maintenance. Blocking or deleting TNFR2 during sepsis decreased the susceptibility to secondary infection. In humans, our data paralleled those in mice; the expression of CTLA-4 was dramatically increased in TNFR2pos Treg after culture in vitro with S. aureus. Our findings describe in vivo mechanisms underlying sepsis-induced immunosuppression and identify TNFR2pos Treg as targets for therapeutic intervention.
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http://dx.doi.org/10.1093/infdis/jiaa225DOI Listing
September 2020

Active Fluctuations of the Nuclear Envelope Shape the Transcriptional Dynamics in Oocytes.

Dev Cell 2019 10 10;51(2):145-157.e10. Epub 2019 Oct 10.

CIRB, Collège de France/CNRS-UMR7241/INSERM-U1050, PSL Research University, Equipe Labellisée FRM, Paris 75005, France. Electronic address:

Nucleus position in cells can act as a developmental cue. Mammalian oocytes position their nucleus centrally using an F-actin-mediated pressure gradient. The biological significance of nucleus centering in mammalian oocytes being unknown, we sought to assess the F-actin pressure gradient effect on the nucleus. We addressed this using a dedicated computational 3D imaging approach, biophysical analyses, and a nucleus repositioning assay in mouse oocytes mutant for cytoplasmic F-actin. We found that the cytoplasmic activity, in charge of nucleus centering, shaped the nucleus while promoting nuclear envelope fluctuations and chromatin motion. Off-centered nuclei in F-actin mutant oocytes were misshaped with immobile chromatin and modulated gene expression. Restoration of F-actin in mutant oocytes rescued nucleus architecture fully and gene expression partially. Thus, the F-actin-mediated pressure gradient also modulates nucleus dynamics in oocytes. Moreover, this study supports a mechano-transduction model whereby cytoplasmic microfilaments could modulate oocyte transcriptome, essential for subsequent embryo development.
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http://dx.doi.org/10.1016/j.devcel.2019.09.010DOI Listing
October 2019

Molecular characterisation of a cellular conveyor belt in Clytia medusae.

Dev Biol 2019 12 8;456(2):212-225. Epub 2019 Sep 8.

Sorbonne Université, MNHN, CNRS, EPHE, Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Paris, France. Electronic address:

The tentacular system of Clytia hemisphaerica medusa (Cnidaria, Hydrozoa) has recently emerged as a promising experimental model to tackle the developmental mechanisms that regulate cell lineage progression in an early-diverging animal phylum. From a population of proximal stem cells, the successive steps of tentacle stinging cell (nematocyte) elaboration, are spatially ordered along a "cellular conveyor belt". Furthermore, the C. hemisphaerica tentacular system exhibits bilateral organisation, with two perpendicular polarity axes (proximo-distal and oral-aboral). We aimed to improve our knowledge of this cellular system by combining RNAseq-based differential gene expression analyses and expression studies of Wnt signalling genes. RNAseq comparisons of gene expression levels were performed (i) between the tentacular system and a control medusa deprived of all tentacles, nematogenic sites and gonads, and (ii) between three samples staggered along the cellular conveyor belt. The behaviour in these differential expression analyses of two reference gene sets (stem cell genes; nematocyte genes), as well as the relative representations of selected gene ontology categories, support the validity of the cellular conveyor belt model. Expression patterns obtained by in situ hybridisation for selected highly differentially expressed genes and for Wnt signalling genes are largely consistent with the results from RNAseq. Wnt signalling genes exhibit complex spatial deployment along both polarity axes of the tentacular system, with the Wnt/β-catenin pathway probably acting along the oral-aboral axis rather than the proximo-distal axis. These findings reinforce the idea that, despite overall radial symmetry, cnidarians have a full potential for elaboration of bilateral structures based on finely orchestrated deployment of an ancient developmental gene toolkit.
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http://dx.doi.org/10.1016/j.ydbio.2019.09.001DOI Listing
December 2019

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination.

Genome Biol 2019 05 21;20(1):100. Epub 2019 May 21.

Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.

Background: The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role.

Results: We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination.

Conclusions: Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis.
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http://dx.doi.org/10.1186/s13059-019-1705-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6528313PMC
May 2019

Zinc Uptake and Storage During the Formation of the Cerebral Cortex in Mice.

Mol Neurobiol 2019 Oct 2;56(10):6928-6940. Epub 2019 Apr 2.

Université Grenoble Alpes, CNRS, CEA, BIG-LCBM, 38000, Grenoble, France.

The cerebral cortex (or neocortex) is a brain structure formed during embryogenesis. The present study seeks to provide a detailed characterization of the Zn homeostatic mechanisms during cerebral cortex formation and development. To reach that goal, we have combined high-throughput RNA-sequencing analysis of the whole murine genome, X-ray fluorescence nanoimaging (XRF), inductively coupled plasma-atomic emission spectrometry (ICP-AES), and live-cell imaging of dissociated cortical neurons loaded with the Zn fluorescent probe FluoZin-3. The transcriptomic analysis was conducted from mRNAs isolated from cortices collected at embryonic (E) days 11 (E11), E13, and E17 and on postnatal day 1 (PN1) pups. This permitted to characterize the temporal pattern of expression of the main genes participating in the cellular transport, storage, and release of Zn during corticogenesis. It appears that cells of the immature cortex express a wide diversity of actors involved in Zn homeostasis with Zip7, SOD1, and metallothioneins being the most abundant transcripts throughout corticogenesis. The quantification of total Zn with XRF and ICP-AES reveals a reduction of Zn levels. Moreover, this is accompanied by a diminution of the size of the internal pools of mobilizable Zn. This study illustrates the tight temporal and spatial regulation of Zn homeostasis during cerebral brain development.
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http://dx.doi.org/10.1007/s12035-019-1581-7DOI Listing
October 2019

Active intermixing of indirect and direct neurons builds the striatal mosaic.

Nat Commun 2018 11 9;9(1):4725. Epub 2018 Nov 9.

Brain Development and Plasticity Team, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.

The striatum controls behaviors via the activity of direct and indirect pathway projection neurons (dSPN and iSPN) that are intermingled in all compartments. While such cellular mosaic ensures the balanced activity of the two pathways, its developmental origin and pattern remains largely unknown. Here, we show that both SPN populations are specified embryonically and intermix progressively through multidirectional iSPN migration. Using conditional mutant mice, we found that inactivation of the dSPN-specific transcription factor Ebf1 impairs selective dSPN properties, including axon pathfinding, while molecular and functional features of iSPN were preserved. Ebf1 mutation disrupted iSPN/dSPN intermixing, resulting in an uneven distribution. Such architectural defect was selective of the matrix compartment, highlighting that intermixing is a parallel process to compartment formation. Our study reveals while iSPN/dSPN specification is largely independent, their intermingling emerges from an active migration of iSPN, thereby providing a novel framework for the building of striatal architecture.
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http://dx.doi.org/10.1038/s41467-018-07171-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226429PMC
November 2018

Cellular Origin, Tumor Progression, and Pathogenic Mechanisms of Cutaneous Neurofibromas Revealed by Mice with Knockout in Boundary Cap Cells.

Cancer Discov 2019 01 22;9(1):130-147. Epub 2018 Oct 22.

Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Paris, France.

Patients carrying an inactive allele develop tumors of Schwann cell origin called neurofibromas (NF). Genetically engineered mouse models have significantly enriched our understanding of plexiform forms of NFs (pNF). However, this has not been the case for cutaneous neurofibromas (cNF), observed in all NF1 patients, as no previous model recapitulates their development. Here, we show that conditional inactivation in -positive boundary cap cells leads to e pNFs and cNFs. This work identifies subepidermal glia as a likely candidate for the cellular origin of cNFs and provides insights on disease mechanisms, revealing a long, multistep pathologic process in which inflammation-related signals play a pivotal role. This new mouse model is an important asset for future clinical and therapeutic investigations of NF1-associated neurofibromas. SIGNIFICANCE: Patients affected by NF1 develop numerous cNFs. We present a mouse model that faithfully recapitulates cNFs, identify a candidate cell type at their origin, analyze the steps involved in their formation, and show that their development is dramatically accelerated by skin injury. These findings have important clinical/therapeutic implications..
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http://dx.doi.org/10.1158/2159-8290.CD-18-0156DOI Listing
January 2019

Genome sequencing and transcriptome analysis of QM9978 strain reveals a distal chromosome translocation to be responsible for loss of expression and loss of cellulase induction.

Biotechnol Biofuels 2017 7;10:209. Epub 2017 Sep 7.

IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852 Rueil-Malmaison, France.

Background: The hydrolysis of biomass to simple sugars used for the production of biofuels in biorefineries requires the action of cellulolytic enzyme mixtures. During the last 50 years, the ascomycete , the main source of industrial cellulase and hemicellulase cocktails, has been subjected to several rounds of classical mutagenesis with the aim to obtain higher production levels. During these random genetic events, strains unable to produce cellulases were generated. Here, whole genome sequencing and transcriptomic analyses of the cellulase-negative strain QM9978 were used for the identification of mutations underlying this cellulase-negative phenotype.

Results: Sequence comparison of the cellulase-negative strain QM9978 to the reference strain QM6a identified a total of 43 mutations, of which 33 were located either close to or in coding regions. From those, we identified 23 single-nucleotide variants, nine InDels, and one translocation. The translocation occurred between chromosomes V and VII, is located upstream of the putative transcription factor , and abolishes its expression in QM9978 as detected during the transcriptomic analyses. Ectopic expression of under the control of its native promoter as well as overexpression of under the control of a strong constitutive promoter restored cellulase expression in QM9978, thus confirming that the translocation event is the reason for the cellulase-negative phenotype. Gene deletion of in the moderate producer strain QM9414 and in the high producer strain Rut-C30 reduced cellulase expression in both cases. Overexpression of in QM9414 and Rut-C30 had no effect on cellulase production, most likely because is already expressed at an optimal level under normal conditions.

Conclusion: We were able to establish a link between a chromosomal translocation in QM9978 and the cellulase-negative phenotype of the strain. We identified the transcription factor as a key regulator of cellulases in whose expression is absent in QM9978. We propose that in , as in , is involved in cellulase induction, although the exact mechanism remains to be elucidated. The data presented here show an example of a combined genome sequencing and transcriptomic approach to explain a specific trait, in this case the QM9978 cellulase-negative phenotype, and how it helps to better understand the mechanisms during cellulase gene regulation. When focusing on mutations on the single base-pair level, changes on the chromosome level can be easily overlooked and through this work we provide an example that stresses the importance of the big picture of the genomic landscape during analysis of sequencing data.
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http://dx.doi.org/10.1186/s13068-017-0897-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5588705PMC
September 2017

Quaking RNA-Binding Proteins Control Early Myofibril Formation by Modulating Tropomyosin.

Dev Cell 2017 09 31;42(5):527-541.e4. Epub 2017 Aug 31.

IBENS, Institut de Biologie de l'Ecole Normale Supérieure, 75005 Paris, France; INSERM U1024, 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France. Electronic address:

Skeletal muscle contraction is mediated by myofibrils, complex multi-molecular scaffolds structured into repeated units, the sarcomeres. Myofibril structure and function have been extensively studied, but the molecular processes regulating its formation within the differentiating muscle cell remain largely unknown. Here we show in zebrafish that genetic interference with the Quaking RNA-binding proteins disrupts the initial steps of myofibril assembly without affecting early muscle differentiation. Using RNA sequencing, we demonstrate that Quaking is required for accumulation of the muscle-specific tropomyosin-3 transcript, tpm3.12. Further functional analyses reveal that Tpm3.12 mediates Quaking control of myofibril formation. Moreover, we identified a Quaking-binding site in the 3' UTR of tpm3.12 transcript, which is required in vivo for tpm3.12 accumulation and myofibril formation. Our work uncovers a Quaking/Tpm3 pathway controlling de novo myofibril assembly. This unexpected developmental role for Tpm3 could be at the origin of muscle defects observed in human congenital myopathies associated with tpm3 mutation.
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http://dx.doi.org/10.1016/j.devcel.2017.08.004DOI Listing
September 2017

Aozan: an automated post-sequencing data-processing pipeline.

Bioinformatics 2017 Jul;33(14):2212-2213

École Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'École Normale Supérieure (IBENS), Plateforme Génomique, Paris, France.

Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports.

Availability And Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www.outils.genomique.biologie.ens.fr/aozan/ . Aozan source code is available on GitHub: https://github.com/GenomicParisCentre/aozan .

Contact: aozan@biologie.ens.fr.
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http://dx.doi.org/10.1093/bioinformatics/btx154DOI Listing
July 2017

IRF5 governs liver macrophage activation that promotes hepatic fibrosis in mice and humans.

JCI Insight 2016 12 8;1(20):e88689. Epub 2016 Dec 8.

Institut National de la Santé et de la Recherche Médicale (INSERM) UMRS 1138, Sorbonne Universités, UPMC Université Paris 06; Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot; and Centre de Recherche des Cordeliers, Paris, France.

Hepatic fibrosis arises from inflammation in the liver initiated by resident macrophage activation and massive leukocyte accumulation. Hepatic macrophages hold a central position in maintaining homeostasis in the liver and in the pathogenesis of acute and chronic liver injury linked to fibrogenesis. Interferon regulatory factor 5 (IRF5) has recently emerged as an important proinflammatory transcription factor involved in macrophage activation under acute and chronic inflammation. Here, we revealed that IRF5 is significantly induced in liver macrophages from human subjects developing liver fibrosis from nonalcoholic fatty liver disease or hepatitis C virus infection. Furthermore, IRF5 expression positively correlated with clinical markers of liver damage, such as plasma transaminase and bilirubin levels. Interestingly, mice lacking IRF5 in myeloid cells (MKO) were protected from hepatic fibrosis induced by metabolic or toxic stresses. Transcriptional reprogramming of macrophages lacking IRF5 was characterized by immunosuppressive and antiapoptotic properties. Consequently, IRF5 MKO mice respond to hepatocellular stress by promoting hepatocyte survival, leading to complete protection from hepatic fibrogenesis. Our findings reveal a regulatory network, governed by IRF5, that mediates hepatocyte death and liver fibrosis in mice and humans. Therefore, modulating IRF5 function may be an attractive approach to experimental therapeutics in fibroinflammatory liver disease.
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http://dx.doi.org/10.1172/jci.insight.88689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5135279PMC
December 2016

Control of Plasma Membrane Permeability by ABC Transporters.

Eukaryot Cell 2015 May 27;14(5):442-53. Epub 2015 Feb 27.

Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA

ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps. Mutant strains lacking these transporter proteins were found to exhibit very different resistance phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A [AbA]) or early (myriocin [Myr]) in the pathway leading to production of these important plasma membrane lipids. These pdr5Δ yor1 strains were highly AbA resistant but extremely sensitive to Myr. We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes, Dnf1/Lem3 and Dnf2/Lem3. Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane. Genetic analyses indicate that lem3Δ mutant strains are highly AbA sensitive and Myr resistant. These phenotypes are fully epistatic to those seen in pdr5Δ yor1 strains. Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1. Microarray experiments found that a pdr5Δ yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon. Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor. Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulates permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2.
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http://dx.doi.org/10.1128/EC.00021-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421010PMC
May 2015

The ß-importin KAP8 (Pse1/Kap121) is required for nuclear import of the cellulase transcriptional regulator XYR1, asexual sporulation and stress resistance in Trichoderma reesei.

Mol Microbiol 2015 Apr 4;96(2):405-18. Epub 2015 Mar 4.

Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, 1060, Austria.

The ascomycete Trichoderma reesei is an industrial producer of cellulolytic and hemicellulolytic enzymes, and serves as a prime model for their genetic regulation. Most of its (hemi-)cellulolytic enzymes are obligatorily dependent on the transcriptional activator XYR1. Here, we investigated the nucleo-cytoplasmic shuttling mechanism that transports XYR1 across the nuclear pore complex. We identified 14 karyopherins in T. reesei, of which eight were predicted to be involved in nuclear import, and produced single gene-deletion mutants of all. We found KAP8, an ortholog of Aspergillus nidulans KapI, and Saccharomyces cerevisiae Kap121/Pse1, to be essential for nuclear recruitment of GFP-XYR1 and cellulase gene expression. Transformation with the native gene rescued this effect. Transcriptomic analyses of Δkap8 revealed that under cellulase-inducing conditions 42 CAZymes, including all cellulases and hemicellulases known to be under XYR1 control, were significantly down-regulated. Δkap8 strains were capable of forming fertile fruiting bodies but exhibited strongly reduced conidiation both in light and darkness, and showed enhanced sensitivity towards abiotic stress, including high osmotic pressure, low pH and high temperature. Together, these data underscore the significance of nuclear import of XYR1 in cellulase and hemicellulase gene regulation in T. reesei, and identify KAP8 as the major karyopherin required for this process.
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http://dx.doi.org/10.1111/mmi.12944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390390PMC
April 2015

Role of the DHH1 gene in the regulation of monocarboxylic acids transporters expression in Saccharomyces cerevisiae.

PLoS One 2014 3;9(11):e111589. Epub 2014 Nov 3.

Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal.

Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170:301-306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111589PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4218774PMC
August 2015

High-frequency promoter firing links THO complex function to heavy chromatin formation.

Cell Rep 2013 Nov 7;5(4):1082-94. Epub 2013 Nov 7.

Centre de Génétique Moléculaire, CNRS-UPR 3404, 91190 Gif sur Yvette, France; Centre for mRNP Biogenesis and Metabolism, Aarhus University, 8000 Aarhus, Denmark.

The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence in situ hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of gene-nuclear pore association and mRNP release to the same high pace of transcription initiation.
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http://dx.doi.org/10.1016/j.celrep.2013.10.013DOI Listing
November 2013

RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans.

BMC Genomics 2012 Aug 16;13:396. Epub 2012 Aug 16.

Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.

Background: Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart.

Results: RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of β-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator.

Conclusion: Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.
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http://dx.doi.org/10.1186/1471-2164-13-396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447688PMC
August 2012

Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress.

Nucleic Acids Res 2012 Jul 29;40(12):5271-82. Epub 2012 Feb 29.

CNRS UPR9073, associated with Univ Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-chimique, F-75005 Paris, France.

Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.
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http://dx.doi.org/10.1093/nar/gks166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384299PMC
July 2012

Physiological and toxic effects of purine intermediate 5-amino-4-imidazolecarboxamide ribonucleotide (AICAR) in yeast.

J Biol Chem 2011 Sep 12;286(35):30994-1002. Epub 2011 Jul 12.

Institut de Biochimie et Génétique Cellulaires Unité Mixte de Recherche 5095, Université Ségalen, Bordeaux F-33077, France.

5-Amino-4-imidazolecarboxamide ribonucleotide 5'-phosphate (AICAR) is a monophosphate metabolic intermediate of the de novo purine synthesis pathway that has highly promising metabolic and antiproliferative properties. Yeast mutants unable to metabolize AICAR are auxotroph for histidine. A screening for suppressors of this phenotype identified recessive and dominant mutants that result in lowering the intracellular AICAR concentration. The recessive mutants affect the adenosine kinase, which is shown here to catalyze the phosphorylation of AICAR riboside in yeast. The dominant mutants strongly enhance the capacity of the alkaline phosphatase Pho13 to dephosphorylate 5-amino-4-imidazole N-succinocarboxamide ribonucleotide 5'-phosphate(SAICAR) into its non-toxic riboside form. By combining these mutants with transcriptomics and metabolomics analyses, we establish that in yeast responses to AICAR and SAICAR are clearly linked to the concentration of the monophosphate forms, whereas the derived nucleoside moieties have no effect even at high intracellular concentration. Finally, we show that AICAR/SAICAR concentrations vary under physiological conditions known to modulate transcription of the purine and phosphate pathway genes.
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http://dx.doi.org/10.1074/jbc.M111.262659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162458PMC
September 2011

Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae.

BMC Genomics 2011 Jun 28;12:331. Epub 2011 Jun 28.

Department of Genetics, Genomics and Microbiology, University of Strasbourg, CNRS, UMR, Strasbourg, France.

Background: Gross chromosomal rearrangements (GCRs) such as aneuploidy are key factors in genome evolution as well as being common features of human cancer. Their role in tumour initiation and progression has not yet been completely elucidated and the effects of additional chromosomes in cancer cells are still unknown. Most previous studies in which Saccharomyces cerevisiae has been used as a model for cancer cells have been carried out in the haploid context. To obtain new insights on the role of ploidy, the cellular effects of GCRs were compared between the haploid and diploid contexts.

Results: A total number of 21 haploid and diploid S. cerevisiae strains carrying various types of GCRs (aneuploidies, nonreciprocal translocations, segmental duplications and deletions) were studied with a view to determining the effects of ploidy on the cellular responses. Differences in colony and cell morphology as well as in the growth rates were observed between mutant and parental strains. These results suggest that cells are impaired physiologically in both contexts. We also investigated the variation in genomic expression in all the mutants. We observed that gene expression was significantly altered. The data obtained here clearly show that genes involved in energy metabolism, especially in the tricarboxylic acid cycle, are up-regulated in all these mutants. However, the genes involved in the composition of the ribosome or in RNA processing are down-regulated in diploids but up-regulated in haploids. Over-expression of genes involved in the regulation of the proteasome was found to occur only in haploid mutants.

Conclusion: The present comparisons between the cellular responses of strains carrying GCRs in different ploidy contexts bring to light two main findings. First, GCRs induce a general stress response in all studied mutants, regardless of their ploidy. Secondly, the ploidy context plays a crucial role in maintaining the stoichiometric balance of the proteins: the translation rates decrease in diploid strains, whereas the excess protein synthesized is degraded in haploids by proteasome activity.
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http://dx.doi.org/10.1186/1471-2164-12-331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157476PMC
June 2011

Metabolic intermediates selectively stimulate transcription factor interaction and modulate phosphate and purine pathways.

Genes Dev 2009 Jun;23(12):1399-407

Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, Bordeaux 33076, France.

Cells use strategic metabolites to sense the metabolome and accordingly modulate gene expression. Here, we show that the purine and phosphate pathways are positively regulated by the metabolic intermediate AICAR (5'-phosphoribosyl-5-amino-4-imidazole carboxamide). The transcription factor Pho2p is required for up-regulation of all AICAR-responsive genes. Accordingly, the binding of Pho2p to purine and phosphate pathway gene promoters is enhanced upon AICAR accumulation. In vitro, AICAR binds both Pho2p and Pho4p transcription factors and stimulates the interaction between Pho2p and either Bas1p or Pho4p in vivo. In contrast, SAICAR (succinyl-AICAR) only affects Pho2p-Bas1p interaction and specifically up-regulates purine regulon genes. Together, our data show that Bas1p and Pho4p compete for Pho2p binding, hence leading to the concerted regulation of cellular nucleotide synthesis and phosphate consumption.
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http://dx.doi.org/10.1101/gad.521809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701576PMC
June 2009

An evaluation of custom microarray applications: the oligonucleotide design challenge.

Nucleic Acids Res 2009 Apr 10;37(6):1726-39. Epub 2009 Feb 10.

INSERM, CNRS, IFR36, Plate-forme Transcriptome, Paris, France.

The increase in feature resolution and the availability of multipack formats from microarray providers has opened the way to various custom genomic applications. However, oligonucleotide design and selection remains a bottleneck of the microarray workflow. Several tools are available to perform this work, and choosing the best one is not an easy task, nor are the choices obvious. Here we review the oligonucleotide design field to help users make their choice. We have first performed a comparative evaluation of the available solutions based on a set of criteria including: ease of installation, user-friendly access, the number of parameters and settings available. In a second step, we chose to submit two real cases to a selection of programs. Finally, we used a set of tests for the in silico benchmark of the oligo sets obtained from each type of software. We show that the design software must be selected according to the goal of the scientist, depending on factors such as the organism used, the number of probes required and their localization on the target sequence. The present work provides keys to the choice of the most relevant software, according to the various parameters we tested.
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http://dx.doi.org/10.1093/nar/gkp053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665234PMC
April 2009

Influence of a walking program on the metabolic risk profile of obese postmenopausal women.

Menopause 2009 May-Jun;16(3):566-75

UFR STAPS, Université P. Sabatier, Toulouse, France.

Objective: Menopause transition is associated with an increased prevalence of metabolic syndrome (MS), which may partly explain the higher coronary heart disease risk. The aim of this study was to examine the impact of a 16-week walking program on the metabolic risk profile of women 50 to 65 years old whose body mass index ranged from 29 to 35 kg/m.

Methods: A total of 153 postmenopausal women were subjected to three sessions per week of 45-minutes of walking at 60% of their heart rate reserve. At baseline, 46 and 84 women were characterized by one and two or more determinants of MS, respectively, whereas 23 women did not show this condition. Body composition, resting blood pressure, fasting lipid-lipoprotein profile, and cardiorespiratory fitness (CRF) were measured before and after exercise.

Results: In the whole sample of 153 women, CRF estimated by V(O2max) increased in response to walking (P < 0.0001). Endurance training promoted body weight and fat mass losses and reduced waist girth and blood pressure, whereas it decreased plasma triglyceride, cholesterol, and low-density lipoprotein cholesterol levels and increased high-density lipoprotein cholesterol concentrations (P < 0.0001). Improvements in lipid-lipoprotein levels were not associated with increases in CRF but seemed to be dependent on reduced body fatness. However, the greatest ameliorations in metabolic risk profile were found in women characterized by two or more determinants of MS at baseline than in the two other groups (0.05 < P < 0.0001).

Conclusion: A moderate-intensity physical activity is thus sufficient to reduce the metabolic risk profile of postmenopausal women characterized by the presence of one or several clinical features of MS but without overt coronary heart disease.
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http://dx.doi.org/10.1097/gme.0b013e31818d4137DOI Listing
July 2009

THO/Sub2p functions to coordinate 3'-end processing with gene-nuclear pore association.

Cell 2008 Oct;135(2):308-21

LEA Laboratory of Nuclear RNA metabolism, Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique - UPR2167, 1, av de la Terrasse, 91190, Gif sur Yvette, France.

During transcription, proteins assemble sequentially with nascent RNA to generate a messenger ribonucleoprotein particle (mRNP). The THO complex and its associated Sub2p helicase are functionally implicated in both transcription and mRNP biogenesis but their precise function remains elusive. We show here that THO/Sub2p mutation leads to the accumulation of a stalled intermediate in mRNP biogenesis that contains nuclear pore components and polyadenylation factors in association with chromatin. Microarray analyses of genomic loci that are aberrantly docked to the nuclear pore in mutants allowed the identification of approximately 400 novel validated target genes that require THO /Sub2p for efficient expression. Our data strongly suggests that the THO complex/Sub2p function is required to coordinate events leading to the acquisition of export competence at a step that follows commitment to 3'-processing.
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http://dx.doi.org/10.1016/j.cell.2008.08.005DOI Listing
October 2008

What is the influence of menopausal status on metabolic profile, eating behaviors, and perceived health of obese women after weight reduction?

Appl Physiol Nutr Metab 2008 Oct;33(5):957-65

UFR STAPS, Universite Paul Sabatier, 118, Route de Narbonne, Toulouse 31062, France.

The duration of the numerous weight-loss studies that combine physical activity and diet varies from 3 to 14 months, and these studies have often considered pre- and postmenopausal women separately. The purpose of this study was to compare the effects of a 3-week weight-reducing program that combines caloric restriction and exercise on the metabolic profile, eating behaviors, and perceived health of sedentary obese pre- and postmenopausal women, after adjustment for age. In 10 pre- and 22 postmenopausal women, before and after weight loss, body composition, fasting lipid-lipoprotein profile, glucose and insulin levels, eating behaviors, and perceived health state were assessed. Body mass index, fat mass, and waist girth decreased after weight reduction in both groups (p < 0.0001). Reductions in fasting serum cholesterol and low-density lipoprotein-cholesterol levels were greater in pre- than in postmenopausal women (p < 0.0001), whereas triacylglycerol, glucose, and high-density lipoprotein-cholesterol levels decreased similarly in both groups (p < 0.05). Neither fasting insulin nor free fatty-acid concentrations were modified after weight loss in either group. Disinhibition (p < 0.005) and hunger scores on the three-factor eating questionnaire (TFEQ) (p < 0.05) and the state-anxiety score on the state-trait anxiety inventory (STAI) questionnaire (p < 0.0005) decreased in both groups, but restriction (TFEQ) increased (p < 0.01) and trait anxiety (STAI) decreased (p < 0.001) after weight reduction only in premenopausal women. Improvements in selected lipid-lipoprotein indices, eating behaviors, and perceived health-state components were better in pre- than in postmenopausal women, suggesting that menopausal status has an influence on some metabolic and behavioral responses to weight loss.
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http://dx.doi.org/10.1139/H08-063DOI Listing
October 2008

Structure and properties of transcriptional networks driving selenite stress response in yeasts.

BMC Genomics 2008 Jul 15;9:333. Epub 2008 Jul 15.

Laboratoire de génétique moléculaire, ENS/CNRS UMR 8541 46 rue d'Ulm, 75005 Paris, France.

Background: Stress responses provide valuable models for deciphering the transcriptional networks controlling the adaptation of the cell to its environment. We analyzed the transcriptome response of yeast to toxic concentrations of selenite. We used gene network mapping tools to identify functional pathways and transcription factors involved in this response. We then used chromatin immunoprecipitation and knock-out experiments to investigate the role of some of these regulators and the regulatory connections between them.

Results: Selenite rapidly activates a battery of transcriptional circuits, including iron deprivation, oxidative stress and protein degradation responses. The mRNA levels of several transcriptional regulators are themselves regulated. We demonstrate the existence of a positive transcriptional loop connecting the regulator of proteasome expression, Rpn4p, to the pleiotropic drug response factor, Pdr1p. We also provide evidence for the involvement of this regulatory module in the oxidative stress response controlled by the Yap1p transcription factor and its conservation in the pathogenic yeast C. glabrata. In addition, we show that the drug resistance regulator gene YRR1 and the iron homeostasis regulator gene AFT2 are both directly regulated by Yap1p.

Conclusion: This work depicted a highly interconnected and complex transcriptional network involved in the adaptation of yeast genome expression to the presence of selenite in its chemical environment. It revealed the transcriptional regulation of PDR1 by Rpn4p, proposed a new role for the pleiotropic drug resistance network in stress response and demonstrated a direct regulatory connection between oxidative stress response and iron homeostasis.
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http://dx.doi.org/10.1186/1471-2164-9-333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515152PMC
July 2008

Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization.

PLoS One 2008 Jun 4;3(6):e2293. Epub 2008 Jun 4.

Laboratoire de Génétique Moléculaire CNRS-UMR8541, Ecole Normale Supérieure, Paris, France.

The asymmetric localization of mRNA plays an important role in coordinating posttranscriptional events in eukaryotic cells. We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which the mRNA binding protein context and the translation efficiency were altered. We identified Puf3p, a Pumilio family RNA-binding protein, as the first trans-acting factor controlling the MLR phenomenon. This allowed the characterization of two classes of genes whose mRNAs are translated to the vicinity of mitochondria. Class I mRNAs (256 genes) have a Puf3p binding motif in their 3'UTR region and many of them have their MLR properties deeply affected by PUF3 deletion. Conversely, mutations in the Puf3p binding motif alter the mitochondrial localization of BCS1 mRNA. Class II mRNAs (224 genes) have no Puf3p binding site and their asymmetric localization is not affected by the absence of PUF3. In agreement with a co-translational import process, we observed that the presence of puromycin loosens the interactions between most of the MLR-mRNAs and mitochondria. Unexpectedly, cycloheximide, supposed to solidify translational complexes, turned out to destabilize a class of mRNA-mitochondria interactions. Classes I and II mRNAs, which are therefore transported to the mitochondria through different pathways, correlated with different functional modules. Indeed, Class I genes code principally for the assembly factors of respiratory chain complexes and the mitochondrial translation machinery (ribosomes and translation regulators). Class II genes encode proteins of the respiratory chain or proteins involved in metabolic pathways. Thus, MLR, which is intimately linked to translation control, and the activity of mRNA-binding proteins like Puf3p, may provide the conditions for a fine spatiotemporal control of mitochondrial protein import and mitochondrial protein complex assembly. This work therefore provides new openings for the global study of mitochondria biogenesis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002293PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387061PMC
June 2008