Institute Of Genomique Fonctionnelle

Montpellier, France

Institute Of Genomique Fonctionnelle

Montpellier, France

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Nabholz B.,Montpellier University | Sarah G.,CIRAD - Agricultural Research for Development | Sabot F.,CIRAD - Agricultural Research for Development | Ruiz M.,CIRAD - Agricultural Research for Development | And 6 more authors.
Molecular Ecology | Year: 2014

The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12 000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented. Using approximate Bayesian computation, we estimated that O. glaberrima experienced a severe bottleneck during domestication. This demographic scenario almost fully accounts for the pattern of genetic diversity across O. glaberrima genome as we detected very few outliers regions where positive selection may have further impacted genetic diversity. Moreover, the large excess of derived nonsynonymous substitution that we detected suggests that the O. glaberrima population suffered from the 'cost of domestication'. In addition, we used this genome-scale data set to demonstrate that (i) O. barthii genetic diversity is positively correlated with recombination rate and negatively with gene density, (ii) expression level is negatively correlated with evolutionary constraint, and (iii) one region on chromosome 5 (position 4-6 Mb) exhibits a clear signature of introgression with a yet unidentified Oryza species. This work represents the first genome-wide survey of the African rice genetic diversity and paves the way for further comparison between the African and the Asian rice, notably regarding the genetics underlying domestication traits. © 2014 John Wiley & Sons Ltd.


Mesirca P.,Institute Of Genomique Fonctionnelle | Mesirca P.,Universites Of Montpellier 1 And 2 | Mesirca P.,French Institute of Health and Medical Research | Torrente A.G.,Institute Of Genomique Fonctionnelle | And 5 more authors.
Frontiers in Physiology | Year: 2015

Pacemaker activity of automatic cardiac myocytes controls the heartbeat in everyday life. Cardiac automaticity is under the control of several neurotransmitters and hormones and is constantly regulated by the autonomic nervous system to match the physiological needs of the organism. Several classes of ion channels and proteins involved in intracellular Ca2+ dynamics contribute to pacemaker activity. The functional role of voltage-gated calcium channels (VGCCs) in heart automaticity and impulse conduction has been matter of debate for 30 years. However, growing evidence shows that VGCCs are important regulators of the pacemaker mechanisms and play also a major role in atrio-ventricular impulse conduction. Incidentally, studies performed in genetically modified mice lacking L-type Cav1.3 (Cav1.3-/-) or T-type Cav3.1 (Cav3.1-/-) channels show that genetic inactivation of these channels strongly impacts pacemaking. In cardiac pacemaker cells, VGCCs activate at negative voltages at the beginning of the diastolic depolarization and importantly contribute to this phase by supplying inward current. Loss-of-function of these channels also impairs atrio-ventricular conduction. Furthermore, inactivation of Cav1.3 channels promotes also atrial fibrillation and flutter in knockout mice suggesting that these channels can play a role in stabilizing atrial rhythm. Genomic analysis demonstrated that Cav1.3 and Cav3.1 channels are widely expressed in pacemaker tissue of mice, rabbits and humans. Importantly, human diseases of pacemaker activity such as congenital bradycardia and heart block have been attributed to loss-of-function of Cav1.3 and Cav3.1 channels. In this article, we will review the current knowledge on the role of VGCCs in the generation and regulation of heart rate and rhythm. We will discuss also how loss of Ca2+ entry through VGCCs could influence intracellular Ca2+ handling and promote atrial arrhythmias. © 2015 Mesirca, Torrente and Mangoni.


Lhoumaud P.,French National Center for Scientific Research | Hennion M.,French National Center for Scientific Research | Gamot A.,French National Center for Scientific Research | Cuddapah S.,U.S. National Institutes of Health | And 11 more authors.
EMBO Journal | Year: 2014

Chromosomal domains in Drosophila are marked by the insulator-binding proteins (IBPs) dCTCF/Beaf32 and cofactors that participate in regulating long-range interactions. Chromosomal borders are further enriched in specific histone modifications, yet the role of histone modifiers and nucleosome dynamics in this context remains largely unknown. Here, we show that IBP depletion impairs nucleosome dynamics specifically at the promoters and coding sequence of genes flanked by IBP binding sites. Biochemical purification identifies the H3K36 histone methyltransferase NSD/dMes-4 as a novel IBP cofactor, which specifically co-regulates the chromatin accessibility of hundreds of genes flanked by dCTCF/Beaf32. NSD/dMes-4 presets chromatin before the recruitment of transcriptional activators including DREF that triggers Set2/Hypb-dependent H3K36 trimethylation, nucleosome positioning, and RNA splicing. Our results unveil a model for how IBPs regulate nucleosome dynamics and gene expression through NSD/dMes-4, which may regulate H3K27me3 spreading. Our data uncover how IBPs dynamically regulate chromatin organization depending on distinct cofactors.


Mesirca P.,Institute Of Genomique Fonctionnelle | Mesirca P.,Universites Of Montpellier 1 And 2 | Mesirca P.,French Institute of Health and Medical Research | Torrente A.G.,Institute Of Genomique Fonctionnelle | And 5 more authors.
Pflugers Archiv European Journal of Physiology | Year: 2014

Cardiac automaticity is a fundamental physiological function in vertebrates. Heart rate is under the control of several neurotransmitters and hormones and is permanently adjusted by the autonomic nervous system to match the physiological demand of the organism. Several classes of ion channels and proteins involved in intracellular Ca2+ handling contribute to pacemaker activity. Voltage-dependent T-type Ca2+ channels are an integral part of the complex mechanism underlying pacemaking. T-type channels also contribute to impulse conduction in mice and humans. Strikingly, T-type channel isoforms are co-expressed in the cardiac conduction system with other ion channels that play a major role in pacemaking such as f- (HCN4) and L-type Cav1.3 channels. Pharmacologic inhibition of T-type channels reduces the spontaneous activity of isolated pacemaker myocytes of the sino-atrial node, the dominant heart rhythmogenic centre. Target inactivation of T-type Ca v3.1 channels abolishes ICa,T in both sino-atrial and atrioventricular myocytes and reduces the daily heart rate of freely moving mice. Cav3.1 channels contribute also to automaticity of the atrioventricular node and to ventricular escape rhythms, thereby stressing the importance of these channels in automaticity of the whole cardiac conduction system. Accordingly, loss-of-function of Cav3.1 channels contributes to severe form of congenital bradycardia and atrioventricular block in paediatric patients. © 2014 Springer-Verlag.


Xiao C.,University of Cincinnati | Ogle S.A.,University of Cincinnati | Schumacher M.A.,University of Cincinnati | Orr-Asman M.A.,University of Cincinnati | And 8 more authors.
Gastroenterology | Year: 2010

Background & Aims: Sonic Hedgehog (Shh) is expressed in the adult stomach, but its role as a gastric morphogen is unclear. We sought to identify mechanisms by which Shh might regulate gastric epithelial cell function and differentiation. Methods: Mice with a parietal cell-specific deletion of Shh (HKCre/ShhKO) were created. Gastric morphology and function were studied in control and HKCre/ShhKO mice between 1 and 8 months of age. Results: In contrast to control mice, HKCre/ShhKO mice developed gastric hypochlorhydria, hypergastrinemia, and a phenotype that resembled foveolar hyperplasia. The fundic mucosa of HKCre/ShhKO mice had an expanded surface pit cell lineage that was documented by increased incorporation of bromodeoxyuridine and was attributed to the hypergastrinemia. Compared with controls, numbers of total mucous neck and zymogen cells were significantly decreased in stomachs of HKCre/ShhKO mice. In addition, zymogen and neck cell markers were coexpressed in the same cell populations, indicating disrupted differentiation of the zymogen cell lineage from the mucous neck cells in the stomachs of HKCre/ShhKO mice. Laser capture microdissection of the surface epithelium, followed by quantitative reverse-transcription polymerase chain reaction, revealed a significant increase in expression of Indian Hedgehog, glioma-associated oncogene homolog 1, Wnt, and cyclin D1. Laser capture microdissection analysis also showed a significant increase in Snail with a concomitant decrease in E-cadherin. Conclusions: In the stomachs of adult mice, loss of Shh from parietal cells results in hypochlorhydria and hypergastrinemia. Hypergastrinemia might subsequently induce increased Hedgehog and Wnt signaling in the surface pit epithelium, resulting in hyperproliferation. © 2010 AGA Institute.


Mouillac B.,Institute Of Genomique Fonctionnelle | Baneres J.L.,Institute Of Genomique Fonctionnelle
Methods in molecular biology (Clifton, N.J.) | Year: 2010

Integral membrane proteins, in particular receptors, regulate numerous physiological functions. The primary difficulty presented by their study in vitro is to obtain them in sufficient amounts in a functional state. Escherichia coli is a host of choice for producing recombinant proteins for structural studies. However, insertion of G-protein coupled receptors into its plasma membrane usually results in bacterial death. An alternative approach consists of targeting recombinant receptors to inclusion bodies, where they accumulate without affecting bacterial growth, and then fold them in vitro . We describe here a general approach that consists of accumulating the receptor in bacterial inclusion bodies, then purifying it under denaturing conditions. A simple assay is then described to screen for refolding conditions of the protein.


Combes M.-C.,Montpellier University | Dereeper A.,Montpellier University | Severac D.,Institute Of Genomique Fonctionnelle | Bertrand B.,Montpellier University | Lashermes P.,Montpellier University
New Phytologist | Year: 2013

Polyploidy has occurred throughout the evolutionary history of plants and led to diversification and plant ecological adaptation. Functional plasticity of duplicate genes is believed to play a major role in the environmental adaptation of polyploids. In this context, we characterized genome-wide homoeologous gene expression in Coffea arabica, a recent allopolyploid combining two subgenomes that derive from two closely related diploid species, and investigated its variation in response to changing environment. The transcriptome of leaves of C. arabica cultivated at different growing temperatures suitable for one or the other parental species was examined using RNA-sequencing. The relative contribution of homoeologs to gene expression was estimated for 9959 and 10 628 genes in warm and cold conditions, respectively. Whatever the growing conditions, 65% of the genes showed equivalent levels of homoeologous gene expression. In 92% of the genes, relative homoeologous gene expression varied < 10% between growing temperatures. The subgenome contributions to the transcriptome appeared to be only marginally altered by the different conditions (involving intertwined regulations of homeologs) suggesting that C. arabica's ability to tolerate a broader range of growing temperatures than its diploid parents does not result from differential use of homoeologs. © 2013 New Phytologist Trust.


Ayoub M.A.,Institute Of Genomique Fonctionnelle | Ayoub M.A.,Universites Montpellier 1 and 2 | Pin J.-P.,Institute Of Genomique Fonctionnelle | Pin J.-P.,Universites Montpellier 1 and 2
Frontiers in Endocrinology | Year: 2013

G protein-coupled receptors are well recognized as being able to activate several signaling pathways through the activation of different G proteins as well as other signaling proteins such as β-arrestins. Therefore, understanding how such multiple GPCR-mediated signaling can be integrated constitute an important aspect. Here, we applied bioluminescence resonance energy transfer (BRET) to shed more light on the G protein coupling profile of trypsin receptor, or protease-activated receptor 2 (PAR2), and its interaction with β-arrestin1. Using YFP and Rluc fusion constructs expressed in COS-7 cells, BRET data revealed a pre-assembly of PAR2 with both Gαi1 and Gαo and a rapid and transient activation of these G proteins upon receptor activation. In contrast, no pre-assembly of PAR2 with Gα12 could be detected and their physical association can be measured with a very slow and sustained kinetics similar to that of β-arrestin1 recruitment. These data demonstrate the coupling of PAR2 with Gαi1, Gαo, and Gα12 in COS-7 cells with differences in the kinetics of GPCR-G protein coupling, a parameter that very likely influences the cellular response. Moreover, this further illustrates that pre-assembly or agonist-induced G protein interaction depends on receptor-G protein pairs indicating another level of complexity and regulation of the signaling of GPCR-G protein complexes and its multiplicity. © 2013 Ayoub and Pin.


Bockaert J.,Institute Of Genomique Fonctionnelle
Medecine/Sciences | Year: 2012

The 2012 Nobel Prize for chemistry has been won by Robert J. Lefkowitz and Brian Kobilka for their work on G protein-coupled receptors (GPCRs). Those receptors (3% of human genome) evolutionary are derived from one 1 or 2 ancestors and are able to recognize external message as different as light, odorants, gustative molecules and intercellular messages such as hormones and neurotransmitters. They are targets of 30-40% of therapeutic drugs. Robert J. Lefkowitz has been one of the leaders of the field from more than 40 years and has built several key concepts of the domain. Brian Kobilka was successful, in 2007, in producing a crystal structure of the ?2-adrenergic receptor. This paved the way for the production of a series of almost 50 GPCR crystal structures both in inactive and active forms.


Cif L.,Montpellier University Hospital Center | Gonzalez-Martinez V.,Montpellier University Hospital Center | Vasques X.,Montpellier University Hospital Center | Vasques X.,Montpellier University | And 5 more authors.
Journal of Neurosurgery | Year: 2012

Object. Deep brain stimulation (DBS) is used for treating various types of dystonia. Multiple electrodes could be proposed to improve the therapeutic outcome enabling the targeting of specific neuronal populations not reached by the electrical field generated by the initially implanted electrode. The authors address the question of the feasibility and safety of staged multiple lead implantations in the sensorimotor internal globus pallidus (GPi) in primary generalized dystonia (PGD). Criteria for patient selection, surgical technique, target selection, electrical settings management, and clinical outcome are presented. Methods. Sixteen patients (8 harbored the DYT1 gene mutation) presented with PGD and were enrolled in this study. Patients underwent clinical assessment using the Burke-Fahn-Marsden Dystonia Rating Scale preoperatively and during follow-up with DBS. Prior to the addition of electrodes, the authors confirmed, by turning off stimulation, that the patient was still benefiting from DBS and that DBS settings adjustment did not provide further improvement. The second target was defined according to the position of the first electrode, to the residual volume within the sensorimotor GPi, and according to residual symptoms. The second surgery followed the same protocol as the first and the new electrode were inserted using the same bur hole as the first electrode. Results. The addition of a new pair of electrodes was followed by significant improvement in the whole population (p = 0.005), as well as in the DYT1-negative subgroup (p = 0.012) but not in the DYT1 subgroup (p = not significant). Nevertheless, some patients did not exhibit significant additional benefit. Seven hardware-related complications occurred during the entire follow-up, 3 prior to it, and 4 after the addition of the second pair of electrodes. Conclusions. The addition of a second pair of electrodes in the GPi in patients with PGD with suboptimal or decaying benefit following the first surgery seems to be a safe procedure and is not followed by an increase in surgery- related complications. This staged procedure may provide further clinical improvement in patients with PGD in whom DBS effect is initially incomplete or when disease progression occurs over time. The position of the additional electrode within the GPi is determined by the available volume within the posteroventral GPi and by the distribution of the dystonic symptoms that need to be controlled.

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