28 research outputs found
Characterization of 3D genomic interactions in fetal pig muscle
Genome sequence alone is not sufficient to explain the overall coordination of nuclear activity in a particular tissue. The nuclear organisation and genomic long-range intra- and inter-chromosomal interactions play an important role in the regulation of gene expression and the activation of tissue- specific gene networks. Here we present an overview of the pig genome architecture in muscle at two late developmental stages. The muscle maturation process occurs between the 90th day and the end of gestation (114 days), a key period for survival at birth. To characterise this period we profiled chromatin interactions genome-wide with in situ Hi-C (High Throughput Chromosome Conformation Capture) in muscle samples collected at 90 and 110 days of gestation, specific moments where a drastic change in gene expression has been reported. About 200 million read pairs per library were generated (3 replicates per condition). This allowed: (a) the design of an experimental Hi-C protocol optimized for frozen fetal tissues, (b) the first Hi-C contact heatmaps in fetal porcine muscle cells, and (c) to profile Topologically Associated Domains (TADs) defined as genomic domains with high levels of chromatin interactions. Using the new assembly version Sus scrofa v11, we could map 82% of the Hi-C reads on the reference genome. After filtering, 49% of valid read pairs were used to infer the genomic interactions in both developmental stages. In addition, ChIP-seq experiments were performed to map the binding of the structural protein CTCF, known to regulate genome structure by promoting interactions between genes and distal enhancers. The Hi-C and ChIP-seq data were analysed in combination with the results of a previous transcriptome analysis, focusing on the hun-dreds of genes that were reported as differentially expressed during muscle maturation. We will report the observed general differences between both developmental stages in terms of transcription and structure
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
The GENETPIG database has been established for storing and disseminating the results of the European project: âGENETPIG: identification of genes controlling economic traits in pig'. The partners of this project have mapped about 630 porcine and human ESTs onto the pig genome. The database collects the mapping results and links them to other sources of mapping data; this includes pig maps as well as available comparative mapping information. Functional annotation of the mapped ESTs is also given when a significant similarity to cognate genes was established. The database is accessible for consultation via the Internet at http://www.infobiogen.fr/services/Genetpi
Evolution des conceptions de l'organisation de l'ADN mitochondrial par des études de la stérilité mùle cytoplasmique des plantes
Notice présente dans BelInra (https://belinra.inra.fr/gestion/catalog.php?categ=isbd&id=83504)il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATIONEvolution des conceptions de l'organisation de l'ADN mitochondrial par des études de la stérilité mùle cytoplasmique des plante
La stérilité male cytoplasmique du tournesol (Helianthus annuus L.) : caractérisation des ADN chloroplastiques
Notice présente dans BelInra (https://belinra.inra.fr/gestion/catalog.php?categ=isbd&id=83503)il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATIONLa stérilité male cytoplasmique du tournesol (Helianthus annuus L.) : caractérisation des ADN chloroplastique
Structure et expression du genome du bacteriophagetempere MV4 de Lactobacillus bulgaricus
SIGLECNRS T Bordereau / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc
Molecular taxonomy of Lactobacillus phages
International audienceForty-eight strains of lactobacilli used as starter strains in the dairy industry were examined for lysogeny after treatment with mitomycin C. Two strains of L. delbrueckii subsp. bulgaricus were able to produce active phages. These temperate phages as well as 4 virulent phages isolated during abnormal fermentations were compared to a previously characterized phage mv4 which is temperate. All these phages were shown to be partially homologous by DNA-DNA hybridization. Genes that code for viral proteins seem to be well conserved since 2 major virion polypeptides of 18 (or 19) kD and 34 kD could be detected in the protein composition of each phage. Immunoblotting studies of the 7 phages using serum raised against phage mv4 confirmed that the proteins of the different phages were related. All these phages can be classified in the previously constituted group a, which now comprises 4 temperate and 15 virulent phages. These results show that some virulent phages appearing during abnormal fermentations and some temperate phages isolated by induction of starter strains can be closely related genetically. Five virulent phages of L. helveticus were also compared according to their restriction pattern and their DNA homology. They were shown to be related to one another, but unrelated to phages of other lactic acid bacteria species
Dynamiques d'expressions et architecture nucléaire des gÚnes IGF2 et de DLK1 pour une meilleure compréhension de la balance myogenÚse/adipogenÚse dans l'espÚce porcine
National audienceNotre objectif est de caractĂ©riser le rĂŽle de lâarchitecture nuclĂ©aire dans la rĂ©gulation de l'expression de gĂšnes dâintĂ©rĂȘt pendant lâadipogĂ©nĂšse et la myogenĂšse. Il a Ă©tĂ© choisi dâĂ©tudier Ă la fois la dynamique dâexpression des gĂšnes IGF2 et DLK1 (gĂšnes clĂ©s dans le dĂ©veloppement des tissus adipeux et musculaires) et lâorganisation nuclĂ©aire de ces gĂšnes au cours de la prolifĂ©ration puis de la diffĂ©renciation des populations de cellules stromales/souches adultes issues du tissu adipeux sous-cutanĂ© ou du muscle longissimus de porcelets, pour mieux comprendre les mĂ©canismes impliquĂ©s dans la balance muscle/gras chez le porc. En effet, il a Ă©tĂ© montrĂ© que lâarchitecture nuclĂ©aire est impliquĂ©e dans la rĂ©gulation de l'expression de nombreux gĂšnes pendant lâadipogĂ©nĂšse (Charo et al., 2016) et la myogenĂšse y compris chez le porc (Lahbib-Mansais et al., 2016). Cependant, il nây a pas dâĂ©tudes qui caractĂ©risent la rĂ©gulation dâIGF2 et DLK1 dans des populations de cellules souches des tissus musculaires et adipeux, triĂ©es en fonction de leurs capacitĂ©s myogĂ©niques ou adipogĂ©niques, et selon le tissu oĂč elles rĂ©sident. A PEGASE, nous avons testĂ© dans une prĂ©cĂ©dente Ă©tude un panel de marqueurs permettant de phĂ©notyper les cellules musculaires et adipeuses et visant Ă aller plus loin dans la discrimination des cellules satellites (CD56+/CD45-) et des cellules fibroadipogĂ©niques (CD56-/CD45-). Au stade prĂ©coce auquel nous rĂ©cupĂ©rons les cellules de porcelets (5-7 jours), les marqueurs CD56 (marqueur myogĂ©nique, prĂ©sent Ă la fois dans le muscle et le tissu adipeux) et CD45 (marqueur hĂ©matopoĂŻĂ©tique) paraissent les plus pertinents. Pour cette Ă©tude, les variations 1) dâexpression gĂ©nique (partenaire 1, PEGASE) et 2) dâassociation gĂ©nique lors dâĂ©tude dâarchitecture nuclĂ©aire (partenaire 2, GenPhySE) sont Ă©tudiĂ©es sur les cellules isolĂ©es des tissus prĂ©levĂ©s sur des porcelets (Landrace x Large White x PiĂ©train, femelles) de 5 jours. Cette approche a nĂ©cessitĂ© de dĂ©velopper des systĂšmes de culture sur lame de verre qui prĂ©servent la structure 3D (sur Matrigel). La culture sur verre nous a confrontĂ© Ă des difficultĂ©s dâadhĂ©rence des cellules, surtout lors de leur diffĂ©renciation, certainement en lien avec la migration cellulaire et la rĂ©organisation intracellulaire inhĂ©rente Ă ces modĂšles de culture. LâĂ©tude sur cellules triĂ©es nâa pas Ă©tĂ© poursuivie. En effet, les cellules CD56- nâadhĂ©rant pas sur lame de verre, nous avons dĂ©cidĂ© de travailler sur lâensemble des cellules stromales sans tri prĂ©alable en rĂ©alisant des mesures sur un point au cours de la prolifĂ©ration et sur deux points au cours de la diffĂ©renciation. A GenPhySE, les premiers rĂ©sultats dâassociation gĂ©nique entre IGF2-DLK1 ont Ă©tĂ© montrĂ©s dans des noyaux de cellules souches non triĂ©es issues de tissu adipeux, au stade de prolifĂ©ration (Jour 3). Lâobservation en microscopie confocale des noyaux marquĂ©s Ă lâaide de deux molĂ©cules fluorescentes distinctes pour chacun des gĂšnes, a permis de mettre en Ă©vidence une association ADN-ADN entre un allĂšle de chacun des gĂšnes. Pour conclure, il a Ă©tĂ© difficile de transposer les systĂšmes de culture cellulaire utilisĂ©s prĂ©cĂ©demment Ă des systĂšmes de culture sur lame de verre permettant de prĂ©server la structure 3D des cellules et de rĂ©aliser les analyses FISH 3D et la microscopie confocale. Des analyses dâassociation gĂ©nique et dâexpression de gĂšnes cibles dont IGF2 et DLK1 par qPCR sont toujours en cours et les derniĂšres analyses sont prĂ©vues pour le printemps 2022
Localization of the tenascin-C gene to pig Chromosome 1
Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-AccessInternational audienc
Swine cytosolic malic enzyme: cDNA cloning, sequencing, and localization
Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-AccessInternational audienc
A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation
The integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development