Éditeur(s) : Université des Antilles AREBio Groupe de recherche BIOSPHERES : BIOlogie, Sciences Physiques & Humaines pour les énergies Renouvelables, l
Extrait de : 1er colloque international BIOSPHERES, du 18 au 20 juin 2019. Université des Antilles
Description : Chlordecone is a persistent organochlorine pesticide widely used between 1972 and 1993 in the French West Indies to control the root borer in banana fields. Chlordecone use resulted in long-term pollution of soils, contamination of waters, of aquatic organisms, and of fields. Chlordecone is known to be neurotoxic, to increase prostate cancer, and to have negative effects on cognitive and motor development during infancy. In Guadeloupe, most of the freshwater species living in contaminated rivers exceed the French legal limit of 20 ?g·kg?1 wet weight. In the present study (ANR MACHLOMA), we chose a transcriptomic approach to study the cellular effects of chlordecone in the giant freshwater prawn Macrobrachium rosenbergii, an important economical species in Guadeloupe.

Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V19065
V19065

Éditeur(s) : HAL CCSD
Résumé : Spermatogenesis in mammals is a complex biological function including cellular processes such as proliferation, meiosis and differentiation, aiming to the production of male gametes in the testis. If the seminiferous epithelium is well described in terms of organization and cellular morphology of cells that compose it, the processes by which undifferentiated diploid germ cells enter meiosis and give haploid cells that undergo many morphological transformations, are not fully decrypted. These processes rely on the coordinated and sequential expression of genes, including specific products for each stage of germ cell development These gene products are essential at each key stage of spermatogenesis. Transcriptomics since the 1990s, and proteomics since the 2000s have contributed to the improved. understanding of these mechanisms. A long term proteomic study aiming at characterizing the proteomes of Sertoli cells and germ cells, and a recent study that characterized and quantified the transcriptome of isolated rat testicular cells at high resolution using de novo sequencing of transcripts (RNA-Seq), have been the basis of my thesis work. The latter study showed the accumulation of long non-Coding RNAs (lncRNAs) and testicular unannotated transcripts (TUTs) at meiotic and post-Meiotic stages of spermatogenesis in the rat. In this context, my thesis work aimed at validating the coding potential of many genes expressed in germ cells using RNA-Seq combined with shotgun proteomics, a so-Called PIT (Proteomics Informed by transcriptomics) approach. In this approach, the protein sequences translated from the transcripts assembled by RNA-Seq in the different testicular cell types are integrated into a custom database of protein sequences used to query mass spectrometry data obtained from proteins of meiotic and post-Meiotic cells. The PIT approach showed that 69 TUTs or lncRNA (corresponding to 44 loci) code for proteins in meiotic cells and post meiotic cells, and we confirmed experimentally the meiotic and post-Meiotic expression for two new transcripts encoding for VAMP9, a protein of the SNARE family, and a new testicular enolase T-ENOL. The post-Meiotic expression of T-ENOL protein was confirmed by immunohistochemistry using a polyclonal antibody raised against the recombinant protein. This approach also allowed us to identify new isoforms of known proteins, specific to each stage of spermatogenesis. Germ cells and Sertoli cells maintain a dialogue which is necessary to the success of spermatogenesis and spermiogenesis. Another part of my work aimed at identifying membrane proteins, in germ cells and residual bodies, that may be involved in the dialogue between Sertoli cells and germ cells, using a ICPL relative quantification proteomic approach. The ICPL analysis enabled us to establish a list of 166 proteins whose expression is differential between pachytene spermatocytes, round spermatids and residual bodies. Their differential expression suggests that these proteins may play a role in spermiogenesis. Thanks to the Gene Ontology annotations, a list of 8 proteins with a putative role in signal transduction, cell recognition or differentiation, thus potentially involved in the dialogue between Sertoli and germ cells was drawn. In addition, I provided a first proteome of rat Sertoli cells, germ cells and residual bodies obtained by shotgun proteomics.
La spermatogenèse chez les mammifères est une fonction biologique complexe incluant des processus de prolifération cellulaire, de méiose et de différenciation uniques visant à la production des gamètes mâles au sein du testicule. Si l’épithélium séminifère est bien décrit sur le plan de son organisation et de la morphologie des cellules qui le composent, les processus par lesquels les cellules germinales diploïdes indifférenciées entrent en méiose pour donner ensuite des cellules haploïdes subissant par la suite de nombreuses transformations morphologiques, ne sont pas totalement décryptés. Ils reposent sur l’expression coordonnée et séquentielle de gènes dont les produits spécifiques de chaque stade de développement des cellules germinales sont essentiels aux étapes clés de la spermatogenèse. La transcriptomique depuis les années 1990 et la protéomique depuis les années 2000 ont contribué à l’amélioration de la connaissance de ces mécanismes. Une étude protéomique visant à caractériser par des approches systématiques et différentielles les protéomes des cellules de Sertoli et de la lignée germinale, et d’autre part une étude récente, réalisée dans notre unité, qui a permis de caractériser et de quantifier le transcriptome des cellules testiculaires isolées de rat en utilisant le séquençage de novo des transcrits (RNA-Seq), ont été à la base de mes travaux de thèse. Cette dernière étude a mis en évidence l’accumulation de longs ARNs non codants (lncRNAs) et de transcrits testiculaires non annotés (TUTs) aux stades méiotique et post- méiotique de la spermatogenèse chez le rat. Dans ce contexte, mon travail a consisté à valider le potentiel codant de nombreux gènes exprimés dans les cellules germinales par une approche dite PIT (Proteomics Informed by Transcriptomics) couplant protéomique Shotgun et RNA-Seq. Dans ce type d’approche, les séquences protéiques déduites des transcrits des différents types cellulaires, assemblés par RNA-Seq, sont intégrées dans une base personnalisée de séquences protéiques utilisée pour interroger les données de spectrométrie de masse obtenues à partir de protéines de cellules méiotiques et post-Méiotiques. L’approche PIT a permis de montrer que 69 TUTs ou lncRNA (correspondant à 44 loci) codent pour des protéines dans les cellules méiotiques et post méiotiques. L’expression post-Méiotique de deux nouveaux transcrits, l’un codant pour la protéine VAMP9, une protéine de la famille SNARE, et l’autre pour une nouvelle énolase T-ENOL a pu être confirmée. L’expression post-Méiotique de T-ENOL a été confirmée par immunohistochimie à l’aide d’un anticorps polyclonal produit contre la protéine recombinante. Cette approche nous a également permis d’identifier de nouvelles isoformes de protéines connues spécifiques de chaque stade de la spermatogenèse. Les cellules germinales et les cellules de Sertoli entretiennent le dialogue nécessaire au bon déroulement de la spermatogenèse. Une autre partie de mon travail a consisté à identifier des protéines membranaires des cellules germinales et des corps résiduels, susceptibles d’intervenir dans le dialogue entre les cellules de Sertoli et les cellules germinales, par une approche protéomique de quantification relative ICPL. Cette approche a permis d’établir une liste de 166 protéines différentiellement exprimées entre les spermatocytes pachytène, les spermatides rondes et les corps résiduels, qui sont susceptibles de jouer un rôle dans la spermiogénèse. Grâce aux annotations de le Gene Ontology, j’ai pu établir une liste de 8 protéines ayant un rôle supposé dans la transduction du signal, la reconnaissance cellulaire ou bien la différenciation. Par ailleurs, j’ai pu établir par protéomique Shotgun un premier protéome des cellules de Sertoli, des cellules germinales et des corps résiduels chez le rat.
https://tel.archives-ouvertes.fr/tel-01127389

Droits : info:eu-repo/semantics/OpenAccess
NNT : 2014REN1S064
tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389
https://tel.archives-ouvertes.fr/tel-01127389/document
https://tel.archives-ouvertes.fr/tel-01127389/file/2014REN1S064.pdf

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Estrogen receptors (ER) α and β are found in both women and men in many tissues, where they have different functions, including having roles in cell proliferation and differentiation of the reproductive tract. In addition to estradiol (E2), a natural hormone, numerous compounds are able to bind ERs and modulate their activities. Among these compounds, phytoestrogens such as isoflavones, which are found in plants, are promising therapeutics for several pathologies. Glyceollins are second metabolites of isoflavones that are mainly produced in soybean in response to an elicitor. They have potentially therapeutic actions in breast cancer by reducing the proliferation of cancer cells. However, the molecular mechanisms driving these effects remain elusive. METHODS: First, to determine the proliferative or anti-proliferative effects of glyceollins, in vivo and in vitro approaches were used. The length of epithelial duct in mammary gland as well as uterotrophy after treatment by E2 and glyceollins and their effect on proliferation of different breast cell line were assessed. Secondly, the ability of glyceollin to activate ER was assessed by luciferase assay. Finally, to unravel molecular mechanisms involved by glyceollins, transcriptomic analysis was performed on MCF-7 breast cancer cells. RESULTS: In this study, we show that synthetic versions of glyceollin I and II exert anti-proliferative effects in vivo in mouse mammary glands and in vitro in different ER-positive and ER-negative breast cell lines. Using transcriptomic analysis, we produce for the first time an integrated view of gene regulation in response to glyceollins and reveal that these phytochemicals act through at least two major pathways. One pathway involving FOXM1 and ERα is directly linked to proliferation. The other involves the HIF family and reveals that stress is a potential factor in the anti-proliferative effects of glyceollins due to its role in increasing the expression of REDD1, an mTORC1 inhibitor. CONCLUSION: Overall, our study clearly shows that glyceollins exert anti-proliferative effects by reducing the expression of genes encoding cell cycle and mitosis-associated factors and biomarkers overexpressed in cancers and by increasing the expression of growth arrest-related genes. These results reinforce the therapeutic potential of glyceollins for breast cancer.
ISSN: 1478-811X

hal-01560288
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560288
DOI : 10.1186/s12964-017-0182-1
PUBMED : 28666461

Éditeur(s) : HAL CCSD
Résumé : Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.
Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.
https://tel.archives-ouvertes.fr/tel-01405400

NNT : 2015YANE0005
tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400/document
https://tel.archives-ouvertes.fr/tel-01405400/file/these_-_tinaut.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
BACKGROUND: Mammalian spermatogenesis is a process that involves a complex expression program in both somatic and germ cells present in the male gonad. A number of studies have attempted to define the transcriptome of male meiosis and gametogenesis in rodents and primates. Few human transcripts, however, have been associated with testicular somatic cells and germ cells at different post-natal developmental stages and little is known about their level of germline-specificity compared with non-testicular tissues. METHODS: We quantified human transcripts using GeneChips and a total of 47 biopsies from prepubertal children diagnosed with undescended testis, infertile adult patients whose spermatogenesis is arrested at consecutive stages and fertile control individuals. These results were integrated with data from enriched normal germ cells, non-testicular expression data, phenotype information, predicted regulatory DNA-binding motifs and interactome data. RESULTS: Among 3580 genes for which we found differential transcript concentrations in somatic and germ cells present in human testis, 933 were undetectable in 45 embryonic and adult non-testicular tissues, including many that were corroborated at protein level by published gene annotation data and histological high-throughput protein immunodetection assays. Using motif enrichment analyses, we identified regulatory promoter elements likely involved in germline development. Finally, we constructed a regulatory disease network for human fertility by integrating expression signals, interactome information, phenotypes and functional annotation data. CONCLUSIONS: Our results provide broad insight into the post-natal human testicular transcriptome at the level of cell populations and in a global somatic tissular context. Furthermore, they yield clues for genetic causes of male infertility and will facilitate the identification of novel cancer/testis genes as targets for cancer immunotherapies.
ISSN: 0268-1161

hal-00877243
https://hal.archives-ouvertes.fr/hal-00877243
DOI : 10.1093/humrep/des301
PUBMED : 22926843

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Glioblastoma (GB) is the most frequent and aggressive type of primary brain tumor. Recurrences are mostly located at the margin of the resection cavity in the peritumoral brain zone (PBZ). Although it is widely believed that infiltrative tumor cells in this zone are responsible for GB recurrence, few studies have examined this zone. In this study, we analyzed PBZ left after surgery with a variety of techniques including radiology, histopathology, flow cytometry, genomic, transcriptomic, proteomic, and primary cell cultures. The resulting PBZ profiles were compared with those of the GB tumor zone and normal brain samples to identify characteristics specific to the PBZ. We found that tumor cell infiltration detected by standard histological analysis was present in almost one third of PBZ taken from an area that was considered normal both on standard MRI and by the neurosurgeon under an operating microscope. The panel of techniques used in this study show that the PBZ, similar to the tumor zone itself, is characterized by substantial inter-patient heterogeneity, which makes it difficult to identify representative markers. Nevertheless, we identified specific alterations in the PBZ such as the presence of selected tumor clones and stromal cells with tumorigenic and angiogenic properties. The study of GB-PBZ is a growing field of interest and this region needs to be characterized further. This will facilitate the development of new, targeted therapies for patients with GB and the development of approaches to refine the per-operative evaluation of the PBZ to optimize the surgical resection of the tumor.
ISSN: 0167-594X

hal-01117083
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01117083/file/Characterizing%20the%20Peritumoral%20Brain%20Zone_accepted.pdf
DOI : 10.1007/s11060-014-1695-8

Résumé : AU COURS DE LA THESE, L'ETUDE DU TRANSCRIPTOME DE SOUCHES GARDEL ET SENEGAL VIRULENTES ET ATTENUEES D'E. RUMINANTIUMA ETE REALISEE. UNE ANALYSE DU TRANSCRIPTOME A DIFFERENTS STADES DE DEVELOPPEMENT, A D'ABORD ETE EFFECTUEE POUR LA SOUCHE GARDEL VIRULENTE. AU STADE CORPS RETICULE (FORME INTRACELLULAIRE NON INFECTIEUSE), UNE SUREXPRESSION DES GENES CODANT POUR DES PROTEINES IMPLIQUEES DANS LE METABOLISME, LE TRANSPORT ET L'ECHANGE DE NUTRIMENTS ET DANS LA RESISTANCE AU STRESS OXYDATIF ETAIT OBSERVEE. IL SEMBLERAIT QUEE. RUMINANTIUMMETTE EN PLACE UN PANEL DE MECANISMES POUR SA SURVIE ET SON DEVELOPPEMENT A L'INTERIEUR DE LA CELLULE HOTE. AU STADE CORPS ELEMENTAIRE (FORME EXTRACELLULAlRE INFECTIEUSE), LE GENE DKSA CODANT POUR UN FACTEUR DE TRANSCRIPTION ETAIT SUREXPRIME. CE GENE A ETE MONTRE COMME ETANT IMPLIQUE DANS LA REGULATION DE FACTEURS DE VIRULENCE. IL SEMBLERAIT . DONC, QU'AU STADE CORPS ELEMENTAIRE, IL Y AIT UNE INDUCTION DE MECANISMES DE VIRULENCE. LA COMPARAISON DE L'EXPRESSION DES GENES AU STADE CORPS ELEMENTAIRE ENTRE SOUCHES VIRULENTES ET ATTENUEES A AUSSI ETE EFFECTUEE. NOS RESULTATS ONT MONTRE UNE MODIFICATION IMPORTANTE DE LA MEMBRANE POUR LES SOUCHES VIRULENTES ET ATTENUEES. POUR LES SOUCHES ATTENUEES, IL A ETE MONTRE UNE SUREXPRESSION DES GENES IMPLIQUES DANS LA BIOGENESE MEMBRANAlRE ET UNE SOUS-EXPRESSION·DES PROTEINES DE LA FAMILLE MULTIGENIQUE MAP. CES RESULTATS SUGGERENT QUE LES PROTEINES MAP JOUENT UN ROLE DE LEURRE VIS-A-VIS DE LA REPONSE IMMUNITAIRE PROTECTRICE. DES PROTEINES MEMBRANAlRES HYPOTHETIQUES SONT SUREXPRIMEES A LA FOIS CHEZ LES SOUCHES VIRULENTES ET ATTENUEES. CERTAINES D'ENTRE ELLES SUREXPRIMEES CHEZ LES SOUCHES ATTENUEES SEMBLENT ETRE DE BONS CANDIDATS VACCINAUX ET DEVRAIENT ETRE ETUDIEES
Transcriptomic study of gardel and senegal both virulent and attenuated e. ruminantium strains was conducted during my phd. an analysis of transcriptome at different stages of development has been first conducted for virulent gardel strain. at reticulate body stage (intracellular form non-infectious), over-expression of genes coding for proteins involved in metabolism, transport and exchange of nutrients and resistance to oxidative stress was observed. at this stage of development, e. ruminantium seems to activate mechanisms for its survival and development within the host cell. at elementary body stage, dksa the gene encoding for a transcription factor was over-expressed. this gene has been shown to be involved in the regulation of virulence factors. it seems, therefore, at the elementary body stage, e. ruminantium induces its virulence factors. secondly, we compare the transcriptome of elementary body between virulent and attenuated strains. our results showed an important membrane modification of attenuated and virulent strains. for attenuated strains, we observed an over-expression of genes involved in membrane biogenesis and a diminution of expression of map multigenic family. it seems that map proteins subvert the protective immune response. hypothetical membrane proteins are over-expressed in both virulent and attenuated strains. some over-expressed proteins in attenuated strains seem to be good vaccine candidates and willstudied.

http://www.theses.fr/2012AGUY0562/document

Éditeur(s) : HAL CCSD BioScientifica
Résumé : International audience
Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the 'proteomics informed by transcriptomics' technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.
ISSN: 1470-1626

hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01214005/file/Linking%20transcriptomics%20and%20proteomics%20in%20spermatogenesis.pdf
DOI : 10.1530/REP-15-0073

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
STUDY QUESTION: Can protein biomarkers of the male genital tract be identified in human seminal plasma? SUMMARY ANSWER: We identified potential biomarkers for each of the organs participating in the secretions of the human seminal plasma. WHAT IS KNOWN ALREADY: The seminal plasma fulfills critical functions for fertility by providing spermatozoa with a protective milieu, promoting their final maturation and modulating the immune responsiveness of the female reproductive tract. It is also considered to be a promising source of biomarkers of male infertility and/or pathologies of the male genital tract. STUDY DESIGN, SIZE, DURATION: This study combines proteomic analyses of normal seminal plasma together with transcriptomic gene expression profiling of human healthy tissues. MATERIALS, SETTING, METHODS: Non-liquefied seminal plasma proteins from a healthy donor were prefractionated using two sequential Proteominer™ libraries. Eight subproteome fractions were collected, trypsin digested and subjected to three successive mass spectrometry analyses for peptide characterization. The list of identified proteins was compared with and merged with other available data sets of the human seminal plasma proteome. The expression of corresponding genes was then investigated using tissue transcriptome profiles to determine where, along the male reproductive tract, these proteins were produced. Finally, tissue specificity of a selected subset of biomarker candidates was validated on human tissues. MAIN RESULTS AND THE ROLE OF CHANCE: We first performed a proteomic analysis of the human seminal plasma and identified 699 proteins. By comparing our protein list with other previous proteomic data sets, we found that 2545 unique proteins have been described so far in the human seminal plasma. We then profiled their expression at the gene level and identified 83 testis, 42 epididymis, 7 seminal vesicle and 17 prostate candidate protein markers. For a subset of testis-specific candidates, i.e. TKTL1, LDHC and PGK2, we further validated their germ cell expression and demonstrated that such markers could distinguish between semen from fertile and infertile men. LIMITATIONS, REASONS FOR CAUTION: While some of the markers we identified are well-known tissue-specific products, further dedicated studies to validate the biomarker status of new candidates will be required. Additionally, whether or not the abundance of these proteins is indeed decreased in some specific pathological situations remains to be determined. WIDER IMPLICATIONS OF THE FINDINGS: Using an integrative genomics approach, we identified biomarker candidates for each of the organs participating in the seminal plasma production. In this study, we essentially focused on germ cell markers and their potential application for the diagnosis of male infertility. Other types of markers also deserve a focused attention given their potential predictive value for various reproductive disorders, notably for prostate cancers. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by the Proteomics Core Facility at Biogenouest and was funded by Conseil Régional de Bretagne, IBiSA and Agence de la Biomédecine grants. The authors declare that there exists a competing financial interest in this work that is related to a patent application on the use of identified germ cell-specific proteins in an antibody-based assay (Fertichip™) to predict the successful testicular biopsy outcomes in human non-obstructive azoospermia.
ISSN: 0268-1161

inserm-00814146
http://www.hal.inserm.fr/inserm-00814146
DOI : 10.1093/humrep/des360
PUBMED : 23024119

Éditeur(s) : HAL CCSD Impact journals
Résumé : International audience
Interleukin (IL)-33 has been recently reported to be strongly pro-fibrogenic in various models of liver disease. Our aim was to study the role of endogenous IL-33 in a diet-induced model of steatohepatitis. IL-33 deficient mice and wild type (WT) littermates received a high-fat diet (HFD), or a standard diet for 12 weeks. The HFD-induced steatohepatitis was associated with an upregulation of IL-33 transcripts and protein. An insulin tolerance test revealed lower systemic insulin sensitivity in IL33-/-HFD mice than in WT-HFD mice. Nevertheless, IL-33 deficiency did not affect the severity of liver inflammation by histological and transcriptomic analyses, nor the quantity of liver fibrosis. Livers from HFD mice had more myeloid populations, markedly fewer NKT cells and higher proportion of ST2+ Treg cells and ST2+ type 2 innate lymphoid cells (ILC2), all unaffected by IL-33 deficiency. In conclusion, deficiency of endogenous IL-33 does not affect the evolution of experimental diet-induced steatohepatitis towards liver fibrosis.
ISSN: 1949-2553

hal-01578584
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01578584
DOI : 10.18632/oncotarget.18335
PUBMED : 28611297

Éditeur(s) : HAL CCSD
Résumé : Ctenophores are one of the four animal phyla positioned outside from the Bilateria. Most ctenophore species are planktonic and gelatinous, and are easily recognisable by their eight comb rows used for swimming. Ctenophore systematics remains nowadays poorly understood. Anatomical characters do not help much in placing them within the animal tree, and similarly the grounds for establishment of their internal phylogeny as well as delimitation of species are notoriously weak due to a paucity of informative morpho-anatomical characters. Until now, the use of molecular data has failed to improve significantly this situation. The aim of this PhD thesis was to bring a contribution to our understanding of ctenophore evolution at different taxonomic scales. At the metazoan level, the position of ctenophores was addressed using a phylogenomic approach. Taxonomic sampling was significantly improved through sequencing and assembly of transcriptomes of 22 non-bilaterian species (belonging to ctenophores, cnidarians and sponges). Two independent datasets were analysed, one consisting in an update of an existing supermatrix of 128 genes, the other one (4235 genes) having been entirely built de novo, thanks to a newly-devised semi-automated protocol intended to eliminate all major potential causes of artefacts (contaminations, paralogies, missing data). Results clearly contradict recent phylogenomic studies which claimed Ctenophora to be the most early-diverging animal lineage, our analyses instead supporting Porifera as the sister-group to other metazoans. The exact position of ctenophores remains however uncertain at this stage, different conditions of analyses yielding three contradictory hypotheses as open possibilities. At the intra-phyletic level, analyses of a ADNr 18S and ITS (internal transcribed spacers) dataset, together with study of duplicated genes and the results of phylogenomic analyses, allowed resolving most phylogenetic relationships between ctenophore orders and families, including the placement of the ctenophore tree root. Finally, at smaller taxonomic scale, in-depth comparison between two species of the genus Pleurobrachia using immunohistochemistry demonstrates the potential of these techniques for uncovering new structural “micro-anatomical” characters useful for diagnosis and identification of ctenophore species. It is our hope that this work will contribute to improving the systematics of a poorly known phylum of great importance for understanding early animal evolution.
Les cténophores représentent l’un des quatre embranchements animaux extérieurs aux Bilateria. La majoritédes espèces sont planctoniques et gélatineuses, et sont reconnaissables à leurs huit rangées de peignes dont lebattement permet la nage. Leur systématique est encore de nos jours mal comprise. L'anatomie descténophores offre peu de caractères aussi bien pour placer la lignée dans l’arbre des métazoaires, que pourétablir les relations de parenté au sein de l’embranchement et délimiter les espèces, et jusqu’à présent lesdonnées moléculaires n’ont pas permis de résoudre ces problèmes de manière satisfaisante. L’objectif de cetravail de thèse est de contribuer à améliorer notre compréhension de l'évolution des cténophores àdifférentes échelles taxonomiques. A l’échelle des métazoaires, la position phylogénétique des cténophores aété abordée par une approche phylogénomique. Un effort significatif a été réalisé pour améliorerl’échantillonnage taxonomique à travers le séquençage et l’assemblage des transcriptomes de 22 espèces denon-Bilateria (cténophores, cnidaires, spongiaires). Deux jeux de données indépendants ont été analysés, lepremier représentant une mise à jour d’une supermatrice existante de 128 gènes ; le second (4235 gènes)ayant été entièrement construit de novo via un protocole original comportant la mise au point de nouvellesméthodes pour traiter de manière semi-automatisée les principales sources potentielles d’artéfact(contaminations, paralogies, données manquantes). Les résultats contredisent certaines études récentes enmontrant que les spongiaires et non les cténophores représentent le groupe-frère des autres métazoaires. Laposition exacte de ces derniers reste à ce stade incertaine (trois options se présentant suivant les analyses). Al’échelle intra-phylétique, l'analyse d'un jeu de données comprenant les marqueurs ADNr 18S et InternalTranscribed Spacers (ITS), associée à des analyses de gènes dupliqués chez les cténophores et aux analysesphylogénomiques précédentes, a permis de résoudre une grande partie des relations phylogénétiques entre lesordres et les familles de cténophores, tout en permettant de préciser la position de la racine. Enfin, à uneéchelle taxonomique plus fine, une comparaison approfondie entre deux espèces du genre Pleurobrachia aumoyen de marquages immunohistochimiques montre le potentiel de ces techniques comme source denouveaux caractères structuraux « micro-anatomiques » à valeur diagnostique pour la délimitation etl’identification des espèces de cténophores. En conclusion, ce travail se veut une contribution au progrès dela systématique d’un embranchement encore méconnu et d’une grande importance pour la compréhensiondes évènements anciens de l’évolution animale.
https://tel.archives-ouvertes.fr/tel-01165014

NNT : 2014PA066448
tel-01165014
https://tel.archives-ouvertes.fr/tel-01165014
https://tel.archives-ouvertes.fr/tel-01165014/document
https://tel.archives-ouvertes.fr/tel-01165014/file/these_archivage_3158995o.pdf

Éditeur(s) : HAL CCSD Endocrine Society
Résumé : International audience
Transcriptional regulation by the estrogen receptor-alpha(ER) has been investigated mainly in breast cancer cell lines, but estrogens such as 17 beta-estradiol (E2) exert numerous extrareproductive effects, particularly in the liver, where E2 exhibits both protective metabolic and deleterious thrombotic actions. To analyze the direct and early transcriptional effects of estrogens in the liver, we determined the E2-sensitive transcriptome and ER cistrome in mice after acute administration of E2 or placebo. These analyses revealed the early induction of genes involved in lipid metabolism, which fits with the crucial role of ER in the prevention of liver steatosis. Characterization of the chromatin state of ER binding sites (BSs) in mice expressing or not ER demonstrated that ER is not required per se for the establishment and/or maintenance of chromatin modifications at the majority of its BSs. This is presumably a consequence of a strong overlap between ER and hepatocyte nuclear factor 4 alpha BSs. In contrast, 40% of the BSs of the pioneer factor forkhead box protein a (Foxa2) were dependent upon ER expression, and ER expression also affected the distribution of nucleosomes harboring dimethylated lysine 4 of Histone H3 around Foxa2 BSs. We finally show that, in addition to a network of liver-specific transcription factors including CCAAT/enhancer-binding protein and hepatocyte nuclear factor 4 alpha, ER might be required for proper Foxa2 function in this tissue.
ISSN: 0888-8809

hal-01357623
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01357623
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01357623/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01357623/file/Changes%20in%20gene%20expression%201%20and%20Estrogen%20Receptor_accepted.pdf
DOI : 10.1210/me.2015-1311

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD BioScientifica
Résumé : International audience
The general rules established from mammalian species for the regulation of spermatogenesis by gonadotropins may not be fully relevant in fish. Particularly, Fsh is as potent as Lh to stimulate steroidogenesis and the Fsh receptor is expressed in Leydig cells. In seasonal breeders, Fsh is likely the major gonadotropin involved in spermatogenesis onset and Lh is required to support spermatogenesis progression and gamete release. However, the genes that relay the action of Fsh and Lh have been poorly investigated in fish. The present study was aimed at identifying gonadotropin-dependent genes expressed in the testis during fish puberty. We cultured pubertal trout testicular explants for 96 h, with or without gonadotropin, and analyzed transcriptome variations using microarrays. Fsh and Lh had similar effects on a large group of genes while other genes were preferentially regulated by one or the other gonadotropin. We showed that most of the responsive genes were expressed in somatic cells and exhibited relevant patterns during the seasonal reproductive cycle. Some genes preferentially modulated by Lh could be involved in testicular cell fate (pvrl1 and bty) or sperm maturation (ehmt2 and racgap1) and will deserve further examination. Besides Fsh's effects on the steroidogenic pathway, our study demonstrates that Fsh coordinates relevant stimulatory and inhibitory paracrine factors known to regulate early germ cell proliferation and differentiation. Some of these genes belong to major regulatory pathways including the Igf pathway (igf1b/igf3 and igfbp6), the Tgfb pathway (amh, inha, inhba, and fstl3), the Wnt pathway (wisp1), and pleiotrophin (mdka).
ISSN: 0952-5041

inserm-00812401
http://www.hal.inserm.fr/inserm-00812401
DOI : 10.1530/JME-12-0197
PUBMED : 23045716

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Millimeter Waves (MMW) will be used in the next-generation of high-speed wireless technologies, especially in future Ultra-Broadband small cells in 5G cellular networks. Therefore, their biocompatibilities must be evaluated prior to their massive deployment. Using a microarray- based approach, we analyzed modifications to the whole genome of a human keratinocyte model that was exposed at 60.4 GHz-MMW at an incident power density (IPD) of 20 mW/cm2 for 3 hours in athermic conditions. No keratinocyte transcriptome modifications were observed. We tested the effects of MMWs on cell metabolism by co-treating MMW-exposed cells with a glycolysis inhibitor, 2-deoxyglucose (2dG, 20 mM for 3 hours), and whole genome expression was evaluated along with the ATP content.We found that the 2dG treatment decreased the cellular ATP content and induced a high modification in the transcriptome (632 coding genes). The affected genes were associated with transcriptional repression, cellular communication and endoplasmic reticulum homeostasis. The MMW/ 2dG co-treatment did not alter the keratinocyte ATP content, but it did slightly alter the transcriptome, which reflected the capacity of MMWto interfere with the bioenergetic stress response. The RT-PCR-based validation confirmed 6 MMW-sensitive genes (SOCS3, SPRY2, TRIB1, FAM46A, CSRNP1 and PPP1R15A) during the 2dG treatment. These 6 genes encoded transcription factors or inhibitors of cytokine pathways, which raised questions regarding the potential impact of long-term or chronic MMW exposure on metabolically stressed cells. © 2016 Soubere Mahamoud et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
ISSN: 1932-6203

hal-01367149
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367149
DOI : 10.1371/journal.pone.0160810
PUBMED : 27529420

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Accumulating evidence suggests that developmental exposure to environmental chemicals may modify the course of brain development, ultimately leading to neuropsychiatric / neurodegenerative disorders later in life. In the present study, we assessed the impact of one of the most frequently used pesticides in both residential and agricultural applications - the synthetic pyrethroid cypermethrin (CYP) - on developmental neurotoxicity (DNT). Female mice were perinatally exposed to low doses of CYP (5 and 20 mg/kg body weight) from gestation to postnatal day 15. Behavioral analyses were performed during the offspring's early life and during adulthood. Postnatal analyses revealed that perinatal exposure to CYP disturbed motor development without modifying sensory and communicative skills. We found that later in life, CYP-exposed offspring expressed maladaptive behaviors in response to highly challenging tasks and abnormal sociability. Transcriptomic analyses performed in the offspring's brain at the end of the exposure, highlighted mitochondrial dysfunction as a relevant pathomechanism underlying CYP-induced DNT. Interestingly, several genes involved in proteostasis maintenance were also shown to be dysregulated suggesting that alterations in biogenesis, folding, trafficking and degradation of proteins may significantly contribute to CYP-related DNT. From a regulatory perspective, this study highlights that behavioral and transcriptomic analyses are complementary tools providing useful direction for better DNT characterization, and as such, should be used together more systematically.
ISSN: 1932-6203

hal-01616489
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01616489
DOI : 10.1371/journal.pone.0184475
PUBMED : 29020013

Éditeur(s) : HAL CCSD BioMed Central
Résumé : [b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species.
ISSN: 1471-2164

hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439
https://hal.archives-ouvertes.fr/hal-01032439/document
https://hal.archives-ouvertes.fr/hal-01032439/file/art_10-1186_1471-2164-15-238.pdf
DOI : 10.1186/1471-2164-15-238

Éditeur(s) : HAL CCSD Cold Spring Harbor Laboratory Press
Résumé : International audience
The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein-coding mRNAs and a considerable amount of different noncoding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), which emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs, and a number of uncharacterized long noncoding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.
ISSN: 1355-8382

hal-00985894
https://hal-univ-rennes1.archives-ouvertes.fr/hal-00985894
DOI : 10.1261/rna.043729.113
PUBMED : 24554440