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Estrogens are steroid hormones produced by the aromatization of androgens by the aromatase enzyme, encoded by theCYP19A1gene. Although generally referred to as “female sex hormones”, estrogen is also produced in the adult testes of many mammals, including humans. To better understand the function of estrogens in the male, we used the rabbit model which is an important biomedical model. First, the expression ofCYP19A1was localized, demonstrating that testicular estrogens are produced by meiotic germ cells inside the seminiferous tubules. Next, the cells expressing ESR1 and ESR2 were identified, showing that estrogens could exert their function on post-meiotic germ cells in the tubules and play a role during sperm maturation, since ESR1 and ESR2 were detected in thecaudaepididymis. Then, CRISPR/Cas9CYP19A1−/−genetically modified rabbits were analyzed.CYP19A1−/−males showed decreased fertility with lower sperm count associated with hypo-spermatogenesis and lower spermatid number. Germ/sperm cell DNA methylation was unchanged, while sperm parameters were affected asCYP19A1−/−males exhibited reduced sperm motility associated with increased flagellar defects. In conclusion, testicular estrogens could be involved in the spermatocyte-spermatid transition in the testis, and in the acquisition of sperm motility in the epididymis.

Background During epididymal transit, spermatozoa go through several functional maturation steps, resulting from interactions with epididymal secretomes specific to each region. In particular, the sperm membrane is under constant remodeling, with sequential attachment and shedding of various molecules provided by the epididymal lumen fluid and epididymosomes, which also deliver sncRNA cargo to sperm. As a result, the payload of sperm sncRNAs changes during the transit from the epididymis caput to the cauda. This work was designed to study the dynamics of cattle sperm sncRNAs from spermatogenesis to final maturation. Results Comprehensive catalogues of sperm sncRNAs were obtained from testicular parenchyma, epididymal caput, corpus and cauda, as well as ejaculated semen from three Holstein bulls. The primary cattle sncRNA sperm content is markedly remodeled as sperm mature along the epididymis. Expression of piRNAs, which are abundant in testis parenchyma, decreases dramatically at epididymis. Conversely, sperm progressively acquires miRNAs, rsRNAs, and tsRNAs along epididymis, with regional specificities. For instance, miRNAs and tsRNAs are enriched in epididymis cauda and ejaculated sperm, while rsRNA expression peaks at epididymis corpus. In addition, epididymis corpus contains mainly 20 nt long piRNAs, instead of 30 nt in all other locations. Beyond the bulk differences in abundance of sncRNAs classes, K-means clustering was performed to study their spatiotemporal expression profile, highlighting differences in specific sncRNAs and providing insights into their putative biological role at each maturation stage. For instance, Gene Ontology analyses using miRNA targets highlighted enriched processes such as cell cycle regulation, response to stress and ubiquitination processes in testicular parenchyma, protein metabolism in epididymal sperm, and embryonic morphogenesis in ejaculated sperm. Conclusions Our findings confirm that the sperm sncRNAome does not simply reflect a legacy of spermatogenesis. Instead, sperm sncRNA expression shows a remarkable level of plasticity resulting probably from the combination of multiple factors such as loss of the cytoplasmic droplet, interaction with epididymosomes, and more surprisingly, the putative in situ production and/or modification of sncRNAs by sperm. Given the suggested role of sncRNA in epigenetic trans-generational inheritance, our detailed spatiotemporal analysis may pave the way for a study of sperm sncRNAs role in embryo development.

Resume Objectifs Selon le concept des « origines developpementales de la sante et des maladies », l’obesite maternelle predispose la descendance aux maladies chroniques. Pour de multiples raisons, une perte de poids preconceptionnelle est recommandee aux femmes obeses. Cependant, les avantages et les potentiels inconvenients pour l’enfant a naitre sont encore mal etudies. Methodes Nous avons evalue le developpement fœtal et analyse l’expression de modificateurs epigenetiques et de genes metaboliques dans le foie et le placenta. Les descendants nes de mere « controle », « obese » ou « perte de poids » ont ete soumis apres le sevrage a un regime controle ou hyperlipidique. Nous avons suivi les parametres metaboliques et les comportements olfactifs jusqu’a l’âge adulte. Resultats Les fœtus de mere obese presentent une restriction de croissance et une alteration de l’expression de modificateurs epigenetiques de la voie d’acetylation des histones. Les phenotypes metaboliques et olfactifs (obesite, dyslipidemie, intolerance au glucose et faible motivation et capacite a trouver une recompense alimentaire) s’expliquent principalement par le regime post-sevrage, mais l’obesite maternelle a un effet notable de conditionnement dependant du sexe : les mâles nes de mere obese developpent une obesite accrue par rapport a leurs congeneres. La perte de poids preconceptionnelle normalise les phenotypes fœtaux et metaboliques decrits ci-dessus, mais certains genes restent differentiels. De plus, elle a des effets inattendus sur les performances olfactives : la sensibilite olfactive peripherique et la motivation induite par le jeune sont reduites. Conclusions Nos resultats confirment les avantages d’une perte de poids preconceptionnelle pour la sante metabolique des descendants, mais revelent de potentiels effets indesirables tels qu’observes pour le comportement olfactif.

Enhanced pre-pubertal nutrition in Holstein bulls increased reproductive hormone production and sperm production potential with no negative effects on sperm quality. However, recent trends in human epigenetic research have identified pre-pubertal period to be critical for epigenetic reprogramming in males. Our objective was to evaluate the methylation changes in sperm of bulls exposed to different pre-pubertal diets. One-week-old Holstein bull calves (n = 9), randomly allocated to 3 groups, were fed either a high, medium or low diet (20%, 17% or 12.2% crude protein and 67.9%, 66% or 62.9% total digestible nutrients, respectively) from 2 to 32 weeks of age, followed by medium nutrition. Semen collected from bulls at two specific time points, i.e. 55-59 and 69-71 weeks, was diluted, cryopreserved and used for reduced representation bisulfite sequencing. Differential methylation was detected for dietary treatment, but minimal differences were detected with age. The gene ontology term, "regulation of Rho protein signal transduction", implicated in sperm motility and acrosome reaction, was enriched in both low-vs-high and low-vs-medium datasets. Furthermore, several genes implicated in early embryo and foetal development showed differential methylation for diet. Our results therefore suggest that sperm epigenome keeps the memory of diet during pre-pubertal period in genes important for spermatogenesis, sperm function and early embryo development.

Estrogens are steroid hormones produced by the aromatization of androgens by the aromatase enzyme, encoded by the CYP19A1 gene. Although generally referred to as “female sex hormones”, estrogen is also produced in the adult testes of many mammals, including humans. To better understand the function of estrogens in the male, we used the rabbit model which is an important biomedical model. First, the expression of CYP19A1 transcripts was localized mainly in meiotic germ cells. Thus, testicular estrogen appears to be produced inside the seminiferous tubules. Next, the cells expressing ESR1 and ESR2 were identified, showing that estrogens could exert their function on post-meiotic germ cells in the tubules and play a role during sperm maturation, since ESR1 and ESR2 were detected in the cauda epididymis. Then, CRISPR/Cas9 CYP19A1−/− genetically modified rabbits were analyzed. CYP19A1−/− males showed decreased fertility with lower sperm count associated with hypo-spermatogenesis and lower spermatid number. Germ/sperm cell DNA methylation was unchanged, while sperm parameters were affected as CYP19A1−/− males exhibited reduced sperm motility associated with increased flagellar defects. In conclusion, testicular estrogens could be involved in the spermatocyte–spermatid transition in the testis, and in the acquisition of sperm motility in the epididymis.

Background Mature sperm carry thousands of RNAs, including mRNAs, lncRNAs, tRNAs, rRNAs and sncRNAs, though their functional significance is still a matter of debate. Growing evidence suggests that sperm RNAs, especially sncRNAs, are selectively retained during spermiogenesis or specifically transferred during epididymis maturation, and are thus delivered to the oocyte at fertilization, providing resources for embryo development. However , a deep characterization of the sncRNA content of bull sperm and its expression profile across breeds is currently lacking. To fill this gap, we optimized a guanidinium–Trizol total RNA extraction protocol to prepare high-quality RNA from frozen bull sperm collected from 40 representative bulls from six breeds. Deep sequencing was performed (40 M single 50-bp reads per sample) to establish a comprehensive repertoire of cattle sperm sncRNA. Results Our study showed that it comprises mostly piRNAs (26%), rRNA fragments (25%), miRNAs (20%) and tRNA fragments (tsRNA, 14%). We identified 5p-halves as the predominant tsRNA subgroup in bull sperm, originating mostly from Gly and Glu isoacceptors. Our study also increased by ~ 50% the sperm repertoire of known miRNAs and identified 2022 predicted miRNAs. About 20% of sperm miRNAs were located within genomic clusters, expanding the list of known polycistronic pri-miRNA clusters and defining several networks of co-expressed miRNAs. Strikingly, our study highlighted the great diversity of isomiRs, resulting mainly from deletions and non-templated additions (A and U) at the 3p end. Substitutions within miRNA sequence accounted for 40% of isomiRs, with G>A, U>C and C>U substitutions being the most frequent variations. In addition, many sncRNAs were found to be differentially expressed across breeds. Conclusions Our study provides a comprehensive overview of cattle sperm sncRNA, and these findings will pave the way for future work on the role of sncRNAs in embryo development and their relevance as biomarkers of semen fertility.

Nutritional changes during developmental windows are of particular concern in offspring metabolic disease. Questions are emerging concerning the role of maternal weight changes before conception, particularly for weight loss, in the development of diet-related disorders. Understanding the physiological pathways affected by the maternal trajectories in the offspring is therefore essential, but a broad overview is still lacking. We recently reported both metabolic and behavioral negative outcomes in offspring born to obese or weight-loss mothers and fed a control of high-fat diet, suggesting long-term modeling of metabolic pathways needing to be further characterized. Using non-targeted LC&ndash, HRMS, we investigated the impact of maternal and post-weaning metabolic status on the adult male offspring&rsquo, s metabolome in three tissues involved in energy homeostasis: liver, hypothalamus and olfactory bulb. We showed that post-weaning diet interfered with the abundance of several metabolites, including 1,5-anhydroglucitol, saccharopine and &beta, hydroxybutyrate, differential in the three tissues. Moreover, maternal diet had a unique impact on the abundance of two metabolites in the liver. Particularly, anserine abundance, lowered by maternal obesity, was normalized by a preconceptional weight loss, whatever the post-weaning diet. This study is the first to identify a programming long-term effect of maternal preconception obesity on the offspring metabolome.

Several studies have demonstrated that overexposure to pesticides can reduce mammalian sperm quality, impairing male fertility. Chlorpyrifos (CPF), a widely used organophosphate pesticide, was shown to impair spermatogenesis by inducing the formation of highly reactive toxic intermediates. To gain further insight into the mechanisms underlying the cytotoxicity and genotoxicity of CPF, bovine spermatozoa were exposed in vitro to environmental CPF concentrations and the motility, in vitro fertilization rates, DNA fragmentation, chromatin alterations, and methylation patterns were assessed. Motility and in vitro fertilization rates were significantly reduced in spermatozoa exposed to CPF, while DNA fragmentation and putative chromatin deconstruction appeared to increase at higher pesticide concentrations. In situ hybridization was carried out with X and Y probes on sperm samples exposed to different CPF concentrations, and subsequent analysis highlighted a significant percentage of spermatozoa with a peculiar morphological malformation, in which a narrowing occurred at the level of the hybridization. Analysis of potential abnormalities in the methylation pattern of NESP55-GNAS and XIST promoters displayed no differentially methylated regions in GNAS promoter relative to the control, whereas spermatozoa exposed to 10 μg/mL CPF had increased methylation variance in one region of imprinted XIST promoter. Our results provide support that CPF can induce a genotoxic effect on spermatozoa, impairig their ability to fertilize and support preimplantation embryo development in vitro. These observations are worrying since altered levels of sporadic methylation in genes of male gametes may affect the success of reproduction and contribute to infertility. Environ. Mol. Mutagen. 60:85-95, 2019. © 2018 Wiley Periodicals, Inc.

International audience; The postpartum period is crucial in dairy cows and is marked by major physiological and metabolic changes that affect milk production, immune response and fertility. Nutrition remains the most important lever for limiting the negative energy balance and its consequences on general health status in highly selected dairy cows. In order to analyze the effect of a commercial micronutrient on intrinsic parameters, performances and the epigenome of dairy cows, 2 groups of 12 Holstein cows were used: 1 fed a standard diet (mainly composed of corn silage, soybean meal and non-mineral supplement) and the other 1 fed the same diet supplemented with the commercial micronutrient (µ-nutrient supplementation) for 4 weeks before calving and 8 weeks thereafter. Milk production and composition, BW, body condition score (BCS), DM intake (DMI) and health (calving score, metritis and mastitis) were recorded over the study period. Milk samples were collected on D15 and D60 post-calving for analyses of casein, Na+ and K+ contents and metalloprotease activity. Milk leukocytes and milk mammary epithelial cells (mMECs) were purified and counted. The viability of mMECs was assessed, together with their activity, through an analysis of gene expression. At the same time points, peripheral blood mononuclear cells (PBMCs) were purified and counted. Using genomic DNA extracted from PBMCs, mMECs and milk leukocytes, we assessed global DNA methylation (Me-CCGG) to evaluate the epigenetic imprinting associated with the µ-nutrient-supplemented diet. The µ-nutrient supplementation increased BCS and BW without modifying DMI or milk yield and composition. It also improved calving condition, reducing the time interval between calving and first service. Each easily collectable cell type displayed a specific pattern of Me-CCGG with only subtle changes associated with lactation stages in PBMCs. In conclusion, the response to the µ-nutrient supplementation improved the body condition without alteration of global epigenetic status in dairy cows.

National audience; La méthylation de l’ADN, est la marque épigénétique la plus étudiée. Plusieurs méthodes pour l’étudier ont été développées, parmi lesquelles le Reduced Representation Bisulfite Sequencing (RRBS), présente certains avantages. Chez les mammifères, ce sont principalement les cytosines suivies d’une guanine (CpG) qui portent le groupement méthyle. Le RRBS permet de cibler les régions riches en CpG grâce à une digestion de l’ADN génomique par l’enzyme Msp1 (C^CGG), suivie d’une étape de sélection de taille. Ces régions riches en CpG appelées ilots CpG, se trouvent souvent dans ou à proximité des régions régulatrices de l’expression des gènes. Le RRBS a été mis en place dans le laboratoire fin 2014 à partir du protocole précédemment décrit (Gu et al., 2011) *. La préparation des librairies nécessite six grandes étapes qui peuvent être source de biais techniques. C’est pourquoi, le RRBS a été automatisé sur un robot STARlet (Hamilton). Cette automatisation permet de gagner 3h20 et libérer du temps manipulateur par rapport à la préparation manuelle, mais surtout cela permet d’augmenter le débit de préparation de librairies (12 à 24 en automatique vs 4 à 8 en manuel/semaines). Une comparaison de différents paramètres de qualité des librairies a été effectuée entre la préparation classique et automatisée, sur deux espèces (lapins et bovins) montrant que l’automatisation permet un gain et une plus grande reproductibilité du nombre de CpG analysés et donc un gain d’information. En deux ans, 388 librairies ont été préparées de façon automatique, pour sept projets différents, sur deux espèces (lapins, bovins) et des types cellulaires variés (spermatozoïdes, placenta, cerveau, monocytes, fibroblastes). Toutes les librairies ont été séquencées par IntegraGen sur HiSeq 4000. Nous avons pu constater une stabilité de plusieurs paramètres de qualité des librairies, dont nous montrerons quelques exemples.

International audience; Highly differentiated mature spermatozoa carry not only genetic but also epigenetic information that is to be transmitted to the embryo. DNA methylation is one epigenetic actor associated with sperm nucleus compaction, gene silencing, and prepatterning of embryonic gene expression. Therefore, the stability of this mark toward reproductive biotechnologies is a major issue in animal production. The present work explored the impact of hormonal induction of spermiation and sperm cryopreservation in two cyprinids, the goldfish (Carassius auratus) and the zebrafish (Danio rerio), using LUminometric Methylation Assay (LUMA). We showed that while goldfish hormonal treatment did increase sperm production, it did not alter global DNA methylation of spermatozoa. Different sperm samples repeatedly collected from the same males for 2 months also showed the same global DNA methylation level. Similarly, global DNA methylation was not affected after cryopreservation of goldfish spermatozoa with methanol, whereas less efficient cryoprotectants (dimethylsulfoxide and 1,2‐propanediol) decreased DNA methylation. In contrast, cryopreservation of zebrafish spermatozoa with methanol induced a slight, but significant, increase in global DNA methylation. In the less compact nuclei, that is, goldfish fin somatic cells, cryopreservation did not change global DNA methylation regardless of the choice of cryoprotectant. To conclude, global DNA methylation is a robust parameter with respect to biotechnologies such as hormonal induction of spermiation and sperm cryopreservation, but it can be altered when the best sperm manipulation conditions are not met.

Notice à reprendre en chantier qualité avec la version finale de l’Editeur; International audience; We identified, through a genome-wide search for new imprinted genes in the human placenta, DSCAM (Down Syndrome Cellular Adhesion Molecule) as a paternally expressed imprinted gene. Our work revealed the presence of a Differentially Methylated Region (DMR), located within intron 1 that might regulate the imprinting in the region. This DMR showed a maternal allele methylation, compatible with its paternal expression. We showed that DSCAM is present in endothelial cells and the syncytiotrophoblast layer of the human placenta. In mouse, Dscam expression is biallelic in foetal brain and placenta excluding any possible imprinting in these tissues. This gene encodes a cellular adhesion molecule mainly known for its role in neurone development but its function in the placenta remains unclear. We report here the first imprinted gene located on human chromosome 21 with potential clinical implications.

International audience

According to the &ldquo, developmental origins of health and disease&rdquo, (DOHaD) concept, maternal obesity predisposes the offspring to non-communicable diseases in adulthood. While a preconceptional weight loss (WL) is recommended for obese women, its benefits on the offspring have been poorly addressed. We evaluated whether preconceptional WL was able to reverse the adverse effects of maternal obesity in a mouse model, exhibiting a modification of foetal growth and of the expression of genes encoding epigenetic modifiers in liver and placenta. We tracked metabolic and olfactory behavioural trajectories of offspring born to control, obese or WL mothers. After weaning, the offspring were either put on a control diet (CD) or a high-fat (HFD). After only few weeks of HFD, the offspring developed obesity, metabolic alterations and olfactory impairments, independently of maternal context. However, male offspring born to obese mother gained even more weight under HFD than their counterparts born to lean mothers. Preconceptional WL normalized the offspring metabolic phenotypes but had unexpected effects on olfactory performance: a reduction in olfactory sensitivity, along with a lack of fasting-induced, olfactory-based motivation. Our results confirm the benefits of maternal preconceptional WL for male offspring metabolic health but highlight some possible adverse outcomes on olfactory-based behaviours.

To produce embryos by nuclear transfer, it needs a great epigenetic reprogramming of somatic nucleus into embryonic nucleus: this reprogramming is highly dependent of oocyte capacity. Thus, each nucleus is placed in a different environment as soon as the oocyte-somatic cell fusion. This way, the cloned animals obtained using the same fibroblast line, have the same nuclear genotype, but are indubitably epigenetically different ([1]). DNA methylation, is one of the more important epigenetic modification analyzed contributes play a role in regulating gene expression and consequently in different biological processes, such as those involved in health and disease. In this study, we analyzed the genome-wide DNA methylation of a purified subpopulation of immune cells, such as monocytes from cloned and controls Holstein (n=5 per group). Born in an experimental INRA’s farm the cows were breed exactly under the same conditions limiting environmental changes. All growth, health and reproductive information has been collected. Cows were hormonally synchronized, the ovulation detected by ultrasonography and blood samples collected at D15 of cycle. Monocyte purification was performed from peripheral blood mononuclear cells obtained by Ficoll gradient, using CD14+ antibody beads. Genome-wide DNA methylation was analyzed by Reduced Representation Bisulfite Sequencing (RRBS; [2]). After sequencing, the reads were analyzed using our dedicated pipeline (https://github.com/FAANG/faang-methylation/tree/master/RRBS-toolkit). After mapping to the reference genome (UMD3.1 assembly), around of 40% of uniquely mapped reads were obtained. Only CpGs covered between 10X and 500X were analyzed and used to calculate a DNA methylation score which was not different between cloned and control groups. However, PCA described a clear separation between cloned and control groups. Differential analysis of the 10 libraries provided differentially methylated cytosine (DMCs) between the two groups, corresponding to DMRs. This study therefore highlights CpGs and regions displaying a specific methylation pattern in cloned cows.

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According to the new paradigm of the Developpemental Origins of Health and Disease (DOHaD), the environmental factors to which an individual is exposed throughout his life can leave an epigenetic footprint on the genome. A crucial period is the early development, where the epigenome is particularly sensitive to the effects of the environment, and during which the individual builds up his health capital that will enable him to respond more or less well to the vagaries of life. The research challenge is to decipher the modes of action and the epigenetic mechanisms put into play by environmental factors that lead to increased disease susceptibility or resilience. The challenge for health is to translate these scientific discoveries into action through, among others, the establishment of preventive recommendations to slow down the growing incidence of non communicable diseases.

The existence of non-genetic and non-cultural mechanisms that transfer information on the memory of parental exposures to various environments, determining the reactivity of the following generations to their environments during their life, are of growing interest. Yet fundamental questions remain about the nature, the roles and relative importance of epigenetic marks and processes, non-coding RNAs, or other mechanisms, and their persistence over generations. A model incorporating the various transmission systems, their cross-talks and windows of susceptibility to the environment as a function of sex/gender of parent and offspring, has yet to be built.

International audience

International audience; Epidemiological studies in humans and animal models (including ruminants and horses) have highlighted the critical role of nutrition on developmental programming. Indeed, it has been demonstrated that the nutritional environment during the periconceptional period and foetal development can altered the postnatal performance of the resultant offspring. This nutritional programming can be exerted by maternal and paternal lineages and can affect offspring beyond the F1 generation. Alterations in epigenetic mechanisms have been proposed as the causative link behind the programming trajectories observed in the offspring. Although a clear cause-effect relationship between epigenetic modifications during early development and later offspring phenotype has not been demonstrated in livestock species, strong associations have been reported for some epigenetic marks (e.g. messenger RNA) that are worth exploring as possible predictors of future offspring phenotype. In this review, we shortly describe the main epigenetic mechanisms studied so far in mammals (i.e. mainly in the mouse) thought to be associated with developmental programming, and discuss the few studies available in mammalian herbivores (e.g. cattle) showing the effect of nutrition on epigenetic marks and the associated phenotype. Clearly, there is a need to develop research on nutritional strategies capable of modulating the epigenetic machinery with positive influence on the phenotype of livestock herbivores. This type of research is needed to alleviate the challenges currently faced by the livestock industry (e.g. impaired fertility of high-yielding dairy cows). This in turn will have a positive influence on animal welfare and productivity of livestock enterprises.

La présence de taureaux subfertiles sur le marché de l’insémination artificielle influence l’efficacité et la durabilité des élevages, en entraînant des pertes de production, une augmentation du taux de réforme des génisses et un gaspillage des ressources. Aujourd’hui, l’évaluation de la fertilité des taureaux, basée sur l’analyse combinée de marqueurs génétiques et de marqueurs morphologiques, cinétiques et métaboliques de la semence, n’est pas suffisante pour identifier les taureaux subfertiles avant leur entrée en production. Notre objectif est d’utiliser l’épigénome de la semence bovine pour identifier de nouveaux marqueurs fiables et précoces de la fertilité mâle.Nous avons mené une analyse pan-génomique de la méthylation de l’ADN spermatique par Reduced Representation Bisulfite Sequencing (RRBS). La préparation des librairies ainsi que l‘analyse bioinformatique et statistique des données ont été automatisées au laboratoire, rendant possible l’étude d’une cohorte de 58 taureaux de races Holstein et Montbéliard. Ces taureaux ont été répartis en trois catégories selon l’adéquation entre une prédiction de fertilité basée sur l’analyse de leur génotype, et leur fertilité réelle sur le terrain : fertiles, subfertiles et déviants (prédits comme fertiles mais subfertiles sur le terrain). Des analyses descriptives réalisées sur l’ensemble des CpG couverts (> 1 million) montrent que les déviants peuvent être distingués des autres animaux chez les Holstein uniquement. En accord avec cette observation, davantage de CpG différentiellement méthylés (DMC) ont été identifiés entre les catégories de fertilité chez les taureaux Holstein que chez les Montbéliard (8884 et 4823, respectivement). De plus, ces DMC présentent une claire tendance à l’hypométhylation chez les déviants Holstein, et sont situés à proximité de gènes impliqués dans le développement embryonnaire précoce. Dans les deux races, les DMC identifiés permettent de prédire de façon robuste le statut de fertilité. Des exemples de validation par pyroséquençage pourront être présentés, soulignant l’importance des paramètres utilisés pour l’analyse statistique des résultats de RRBS. Enfin, nous aborderons la problématique de l’intégration avec le génotype, qui illustre l’effet direct et indirect de polymorphismes de séquence sur la méthylation de l’ADN.En conclusion, cette étude montre que des profils de méthylation de l’ADN spermatique peuvent être associés à la fertilité chez le bovin. Ces résultats seront complétés par l’analyse de microARN (voir Sellem et al.) et de modifications post-traductionnelles d’histones. L’ensemble des biomarqueurs identifiés serviront de base au développement d’outils technologiques et statistiques pouvant être utilisés en routine pour améliorer la prédiction de la fertilité mâle.

La santé et la fertilité des vaches laitières sont au cœur des préoccupations de la filière professionnelle dans un objectif d’efficience, de quantité et de qualité de la production de lait. La mise en place d’une lactation performante se superpose aux profonds changements hormonaux et métaboliques de la période postpartum, se traduisant par une balance énergétique négative. Les conséquences en sont souvent une altération de la fertilité et une immunodépression qui accroit la susceptibilité aux pathologies. Dans les élevages, il existe encore une grande variabilité d’état général et de performances chez les vaches laitières malgré la sélection génomique. Il est proposé que des modifications de la méthylation de l’ADN puissent contribuer à cette variabilité phénotypique individuelle. En effet, la méthylation de l’ADN, en tant que processus épigénétique, est impliquée dans la régulation transcriptionnelle des gènes, et présente une certaine plasticité face aux contraintes environnementales. Nous avons fait l’hypothèse que des signatures épigénétiques portées par les cellules du sang, pourraient refléter l’état de santé des vaches et pourraient être modifiées en réponse à différents facteurs intrinsèques (parité, stades physiologiques…) et aux contraintes environnementales. Ces signatures ont été recherchées dans une population de cellules du sang particulière : les monocytes. Ces cellules, accessibles par prélèvements sanguins et purification en présence d’un anticorps spécifique, constituent la première ligne de réponse d’immunité innée face aux infections aigües participant à la dégradation de l’état de santé des vaches en postpartum. Pour tester l’hypothèse de signatures épigénétiques monocytaires, une analyse du méthylome par « Reduced Representation Bisulfite Sequencing », (RRBS) dans diverses situations d’élevage a été réalisée. En utilisant des ADN génomiques de vaches incluses dans plusieurs protocoles, 22 banques ont été construites et séquencées. Leur analyse a été réalisée en utilisant un pipeline d’analyses bioinformatique et biostatistique développé au laboratoire. En moyenne 1 250 000 CpG sont pris en considération et permettent l’identification et la localisation de cytosines différentiellement méthylées (DMC) : i) 27143 DMC en comparant les méthylomes de différents types cellulaires (monocytes versus fibroblastes et PBMC) ii) 4788 DMC en réponse à un challenge nutritionnel basé sur la distribution du complément alimentaire GENIAL®, fabriqué et distribué en élevage par nos partenaires PILARDIERE et XR-Repro. iii) 2615 et 4616 DMC en réponse au challenge infectieux pour le groupe de vaches témoins et le groupe en restriction alimentaire respectivement (protocole coordonné par Christine Leroux et José Pires (RUMINFLAME, INRA, Theix) combinant une restriction alimentaire et un challenge immunitaire, par injection de LipoPolySaccharide). iv) 4420 DMC issues de la comparaison entre méthylomes de vaches à génome constant (issues du transfert nucléaire, clones) et de vaches à génome variable mais de même âge et élevées dans les mêmes conditions que les clones. Pour certaines régions différentiellement méthylées (DMR) ciblant le promoteur de gènes, le statut de méthylation a été confirmé par conversion bisulfite et pyroséquençage. L’expression des gènes associés a été étudiée. Une anti corrélation significative est observée entre méthylation et expression signant la fonctionnalité de ces régions. En comparant les 11 méthylomes monocytaires, il est montré que 21% des CpG sont extrêmement stables et ne présentent qu’une faible variation de méthylation entre échantillons ( 20%).L’ensemble de ces informations peut être pris en considération pour la conception d’un outil d’épigénotypage. A l’avenir, il serait aussi possible d’utiliser cet outil en routine afin d’appréhender les variations du méthylome monocytaire dans différentes conditions d’élevage.

Daniel Le Bourhis, present adress: ALLICE, Nouzilly, France Sandrine Balzergue, present adress: IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV; International audience; Cloning enables the generation of both clinically normal and pathological individuals from the same donor cells, and may therefore be a DNA sequence-independent driver of phenotypic variability. We took advantage of cattle clones with identical genotypes but different developmental abilities to investigate the role of epigenetic factors in perinatal mortality, a complex trait with increasing prevalence in dairy cattle. We studied livers from pathological clones dying during the perinatal period, clinically normal adult clones with the same genotypes as perinatal clones and conventional age-matched controls. The livers from deceased perinatal clones displayed histological lesions, modifications to quantitative histomorphometric and metabolic parameters such as glycogen storage and fatty acid composition, and an absence of birth-induced maturation. In a genome-wide epigenetic analysis, we identified DNA methylation patterns underlying these phenotypic alterations and targeting genes relevant to liver metabolism, including the type 2 diabetes gene TCF7L2. The adult clones were devoid of major phenotypic and epigenetic abnormalities in the liver, ruling out the effects of genotype on the phenotype observed. These results thus provide the first demonstration of a genome-wide association between DNA methylation and perinatal mortality in cattle, and highlight epigenetics as a driving force for phenotypic variability in farmed animals.

Thématique: épigénétique; We propose a new bioinformatics pipeline for livestock methylome analysis using data gene-rated through Reduced Representation Bisulfite Sequencing (RRBS). This pipeline is currently used by biologists to analyse paired-end RRBS libraries from various rabbit and bovine tissues1. Here we present the comparison between results obtained by this pipeline and results publis-hed by Choi et al. 2 in pig.

International audience

Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bovine spermatozoa is still scarce. In the context of genomic selection, more information on the epigenetic features transferred to the embryo alongside the paternal genetic heritage is necessary, in order to improve semen quality control procedures and bull fertility. We characterized the bull sperm methylome relative to bovine fibroblasts and monocytes using reduced restriction bisulfite sequencing (RRBS). A wide majority of differentially methylated cytosines (DMCs) were less methylated in sperm than in somatic cells. Consistent with previous studies in other species, these hypomethylated DMCs were enriched for genes relevant to the germline differentiation program and sperm functions. The most remarkable observation was a dramatic enrichment for repeats and particularly for satellites, which may partly account for the lower global methylation we observed in bull sperm relative to sperm from other species (LUminometric Methylation Assay). We next investigated whether fertility biomarkers could be identified in the sperm methylome. Based on field fertility indicators, we compared fertile ejaculates, subfertile ejaculates and ejaculates from bulls with a disappointing career in contradiction with genomic predictions (Montbéliarde breed, n=10/group). The median age at production was consistent among groups and the phenotypic characterization revealed no significant differences except for the proportion of motile sperm, which was reduced in disappointing bulls. We identified 4823 DMCs targeting genes involved in signaling pathways, angiogenesis and the response to growth factors. Since DNA methylation is affected by the CpG content of the genome and its alteration by DNA polymorphism, an integrative approach was conducted to identify CpGs and SNPs in correlation, which revealed both direct and indirect interactions between the genome and the epigenome.

Background Maternal obesity impacts fetal growth and pregnancy outcomes. To counteract the deleterious effects of obesity on fertility and pregnancy issue, preconceptional weight loss is recommended to obese women. Whether this weight loss is beneficial/detrimental for offspring remains poorly explored. Epigenetic mechanisms could be affected by maternal weight changes, perturbing expression of key developmental genes in the placenta or fetus. Our aim was to investigate the effects of chronic maternal obesity on feto-placental growth along with the underlying epigenetic mechanisms. We also tested whether preconceptional weight loss could alleviate these effects. Results Female mice were fed either a control diet (CTRL group), a high-fat diet (obese (OB) group), or a high-fat diet switched to a control diet 2 months before conception (weight loss (WL) group). At mating, OB females presented an obese phenotype while WL females normalized metabolic parameters. At embryonic day 18.5 (E18.5), fetuses from OB females presented fetal growth restriction (FGR; −13 %) and 28 % of the fetuses were small for gestational age (SGA). Fetuses from WL females normalized this phenotype. The expression of 60 epigenetic machinery genes and 32 metabolic genes was measured in the fetal liver, placental labyrinth, and junctional zone. We revealed 23 genes altered by maternal weight trajectories in at least one of three tissues. The fetal liver and placental labyrinth were more responsive to maternal obesity than junctional zone. One third (18/60) of the epigenetic machinery genes were differentially expressed between at least two maternal groups. Interestingly, genes involved in the histone acetylation pathway were particularly altered (13/18). In OB group, lysine acetyltransferases and Bromodomain-containing protein 2 were upregulated, while most histone deacetylases were downregulated. In WL group, the expression of only a subset of these genes was normalized. Conclusions This study highlights the high sensitivity of the epigenetic machinery gene expression, and particularly the histone acetylation pathway, to maternal obesity. These obesity-induced transcriptional changes could alter the placental and the hepatic epigenome, leading to FGR. Preconceptional weight loss appears beneficial to fetal growth, but some effects of previous obesity were retained in offspring phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0188-3) contains supplementary material, which is available to authorized users.

International audience; The effect of the Developmental Origins of Health and Disease on the spread of non-communicable diseases is recognised by world agencies such as the United Nations and the World Health Organization. Early environmental effects on offspring phenotype also apply to domestic animals and their production traits. Herein, we show that maternal nutrition not only throughout pregnancy, but also in the periconception period can affect offspring phenotype through modifications of gametes, embryos and placental function. Because epigenetic mechanisms are key processes in mediating these effects, we propose that the study of epigenetic marks in gametes may provide additional information for domestic animal selection.

Fernando H. Biase: present adress: Department of Animal Sciences, Aubrun University, Etats Unis; A major unresolved issue in the cloning of mammals by somatic cell nuclear transfer (SCNT) is the mechanism by which the process fails after embryos are transferred to the uterus of recipients before or during the implantation window. We investigated this problem by using RNA sequencing (RNA-seq) to compare the transcriptomes in cattle conceptuses produced by SCNT and artificial insemination (AI) at day (d) 18 (preimplantation) and d 34 (postimplantation) of gestation. In addition, endometrium was profiled to identify the communication pathways that might be affected by the presence of a cloned conceptus, ultimately leading to mortality before or during the implantation window. At d 18, the effects on the transcriptome associated with SCNT were massive, involving more than 5,000 differentially expressed genes (DEGs). Among them are 121 genes that have embryonic lethal phenotypes in mice, cause defects in trophoblast and placental development, and/or affect conceptus survival in mice. In endometria at d 18

International audience; Lactation performance is dependent on both the genetic characteristics and the environmental conditions surrounding lactating cows. However, individual variations can still be observed within a given breed under similar environmental conditions. The role of the environment between birth and lactation could be better appreciated in cloned cows, which are presumed to be genetically identical, but differences in lactation performance between cloned and noncloned cows first need to be clearly evaluated. Conflicting results have been described in the literature, so our aim was to clarify this situation. Nine cloned Prim' Holstein cows were produced by the transfer of nuclei from a single fibroblast cell line after cell fusion with enucleated oocytes. The cloned cows and 9 noncloned counterparts were raised under similar conditions. Milk production and composition were recorded monthly from calving until 200 d in milk. At 67 d in milk, biopsies were sampled from the rear quarter of the udder, their mammary epithelial cell content was evaluated, and mammary cell renewal, RNA, and DNA were then analyzed in relevant samples. The results showed that milk production did not differ significantly between cloned and noncloned cows, but milk protein and fat contents were less variable in cloned cows. Furthermore, milk fat yield and contents were lower in cloned cows during early lactation. At around 67 DIM, milk fat and protein yields, as well as milk fat, protein, and lactose contents, were also lower in cloned cows. These lower yields could be linked to the higher apoptotic rate observed in cloned cows. Apoptosis is triggered by insulin-like factor growth binding protein 5 (IGFBP5) and plasminogen activator inhibitor (PAI), which both interact with CSN1S2. During our experiments, CSN1S2 transcript levels were lower in the mammary gland of cloned cows. The mammary cell apoptotic rate observed in cloned cows may have been related to the higher levels of DNA (cytosine-5-)-methyltransferase 1 (DNMT1) transcripts, coding for products that maintain the epigenetic status of cells. We conclude, therefore, that milk production in cloned cows differs slightly from that of noncloned cows. These differences may be due, in part, to a higher incidence of subclinical mastitis. They were associated with differences in cell apoptosis and linked to variations in DNMT1 mRNA. However, milk protein and fat contents were more similar among cloned cows than among noncloned cows.

L’empreinte parentale est un phenomene epigenetique complexe qui regule l’expression monoallelique de certains genes en fonction de l’origine parentale de l’allele. Les genes soumis a empreinte (GSE) participent au developpement placentaire et fœtal. Des defauts d’empreinte de certains GSE entrainent des syndromes cliniques associant une pathologie placentaire a l’origine notamment d’un defaut de croissance fœtale, et des manifestations neuro-developpementales. Environ 70 GSE ont ete identifies a ce jour chez l’homme. Nous avons developpe une strategie de criblage haut debit pour identifier de nouveaux GSE dans le placenta humain. Une premiere serie de validation a permis de confirmer le statut d’empreinte d’une dizaine de nouveaux genes [1] . Recemment, nous avons revele le statut de GSE pour le gene DSCAM (Down Syndrome Cellular Adhesion Molecule). Ce gene, qui se trouve dans la region critique du syndrome de Down, est ainsi le premier GSE identifie sur le chromosome 21. Notre etude montre que c’est l’allele paternel qui est exprime dans le placenta. Des resultats preliminaires nous laissent penser que l’empreinte de ce gene pourrait etre regulee par une region differentiellement methylee en amont du gene. L’etude par immunohistochimie de coupes placentaires montre une expression dans les cellules endotheliales et le syncytiotrophoblaste pouvant suggerer un role dans l’angiogenese placentaire via son ligand Netrin. Une etude est en cours a partir d’un modele cellulaire de trophoblaste avant et apres syncytialisation pour analyser son role dans ce type cellulaire. Par ailleurs, DSCAM est connu pour son role dans la mise en place des connections inter-neurones [2] . Une etude est en cours sur des modeles murins afin d’analyser le statut d’empreinte de ce gene dans le tissu nerveux et les consequences d’un defaut d’expression de son ligand Netrin sur le developpement placentaire.

Most dairy cows are inseminated and sub-fertile bulls can have an overall dramatic negative impact on the sustainability of the dairy sector. The bull fertility prediction, through efficient quality control (QC) procedures is thus crucial for the cattle breeding sector. Over the last decades, several biomarkers and quality control procedures have been proposed to guarantee semen fertility, including assessment of key functional parameters using flow cytometry. However, their relevance for routine QC has yet to be ascertained and their predictive value is too limited to confidently discard subfertile bulls. Thus, studies have been conducted by LabCom SeQuaMol to explore to what extent the bull sperm epigenome may be relevant to improve fertility prediction. In this respect, this PhD thesis was focused on small noncoding RNAs (sncRNAs), which have been shown to play a role in spermatogenesis and fertilization. We aimed at improving the scientific knowledge on bull sperm sncRNA content in order to develop a routine tool to predict bull fertility. The work has been organized according to three main themes: providing a comprehensive overview of cattle sperm sncRNA, studying their expression dynamics during sperm maturation along epididymis and identifying biomarkers associated with bull fertility.; L’utilisation de taureaux subfertiles entraîne des pertes de production, une augmentation du taux de réforme des vaches pour infertilité et un gaspillage des ressources. C’est pourquoi le contrôle qualité de la semence utilisée en Insémination Animale est une préoccupation majeure des entreprises de sélection. Divers protocoles de contrôle qualité ont été développés au cours des dernières décennies, exploitant des biomarqueurs et des paramètres fonctionnels clés mesurés par cytométrie en flux. Toutefois, la capacité prédictive de ces tests reste limitée et ne permet pas d’identifier les taureaux subfertiles. C’est pourquoi des travaux ont été entrepris dans le cadre du LabCom SeQuaMol, afin d’explorer l’intérêt de l’épigénome spermatique comme biomarqueur de fertilité chez les taureaux. Ainsi, les travaux menés au cours de cette thèse ont portés sur les petits ARNs non codants (sncRNA), dont le rôle au cours de la spermatogénèse et de la fécondation a été suggéré et démontré. L’amélioration des connaissances sur le contenu en sncRNA du spermatozoïde bovin éjaculé avait comme objectif pratique de développer un outil permettant de fiabiliser la prédiction en routine de la fertilité des taureaux. Les travaux ont été organisés selon trois axes : l’établissement du contenu exhaustif en sncRNA du sperme bovin éjaculé, l’étude de la dynamique d’expression de ces sncRNAs au cours de la maturation épididymaire et l'identification in fine de biomarqueurs associés à la fertilité des taureaux.

The presence of subfertile bulls in the market of Animal Insemination negatively influences the efficacy of breeding farms. The evaluation of bull fertility, based on the combined analysis of genetic, morphological, kinetic and metabolic markers of the semen, is not sufficient to identify subfertile bulls before entering semen production. It suggests the implication of other factors, especially epigenetic ones. Within the epigenetic markers, DNA methylation holds a crucial position: indeed, its reprogramming is indispensable to the fundamental processes that are germinal cell differentiation, spermatogenesis and the embryonic development. Whereas several studies have showed that the alteration of spermatic methylation profiles are associated with subfertility in humans, only a little data exists concerning bovines. The aim of this thesis is the characterization of the methylome of bovine semen and the identification of new reliable markers of male fertility at an early stage. This study is part of a larger project called SeQuaMol (Molecular Quality of Semen) which rely on a common laboratory between INRA and the ALLICE federation. The characterization of the bovine sperm methylome was achieved by using a multiscale approach (global, pangenomic and sequencespecific). The analyses made it possible to observe the hypomethylation of the bovine semen. Hypomethylation affects genes that are crucial for the differentiation of the germline, spermatic functions, and also on satellite sequences.The identification fertility biomarkers was carried out by using a pangenomic approach (Reduced Representation Bisulfite Sequencing, RRBS). The analysis has been performed on a cohort of 94 bulls, including subjects of the Holstein race and Montbeliard race, categorized according to the adequacy between a genetic indicator of fertility and their actual fertility. The process also includes bulls from 4 other breeds in order to obtain an estimate of the genetic variability linked to the breed. This analysis has required the optimization and the automation of the protocol for the high throughput preparation of RRBS libraries, as well as the development of the whole bioinformatic pipeline and data statistics. Several thousands of biomarkers of fertility have been identified, which allow to predict in a robust way the fertility status. Furthermore, a process of integration of genotype and epigenotype data has been started, which underlines the potential interaction between these levels of information. Finally, we have highlighted the influence of the age of semen production on the methylome. Altogether, theses data suggest that modifications of the semen methylome can affect genes that are involved in the process of early and late embryo development, and parts of the functioning of the sperm cell. The biomarkers identified will form a basis for the pursuit of the SeQuaMol project, of which the completion will be the development of technological and statistical tools that may be used routinely to improve male’s fertility prediction.; La présence de taureaux sub-fertiles sur le marché de l’Insémination Animale (IA) influence négativement l’efficacité des élevages. L’évaluation de la fertilité des taureaux, basée sur l’analyse combinée de marqueurs génétiques, morphologiques, cinétiques et métaboliques de la semence, n’est pas suffisante pour identifier les taureaux sub-fertiles avant leur entrée en production. Cela suggère l’implication d’autres facteurs, notamment d’origines épigénétiques. Parmi les marques épigénétiques, la méthylation de l’ADN tient une place essentielle : son remaniement est en effet indispensable aux processus fondamentaux que sont la différenciation des cellules germinales, la spermatogénèse et le développement embryonnaire précoce. Alors que chez l’Homme, de nombreuses études ont montré que des altérations des profils de méthylation spermatiques sont associées à la sub-fertilité, très peu de données existent chez le bovin. L’objectif de ce travail de thèse est la caractérisation du méthylome de la semence bovine et l’identification de nouveaux marqueurs fiables de la fertilité mâle à un stade précoce. Cette étude s’inscrit dans un large projet intitulé SeQuaMol (pour « Qualité Moléculaire de la Semence »), mis en place au sein d’un laboratoire commun entre l’INRA et la fédération ALLICE. La caractérisation du méthylome spermatique bovin a été réalisée en utilisant une approche multi-échelle (globale, pangénomique et séquence-spécifique). Les analyses ont permis de révéler l’hypométhylation très marquée du spermatozoïde bovin. L’hypométhylation affecte des gènes importants pour la différenciation de la lignée germinale, les fonctions spermatiques, ainsi que des séquences satellites. L’identification de biomarqueurs de la fertilité a été réalisée en utilisant une approche pangénomique (Reduced Representation Bisulfite Sequencing, RRBS). L’analyse a été effectuée sur une cohorte de 94 taureaux, dont les individus de races Holstein et Montbéliard ont été catégorisés en fonction de l’adéquation entre un indicateur génétique de la fertilité et leur fertilité réelle. Le dispositif inclus également des taureaux de 4 autres races pour obtenir une estimation de la variabilité épigénétique liée à la race. Cette analyse a nécessité l’optimisation et l’automatisation du protocole pour la préparation des banques RRBS à haut-débit, ainsi que la mise au point de l’ensemble de la procédure de traitement bio-informatique et statistique des données. Plusieurs milliers de biomarqueurs de la fertilité ont été identifiés et permettent de prédire de façon robuste le statut de fertilité. De plus, une démarche d’intégration des données de génotype et d’épigénotype a été amorcée, soulignant les interactions potentielles en ces strates d’informations. Enfin, nous avons mis en évidence l’influence de l’âge à la production de semence sur le méthylome. L’ensemble de ces données souligne que les modifications du méthylome spermatique peuvent affecter des gènes impliqués dans les processus précoces et plus tardifs du développement, ainsi que quelques voies du fonctionnement du spermatozoïde. L’ensemble des biomarqueurs identifiés serviront de base à la poursuite du projet SeQuaMol, dont l’aboutissement sera le développement d’outils technologiques et statistiques pouvant être utilisés en routine pour améliorer la prédiction de la fertilité mâle.

In dairy breeding the health and fertility of cows are the main concern with the aims to maintain milk quantity and quality and to reduce the interval between calving in a high competitive economical context. Postpartum period is marked by major honnonal and metabolic changes that affect productivity, immune responses and fertility. The consequences of immune response deterioration are an increasing susceptibility to diseases (mast itis, metritis, endometritis...). Genomic selection in livestock improves the perfonnance of the population but does not exclude phenotypic variability at the level of livestock and the individual. It is proposed that DNA methylation could contribute to this individual phenotype variability. Indeed, DNA methylation is an epigenetic process involved in transcriptional regulation of genes displaying certain plasticity in front of environmental constraints. We assumed the epigenetic signatures carried by blood cells, could reflect overall health and could be modified in response to intrinsic factors (parity, stages...) and to enviro nmental changes. These signatures were researched in a particular blood ceIls surpopulation: the monocytes. These cells, obtained by blood sampling and purification with a specifie antibody, are the first line of defense against acute infections participating in health status deterioration of postpartum cows. To test the monocyte epigenetic signatures hypothesis, monocyte methylome were analyzed by «Reduced Representation Bisulfite Sequencing» (RRBS), in various breeding conditions. Using genomic DNA form cows included in several protocols, 22 libraries were constructed and sequenced. Their analyses were accomplished using a «homemade» pipeline which integrates bioinformatics and biostatistics analyses. On average, 1 250 000 CpGs were analyzed in order to identify differetially methylated cytosines (DMCs): i) 27143 DMC by comparison between different cells types (monocytes versus fibroblasts and PBMC) ii) 4788 DMCs in response to nutritional challenge based on the dietary supplement. GENIAL®, produced and distributed in breeding by our partner PILARDIERE and XR-Repro (in collaboration with Marion Boutinaud, INRA, Rennes). iii) 2615 and 4616 DMCs in response to infectious challenge with LipoPolySaccharide injection for control cows group fed normal diet and for dietary restriction cows group. respectively (collaboration with Christine Leroux and José Pires, RUMINFLAME, INRA, Theix; and Gilles Foucras (ENVT, Toulouse)). iv) 4420 DMCs from the comparison between constant genomic cow (Somatic cell nuclear transfer, clones) and variable genomic cows but with the same age and raised in the same conditions than clones. From DMCs, we identified differentially methylated regions (DMR s) defined as region with at least 3 DMCs inside 100 bp. For some DM Rs targeting gene promoter, the methylation status was validated by bisulfite conversion and pyrosequencing. Gene associated expression were also investigated. A significant negati ve correlation has been observed between methylation and expression, highlighting the functional relevance of these DMRs in gene transcription control. By comparing the 11 monocyte methylomes, 21% of CpGs present a remarkable constant methylation level with weak variability between samples (< 10%). On the other hand, 2.9% of CpGs show a strong variation (>20%).Taking together, these data can provide a list of relevant DMCs for an epigenetic tool conception. ln the future, it would be possible 10 use this tool for a routine analysis in order to grasp monocyte methylome variations in different breeding management.; La santé et la fertilité des vaches laitières sont au cœur des préoccupations de la filière professionnelle dans un objectif d’efficience, de quantité et de qualité de la production de lait. La mise en place d’une lactation performante se superpose aux profonds changements hormonaux et métaboliques de la période postpartum, se traduisant par une balance énergétique négative. Les conséquences en sont souvent une altération de la fertilité et une immunodépression qui accroit la susceptibilité aux pathologies. Dans les élevages, il existe encore une grande variabilité d’état général et de performances chez les vaches laitières malgré la sélection génomique. Il est proposé que des modifications de la méthylation de l’ADN, en tant que processus épigénétique, est impliquée dans la régulation transcriptionnelle de gènes, et présente une certaine plasticité face aux contraintes environnementales. Nous avons fait l’hypothèse que des signatures épigénétiques portées sur les cellules du sang, pourraient refléter l’état de santé des vaches et pourraient être modifiées en réponse à différents facteurs intrinsèques (parité, stades physiologiques…) et aux contraintes environnementales. Ces signatures ont été recherchées dans une population de cellules du sang particulière : les monocytes. Ces cellules accessibles par prélèvements sanguins et purification en présence d’un anticorps spécifique, constituent la première ligne de réponse d’immunité innée face aux infections aigües participant à l’hypothèse de signatures épigénétiques monocytaires, une analyse du méthylome par « Reduced Representation Bisulfite Sequencing », (RRBS) dans diverses situations d’élevage a été réalisée. En utilisant des ADN génomiques de vaches incluses dans plusieurs protocoles, 22 banques ont été construites et séquencées. Leur analyse a été réalisée en utilisant un pipeline d’analyses bioinformatique et biostatistique développé au laboratoire. En moyenne, 1 250 000 CpG sont pris en considération en permettent l’identification et la localisation de cytosines différentiellement (DMC) : i) 27143 DMC en comparant les méthylomes de différents types cellulaires (monocytes versus fibroblastes et l’IBIVIC) ii) 4788 DMC en réponse à un challenge nutritionnel basé sur la distribution du complément alimentaire GENIAL®, fabriqué et distribué en élevage par nos partenaires PILADIERE et XR-Repro. Iii) 2615 et 4616 DMC en réponse au challenge infectieux pour le groupe de vaches témoins et le groupe en restriction alimentaire respectivement (protocole coordonné par Christine Leroux et José Pires (RUMINFLAME, INRA Theix) combinant une restriction alimentaire et un challenge immunitaire, par injection de LipoPolySaccharide). Iv) 4420 DMC issues de la comparaison entre méthylomes de vaches à génome constant (issues du transfert nucléaire, clones) et de vaches à génome variable mais de même âge et élevées dans les mêmes conditions que les clones. Pour certaines régions différentiellement méthylées (DMR) ciblant le promoteur de gènes, le statut de méthylation a été confirmé par conversion bisulfite et pyroséquençage. L’expression des gènes associés a été étudiée. Une anti corrélation significative est observée entre méthylation et expression signant la fonctionnalité de ces régions. En comparant les 11 méthylomes monocytaires, il est montrée que 21% des CpG sont extrêmement stables et ne présentent qu’une faible variation de méthylation entre échantillons (20%). L’ensemble de ces informations peut être pris en considération pour la conception d’un outil d’épigénotypage. A l’avenir, il serait aussi possible d’utiliser cet outil en routine afin d’appréhender les variations du méthylome monocytaire dans différentes conditions d’élevage.