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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.

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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.

Epigenetics : a reading of the genome through stable / temporary / inheritable modifications Epigenetics refers to molecular processes checking the reading of the genome. These processes, including DNA methylation, the histone post translational modifications, as well as small and long non coding ARN, constitute the epigenetic machinery and participate to nuclear architecture. Stable, flexible, and quickly variable, the epigenetic status of cell nucleus is dynamic. After the fertilization, the parental genomes undergo epigenetic reprogramming, orchestrating the gene expression essential to the embryonic development. During the embryo development, the waves of cellular differentiation involved in organogenesis, come along with the implementation of cell-specific epigenome. Its stability is insured by the heritability of the epigenetic marks through the mitosis (and meiosis). It provides the maintenance of cell function associated with the stability of gene expression profile. Flexibility and/or reversibility of these marks take place in answer to diverse environmental changes. The importance of these processes is suggested by fetal programming, underlined the impact of in utero life on adult health and diseases. In order to exemplify these concepts, we will analyze the role played by the epigenetic programming during the spermatogenesis. Thus, epigenetics acts such as cell memory and origin of diversity between the individuals., L’épigénétique se réfère à un ensemble de processus moléculaires contrôlant le fonctionnement du génome. Ces processus, mettant en jeu la méthylation de l’ADN, les modifications post-traductionnelles des histones, de petits et grands ARN non codants, constituent la machinerie épigénétique et participent à l’architecture nucléaire. Stable mais aussi flexible, et variant rapidement, le statut epigénétique du noyau cellulaire est dynamique. Dès la fécondation, les patrimoines génétiques parentaux subissent une reprogrammation épigénétique orchestrant l’expression génique indispensable au développement embryonnaire. Au cours du développement, les vagues de différenciation cellulaire, nécessaires à l’organogénèse, s’accompagnent de la mise en place d’épigénomes cellulaires spécifiques dont la stabilité est assurée par l’héritabilité des marques épigénétiques à travers la mitose (voire la méiose). Ceci garantit le maintien de la fonction cellulaire de par la stabilité du profil de gènes exprimés. Flexibilité et/ou réversibilité de ces marques peuvent intervenir en réponse à divers changements environnementaux. Cette caractéristique prend toute sa dimension dans les processus de programmation foetale, soulignant l’empreinte de la vie in utero sur le devenir de la descendance. Afin d’illustrer l’ensemble de ces notions, nous prendrons divers exemples de biologie du développement avec une attention particulière concernant la place de la programmation épigénétique au cours de la spermatogenèse. L’épigénétique peut être considérée comme mémoire cellulaire et source de diversité entre les individus., Jammes Hélène. Épigénétique : une lecture du génome via des modifications stables / transitoires et transmissibles . In: Bulletin de l'Académie Vétérinaire de France tome 167 n°2, 2014. pp. 109-118.

SUMMARY We determined if somatic cell nuclear transfer (SCNT) cloning is associated with WNT-related gene expression in cattle development, and if the expression of genes in the WNT pathway changes during the peri-implantation period. Extra-embryonic and endometrial tissues were collected at gestation days 18 and 34 (d18, d34). WNT5A, FZD4, FZD5, LRP5, CTNNB1, GNAI2, KDM1A, BCL2L1, and SFRP1 transcripts were localized in extra-embryonic tissue, whereas SFRP1 and DKK1 were localized in the endometrium. There were no differences in the localization of these transcripts in extra-embryonic tissue or endometrium from SCNT or artificial insemination (AI) pregnancies. Expression levels of WNT5A were 11-fold greater in the allantois of SCNT than AI samples. In the trophoblast, expression of WNT5A, FZD5, CTNNB1, and DKK1 increased significantly from d18 to d34, whereas expression of KDM1A and SFRP1 decreased, indicating that implantation is associated with major changes in WNT signaling. SCNT was associated with altered WNT5A expression in trophoblasts, with levels increasing 2.3-fold more in AI than SCNT conceptuses from d18 to d34. In the allantois, expression of WNT5A increased 6.3-fold more in SCNT than AI conceptuses from d18 to d34. Endometrial tissue expression levels of the genes tested did not differ between AI or SCNT pregnancies, although expression of individual genes showed variation across developmental stages. Our results demonstrate that SCNT is associated with altered expression of specific WNT-related genes in extra-embryonic tissue in a time- and tissue-specific manner. The pattern of gene expression in the WNT pathway suggests that noncanonical WNT signal transduction is important for implantation of cattle conceptuses. Mol. Reprod. Dev. 80: 977–987, 2013. © 2013 Wiley Periodicals, Inc.

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

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.

After fertilization, lineage specification is governed by a complicated molecular network in which permissiveness and repression of expression of pluripotency- and differentiation-associated genes are regulated by epigenetic modifications. DNA methylation operates as a very stable repressive mark in this process. In this study, we investigated the relationship between DNA methylation and expression of pluripotency-associated genes (OCT4, NANOG and SOX2), a trophectoderm (TE)-specific gene (ELF5), and genes associated with neural differentiation (SOX2 and VIMENTIN) in porcine Day 10 (E10) epiblast, hypoblast, and TE as well as in epiblast-derived neural progenitor cells (NPCs). We found that OCT4, NANOG, and SOX2 were highly expressed in the epiblast and hypoblast, while VIMENTIN was only highly expressed in the epiblast. Moreover, low expression of OCT4, NANOG, SOX2 and VIMENTIN was noted in the TE. Most CpG sites of OCT4, NANOG, SOX2 and VIMENTIN displayed low methylation levels in the epiblast and hypoblast and, strikingly, also in the TE. Hence, the expression patterns of these genes were not directly related to levels of DNA methylation in the TE in contrast to the situation in the mouse. In contrast, ELF5 was exclusively expressed in the TE and was correspondingly hypomethylated in this tissue. In NPCs, we observed down-regulation of NANOG and OCT4 expression, which correlated with hypermethylation of their promoters, whereas VIMENTIN displayed up-regulation in accordance with hypomethylation of its promoter. In conclusion, DNA methylation is an inconsistently operating epigenetic mechanism in porcine E10 blastocysts, whereas in porcine epiblast-derived NPCs, expression of pluripotency-associated and differentiation genes appear to be regulated by this modification.

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.

The H19 gene produces a non-coding RNA, which is abundantly expressed during embryonic development and down-regulated after birth. Although this gene was discovered over 20 years ago, its function has remained unclear. Only recently a role was identified for the non-coding RNA and/or its microRNA partner, first as a tumour suppressor gene in mice, then as a trans-regulator of a group of co-expressed genes belonging to the imprinted gene network that is likely to control foetal and early postnatal growth in mice. The mechanisms underlying this transcriptional or post-transcriptional regulation remain to be discovered, perhaps by identifying the protein partners of the full-length H19 RNA or the targets of the microRNA. This first in vivo evidence of a functional role for the H19 locus provides new insights into how genomic imprinting helps to control embryonic growth.

Mouse embryonic pluripotent stem cells can be obtained from the inner cell mass at the blastocyst stage (embryonic stem cells, ESCs) or from the late epiblast of postimplantation embryos (epiblast stem cells, EpiSCs). During normal development, the transition between these two stages is marked by major epigenetic and transcriptional changes including DNA de novo methylation. These modifications represent an epigenetic mark conserved in ESCs and EpiSCs. Pluripotent ESCs derived from blastocysts generated by nuclear transfer (NT) have been shown to be correctly reprogrammed. However, NT embryos frequently undergo abnormal development. In the present study, we have examined whether pluripotent cells could be derived from the epiblast of postimplantation NT embryos and whether the reprogramming process would affect the epigenetic changes occurring at this stage, which could explain abnormal development of NT embryos. We showed that EpiSCs could be derived with the same efficiency from NT embryos and from their fertilized counterparts. However, gene expression profile analyses showed divergence between fertilized- and nuclear transfer-EpiSCs with a surprising bias in the distribution of the differentially expressed genes, 30% of them being localized on chromosome 11. A majority of these genes were downregulated in NT-EpiSCs and imprinted genes represented a significant fraction of them. Notably, analysis of the epigenetic status of a downregulated imprinted gene in NT-EpiSCs revealed complete methylation of the two alleles. Therefore, EpiSCs derived from NT embryos appear to be incorrectly reprogrammed, indicating that abnormal epigenetic marks are imposed on cells in NT embryos during the transition from early to late epiblast.

Children conceived through assisted reproductive technologies (ART) now account for a noteworthy proportion (-2.4%) of births in France. Considerable attention is being paid to the outcome of ART pregnancies. The vast majority of these children are apparently normal. However, they are at an increased risk of minor birth defects, low birth weight, and rare imprinting disorders such as Beckwith-Wiedemann syndrome (BWS), Angelman syndrome (AS) and Silver Russel syndrome (SRS). Animal models are important for investigating the possible role of each step of ART (ovarian stimulation, gamete manipulation, in vitro fertilization, embryo culture and embryo transfer) in epigenetic reprogramming This review discusses these issues in the context of epigenetic and developmental abnormalities observed in animals following ART More research is needed on ART-induced errors, focusing not only on genomic imprinting but also on non-imprinted loci, which may help explain some of the more subtle longer-term health effects emerging from studies with animal models.

Resume Les modeles animaux montrent bien qu’un certain nombre de « stress precoces » tels que l’hyperglycemie maternelle (grossesses diabetiques), la sous-alimentation maternelle, l’obesite maternelle, la corticotherapie, l’insuffisance uteroplacentaire, l’hypoxie intra-uterine, conduisent a des adaptations metaboliques (notion de programmation ou empreinte, metabolique). Il existe un denominateur commun entre tous ces modeles d’etiologies tres differentes : lorsque les femelles de la generation F1 sont rendues gestantes, elles developpent une hyperglycemie gestationnelle et leur descendants (F2) sont intolerants au glucose. C’est ainsi que se met en place une veritable heritabilite de l’intolerance glucidique transmise de generation en generation. Cela suggere fortement qu’une hyperglycemie meme modeste, subie pendant la vie fœtale et/ou neonatale, contribue a la programmation du pancreas endocrine. Nous montrons qu’un tel scenario s’applique au rat GK/Par, modele de diabete de type 2 (DT2) spontane. En effet, a chaque generation, les meres GK/Par exposent leur descendance a une hyperglycemie moderee tout au long de la gestation et de l’allaitement. Nous proposons que l’hyperglycemie gestationnelle maternelle contribue a etablir, puis au cours des generations successives, a maintenir stable, l’heritabilite du phenotype « masse beta reduite », phenotype crucial dans la pathogenese du DT2. Des mecanismes epigenetiques pourraient rendre compte de l’empreinte pancreatique. Il est propose que des perturbateurs metaboliques intra-uterins puissent provoquer des changements transmissibles et cellule-specifiques de l’etat de methylation du promoteur et/ou de conformation de la chromatine (deacetylation des histones) de certains genes cruciaux pour la survie (Igf2, Igf1-R) et/ou la differenciation (Pdx1) des cellules beta. Cela conduirait a des changements perennes du niveau d’expression de ces genes.

Resume Des l’introduction des techniques d’Assistance medicale a la procreation (AMP), de nombreuses etudes ont ete menees pour evaluer leur impact sur la sante des enfants ainsi concus. La notion de risque epigenetique a ete evoquee et un lien entre AMP et pathologies associees a des anomalies de l’empreinte parentale a ete suggere : en particulier, dans le cas des syndromes de Beckwith-Wiedemann (BWS), d’Angelman (AS) et de Silver-Russell (SRS). Le cycle des marques epigenetiques (ecrasement dans les lignees germinales primordiales, etablissement de l’empreinte au cours des gametogeneses, lecture et maintien de l’empreinte dans les cellules somatiques) accompagne toutes les phases de la reproduction, la gametogenese, la maturation gametique, la fecondation et le developpement embryonnaire precoce. L’objectif de cette revue est de recenser toutes les informations issues de l’experimentation animale pouvant contribuer a une meilleure connaissance des perturbations de l’empreinte parentale, en liaison avec les differentes techniques utilisees en AMP et fournir des informations utiles dans la perspective d’ameliorer la prise en charge des couples engages dans un projet parental.