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 individualsL’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 individu

In Vitro Fertilization and Embryo Culture Strongly Impact the Placental Transcriptome in the Mouse Model

BACKGROUND: Assisted Reproductive Technologies (ART) are increasingly used in humans; however, their impact is now questioned. At blastocyst stage, the trophectoderm is directly in contact with an artificial medium environment, which can impact placental development. This study was designed to carry out an in-depth analysis of the placental transcriptome after ART in mice. METHODOLOGY/PRINCIPAL FINDINGS: Blastocysts were transferred either (1) after in vivo fertilization and development (control group) or (2) after in vitro fertilization and embryo culture. Placentas were then analyzed at E10.5. Six percent of transcripts were altered at the two-fold threshold in placentas of manipulated embryos, 2/3 of transcripts being down-regulated. Strikingly, the X-chromosome harbors 11% of altered genes, 2/3 being induced. Imprinted genes were modified similarly to the X. Promoter composition analysis indicates that FOXA transcription factors may be involved in the transcriptional deregulations. CONCLUSIONS: For the first time, our study shows that in vitro fertilization associated with embryo culture strongly modify the placental expression profile, long after embryo manipulations, meaning that the stress of artificial environment is memorized after implantation. Expression of X and imprinted genes is also greatly modulated probably to adapt to adverse conditions. Our results highlight the importance of studying human placentas from ART

Hypoxia-activated genes from early placenta are elevated in preeclampsia, but not in Intra-Uterine Growth Retardation.

BACKGROUND: As a first step to explore the possible relationships existing between the effects of low oxygen pressure in the first trimester placenta and placental pathologies developing from mid-gestation, two subtracted libraries totaling 2304 cDNA clones were constructed. For achieving this, two reciprocal suppressive/subtractive hybridization procedures (SSH) were applied to early (11 weeks) human placental villi after incubation either in normoxic or in hypoxic conditions. The clones from both libraries (1440 hypoxia-specific and 864 normoxia-specific) were spotted on nylon macroarrays. Complex cDNAs probes prepared from placental villi (either from early pregnancy, after hypoxic or normoxic culture conditions, or near term for controls or pathological placentas) were hybridized to the membranes. RESULTS: Three hundred and fifty nine clones presenting a hybridization signal above the background were sequenced and shown to correspond to 276 different genes. Nine of these genes are mitochondrial, while 267 are nuclear. Specific expression profiles characteristic of preeclampsia (PE) could be identified, as well as profiles specific of Intra-Uterine Growth Retardation (IUGR). Focusing on the chromosomal distribution of the fraction of genes that responded in at least one hybridization experiment, we could observe a highly significant chromosomal clustering of 54 genes into 8 chromosomal regions, four of which containing imprinted genes. Comparative mapping data indicate that these imprinted clusters are maintained in synteny in mice, and apparently in cattle and pigs, suggesting that the maintenance of such syntenies is requested for achieving a normal placental physiology in eutherian mammals. CONCLUSION: We could demonstrate that genes induced in PE were also genes highly expressed under hypoxic conditions (P = 5 x 10(-5)), which was not the case for isolated IUGR. Highly expressed placental genes may be in syntenies conserved interspecifically, suggesting that the maintenance of such clusters is requested for achieving a normal placental physiology in eutherian mammals

Non-random, individual-specific methylation profiles are present at the sixth CTCF binding site in the human H19/IGF2 imprinting control region

Expression of imprinted genes is classically associated with differential methylation of specific CpG-rich DNA regions (DMRs). The H19/IGF2 locus is considered a paradigm for epigenetic regulation. In mice, as in humans, the essential H19 DMR—target of the CTCF insulator—is located between the two genes. Here, we performed a pyrosequencing-based quantitative analysis of its CpG methylation in normal human tissues. The quantitative analysis of the methylation level in the H19 DMR revealed three unexpected discrete, individual-specific methylation states. This epigenetic polymorphism was confined to the sixth CTCF binding site while a unique median-methylated profile was found at the third CTCF binding site as well as in the H19 promoter. Monoallelic expression of H19 and IGF2 was maintained independently of the methylation status at the sixth CTCF binding site and the IGF2 DMR2 displayed a median-methylated profile in all individuals and tissues analyzed. Interestingly, the methylation profile was genetically transmitted. Transgenerational inheritance of the H19 methylation profile was compatible with a simple model involving one gene with three alleles. The existence of three individual-specific epigenotypes in the H19 DMR in a non-pathological situation means it is important to reconsider the diagnostic value and functional importance of the sixth CTCF binding site

A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific

peer-reviewedBackground: Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species.Background: Spermatozoa have a remarkable epigenResults: The quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats. Conclusions: These results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis

Le développement de la glande mammaire et son contrôle hormonal dans l'espèce bovine

National audienceLa fonction de lactation, c’est-à-dire la production de lait, est l’aboutissement d’un long processus de développement et de différenciation des tissus mammaires. De la vie embryonnaire à la première lactation, la glande mammaire prend forme étape par étape. Chacune de ces étapes est contrôlée par une association d’hormones dans des rapports de concentrations bien définis et agissant de manière séquentielle. La mammogenèse dépend principalement des hormones stéroïdes en synergie avec la prolactine et l’hormone de croissance ; la lactogenèse de la prolactine et des glucocorticoïdes ; enfin, la galactopoïèse est sous le contrôle de la prolactine, de l’hormone de croissance et des glucocorticoïdes

Le récepteur de la GH peut-il constituer un marqueur de la variabilité des capacités de croissance entre types génétiques ? Etude chez le bovin et le lapin

Cet article fait partie du dossier : Le déterminisme génétique du développement musculaireNational audienc

Potential uses of milk epithelial cells : a review

International audienc

Potential uses of milk epithelial cells: a review

Secretions collected from the mammary gland of different species contain heterogeneous populations of cells including lymphocytes, neutrophils, macrophages and epithelial cells in different species. Several factors influence the somatic cell count in milk and the distribution of cell types, such as species, infection status, physiological status and management practices. The epithelial cells are shed into milk during the lactation process. Most of them are viable and exhibit the characteristics of fully differentiated alveolar cells. Primary cultures of epithelial cells from colostrum and milk of humans, baboons, cows and goats together with established cell lines from human and goat milk, provide a good model for the study of lactogenesis, immunity transmission, cancer research and infection by viruses. The RNA extracted from milk cells have been shown to be representative of gene expression in the mammary gland and thus provide a source of material for molecular studies of gene expression and environmental interactions.Utilisations potentielles des cellules épithéliales du lait. Les sécrétions de la glande mammaire de différentes espèces, contiennent une population hétérogène de cellules incluant des cellules du système immunitaire et des cellules épithéliales. Divers facteurs influencent le nombre de cellules somatiques dans le lait et la distribution de chaque type cellulaire, en particulier l'espèce, le stade physiologique, l'état sanitaire et les conduites d'élevage. Les cellules épithéliales se détachent de l'épithélium mammaire au cours du processus de sécrétion du lait. Cependant, une grande majorité d'entre elles sont viables et présentent des caractéristiques de cellules alvéolaires totalement différenciées. En culture primaire ou en lignées cellulaires, elles constituent un modèle d'étude de l'action hormonale, de marqueurs de la cancérogenèse, de la transmission de l'immunité et d'infections virales. Les ARN totaux extraits des cellules du lait constituent une source de matériel représentatif de l'expression des gènes dans la glande mammaire et devraient permettre des études globales d'expression des gènes en interaction avec l'environnement de l'animal