Assessing the influence of distinct culture media on human pre-implantation development using single-embryo transcriptomics

The use of assisted reproductive technologies is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. In particular, embryos within their first days of development are highly sensitive to their micro-environment, and it is unknown how their transcriptome adapts to different embryo culture compositions. Here, we determined the impact of culture media composition on gene expression in human pre-implantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of the post-fertilization culture in different commercially available media (Ferticult, Global, and SSM), we revealed medium-specific differences in gene expression changes. Embryos cultured pre-compaction until day 2 in Ferticult or Global media notably displayed 266 differentially expressed genes, which were related to essential developmental pathways. Herein, 19 of them could have a key role in early development, based on their previously described dynamic expression changes across development. When embryos were cultured after day 2 in the same media considered more suitable because of its amino acid enrichment, 18 differentially expressed genes thought to be involved in the transition from early to later embryonic stages were identified. Overall, the differences were reduced at the blastocyst stage, highlighting the ability of embryos conceived in a suboptimal in vitro culture medium to mitigate the transcriptomic profile acquired under different pre-compaction environments

Allele-specific demethylation at an imprinted mammalian promoter

A screen for imprinted genes on mouse Chromosome 7 recently identified Inpp5f_v2, a paternally expressed retrogene lying within an intron of Inpp5f. Here, we identify a novel paternally expressed variant of the Inpp5f gene (Inpp5f_v3) that shows a number of unusual features. Inpp5f_v3 initiates from a CpG-rich repeat region adjoining two B1 elements, despite previous reports that SINEs are generally excluded from imprinted promoters. Accordingly, we find that the Inpp5f_v3 promoter acquires methylation around the time of implantation, when many repeat families undergo de novo epigenetic silencing. Methylation is then lost specifically on the paternally derived allele during the latter stages of embryonic development, resulting in imprinted transcriptional activation on the demethylated allele. Methylation analyses in embryos lacking maternal methylation imprints suggest that the primary imprinting mark resides within an intronic CpG island ∼1 kb downstream of the Inpp5f_v3 transcriptional start site. These data support the hypothesis that SINEs can influence gene expression by attracting de novo methylation during development, a property likely to explain their exclusion from other imprinted promoters

Assessing the influence of distinct culture media on human pre-implantation development using single-embryo transcriptomics

The use of assisted reproductive technologies is consistently rising across the world. However, making an informed choice on which embryo culture medium should be preferred to ensure satisfactory pregnancy rates and the health of future children critically lacks scientific background. In particular, embryos within their first days of development are highly sensitive to their micro-environment, and it is unknown how their transcriptome adapts to different embryo culture compositions. Here, we determined the impact of culture media composition on gene expression in human pre-implantation embryos. By employing single-embryo RNA-sequencing after 2 or 5 days of the post-fertilization culture in different commercially available media (Ferticult, Global, and SSM), we revealed medium-specific differences in gene expression changes. Embryos cultured pre-compaction until day 2 in Ferticult or Global media notably displayed 266 differentially expressed genes, which were related to essential developmental pathways. Herein, 19 of them could have a key role in early development, based on their previously described dynamic expression changes across development. When embryos were cultured after day 2 in the same media considered more suitable because of its amino acid enrichment, 18 differentially expressed genes thought to be involved in the transition from early to later embryonic stages were identified. Overall, the differences were reduced at the blastocyst stage, highlighting the ability of embryos conceived in a suboptimal in vitro culture medium to mitigate the transcriptomic profile acquired under different pre-compaction environments

Évolution de l’empreinte parentale chez les mammifères

L’empreinte parentale ou empreinte génomique impose un mode de reproduction sexué obligatoire chez les mammifères. Ce phénomène résulte de l’expression mono-allélique et monoparentale d’un groupe de gènes. Ce mécanisme de régulation génique concerne les mammifères vivipares comme les euthériens et, dans une moindre mesure, les marsupiaux. Les mammifères ovipares, ou monotrèmes, ne semblent pas dotés d’empreinte parentale. Cette restriction phylogénétique conforte l’hypothèse selon laquelle l’émergence de l’organe placentaire aurait imposé une pression sélective pour l’acquisition de l’empreinte. Ces arguments physiologiques ont été plus récemment étayés par des arguments génomiques, grâce au séquençage du génome de l’étrange ornithorynque, un des rares monotrèmes encore existants. De nombreuses coïncidences temporelles et fonctionnelles existent entre l’apparition de l’empreinte et l’accumulation d’éléments transposables. Les analyses comparatives systématiques du génome de différentes espèces de mammifères, classiques et exotiques, sont essentielles à notre connaissance de l’émergence et de l’évolution de l’empreinte

Sperme express

L’émergence de cellules souches germinales est une décision cellulaire fondamentale pour la perpétuation de l’espèce. Les processus de spécification et de différenciation de la lignée germinale restent cependant mal caractérisés chez les mammifères en raison du nombre très limité des cellules fondatrices et de leur apparition précoce au cours du développement embryonnaire. Leur accès est de plus restreint dans l’espèce humaine pour des raisons éthiques évidentes. Le développement d’un système de dérivation in vitro de cellules souches germinales à partir de cellules ES est une priorité pour l’analyse fondamentale des mécanismes sousjacents à la spécification et à la mise en place de l’identité épigénétique de ces cellules. La disponibilité de ce modèle cellulaire permettrait de plus l’évaluation in vitro des effets génotoxiques de certains agents environnementaux et médicamenteux sur le développement gamétique. Cet outil promet enfin des avancées importantes en médecine reproductive, avec la perspective de recoloniser les gonades d’hommes stériles ou de produire in vitro des ovocytes compétents pour la fécondation ou le transfert nucléaire. La dérivation de cellules souches germinales mâles à partir de cellules ES et leur différenciation in vitro ont récemment été réalisées chez la souris. Les défauts d’identité cellulaire et épigénétiques que présentent ces gamètes synthétiques mettent en évidence les contraintes spatiales et temporelles requises pour la spécification germinale et devraient permettre aux spécialistes de développer des protocoles plus adaptés

Cultural relativism: maintenance of genomic imprints in pluripotent stem cell culture systems

International audienc

The diverse roles of DNA methylation in mammalian development and disease

International audienc

Small RNA guides for de novo DNA methylation in mammalian germ cells

Germline genomic methylation is essential for gamete identity and integrity in mammals. The study by Kuramochi-Miyagawa and colleagues (908–917) in the previous issue of Genes & Development links the process of DNA methylation-dependent repression of retrotranspons with the presence of piwi-interacting RNAs (piRNAs) in fetal male germ cells undergoing de novo methylation