The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals.

Many loci maintain parent-of-origin DNA methylation only briefly after fertilization during mammalian development: Whether this form of transient genomic imprinting can impact the early embryonic transcriptome or even have life-long consequences on genome regulation and possibly phenotypes is currently unknown. Here, we report a maternal germline differentially methylated region (DMR) at the mouse Gpr1/Zdbf2 (DBF-type zinc finger-containing protein 2) locus, which controls the paternal-specific expression of long isoforms of Zdbf2 (Liz) in the early embryo. This DMR loses parental specificity by gain of DNA methylation at implantation in the embryo but is maintained in extraembryonic tissues. As a consequence of this transient, tissue-specific maternal imprinting, Liz expression is restricted to the pluripotent embryo, extraembryonic tissues, and pluripotent male germ cells. We found that Liz potentially functions as both Zdbf2-coding RNA and cis-regulatory RNA. Importantly, Liz-mediated events allow a switch from maternal to paternal imprinted DNA methylation and from Liz to canonical Zdbf2 promoter use during embryonic differentiation, which are stably maintained through somatic life and conserved in humans. The Gpr1/Zdbf2 locus lacks classical imprinting histone modifications, but analysis of mutant embryonic stem cells reveals fine-tuned regulation of Zdbf2 dosage through DNA and H3K27 methylation interplay. Together, our work underlines the developmental and evolutionary need to ensure proper Liz/Zdbf2 dosage as a driving force for dynamic genomic imprinting at the Gpr1/Zdbf2 locus.

Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes.

Identifying loci with parental differences in DNA methylation is key to unraveling parent-of-origin phenotypes. By conducting a MeDIP-Seq screen in maternal-methylation free postimplantation mouse embryos (Dnmt3L-/+), we demonstrate that maternal-specific methylation exists very scarcely at midgestation. We reveal two forms of oocyte-specific methylation inheritance: limited to preimplantation, or with longer duration, i.e. maternally imprinted loci. Transient and imprinted maternal germline DMRs (gDMRs) are indistinguishable in gametes and preimplantation embryos, however, de novo methylation of paternal alleles at implantation delineates their fates and acts as a major leveling factor of parent-inherited differences. We characterize two new imprinted gDMRs, at the Cdh15 and AK008011 loci, with tissue-specific imprinting loss, again by paternal methylation gain. Protection against demethylation after fertilization has been emphasized as instrumental in maintaining parent-of-origin methylation inherited from the gametes. Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life.

Effects of assisted reproductive technologies on transposon regulation in the mouse pre-implanted embryo.

STUDY QUESTION: Do assisted reproductive technologies (ARTs) impact on the expression of transposable elements (TEs) in preimplantation embryos? SUMMARY ANSWER: The expression of all TE families is globally increased with mouse embryo culture with differences according to culture medium composition. WHAT IS KNOWN ALREADY: Mammalian genomes are subject to global epigenetic reprogramming during early embryogenesis. Whether ARTs could have consequences on this period of acute epigenetic sensitivity is the matter of intense research. So far, most studies have examined the impact of ARTs on the regulation of imprinted genes. However, very little attention has been given to the control of TEs, which exceed by far the number of genes and account for half of the mammalian genomic mass. This is of particular interest as TEs have the ability to modulate gene structure and expression, and show unique regulatory dynamics during the preimplantation period. STUDY DESIGN, SIZE, DURATION: Here, we evaluated for the first time the impact of ART procedures (superovulation, in-vitro fertilisation and embryo culture) on the control of different TE types throughout preimplantation development of mouse embryos. We also made use of a mouse model carrying a LINE-1 retrotransposition-reporter transgene to follow parental patterns of transmission and mobilisation. PARTICIPANTS/MATERIALS, SETTING, METHODS: Hybrid B6CBA/F1 mice were used for the expression analyses. Relative TE expression was evaluated by using the nCounter quantification methodology (Nanostring®). This quantitative method allowed us to simultaneously follow 15 TE targets. Another technique of quantification (RTqPCR) was also used.A mouse model carrying a LINE-1 retrotransposition-reporter transgene (LINE-1 GF21) was used to follow parental patterns of transmission and mobilisation. MAIN RESULTS AND THE ROLE OF CHANCE: We found that the superovulation step did not modify the dynamics nor the level of TE transcription across the preimplantation period. However, upon in-vitro culture, TE expression was globally increased at the blastocyst stage in comparison with in-vivo development. Finally, by monitoring the transmission and mobilisation of a transgenic LINE-1 transposon, we found that in-vitro fertilisation may alter the mendelian rate of paternal inheritance. LARGE SCALE DATA: N/A. LIMITATIONS, REASONS FOR CAUTION: Even though the Nanostring results concerning the dynamics of transcription throughout preimplantation development were based on pools of embryos originating from several females, only two pools were analysed per developmental stage. However, at the blastocyst stage, consistent expressional results were found between the Nanostring technology and the other technique of quantification used, RTqPCR. WIDER IMPLICATIONS OF THE FINDINGS: Our findings highlight the sensitivity of TEs to the ART environment and their great potential as biomarkers of culture medium-based effects. STUDY FUNDING/COMPETING INTEREST(S): This work was supported by funding from the 'Agence de la Biomedecine', 'Conseil Régional de Bourgogne' and 'RCT grant from INSERM-DGOS'. The authors have no conflicts of interest to declare.

Plasticity in Dnmt3L-dependent and -independent modes of de novo methylation in the developing mouse embryo.

A stimulatory DNA methyltransferase co-factor, Dnmt3L, has evolved in mammals to assist the process of de novo methylation, as genetically demonstrated in the germline. The function of Dnmt3L in the early embryo remains unresolved. By combining developmental and genetic approaches, we find that mouse embryos begin development with a maternal store of Dnmt3L, which is rapidly degraded and does not participate in embryonic de novo methylation. A zygotic-specific promoter of Dnmt3l is activated following gametic methylation loss and the potential recruitment of pluripotency factors just before implantation. Importantly, we find that zygotic Dnmt3L deficiency slows down the rate of de novo methylation in the embryo by affecting methylation density at some, but not all, genomic sequences. Dnmt3L is not strictly required, however, as methylation patterns are eventually established in its absence, in the context of increased Dnmt3A protein availability. This study proves that the postimplantation embryo is more plastic than the germline in terms of DNA methylation mechanistic choices and, importantly, that de novo methylation can be achieved in vivo without Dnmt3L.

DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation.

As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.

Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo.

Nodal, a secreted factor known for its conserved functions in cell-fate specification and the establishment of embryonic axes, is also required in mammals to maintain the pluripotency of the epiblast, the tissue that gives rise to all fetal lineages. Although Nodal is expressed as early as E3.5 in the mouse embryo, its regulation and functions at pre- and peri-implantation stages are currently unknown. Sensitive reporter transgenes for two Nodal cis-regulatory regions, the PEE and the ASE, exhibit specific expression profiles before implantation. Mutant and inhibitor studies find them respectively regulated by Wnt/ß-catenin signaling and Activin/Nodal signaling, and provide evidence for localized and heterogeneous activities of these pathways in the inner cell mass, the epiblast and the primitive endoderm. These studies also show that Nodal and its prime effector, FoxH1, are not essential to preimplantation Activin/Nodal signaling. Finally, a strong upregulation of the ASE reporter in implanting blastocysts correlates with a downregulation of the pluripotency factor Nanog in the maturing epiblast. This study uncovers conservation in the mouse blastocyst of Wnt/ß-catenin and Activin/Nodal-dependent activities known to govern Nodal expression and the establishment of polarity in the blastula of other deuterostomes. Our results indicate that these pathways act early on to initiate distinct cell-specification processes in the ICM derivatives. Our data also suggest that the activity of the Activin/Nodal pathway is dampened by interactions with the molecular machinery of pluripotency until just before implantation, possibly delaying cell-fate decisions in the mouse embryo.

The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates.

Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.

Persistent cell migration and adhesion rely on retrograde transport of ß(1) integrin.

Integrins have key functions in cell adhesion and migration. How integrins are dynamically relocalized to the leading edge in highly polarized migratory cells has remained unexplored. Here, we demonstrate that ß1 integrin (known as PAT-3 in Caenorhabditis elegans), but not ß3, is transported from the plasma membrane to the trans-Golgi network, to be resecreted in a polarized manner. This retrograde trafficking is restricted to the non-ligand-bound conformation of ß1 integrin. Retrograde trafficking inhibition abrogates several ß1-integrin-specific functions such as cell adhesion in early embryonic development of mice, and persistent cell migration in the developing posterior gonad arm of C. elegans. Our results establish a paradigm according to which retrograde trafficking, and not endosomal recycling, is the key driver for ß1 integrin function in highly polarized cells. These data more generally suggest that the retrograde route is used to relocalize plasma membrane machinery from previous sites of function to the leading edge of migratory cells.