Collecting two-cell- to compacted morula-stage embryos

Dux facilitates post-implantation development, but is not essential for zygotic genome activation†

Double homeobox genes are unique to eutherian mammals. It has been proposed that the DUXC clade of the double homeobox gene family, which is present in multicopy long tandem arrays, plays an essential role in zygotic genome activation (ZGA). We generated a deletion of the tandem array encoding the DUXC gene of mouse, Double homeobox (Dux), and found it surprisingly to be homozygous viable and fertile. We characterize the embryonic development and ZGA profile of knockout (KO) embryos, finding that zygotic genome activation still occurs, with only modest alterations in 2-cell embryo gene expression, no defect in in vivo preimplantation development, but an increased likelihood of post-implantation developmental failure, leading to correspondingly smaller litter sizes in the KO strain. While all known 2-cell specific Dux target genes are still expressed in the KO, a subset is expressed at lower levels. These include numerous genes involved in methylation, blastocyst development, and trophectoderm/placental development. We propose that rather than driving ZGA, which is a process common throughout the animal kingdom, DUXC genes facilitate a process unique to eutherian mammals, namely the post-implantation development enabled by an invasive placenta.

ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains

BACKGROUND

KRAB zinc finger proteins (KZFPs) represent one of the largest families of DNA-binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental origin at genomic imprints. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at imprints, unique and repetitive regions of the genome.

RESULTS

Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though the loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibit alterations in expression. Comparison of ZFP57 mutants with DNA methyltransferase-deleted ES cells (TKO) identifies a remarkably similar pattern of H3K9me3 loss across the genome. These data define regions where H3K9me3 is secondary to DNA methylation and we propose that ZFP57 is the principal if not sole methylation-sensitive KZFP in mouse ES cells. Finally, we examine dynamics of DNA and H3K9 methylation during pre-implantation development and show that sites bound by ZFP57 in ES cells maintain DNA methylation and H3K9me3 at imprints and at non-imprinted regions on the maternally inherited chromosome throughout preimplantation development.

CONCLUSION

Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline-derived imprinting control regions.

Mouse Embryo Cryopreservation by High-Osmolality Vitrification

In conventional vitrification methods, the embryos are vitrified under considerable supercooling (i.e., under nonequilibrium conditions). This protocol is a refinement of newer equilibrium vitrification methods. The equilibrium vitrification solution contains a high concentration of cryoprotectants that increase its osmolality and allows vitrified embryos to survive not only during storage in liquid nitrogen (LN₂) at -196°C but also during temporary holding at -80°C (for at least 5 mo). This high-osmolality vitrification (HOV) method is as simple as conventional vitrification and provides essentially the same high postwarming survival rate. It has several advantages over conventional vitrification: (1) Cryopreserved embryos are less likely to be damaged during handling for warming; (2) samples can be temporarily evacuated to a -80°C freezer and can be successfully recovered after 5 mo at -80°C; (3) samples can be arranged and sorted at -80°C; and (4) vitrified embryos can be transported using dry ice. Also included here is an alternative protocol that describes the use of straws instead of cryotubes.

Mouse Embryo Cryopreservation by Rapid Cooling

Embryo cryopreservation has been used to archive mouse strains. Protocols have evolved over this time and now vary considerably in terms of cryoprotectant solution, cooling and warming rates, methods to add and remove cryoprotectant, container or carrier type, volume of cryoprotectant, the stage of preimplantation development, and the use of additional treatments such as blastocyst puncture and microinjection. The rapid cooling methods use concentrated solutions of cryoprotectants to reduce the water content of the cell before cooling commences, thus preventing the formation of ice crystals. Embryos are equilibrated with the cryoprotectants, loaded into a carrier, and then rapidly cooled (e.g., by being plunged directly into LN₂ or onto a surface cooled in LN₂). The rapid cooling methods eliminate the need for controlled-rate freezers and seeding procedures. However, they are much more sensitive to minor variations when performing the steps. The rapid-cooling protocol described here is suitable for use with plastic insemination straws. Because it uses relatively large volumes, it is less technically demanding than some other methods that use minivolume devices.

Mouse Embryo Cryopreservation by Slow Freezing

This embryo cryopreservation protocol is used by The Jackson Laboratory and several other repositories around the world. This protocol has clearly withstood the test of time; >2 million embryos from thousands of strains have been cryopreserved using this method. It requires a controlled-rate freezer, but is simple, effective, and can be applied to cryopreserve embryos from the two-cell to the blastocyst stage. Thawing requires neither special media nor equipment because the insemination straw contains all of the needed elements, making this very useful for distributing cryopreserved embryos. Embryo survival rates of greater than 90% can be expected when this method is used, making it reliable and enabling staff with prior embryo-handling experience to become proficient quickly.

Shipment of Live Preimplantation-Stage Mouse Embryos

Sharing genetically modified mouse models is a very important part of collaboration between researchers. Shipping live animals around the world is inconvenient, expensive, and cumbersome because of the variety of international regulations and paperwork. The issue of health status differences between animal facilities is of great importance; traditionally, imported animals are quarantined to determine their health status and avoid the introduction of undesirable pathogens. The shipment of preimplantation-stage embryos for immediate transfer into pseudopregnant recipients upon arrival is a commonly used method for transportation. Time coordination on both sides is critical in this case, but the shipment can be done by any courier and the container does not need to be returned. This protocol has been used since the early 1990s to rederive dozens of mouse strains.

Derivation of Mouse Embryonic Stem (ES) Cell Lines Using Small-Molecule Inhibitors of Erk and Gsk3 Signaling (2i)

The efficiency of embryonic stem (ES) cell derivation is very high if embryos are incubated, from the eight-cell stage, in the presence of the two inhibitors of signaling via the Erk and Gsk3 pathways (PD0325901 and CHIR99021, respectively, known as "2i"). The success rate may vary, depending on the quality of the embryos and the speed with which they are processed, but it is not unusual to obtain ES cell lines from all embryos allocated to the study, even from the least permissive strains. Furthermore, ES cells can be efficiently obtained from any complex genetic mouse model or for in vitro analysis and additional genetic manipulation in any background of choice.

Class II major histocompatibility complex mutant mice to study the germ-line bias of T-cell antigen receptors

The interaction of αβ T-cell antigen receptors (TCRs) with peptides bound to MHC molecules lies at the center of adaptive immunity. Whether TCRs have evolved to react with MHC or, instead, processes in the thymus involving coreceptors and other molecules select MHC-specific TCRs de novo from a random repertoire is a longstanding immunological question. Here, using nuclease-targeted mutagenesis, we address this question in vivo by generating three independent lines of knockin mice with single-amino acid mutations of conserved class II MHC amino acids that often are involved in interactions with the germ-line-encoded portions of TCRs. Although the TCR repertoire generated in these mutants is similar in size and diversity to that in WT mice, the evolutionary bias of TCRs for MHC is suggested by a shift and preferential use of some TCR subfamilies over others in mice expressing the mutant class II MHCs. Furthermore, T cells educated on these mutant MHC molecules are alloreactive to each other and to WT cells, and vice versa, suggesting strong functional differences among these repertoires. Taken together, these results highlight both the flexibility of thymic selection and the evolutionary bias of TCRs for MHC.