In mammals, extensive chromatin reorganization is essential for reprogramming terminally committed gametes to a totipotent state during preimplantation development. However, the global chromatin landscape and its dynamics in this period remain unexplored. Here we report a genome-wide map of accessible chromatin in mouse preimplantation embryos using an improved assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach with CRISPR/Cas9-assisted mitochondrial DNA depletion. We show that despite extensive parental asymmetry in DNA methylomes, the chromatin accessibility between the parental genomes is globally comparable after major zygotic genome activation (ZGA). Accessible chromatin in early embryos is widely shaped by transposable elements and overlaps extensively with putative cis-regulatory sequences. Unexpectedly, accessible chromatin is also found near the transcription end sites of active genes. By integrating the maps of cis-regulatory elements and single-cell transcriptomes, we construct the regulatory network of early development, which helps to identify the key modulators for lineage specification. Finally, we find that the activities of cis-regulatory elements and their associated open chromatin diminished before major ZGA. Surprisingly, we observed many loci showing non-canonical, large open chromatin domains over the entire transcribed units in minor ZGA, supporting the presence of an unusually permissive chromatin state. Together, these data reveal a unique spatiotemporal chromatin configuration that accompanies early mammalian development.

The landscape of accessible chromatin in mammalian preimplantation embryos

During mouse preimplantation embryo development, totipotent blastomeres generate the first three cell lineages of the embryo: trophectoderm, epiblast and primitive endoderm. In recent years, studies have shown that this process appears to be regulated by differences in cell-cell interactions, gene expression and the microenvironment of individual cells, rather than the active partitioning of maternal determinants. Precisely how these differences first emerge and how they dictate subsequent molecular and cellular behaviours are key questions in the field. As we review here, recent advances in live imaging, computational modelling and single-cell transcriptome analyses are providing new insights into these questions.

/pdf/lineage-specification-in-the-mouse-preimplantation-embryo-5coam5rjxc.pdf

Lineage specification in the mouse preimplantation embryo.

New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation

Pluripotent epiblast (EPI) cells, present in the inner cell mass (ICM) of the mouse blastocyst, are progenitors of both embryonic stem (ES) cells and the fetus. Discovering how pluripotency genes regulate cell fate decisions in the blastocyst provides a valuable way to understand how pluripotency is normally established. EPI cells are specified by two consecutive cell fate decisions. The first decision segregates ICM from trophectoderm (TE), an extraembryonic cell type. The second decision subdivides ICM into EPI and primitive endoderm (PE), another extraembryonic cell type. Here, we investigate the roles and regulation of the pluripotency gene Sox2 during blastocyst formation. First, we investigate the regulation of Sox2 patterning and show that SOX2 is restricted to ICM progenitors prior to blastocyst formation by members of the HIPPO pathway, independent of CDX2, the TE transcription factor that restricts Oct4 and Nanog to the ICM. Second, we investigate the requirement for Sox2 in cell fate specification during blastocyst formation. We show that neither maternal (M) nor zygotic (Z) Sox2 is required for blastocyst formation, nor for initial expression of the pluripotency genes Oct4 or Nanog in the ICM. Rather, Z Sox2 initially promotes development of the primitive endoderm (PE) non cell-autonomously via FGF4, and then later maintains expression of pluripotency genes in the ICM. The significance of these observations is that 1) ICM and TE genes are spatially patterned in parallel prior to blastocyst formation and 2) both the roles and regulation of Sox2 in the blastocyst are unique compared to other pluripotency factors such as Oct4 or Nanog.

/pdf/hippo-pathway-members-restrict-sox2-to-the-inner-cell-mass-6r7xtwiwaw.pdf

HIPPO Pathway Members Restrict SOX2 to the Inner Cell Mass Where It Promotes ICM Fates in the Mouse Blastocyst

Liver disease causing end organ failure is a growing cause of mortality. In most cases, the only therapy is liver transplantation. However, liver transplantation is a complex undertaking and its success is dependent on a number of factors. In particular, liver transplantation is subject to the risks of ischaemia-reperfusion injury (IRI). Liver IRI has significant effects on the function of a liver after transplantation. The cellular and molecular mechanisms governing IRI in liver transplantation are numerous. They involve multiple cells types such as liver sinusoidal endothelial cells, hepatocytes, Kupffer cells, neutrophils and platelets acting via an interconnected network of molecular pathways such as activation of toll-like receptor signalling, alterations in micro-RNA expression, production of ROS, regulation of autophagy and activation of hypoxia-inducible factors. Interestingly, the cellular and molecular events in liver IRI can be correlated with clinical risk factors for IRI in liver transplantation such as donor organ steatosis, ischaemic times, donor age, and donor and recipient coagulopathy. Thus, understanding the relationship of the clinical risk factors for liver IRI to the cellular and molecular mechanisms that govern it is critical to higher levels of success after liver transplantation. This in turn will help in the discovery of therapeutics for IRI in liver transplantation - a process that will lead to improved outcomes for patients suffering from end-stage liver disease.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/liv.14091

Ischaemia reperfusion injury in liver transplantation: Cellular and molecular mechanisms.

In many invertebrate and vertebrate species, cell fates are assigned through the cellular inheritance of differentially localized maternal determinants. Whether mammalian embryogenesis is also regulated by deterministic mechanisms is highly controversial. The caudal domain transcription factor CDX2 has been reported to act as a maternal determinant regulating cell fate decisions in mouse development. However, this finding is contentious because of reports that maternal Cdx2 is not essential for development. Notably, all of the previously published studies of maternal Cdx2 relied on injected RNA interference constructs, which could introduce experimental variation. Only deletion of the maternal gene can unambiguously resolve its requirement in mouse development. Here, we genetically ablated maternal Cdx2 using a Cre/lox strategy, and we definitively establish that maternal Cdx2 is not essential for mouse development.

/pdf/maternal-cdx2-is-dispensable-for-mouse-development-4hxkuqnyl6.pdf

Maternal Cdx2 is dispensable for mouse development

Diverse pluripotent stem cell lines have been derived from the mouse, including embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), embryonal carcinoma cells (ECCs), and epiblast stem cells (EpiSCs). While all are pluripotent, these cell lines differ in terms of developmental origins, morphology, gene expression, and signaling, indicating that multiple pluripotent states exist. Whether and how the pluripotent state influences the cell line's developmental potential or the competence to respond to differentiation cues could help optimize directed differentiation protocols. To determine whether pluripotent stem cell lines differ in developmental potential, we compared the capacity of mouse ESCs, iPSCs, ECCs, and EpiSCs to form trophoblast. ESCs do not readily differentiate into trophoblast, but overexpression of the trophoblast-expressed transcription factor, CDX2, leads to efficient differentiation to trophoblast and to formation of trophoblast stem cells (TSCs) in the presence of fibrobla...

/pdf/cdx2-efficiently-induces-trophoblast-stem-like-cells-in-1iko9lazw2.pdf

Stephanie Blij

Papers

HIPPO Pathway Members Restrict SOX2 to the Inner Cell Mass Where It Promotes ICM Fates in the Mouse Blastocyst

Maternal Cdx2 is dispensable for mouse development

Cdx2 Efficiently Induces Trophoblast Stem-Like Cells in Naïve, but Not Primed, Pluripotent Stem Cells