Misteli Guerreiro, I. | bioRxiv Science

bioRxiv2019

Self-organization of post-implantation-like embryonic tissues from blastoids

The early mammalian embryo (blastocyst) contains three co-developing types of stem cells. Two supporting extraembryonic types - the trophectoderm and the primitive endoderm - encase and guide the pluripotent epiblast that eventually forms all body tissues. Unlike embryos, stem cell-based models of the embryo can be generated in large numbers and subjected to high-content screens as a basis for basic and biomedical discoveries (Rivron et al., 2018a; Vrij et al., 2016b). Here, we show that aggregates of naive Embryonic stem cells cultured in chemically-defined conditions and exposed to combinatorial screens of signaling molecules, rapidly (48 hours) and efficiently (80%) set apart PrE-like cells. These cells produce a basal lamina, generate progenitors resembling both visceral and parietal endoderm, and polarize co-developing Epiblast cells to form a proamniotic cavity. In blastoids, stem cell-based models of the early blastocyst (Rivron et al., 2018b), this combination of signals increases the ratio and number of Gata6+/Nanog+ cells and promotes the survival, growth and morphogenesis of a post-implantation-like Epiblast in vitro. Modeling early embryonic development in chemically-defined in vitro conditions shows that the primitive endoderm forms via a specific combination of signaling pathways and sufficient to drive the development of the Epiblast.

developmental biology↗

bioRxiv2018

Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation

Mammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking-and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.

genomics↗