Jennifer Nichols

This study compares single-cell transcriptomes of human, marmoset, and mouse embryos to identify conserved and divergent features of preimplantation development.

The paper shows that during exit from pluripotency, coexpression of DNMT3s and TETs drives genome-scale DNA methylation oscillations, with amplitude dependent on CpG density, observed both in vitro and in vivo.

The paper develops a mouse pluripotent stem cell micropattern system to study regionalized fate specification and patterning, revealing how signals direct distinct identities and spatial organization.

Reanalysis of three human embryo scRNA-seq datasets resolves cell-type ambiguities, defines epiblast and primitive endoderm prototypes, and identifies t2iLGö and 5i/L/A naïve stem cells as epiblast-like.

The paper tracks the transition of mouse embryonic stem cells from ground state pluripotency to a formative phase, showing acute exit from naive status and transcriptome changes similar to early post-implantation epiblast.