Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a ‘T’-shaped model of specification. Here, we examine whether the acquisition of these two states in vitro, by nuclear reprogramming, share similar dynamics/trajectories. Using a comparative parallel multi-omics analysis (i.e., bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on cells undergoing reprogramming to pluripotency and TSC state we show that each reprogramming system exhibits specific trajectories from the onset of the process, suggesting ‘V’-shaped model. We describe in detail the various trajectories toward the two states and illuminate reprogramming stage-specific markers, blockers, facilitators and TSC subpopulations. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these regions are initially defined but retain inactive by the elimination of H3K27ac.
Bibliographical noteFunding Information:
Y.B. is supported by research grants from the European Research Council (ERC, #676843), the Israel Science Foundation (ISF, #823/14), EMBO Young Investigator Programme (YIP), DKFZ-MOST (CA 177), Howard Hughes Medical Institute International Research Scholar (HHMI, #55008727) and by a generous gift from Ms. Nadia Guth Biasini. T.K. is supported by the Israel Science Foundation (ISF, #913/15 and #1250/18), and by a CIDR Data Science grant. A.R. is supported by the British GROWTH fellowship. N.L. is supported by CIDR Data Science and Leibniz fellowships.
© 2022, The Author(s).