Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities

Vidur Garg; Yang Yang; Sonja Nowotschin; Manu N. Setty; Ying-Yi Kuo; Roshan Sharma; Alexander Polyzos; Eralda Salataj; Dylan Murphy; Amy Jang; Dana Pe’er; Effie Apostolou; Anna‐Katerina Hadjantonakis

doi:10.1101/2023.03.28.534648

Developmental BiologybioRxivMar 28, 2023

Preprint

Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities

Vidur Garg iD, Yang Yang iD, Sonja Nowotschin iD, Manu N. Setty iD, Ying-Yi Kuo iD, Roshan Sharma iD, Alexander Polyzos iD, Eralda Salataj iD, Dylan Murphy iD, Amy Jang, Dana Pe’er iD, Effie Apostolou iD, Anna‐Katerina Hadjantonakis iD

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Abstract

Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells - in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.