The regulatory architecture of the primed pluripotent cell state

Bo I. Li, Mariano J. Alvarez, Hui Zhao, Napon Chirathivat, Andrea Califano () and Michael M. Shen ()
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Bo I. Li: Department of Medicine
Mariano J. Alvarez: Systems Biology
Hui Zhao: Department of Medicine
Napon Chirathivat: Department of Medicine
Andrea Califano: Department of Medicine
Michael M. Shen: Department of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract Despite extensive research, the gene regulatory architecture governing mammalian cell states remains poorly understood. Here we present an integrative systems biology approach to elucidate the network architecture of primed state pluripotency. Using an unbiased methodology, we identified and experimentally confirmed 132 transcription factors as master regulators (MRs) of mouse epiblast stem cell (EpiSC) pluripotency, many of which were further validated by CRISPR-mediated functional assays. To assemble a comprehensive regulatory network, we silenced each of the 132 MRs to assess their effects on the other MRs and their transcriptional targets, yielding a network of 1273 MR → MR interactions. Network architecture analyses revealed four functionally distinct MR modules (communities), and identified key Speaker and Mediator MRs based on their hierarchical rank and centrality. Our findings elucidate the de-centralized logic of a “communal interaction” model in which the balanced activities of four MR communities maintain primed state pluripotency.

Date: 2025
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DOI: 10.1038/s41467-025-57894-4

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