A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Cell Systems |
| Vol/bind | 14 |
| Udgave nummer | 9 |
| Sider (fra-til) | 788-805.e8 |
| ISSN | 2405-4712 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
We thank N. Festuccia for EsrrbΔ ESCs and the Esrrb-tdT targeting construct and all members of the Brickman laboratory for continuous critical discussion, specifically J.A.R. Herrera for bioinformatics advice and pipeline development and M. Rothová for their technical expertise and support on MARS-seq. We thank H. Neil, M. Michaut, and the reNEW Genomics Platform for exquisite assistance, support, and use of instruments, L. Mariani for assistance with mesoderm differentiation, J. Zylicz for TSCs, K. Stewart-Morgan for advice on ATAC protocols and the manuscript, G. dela Cruz and P. van Dieken for their technical support and advice on flow cytometry cell sorting, J. M. Bulkescher for microscopy support, and R. Bone for in-house processing/analysis of published ATAC-sequencing and post-implantation single-cell RNA-seq, respectively. MP was supported by a PhD studentship from the Lundbeck Foundation (R286-2018-1534). Work in the Brickman lab was funded by grants from the Lundbeck Foundation (R198-2015-412, R370-2021-617, and R400-2022-769), the Independent Research Fund Denmark (DFF-8020-00100B, DFF-0134-00022B, and DFF-2034-00025B), the Danish National Research Foundation (DNRF116), and the Novo Nordisk Foundation (NNF21OC0070898). The Novo Nordisk Foundation Center for Stem Cell Medicine is supported by Novo Nordisk Foundation (grant number NNF21CC0073729 and previously NNF17CC0027852). Work in the Trusina lab was funded by the Danish National Research Foundation (DNRF116). T.E.K. W.B.H. A.T. and J.M.B. conceived the study. T.E.K. W.B.H. and J.M.B. designed and interpreted experiments. T.E.K. performed all experiments, except the Esrrb truncation/mutant assessment, which was done by M.L. and the embryo work, which was done by M.L.-A. and M. Perera. T.E.K. carried out the bioinformatics analysis, except for processing of single-cell sequencing data and in-house analysis of Nowotschin et al. which was performed by M. Proks. T.E.K. A.T. A.V.N. and L.L.M. wrote and analyzed the in silico models. T.E.K. and J.M.B. wrote the manuscript with input from all other authors. The authors declare no competing interests. One or more of the authors of this paper self-identifies as a member of the LGBTQ+ community. We support inclusive, diverse, and equitable conduct of research.
Funding Information:
We thank N. Festuccia for EsrrbΔ ESCs and the Esrrb-tdT targeting construct and all members of the Brickman laboratory for continuous critical discussion, specifically J.A.R. Herrera for bioinformatics advice and pipeline development and M. Rothová for their technical expertise and support on MARS-seq. We thank H. Neil, M. Michaut, and the reNEW Genomics Platform for exquisite assistance, support, and use of instruments, L. Mariani for assistance with mesoderm differentiation, J. Zylicz for TSCs, K. Stewart-Morgan for advice on ATAC protocols and the manuscript, G. dela Cruz and P. van Dieken for their technical support and advice on flow cytometry cell sorting, J. M. Bulkescher for microscopy support, and R. Bone for in-house processing/analysis of published ATAC-sequencing and post-implantation single-cell RNA-seq, respectively. MP was supported by a PhD studentship from the Lundbeck Foundation ( R286-2018-1534 ). Work in the Brickman lab was funded by grants from the Lundbeck Foundation ( R198-2015-412 , R370-2021-617 , and R400-2022-769 ), the Independent Research Fund Denmark ( DFF-8020-00100B , DFF-0134-00022B , and DFF-2034-00025B ), the Danish National Research Foundation ( DNRF116 ), and the Novo Nordisk Foundation ( NNF21OC0070898 ). The Novo Nordisk Foundation Center for Stem Cell Medicine is supported by Novo Nordisk Foundation (grant number NNF21CC0073729 and previously NNF17CC0027852 ). Work in the Trusina lab was funded by the Danish National Research Foundation ( DNRF116 ).
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