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Probing cell identity hierarchies by fate titration and collision during direct reprogramming
Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate con...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9476893/ https://www.ncbi.nlm.nih.gov/pubmed/36106915 http://dx.doi.org/10.15252/msb.202211129 |
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author | Hersbach, Bob A Fischer, David S Masserdotti, Giacomo Deeksha, Mojžišová, Karolina Waltzhöni, Thomas Rodriguez‐Terrones, Diego Heinig, Matthias Theis, Fabian J Götz, Magdalena Stricker, Stefan H |
author_facet | Hersbach, Bob A Fischer, David S Masserdotti, Giacomo Deeksha, Mojžišová, Karolina Waltzhöni, Thomas Rodriguez‐Terrones, Diego Heinig, Matthias Theis, Fabian J Götz, Magdalena Stricker, Stefan H |
author_sort | Hersbach, Bob A |
collection | PubMed |
description | Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide‐seq. Collide‐seq revealed the lack of a common mechanism through which fibroblast‐specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide‐seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms. |
format | Online Article Text |
id | pubmed-9476893 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94768932022-09-21 Probing cell identity hierarchies by fate titration and collision during direct reprogramming Hersbach, Bob A Fischer, David S Masserdotti, Giacomo Deeksha, Mojžišová, Karolina Waltzhöni, Thomas Rodriguez‐Terrones, Diego Heinig, Matthias Theis, Fabian J Götz, Magdalena Stricker, Stefan H Mol Syst Biol Articles Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide‐seq. Collide‐seq revealed the lack of a common mechanism through which fibroblast‐specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide‐seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms. John Wiley and Sons Inc. 2022-09-15 /pmc/articles/PMC9476893/ /pubmed/36106915 http://dx.doi.org/10.15252/msb.202211129 Text en © 2022 The Authors. Published under the terms of the CC BY 4.0 license. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Hersbach, Bob A Fischer, David S Masserdotti, Giacomo Deeksha, Mojžišová, Karolina Waltzhöni, Thomas Rodriguez‐Terrones, Diego Heinig, Matthias Theis, Fabian J Götz, Magdalena Stricker, Stefan H Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title | Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title_full | Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title_fullStr | Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title_full_unstemmed | Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title_short | Probing cell identity hierarchies by fate titration and collision during direct reprogramming |
title_sort | probing cell identity hierarchies by fate titration and collision during direct reprogramming |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9476893/ https://www.ncbi.nlm.nih.gov/pubmed/36106915 http://dx.doi.org/10.15252/msb.202211129 |
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