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Probing cell identity hierarchies by fate titration and collision during direct reprogramming.
Mol. Syst. Biol. 18:e11129 (2022)
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.
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
Direct Reprogramming ; Collide-seq ; Fate Conversion ; Reprogramming ; Scrna-seq
ISSN (print) / ISBN
1744-4292
e-ISSN
1744-4292
Journal
Molecular Systems Biology
Quellenangaben
Volume: 18,
Issue: 9,
Article Number: e11129
Publisher
EMBO Press
Non-patent literature
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Reviewing status
Peer reviewed