Open AccessProbing cell identity hierarchies by fate titration and collision during direct reprogramming
Author(s) -
Hersbach Bob A,
Fischer David S,
Masserdotti Giacomo,
Mojžišová Karolina,
Waltzhöni Thomas,
RodriguezTerrones Diego,
Heinig Matthias,
Theis Fabian J,
Götz Magdalena,
Stricker Stefan H
Publication year - 2022
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.202211129
Subject(s) - reprogramming , biology , cell fate determination , identity (music) , computational biology , titration , collision , microbiology and biotechnology , cell , evolutionary biology , genetics , transcription factor , gene , computer science , computer security , physics , inorganic chemistry , chemistry , acoustics
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.