ArticleMolecular systems biology2022
Probing cell identity hierarchies by fate titration and collision during direct reprogramming.
Article in Molecular systems biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
- Protocol for identifying cellular reprogramming minimal networks using combinatorial transcription factor screening.STAR protocols · 2026Article
- Investigating the ageing-Parkinson's disease nexus: standardisation of in vitro models and techniques by the PD-AGE network.NPJ Parkinson's disease · 2025Review
- Cell identity and 5-hydroxymethylcytosine.Epigenetics & chromatin · 2025Review
- Proliferation history and transcription factor levels drive direct conversion to motor neurons.Cell systems · 2025Article
- Fate erasure logic of gene networks underlying direct neuronal conversion of somatic cells by microRNAs.Cell reports · 2025Article
- A Snapshot of Early Transcriptional Changes Accompanying the Pro-Neural Phenotype Switch by NGN2, ASCL1, SOX2, and MSI1 in Human Fibroblasts: An RNA-Seq Study.International journal of molecular sciences · 2024Article
- Epigenetic Dynamics in Reprogramming to Dopaminergic Neurons for Parkinson's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Review
- A logic-incorporated gene regulatory network deciphers principles in cell fate decisions.eLife · 2024Article
- Insights and applications of direct neuronal reprogramming.Current opinion in genetics & development · 2023Review
- Proliferation history and transcription factor levels drive direct conversion.bioRxiv : the preprint server for biology · 2023Article
- Dissecting and improving gene regulatory network inference using single-cell transcriptome data.Genome research · 2023Article
- The CUT&RUN suspect list of problematic regions of the genome.Genome biology · 2023Article
- Deterministic and probabilistic fate decisions co-exist in a single retinal lineage.The EMBO journal · 2023Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- Probing cell identity hierarchies by fate titration and collision during direct reprogramming.Molecular systems biology · 2022Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.