Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee1,3,
- Qingqing Guo1,3,
- Mijeong Kim1,3,
- Joonhyuk Choi1,
- Alia Segura1,
- Alper Genceroglu1,
- Lucy LeBlanc1,
- Nereida Ramirez1,
- Yu Jin Jang1,
- Yeejin Jang1,
- Bum-Kyu Lee2,
- Edward M. Marcotte1 and
- Jonghwan Kim1
- 1Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
- 2Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
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↵3 These authors contributed equally to this work.
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277926.123.
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Freely available online through the Genome Research Open Access option.
- Received March 27, 2023.
- Accepted February 21, 2024.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
