Lee Muyoung, Guo Qingqing, Kim Mijeong, Choi Joonhyuk, Segura Alia, Genceroglu Alper, LeBlanc Lucy, Ramirez Nereida, Jang Yu Jin, Jang Yeejin, Lee Bum-Kyu, Marcotte Edward M, Kim Jonghwan
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA.
Genome Res. 2024 Apr 25;34(3):484-497. doi: 10.1101/gr.277926.123.
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.
转录调控通过转录因子（TFs）与其染色体靶标的相互作用来控制细胞功能。然而，以可诱导的方式理解多种TFs的命运转换潜力仍然有限。在此，我们引入iTF-seq作为一种在单细胞水平上鉴定能够将细胞命运改变为特定谱系的单个TFs的方法。iTF-seq能够对转录组变化进行时间进程监测，并且利用生物素化的单个TFs，它提供了一种多组学方法来理解TF介导的细胞命运变化背后的机制。我们在小鼠胚胎干细胞中进行的iTF-seq研究鉴定出多个TFs，它们在诱导一天内引发快速的转录组变化，表明细胞发生分化。此外，表达这些强效TFs的细胞通常显示出较慢的细胞周期和增加的细胞死亡。使用bioChIP-seq的进一步分析表明，GCM1和OTX2在细胞命运转换过程中通过增加基因可及性并激活谱系特异性基因的表达，充当先锋因子和激活剂。iTF-seq在绘制细胞命运转换图谱和理解细胞命运转换机制方面都具有实用性。
