Systematic mapping of TF-mediated cell fate changes by a pooled inductioncoupled with scRNA-seq and multi-omics approaches

Transcriptional regulation controls various cellular functions via the interactionsbetween cell-type-specific transcription factors (TFs) and their chromosomaltargets. While multiple TFs capable of converting cell fates from one to anotherhave been reported, only a few systematic studies aiming to understand thefate conversion potential of numerous individual TFs have been reported. Here,we propose an iTF-seq method (pooled induction of individual TFs followed bysingle-cell RNA sequencing) to identify potent TFs capable of converting cellfates and elucidate their lineage specification potential at a single-cell level.Enabling metabolic biotinylation of TFs during the process, the method allowssubsequent multi-omics approaches to understand underlying actionmechanisms of TFs during cell fate changes. Our pilot iTF-seq of 80 TFs inmouse embryonic stem (ES) cells has identified multiple previously known andunknown TFs triggering transcriptome changes within one day of TF induction.Subsequent tests revealed that Gcm1 and Otx2 function as activators andpioneer factors, while they resulted in distinct cell fates and gene expressionprograms upon induction. Overall design: BioChIP-seq was performed on Gcm1 and Otx2 SBFB cells after 24h of Dox induction with uninduced control cells as well as Nanog FB mESCs. ATAC-seq was performed on Gcm1 and Otx2 SBFB cells after 24h of Dox induction with uninduced control cells.