TCF1 dosage determines cell fate during T cell development. [scATAC-Seq]

Loss of function studies have shown that transcription factor T cell factor-1 (TCF1), encoded by the Tcf7 gene, is essential for T cell development in the thymus. We discovered that the Tcf7 expression level is regulated by E box DNA binding proteins, independent of Notch, and regulates ab and gd T cell development. Systematic interrogation of the five E-protein binding elements (EPE1-5) in the Tcf7 enhancer region showed lineage-specific utilization. Specifically, loss-of-function analysis revealed that only EPE3 plays a critical role in supporting ab T cell development, while EPE1, 3 and 5 regulate gd T cell maturation and functional cell fate decision. The importance of EPE3 in supporting both lineages may stem from its unique capacity to interact with the Tcf7 transcriptional start site. Together these studies demonstrate that the precise dosage of TCF1 expression mediated by distinct EPEs generates a balanced output of T cells from the thymus. Overall design: 100,000 sorted WT-DN and ?EPE3-DN thymocytes were processed to isolate nuclei. Using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 and the Chromium Next GEM Chip H Single Cell Kit v1.1, thymocyte nuclei, at 7,000 nuclei per µl, were loaded onto a Chromium controller to generate single-nuclei GEMs after which library construction is performed according to the manufacturer's protocol.