An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development

alpha beta lineage T cells, most of which are CD4(+) or CD8(+) and recognize MHC I- or MHC II-presented antigens, are essential for immune responses and develop from CD4(+) CD8(+) thymocytes. The absence of in vitro models and the heterogeneity of alpha beta thymocytes have hampered analyses of their intrathymic differentiation. Here, combining single-cell RNA and ATAC (chromatin accessibility) sequencing, we identified mouse and human cep thymocyte developmental trajectories, We demonstrated asymmetric emergence of CD4(+) and CD8(+) lineages, matched differentiation programs of agonist-signaled cells to their MHC specificity, and identified correspondences between mouse and human transcriptomic and epigenomic patterns. Through computational analysis of single-cell data and binding sites for the CD4(+) -lineage transcription factor Thpok, we inferred transcriptional networks associated with CD4(+) - or CD8(+) -lineage differentiation, and with expression of Thpok or of the CD8(+)-lineage factor Runx3. Our findings provide insight into the mechanisms of CD4(+) and CD8(+) T cell differentiation and a foundation for mechanistic investigations of ocI T cell development.