TCR gene rearrangement coincides with the acquisition of co-receptors. A key intermediate in T-cell development is a thymocyte that expresses both of the TCR co-receptors, CD4 and CD8, as well as a functional TCR-CD3 complex. These cells, called double positive (CD4CD8+) cells, are found only as developmental intermediates in the thymus. As the T cells mature, they lose either CD4 or CD8 to become single-positive cells. The choice of which co-receptor (CD4 or CD8) to express determines whether a T cell will recognize class I or class II MHC molecules. The question of how a CD4CD8+ cell is instructed to become a CD8 (class I MHC-restricted) T cell or a CD4 (class II MHC-restricted) T cell is not entirely settled, but we know that the transcription factors ThPOK and Runx3 play fundamental roles. ThPOK and Runx3 are regulated by TCR signaling. Cells that transiently express ThPOK will commit to the CD4 lineage and repress Runx3 expression. On the other hand, if ThPOK expression is not induced, Runx3 expression is high, and cells commit to the CD8 lineage. In mice, a loss-of-function mutation in the ThPOK gene abrogates CD4 T-cell development, and all thymocytes become CD8-expressing T cells.
A third type of CD4 T cells also develop in the thymus, named natural (or thymically derived) regulatory T cells (Tregs), but their function differs from that of the classic, conventional CD4 helper T cells, as will be described below. The development and function of natural Tregs requires the transcription factor FoxP3, which is also regulated to some extent by TCR signaling. While the avidity model of T-cell selection also applies to the development of natural Tregs, the threshold for negative selection seems to be higher for natural Tregs: thymocytes that recognize self antigen with high affinity yet escape negative selection further commit to the natural Treg lineage. Finally, the thymus gives rise to unconventional (and less numerous) types of T cells, such as invariant natural killer T cells (iNKT) that express the NK cell marker NK1.1 and are selected on the nonclassic MHC molecule CD1, which presents lipid antigens, as well as intraepithelial lymphocytes that will colonize the mucosal surfaces of the intestine. After the final stages of maturation, T cells of all types are exported to the peripheral lymphoid organs.