The genetic mechanisms that promote lineage commitment and eliminate autoreactive cells in the thymus are not well understood. To better understand this process, we have identified and quantitated transcripts in the two major thymocyte lineages by using serial analysis of gene expression. Approximately 25 genes displayed almost complete segregation to one or the other T cell lineage. Commitment to the CD4 lineage was marked by upregulation of genes associated with increased survival and chaperone function followed by expression of genes that regulate nucleosome remodeling and T cell receptor signaling. Differentiation within the CD8 lineage, on the other hand, was marked by up-regulation of genes that regulate lymphocyte homing, followed by quenching of genes that inhibit apoptosis. Definition of differential gene expression during development of the two major thymocyte lineages will allow insight into mechanisms of T cell development after positive and negative selection.serial analysis of gene expression ͉ genetic profiling ͉ CD4͞CD8 ͉ lineage commitment T he two major T cell lineages that regulate adaptive immunity are generated and purged of clones bearing autoreactive T cell receptors (TCR) in the thymus (1). Although the molecular basis of TCR expression on thymocytes and T cells is relatively well understood, the mechanisms that orchestrate development and selection of TCR-bearing thymocytes have not been clearly defined. Delineation of the expression and potential function of genes expressed during the development of each lineage represents an important step in understanding this process.Thymocyte differentiation begins with migration of common lymphoid progenitor cells from hematopoietic stem cells in adult bone marrow or fetal liver into the thymus, where they undergo cellular maturation and TCR-based selection. Distinct developmental compartments have been defined according to expression of the CD4 and CD8 coreceptors on differentiating thymocytes. The earliest compartment is composed of CD4 Ϫ 8 Ϫ double negative (DN) thymocytes, which give rise to CD4 ϩ CD8 ϩ double positive (DP) intermediates, which yield mature CD4 ϩ CD8 Ϫ (CD4) or CD4 Ϫ CD8 ϩ (CD8) single positive (SP) mature progeny. The DN stage of thymocyte differentiation is marked by genetic events that prepare cells for TCR-based selection by self-MHC, including expression of recombination activating genes (RAG-1 and RAG-2) and initiation of TCR gene rearrangements. These genetic events can be demarcated according to surface markers expressed sequentially on DN thymocytes (stages DN1-DN4) in order of their appearance during development (2, 3). DN1 and DN2 thymocytes proliferate before RAG-1͞-2 expression (4, 5), whereas the DN3 3 DN4 developmental step is accompanied by expression of a pre-TCR that inhibits further RAG-1͞-2 activity and promotes a second proliferative burst of cells that express both CD4 and CD8, marking transition into the DP compartment (6).Thymocytes that express the DP phenotype (by far the most abundant in the thymus) ...