Rules for gene usage inferred from a comparison of large-scale gene expression profiles of T and B lymphocyte development.

Ribonucleic acid expression profiles of seven consecutive stages of mouse thymocyte development were generated on high density oligonucleotide arrays. Previously known expression patterns of several genes were confirmed. Ten percent (1,304 of more than 13,000) of the monitored genes were found with 99% confidence to be differentially expressed across all T cell developmental stages. When compared with 1,204 genes differentially expressed in five consecutive B lineage developmental stages of bone marrow, >40% (546 genes) appeared to be shared by both lineages. However, when four pools of functionally distinct cell stages were compared between B and T cell development, DJ-rearranged precursor cells and resting immature precursor cells before and after surface Ag receptor expression shared less than 10%, mature resting lymphocytes between 15 and 20%, and only cycling precursors responding to precursor lymphocyte receptor deposition shared >50% of these differentially expressed genes. Three general rules emerge from these results: 1) proliferation of cells at comparable stages is in majority executed by the same genes; 2) intracellular signaling and intercellular communication are effected largely by different genes; and 3) most genes are not used strictly at comparable, but rather at several, stages, possibly in different functional contexts.