Isolation, expression, and sequence of the TAP/Ly-6A.2 chromosomal gene

The murine Ly-6 locus controls the expression of a number of genes. One of the products of the Ly-6 locus, Ly-6A.2, has been implicated in the process of T cell activation. We have identified the chromosomal sequences encoding the Ly-6A.2 molecule using very stringent hybridization and washing conditions. We confirmed that this gene encoded the Ly-6A.2 molecule by transfection studies using a cell line genetically negative for the Ly-6A.2 gene as a DNA recipient. Sequence analysis showed that the Ly-6A.2 gene is made up of four exons. The start site of transcription was determined by primer extension analysis. The first exon does not contain protein coding sequences. The structure of the Ly-6A.2 gene supports previous speculation that various Ly-6 RNA can be generated by alternate splicing events. The Ly-6A.2 chromosomal gene is closely related to the previously characterized Ly-6C.1 chromosomal gene in the intron, exon, and 5' flanking regions. This analysis indicates that these genes have arisen as a consequence of gene duplication. Although endogenous Ly-6A.2 and Ly-6C genes are IFN responsive, only the latter contains a clearly identifiable IFN responsive element. A transfected Ly-6A.2 chromosomal gene that contains 3.9 kb of 5'-untranslated sequence is IFN responsive. However, a shorter chromosomal clone containing only 940 bp of 5' sequence is constitutively expressed in transfectants but does not respond to IFN.