Comparative analysis of the promoter regions and transcriptional start sites of mouse Ly49 genes

Despite numerous studies on the function of Ly49 natural killer cell recept ors in the mouse, relatively little is known about how these genes are regu lated at the transcriptional level. In the present study, we sequenced and compared 800 bp of the promoter region of nine Ly49 genes from C57B1/6 mice . This comparison showed that there is a high degree of sequence identity b etween the genes, and also revealed a region which is conserved between the mouse genes and the human Ly49L gene, indicating a potential core promoter region. This analysis also found that Ly49B and W differ from the other ge nes in having long interspersed repetitive sequence in their promoter regio n which suggests a gene conversion or rearrangement involving these two gen es. In addition, we performed 5' rapid amplification of cDNA ends on four L y49 genes to localize transcriptional start sites. These experiments showed that the transcriptional initiation sites art: heterogeneous for all of th e genes examined, and that a large majority of Ly49G transcripts originate from the second exori as well as its first. intron. Although potential TATA boxes have been previously identified for some of the genes, we did not fi nd evidence that a majority of transcripts initiate at the expected distanc e downstream of these boxes. Our data suggest that differences in the locat ion of transcriptional start sites contribute to the observed complexity in receptor repertoire patterns.