Feature mapping of the HLA class I region: localization of the POU5F1 and TCF19 genes

The class I region of the human leukocyte antigen (HLA) complex located on chromosome 6p21.3 is gene dense. To define the gene content of the class I region, we are constructing genomic DNA feature maps. Here we report mapping of the POU5F1 and TCF19 genes to an approximately 0.2-Mb region between the HLA-C and the S genes. Localization of these genes was facilitated by subcloning genomic DNA fragments from the 0.2-Mb region into a transposon gamma delta-based vector, selecting transposon-mediated deletions in vivo in Escherichia coli, and sequencing a nested subset chosen for their uniform distribution of deletion endpoints. The POU5F1 and TCF19 genes are located approximately 130 kb telomeric of the HLA-C locus, approximately 0.6 kb apart from each other. Complete sequencing of a 5.5-kb EcoRI fragment containing the TCF19 gene revealed that it is composed of three exons, bounded by consensus splice signals. These experiments illustrate that the transposon-based nested deletion sequencing method provides an easy and efficient approach to feature mapping genomic fragments and to high-resolution analysis of selected subportions.