Orientation of HLA-DNA gene and identification of a CpG island-associated gene adjacent to DNA in human major histocompatibility complex class II region.

We have constructed the detailed physical map of the HLA class II gene region by the pulsed field gel electrophoresis (PFGE) and cosmid walking technique. In this process, the DNA gene was found to be located telomeric to DPA1 with the 5'----3' orientation which is the same as the DPA1 and DPA2 genes, but opposite to the DQA1, DQA2 and DRA genes. This orientation is reverse to that of the counterpart gene in the rabbit major histocompatibility complex region. About 30 kb downstream from the DNA gene towards DOB, a CpG island characterized by clustered sites for rare cutting restriction enzymes and frequently associated with the 5' end of housekeeping genes was identified by PFGE and cosmid walking. From a complementary DNA (cDNA) library constructed from a Epstein-Barr virus-transformed B-cell line, a cDNA clone was isolated using the genetic probe from this CpG island. Its nucleotide sequences suggested that it represented a new non-HLA gene with a single copy which was of little genetic polymorphism and named NAT (DNA-associated transcript). Northern blot analysis showed that the NAT gene was expressed with a 4-kb transcript in all of tissues examined so far.