Inactivation of the H-2Klk gene could involve the substitutions of methylated CpGs.

By the isolation of overlapping cosmid clones and 'chromosome walking' studies from the H-2Kk gene, we have obtained cosmid clones encoding the H-2Klk gene from two separate cosmid libraries. The nucleotide sequence of one of the clones was determined. The cloned H-2Klk gene could be transcribed in vitro to give a normal H-2 class I mRNA of 1.7 kb. However, the deletion of four nucleotides in exon 3 of the H-2Klk gene results in a translation termination codon at the beginning of exon 4. In agreement with this, when expressed in human cells, the H-2Klk gene gave a truncated, cytoplasmic polypeptide of Mr 36,000. Therefore, although the H-2Klk gene is homologous to other class I MHC genes in its molecular organization and nucleotide sequence, it is a pseudogene. When compared to the nucleotide sequence of the H-2Kk gene, the H-2Klk gene has undergone many substitutions of methylated CpG residues (meCpG). This represents further evidence to suggest that this gene is inactive.