Genomic features of human PKR: alternative splicing and a polymorphic CGG repeat in the 5'-untranslated region

The double-stranded RNA-dependent protein kinase (PKR) is a serine/threonine kinase that plays an important role in the antiviral activities of interferon (IFN). To determine the organization and regulation of the PKR locus, lambda phage and bacterial artificial chromosome (BAC) clones containing the human PKR gene were isolated. Characterization of these clones revealed that PKR has 17 exons and 16 introns dispersed in a genomic region of 50 kb. Sequence analysis of the PKR 5'-flanking region identified a canonical IFN-stimulated response element (ISRE), GAAAACGAAACT. Transient transfection of PKR promoter constructs linked to a luciferase reporter gene into human T98G cells indicated that this 5'-flanking region is capable of functioning as a basal promoter that is also inducible by IFN-alpha and IFN-beta but not IFN-gamma. Interestingly, the PKR gene contains a polymorphic CGG trinucleotide repeat in exon 1. In addition, four PKR alleles, varying in repeat number from 7 to 10, were detected in 30 individual chromosomes. The PKR gene undergoes alternative splicing of exon 2, which gives rise to two forms of 5'-untranslated exons of different length. Although the human and murine PKR proteins have high homology, comparison of their gene structures reveals divergence in 5'-flanking regions, suggesting distinct regulation at the genomic level.