Multiple transcripts for rat nucleoside diphosphate kinase alpha isoform are structurally categorized into two groups that exhibit cell-specific expression and distinct translation potential.

Rat nucleoside diphosphate (NDP) kinase is composed of two isoforms (alpha and beta) encoded by independent genes. The mRNAs are expressed ubiquitously; however, the level of expression is tissue-dependent and is also up- or down-regulated under certain conditions, including growth stimulation, differentiation, and tumor metastasis. To address the regulatory mechanisms of gene expression for the rat NDP kinase major isoform alpha (an nm23-H2/PuF homologue), we identified the transcription initiation sites in detail by RNase protection and 5'-rapid amplification of DNA ends and located the core promoter region by chloramphenicol acetyltransferase assay. The transcripts, initiated from an extraordinarily wide range of sites, were categorized into two groups; one transcribed from an upstream region was spliced in the untranslated region (group 1), whereas the other initiated in the downstream region was not (group 2). RNase protection demonstrated that the group 1 mRNA was the dominant form present in all tissues except heart and skeletal muscle. In situ hybridization revealed cell-specific expression of these mRNA species. Furthermore, they differed in the translational efficiency (the group 2 alpha > beta > the group 1 alpha). These findings suggest that the regulation of the NDP kinase expression at both transcriptional and posttranscriptional steps could be fundamentally governed by the selection of transcription initiation sites.