Recently, we reported the organization of the thirteen exons of the human
DNA polymerase beta (beta-pol) gene and the sequences of the exon-intron junctions. Splice variants of human beta-pol
mRNA have been postulated to be related to
cancer development. Here, we report the characterization of
isoforms of human beta-pol
mRNA in different cells by reverse transcription polymerase chain reaction (RT-PCR). DNA sequence analysis of RT-PCR products revealed eight alternative splicing
mRNA isoforms in the
brain cancer cell line, SK-N-MC. These various
isoforms were consistent with alternative splicing of four exons (II, IV, V, and VI) and with a 105-nucleotide insertion (exon alpha) between exons VI and VII. We also found an
isoform with a 19-nucleotide sequence inserted into the exon IV and V junction, which resulted from usage of a different
3' splice site. Seven of the
isoforms resulted in truncated open reading frame (ORF); five corresponded to deduced
peptide of
amino acids 1-20 of beta-pol and two corresponded to
amino acids 1-60 of beta-pol. Only one of the right
mRNA isoforms, that with the exon alpha insertion, was in-frame with the entire wild-type ORF resulting in a deduced
protein of 370 residues, compared with the wild-type
protein of 335 residues and 39 kD. This longer ORF was shown to be capable of encoding a beta-
pol protein, larger than wild-type beta-pol, that cross-reacted with beta-pol antibody and exhibited beta-pol enzymatic activity. The
mRNA isoform with the exon alpha insertion was not
tumor specific because it as detected in low abundance in all cells tested, except the colon cell line CCD18 Co where the
isoform was absent. The genomic location of exon alpha is in intron VI, 990 bp upstream of exon VII and flanked by consensus splice sites. Thus, this 105-bp genomic sequence is a beta-pol exon present in a low-abundance beta-pol
mRNA isoform capable of encoding an approximately 42-kD beta-pol.