In silico analysis of the 5' region of the Vitamin D receptor gene: functional implications of evolutionary conservation

In recent years, the complexity of the 5' region of the Vitamin D receptor (VDR) gene has become apparent. Six exons, 1a-1f, lie upstream of the translation start codon in exon 2. Transcription has been reported beginning in exons 1f, 1a, 1d and 1c and alternative splicing can produce a large number of alternative mRNA transcripts. Exon 1d transcripts can code for two alternative proteins. This pattern of transcription produces several potential promoter regions. We have used a number of in silico tools to study the evolutionary conservation of the exon and promoter sequences of the 5' region. Those exons involved in the alternative VDR proteins, exons 1d and 1c, were well conserved from mouse and rat, unlike exons 1f, 1e and 1b which showed little homology. Exon 1a was also well conserved. Furthermore, 1a was shown to be within a strong CpG island and TraFac revealed a Sp1-MazR-Sp1-MazR cluster of transcription factor binding sites immediately upstream of exon 1a, a common motif in strong promoters. The promoter region upstream of 1f showed a highly conserved pattern of transcription factor binding sites and was also shown to be within a CpG island. No significant clusters of conserved sites were observed in the 1c promoter region, despite reports of 1c promoter activity.