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

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In silico analysis of the 5' region of the Vitamin D receptor gene : functional implications of evolutionary conservation. / Halsall, J A; Osborne, J E; Hutchinson, P E; Pringle, J H.

In: The Journal of Steroid Biochemistry and Molecular Biology, Vol. 103, No. 3-5, 03.2007, p. 352-6.

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@article{266e21ab46824d31a55b6dd2e77aab08,
title = "In silico analysis of the 5' region of the Vitamin D receptor gene: functional implications of evolutionary conservation",
abstract = "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.",
keywords = "Animals, Computational Biology, Evolution, Molecular, Exons, Genome, Humans, Promoter Regions, Genetic, Receptors, Calcitriol",
author = "Halsall, {J A} and Osborne, {J E} and Hutchinson, {P E} and Pringle, {J H}",
year = "2007",
month = mar,
doi = "10.1016/j.jsbmb.2006.12.046",
language = "English",
volume = "103",
pages = "352--6",
journal = "The Journal of Steroid Biochemistry and Molecular Biology",
issn = "0960-0760",
publisher = "Elsevier",
number = "3-5",

}

RIS

TY - JOUR

T1 - In silico analysis of the 5' region of the Vitamin D receptor gene

T2 - functional implications of evolutionary conservation

AU - Halsall, J A

AU - Osborne, J E

AU - Hutchinson, P E

AU - Pringle, J H

PY - 2007/3

Y1 - 2007/3

N2 - 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.

AB - 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.

KW - Animals

KW - Computational Biology

KW - Evolution, Molecular

KW - Exons

KW - Genome

KW - Humans

KW - Promoter Regions, Genetic

KW - Receptors, Calcitriol

U2 - 10.1016/j.jsbmb.2006.12.046

DO - 10.1016/j.jsbmb.2006.12.046

M3 - Article

C2 - 17240138

VL - 103

SP - 352

EP - 356

JO - The Journal of Steroid Biochemistry and Molecular Biology

JF - The Journal of Steroid Biochemistry and Molecular Biology

SN - 0960-0760

IS - 3-5

ER -