Human Molecular Genetics Advance Access originally published online on April 20, 2005
Human Molecular Genetics 2005 14(12):1579-1585; doi:10.1093/hmg/ddi166
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Allele-specific transcript quantification detects haplotypic variation in the levels of the SDF-1 transcripts
1Department of Human Genetics, Graduate School of Medicinen and 2Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan and 3Department of Pediatrics, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
* To whom correspondence should be addressed at: Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Tel: +81 358414633; Fax: +81 338187547; Email: tishida{at}biol.s.u-tokyo.ac.jp
Received February 2, 2005; Revised April 2, 2005; Accepted April 14, 2005
It has been suggested that SDF1-G801A, a single nucleotide polymorphism (SNP) in the 3' untranslated region (UTR) of the SDF1 gene, is associated with susceptibility to diseases such as AIDS and type-I diabetes. However, experimental studies examining the effect of SDF1-G801A on SDF-1 expression have not supported its functional importance. In this study, to examine whether other polymorphisms have a cis-acting effect on SDF1 expression, we carried out haplotype analyses of the SDF1 gene and the allele-specific transcript quantification utilizing Epstein–Barr virus-transformed lymphoblastoid cell lines with heterozygous genotype for SDF1-G801A. Haplotype-based analyses on the proportion of the allele-specific transcripts revealed the presence of haplotypes associated with a decreased amount of the transcripts. In addition, we observed haplotypic variation in response to dibutyl cyclic AMP and tetradecanoyl phorbol acetate that enhances the levels of SDF-1 transcripts probably through activation of transcription factors. Showing evidence that polymorphisms other than the SDF1-G801A have a cis-acting effect on expression of SDF-1 transcripts, the results of this study contribute to the interpretation of previous disease-association studies and to the selection of SNP markers for future studies. As shown in this study, allele-specific transcript quantification coupled with haplotype analyses can be an effective tool for detecting cis-acting polymorphisms in expressional regulation.
This study constitutes part of a doctoral dissertation (R. Kimura) submitted to the University of Tokyo.
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