Human Molecular Genetics Advance Access published online on April 20, 2005
Human Molecular Genetics, doi:10.1093/hmg/ddi166
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1 Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
* To whom correspondence should be addressed. It has been suggested that the SDF1-G801A, a SNP in the 3' untranslated region of the SDF1 gene, is associated with susceptibility to diseases such as AIDS and type-I diabetes. Experimental studies examining an effect of the SDF1-G801A on SDF-1 expression, however, 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 the heterozygous genotype for the SDF1-G801A. Haplotype-based analyses on proportion of the allele-specific transcripts revealed the presence of haplotypes associated with the decreased amount of the transcripts. In addition, we observed haplotypic variation in response to dibutyl cyclic AMP and tetradecanoyl phorbol acetate that enhance the levels of SDF-1 transcripts probably through activation of transcription factors. Showing evidence that polymorphisms other than the SDF1-G801A have the cis-acting effect on expression of SDF-1 transcripts, the results of this study contribute to interpretation of previous disease-association studies and to selection of SNP markers for future studies. As shown in this study, the allele-specific transcript quantification coupled with haplotype analyses can be an effective tool for detecting cis-acting polymorphisms in expressional regulation.
Received February 2, 2005
Revised April 4, 2005
Accepted April 7, 2005
Article
Allele-specific transcript quantification detects haplotypic variation in the levels of the SDF-1 transcripts
2 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
3 Department of Pediatrics, Faculty of Medicine, Diponegoro University, Semarang, Indonesia.
4 Department of Biological Sciences, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Tokyo, Japan.
Takafumi Ishida, E-mail: tishida{at}biol.s.u-tokyo.ac.jp
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