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The Bardet–Biedl Syndrome 7 (<i>Bbs7</i>) gene was identified as the most likely candidate gene causing juvenile obesity in the Berlin Fat Mouse Inbred (BFMI) line. <i>Bbs7</i> expression is significantly lower in the brain, adipose tissue, and liver of BFMI mice compared to lean C57BL/6NCrl (B6N) mice. A DNA sequence comparison between BFMI and B6N revealed 16 sequence variants in the <i>Bbs7</i> promoter region. Here, we tested if these mutations contribute to the observed differential expression of <i>Bbs7</i>. In a cell-based dual-luciferase assay, we compared the effects of the BFMI and the B6N haplotypes of different regions of the <i>Bbs7</i> promotor on the reporter gene expression. A single-nucleotide polymorphism (SNP) was identified causing a significant reduction in the reporter gene expression. This SNP (rs29947545) is located in the 5′ UTR of <i>Bbs7</i> at Chr3:36.613.350. The SNP is not unique to BFMI mice but also occurs in several other mouse strains, where the BFMI allele is not associated with lower <i>Bbs7</i> transcript amounts. Thus, we suggest a compensatory mutation in the other mouse strains that keeps <i>Bbs7</i> expression at the normal level. This compensatory mechanism is missing in BFMI mice and the cell lines tested.