Arkova O.V. Rasskazov D.A. Drachkova I.А. Ponomarenko P.M. Arshinova T.V. Ponomarenko M.P. Savinkova L.K. Kolchanov N.A.
Obesity-related putative SNP-markers rs200487063, rs34104384, and rs201381696 change the affinity of the TATA-binding protein to the human LEP promoter significantly
Reporter: Arkova O.V.
Consideration of SNP markers of resistance, susceptibility, or hypersensitivity to a certain kind of therapy helps doctors alleviate patients' suffering and improve treatment quality. Only medical practice can establish SNP markers by genotyping patients and detecting SNP alleles significantly more frequent than in healthy persons. Search for relevant SNPs can be accelerated by computer-based analysis of hundreds of millions of SNPs in the 1000 Genomes project. We have used the SNP_TATA_Comparator (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl) to assess the significance (Z-score) of changes in the affinity of the TATA-binding protein (TBP) to the human LEP promoter for all unannotated SNPs in its [-70; -20] region, where all proven TATA boxes fall. These changes determine deviations in the level of the adipose tissue hormone leptin, which regulates energy metabolism. We have found a putative SNP-marker, rs201381696, for leptin deficiency. Earlier, this deficiency was clinically associated with leptin/insulin resistance in diet-induced obesity. Two other putative SNP markers, rs200487063 and rs34104384, determine elevated leptin levels. Earlier, the high level of leptin was clinically observed in patients with obesity-associated hypertension. The significance (α<0.05) of the difference of TBP affinities to the minor and ancestral alleles of rs200487063, rs201381696, and rs34104384 is confirmed by the electrophoretic mobility shift assay under nonequilibrium conditions in vitro. We have also measured the half-lives and the association and dissociation rate constants of TBP/DNA complexes for these SNPs. Our in silico and in vitro analysis show that rs566757746, rs560478489, and rs545535648 insignificantly affect the anchoring TBP/DNA complex, whose binding to RNA polymerase II triggers the assembly of the preinitiation complex of the human LEP gene. With the current state of the art, the choice of rs200487063, rs201381696, and/or rs34104384 for testing as obesity-related SNP markers according to appropriate biomedical standards and protocols appears to be better substantiated than the rest SNPs rs566757746, rs560478489, or rs545535648 of this gene promoter.
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