Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

• Published in: BioMed research international Vol. 2016; no. 2016; pp. 1 - 21
• Main Authors: Ponomarenko, Mikhail, Kolchanov, Nikolay, Chadaeva, Irina, Podkolodny, Nikolay L., Podkolodnaya, Olga, Savinkova, Ludmila, Sharypova, Ekaterina, Suslov, Valentin, Rasskazov, Dmitry, Ponomarenko, M. P., Tverdokhleb, Natalya N.
• Format: Journal Article
• Language: English
• Published: Cairo, Egypt Hindawi Publishing Corporation 01-01-2016; John Wiley & Sons, Inc
• Subjects: Analysis; Circadian Clocks - genetics; Diabetics; Genes; Genetic aspects; Genetic Markers - genetics; Genetic Predisposition to Disease - genetics; Genomes; Genomics; Heart attack; Humans; Lung cancer; Polymorphism, Single Nucleotide - genetics; Promoter Regions, Genetic - genetics; Promoters (Genetics); Protein binding; Single nucleotide polymorphisms; TATA-Box Binding Protein - genetics; Web services
• ISSN: 2314-6133; 2314-6141
• DOI: 10.1155/2016/8642703

Variations in human genome (e.g., single nucleotide polymorphisms, SNPs) may be associated with hereditary diseases, their complications, comorbidities, and drug responses. Using Web service SNP_TATA_Comparator presented in our previous paper, here we analyzed immediate surroundings of known SNP markers of diseases and identified several candidate SNP markers that can significantly change the affinity of TATA-binding protein for human gene promoters, with circadian consequences. For example, rs572527200 may be related to asthma, where symptoms are circadian (worse at night), and rs367732974 may be associated with heart attacks that are characterized by a circadian preference (early morning). By the same method, we analyzed the 90 bp proximal promoter region of each protein-coding transcript of each human gene of the circadian clock core. This analysis yielded 53 candidate SNP markers, such as rs181985043 (susceptibility to acute Q fever in male patients), rs192518038 (higher risk of a heart attack in patients with diabetes), and rs374778785 (emphysema and lung cancer in smokers). If they are properly validated according to clinical standards, these candidate SNP markers may turn out to be useful for physicians (to select optimal treatment for each patient) and for the general population (to choose a lifestyle preventing possible circadian complications of diseases).