title: Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters.
abstract: 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).
authors.affiliation: Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Ponomarenko
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Rasskazov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Valentin
authors.initials: V
authors.lastname: Suslov
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Sharypova
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Ludmila
authors.initials: L
authors.lastname: Savinkova
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Podkolodnaya
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Nikolay L
authors.initials: NL
authors.lastname: Podkolodny
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Natalya N
authors.initials: NN
authors.lastname: Tverdokhleb
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Irina
authors.initials: I
authors.lastname: Chadaeva
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Mikhail
authors.identifier: 0000-0003-1663-318X
authors.initials: M
authors.lastname: Ponomarenko
authors.affiliation: Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Kolchanov
mesh_terms: D057906:Circadian Clocks / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics*; D020022:Genetic Predisposition to Disease / Q000235:genetics; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D035181:TATA-Box Binding Protein / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D035181:TATA-Box Binding Protein