Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Mikhail P Ponomarenko; Olga Arkova; Dmitry Rasskazov; Petr Ponomarenko; Ludmila Savinkova; Nikolay Kolchanov

doi:10.3389/fimmu.2016.00130

Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

Front Immunol. 2016 Apr 4:7:130. doi: 10.3389/fimmu.2016.00130. eCollection 2016.

Authors

Mikhail P Ponomarenko¹, Olga Arkova², Dmitry Rasskazov², Petr Ponomarenko³, Ludmila Savinkova², Nikolay Kolchanov¹

Affiliations

¹ Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
² Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences , Novosibirsk , Russia.
³ Children's Hospital Los Angeles , Los Angeles, CA , USA.

Abstract

Some variations of human genome [for example, single nucleotide polymorphisms (SNPs)] are markers of hereditary diseases and drug responses. Analysis of them can help to improve treatment. Computer-based analysis of millions of SNPs in the 1000 Genomes project makes a search for SNP markers more targeted. Here, we combined two computer-based approaches: DNA sequence analysis and keyword search in databases. In the binding sites for TATA-binding protein (TBP) in human gene promoters, we found candidate SNP markers of gender-biased autoimmune diseases, including rs1143627 [cachexia in rheumatoid arthritis (double prevalence among women)]; rs11557611 [demyelinating diseases (thrice more prevalent among young white women than among non-white individuals)]; rs17231520 and rs569033466 [both: atherosclerosis comorbid with related diseases (double prevalence among women)]; rs563763767 [Hughes syndrome-related thrombosis (lethal during pregnancy)]; rs2814778 [autoimmune diseases (excluding multiple sclerosis and rheumatoid arthritis) underlying hypergammaglobulinemia in women]; rs72661131 and rs562962093 (both: preterm delivery in pregnant diabetic women); and rs35518301, rs34166473, rs34500389, rs33981098, rs33980857, rs397509430, rs34598529, rs33931746, rs281864525, and rs63750953 (all: autoimmune diseases underlying hypergammaglobulinemia in women). Validation of these predicted candidate SNP markers using the clinical standards may advance personalized medicine.

Keywords: SNP marker; TATA-binding protein; TBP-binding site; expression change; gender-biased autoimmune disease; gene; promoter; single nucleotide polymorphism.