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Uvarova AN, Tkachenko EA, Stasevich EM, Zheremyan EA, Korneev KV, Kuprash DV. Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1002-1013. [PMID: 38981696 DOI: 10.1134/s0006297924060026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 07/11/2024]
Abstract
Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis on specific genetic variants within the non-coding sequences. A particular focus is on the methods for identification of transcription factors with binding efficiency dependent on polymorphic variations. Despite remarkable progress in bioinformatic resources enabling prediction of the impact of polymorphisms on the disease pathogenesis, there is still the need for experimental approaches to investigate this issue.
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Affiliation(s)
- Aksinya N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Elena A Tkachenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ekaterina M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia
| | - Elina A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Kirill V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dmitry V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Klimova NV, Oshchepkova E, Chadaeva I, Sharypova E, Ponomarenko P, Drachkova I, Rasskazov D, Oshchepkov D, Ponomarenko M, Savinkova L, Kolchanov NA, Kozlov V. Disruptive Selection of Human Immunostimulatory and Immunosuppressive Genes Both Provokes and Prevents Rheumatoid Arthritis, Respectively, as a Self-Domestication Syndrome. Front Genet 2021; 12:610774. [PMID: 34239535 PMCID: PMC8259950 DOI: 10.3389/fgene.2021.610774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Using our previously published Web service SNP_TATA_Comparator, we conducted a genome-wide study of single-nucleotide polymorphisms (SNPs) within core promoters of 68 human rheumatoid arthritis (RA)-related genes. Using 603 SNPs within 25 genes clinically associated with RA-comorbid disorders, we predicted 84 and 70 candidate SNP markers for overexpression and underexpression of these genes, respectively, among which 58 and 96 candidate SNP markers, respectively, can relieve and worsen RA as if there is a neutral drift toward susceptibility to RA. Similarly, we predicted natural selection toward susceptibility to RA for 8 immunostimulatory genes (e.g., IL9R) and 10 genes most often associated with RA (e.g., NPY). On the contrary, using 25 immunosuppressive genes, we predicted 70 and 109 candidate SNP markers aggravating and relieving RA, respectively (e.g., IL1R2 and TGFB2), suggesting that natural selection can simultaneously additionally yield resistance to RA. We concluded that disruptive natural selection of human immunostimulatory and immunosuppressive genes is concurrently elevating and reducing the risk of RA, respectively. So, we hypothesize that RA in human could be a self-domestication syndrome referring to evolution patterns in domestic animals. We tested this hypothesis by means of public RNA-Seq data on 1740 differentially expressed genes (DEGs) of pets vs. wild animals (e.g., dogs vs. wolves). The number of DEGs in the domestic animals corresponding to worsened RA condition in humans was significantly larger than that in the related wild animals (10 vs. 3). Moreover, much less DEGs in the domestic animals were accordant to relieved RA condition in humans than those in the wild animals (1 vs. 8 genes). This indicates that the anthropogenic environment, in contrast to a natural one, affects gene expression across the whole genome (e.g., immunostimulatory and immunosuppressive genes) in a manner that likely contributes to RA. The difference in gene numbers is statistically significant as confirmed by binomial distribution (p < 0.01), Pearson's χ2 (p < 0.01), and Fisher's exact test (p < 0.05). This allows us to propose RA as a candidate symptom within a self-domestication syndrome. Such syndrome might be considered as a human's payment with health for the benefits received during evolution.
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Affiliation(s)
- Natalya V Klimova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Evgeniya Oshchepkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Ekaterina Sharypova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Petr Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Irina Drachkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Dmitry Rasskazov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Research Institute of Fundamental and Clinical Immunology (RIFCI SB RAS), Novosibirsk, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Nikolay A Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI SB RAS), Novosibirsk, Russia
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Abramov S, Boytsov A, Bykova D, Penzar DD, Yevshin I, Kolmykov SK, Fridman MV, Favorov AV, Vorontsov IE, Baulin E, Kolpakov F, Makeev VJ, Kulakovskiy IV. Landscape of allele-specific transcription factor binding in the human genome. Nat Commun 2021; 12:2751. [PMID: 33980847 PMCID: PMC8115691 DOI: 10.1038/s41467-021-23007-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/12/2021] [Indexed: 12/28/2022] Open
Abstract
Sequence variants in gene regulatory regions alter gene expression and contribute to phenotypes of individual cells and the whole organism, including disease susceptibility and progression. Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Differential transcription factor binding in heterozygous genomic loci provides a natural source of information on such regulatory variants. We present a novel approach to call the allele-specific transcription factor binding events at single-nucleotide variants in ChIP-Seq data, taking into account the joint contribution of aneuploidy and local copy number variation, that is estimated directly from variant calls. We have conducted a meta-analysis of more than 7 thousand ChIP-Seq experiments and assembled the database of allele-specific binding events listing more than half a million entries at nearly 270 thousand single-nucleotide polymorphisms for several hundred human transcription factors and cell types. These polymorphisms are enriched for associations with phenotypes of medical relevance and often overlap eQTLs, making candidates for causality by linking variants with molecular mechanisms. Specifically, there is a special class of switching sites, where different transcription factors preferably bind alternative alleles, thus revealing allele-specific rewiring of molecular circuitry. Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Here the authors present a meta-analysis empowered by a new statistical method covering thousands of ChIP-Seq experiments resulting in the identification of more than 500 thousand allele-specific binding (ASB) events in the human genome.
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Affiliation(s)
- Sergey Abramov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexandr Boytsov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria Bykova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry D Penzar
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan Yevshin
- Federal Research Center for Information and Computational Technologies, Novosibirsk, Russia.,Sirius University of Science and Technology, Sochi, Russia.,BIOSOFT.RU LLC, Novosibirsk, Russia
| | - Semyon K Kolmykov
- Federal Research Center for Information and Computational Technologies, Novosibirsk, Russia.,Sirius University of Science and Technology, Sochi, Russia.,BIOSOFT.RU LLC, Novosibirsk, Russia
| | - Marina V Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ilya E Vorontsov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Eugene Baulin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Mathematical Problems of Biology RAS-The Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Fedor Kolpakov
- Federal Research Center for Information and Computational Technologies, Novosibirsk, Russia.,Sirius University of Science and Technology, Sochi, Russia.,BIOSOFT.RU LLC, Novosibirsk, Russia
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center Kurchatov Institute, Moscow, Russia. .,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia. .,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia. .,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Ponomarenko MP, Sharypova EB, Drachkova IA, Savinkova LK, Chadaeva IV, Rasskazov DA, Ponomarenko PM, Osadchuk LV, Osadchuk AV. [Candidate SNP-markers altering TBP binding affinity for promoters of the Y-linked genes CDY2A, SHOX, and ZFY are lowering many indexes of reproductive potential in men]. Vavilovskii Zhurnal Genet Selektsii 2020; 24:785-793. [PMID: 33959695 PMCID: PMC8094035 DOI: 10.18699/vj20.674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Репродуктивный потенциал – уровень физического и психического состояния организма, позволяю-
щий при достижении социальной зрелости воспроизводить здоровое потомство. В узком биомедицинском смыс-
ле определение включает комплекс функциональных показателей репродуктивной системы, но в более широком
смысле его можно рассматривать как совокупность физиологических, поведенческих, адаптивных, ментальных, ан-
тропометрических и генетических характеристик особи, способствующих размножению. Целью настоящей работы
было расширить область применимости созданного ранее Web-сервиса SNP_TATA_Z-tester для поиска кандидатных
маркеров однонуклеотидного полиморфизма (SNP) на хромосоме Y человека, связанных с мужским репродуктив-
ным потенциалом (МРП). В поиске кандидатных SNP-маркеров для МРП мы сосредоточились на генах хромосомы Y
человека. Изучены 35 SNP в промоторах генов CDY2A, SHOX и ZFY, представляющих все три типа генов хромосомы Y
человека: уникальный, псевдоаутосомный и паралог гена хромосомы X человека соответственно. Предсказаны
11 кандидатных SNP-маркеров ослабления МРП из-за изменения сродства TATA-связывающего белка (TBP) к этим
промоторам. Выборочно верифицированы in vitro величины сродства «TBP-промотор», предсказанные в этой рабо-
те. Установлена достоверная корреляция (r = 0.94, p < 0.005) между ними и результатами измерения in vitro сродства
ТВР человека к олигонуклеотидам, идентичным сайтам ТВР-связывания исследуемых промоторов. Проведя поиск в
базе данных PubMed по ключевым словам, мы нашли клиническое описание патологических состояний человека,
соответствующих изменению экспрессии генов, несущих предсказанные нами кандидатные SNP-маркеры. Среди
них оказались такие патологии, как нарушение сперматогенеза (ZFY: rs1388535808 и rs996955491), задержка поло-
вого созревания (CDY2A: rs200670724), нарушения эмбриогенеза (SHOX: rs28378830) и непропорционально низкий
рост с деформациями Маделунга (SHOX: rs1452787381). Они свидетельствуют, что в случае SNP-промоторов генов
хромосомы Y человека следует ожидать изменений широкого круга показателей МРП, выходящих далеко за рамки
генетического контроля собственно мужской репродуктивной функции.
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Affiliation(s)
- M P Ponomarenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - E B Sharypova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I A Drachkova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L K Savinkova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I V Chadaeva
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D A Rasskazov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P M Ponomarenko
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L V Osadchuk
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Osadchuk
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Identification of Prognostic Immune Genes in Bladder Urothelial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7510120. [PMID: 32420368 PMCID: PMC7201587 DOI: 10.1155/2020/7510120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022]
Abstract
Background The aim of this study is to identify possible prognostic-related immune genes in bladder urothelial carcinoma and to try to predict the prognosis of bladder urothelial carcinoma based on these genes. Methods The Cancer Genome Atlas (TCGA) expression profile data and corresponding clinical traits were obtained. Differential gene analysis was performed using R software. Reactome was used to analyze the pathway of immune gene participation. The differentially expressed transcription factors and differentially expressed immune-related genes were extracted from the obtained list of differentially expressed genes, and the transcription factor-immune gene network was constructed. To analyze the relationship between immune genes and clinical traits of bladder urothelial carcinoma, a multifactor Cox proportional hazards regression model based on the expression of immune genes was established and validated. Results Fifty-eight immune genes were identified to be associated with the prognosis of bladder urothelial carcinoma. These genes were enriched in Cytokine Signaling in Immune System, Signaling by Receptor Tyrosine Kinases, Interferon alpha/beta signaling, and other immune related pathways. Transcription factor-immune gene regulatory network was established, and EBF1, IRF4, SOX17, MEF2C, NFATC1, STAT1, ANXA6, SLIT2, and IGF1 were screened as hub genes in the network. The model calculated by the expression of 16 immune genes showed a good survival prediction ability (p < 0.05 and AUC = 0.778). Conclusion A transcription factor-immune gene regulatory network related to the prognosis of bladder urothelial carcinoma was established. EBF1, IRF4, SOX17, MEF2C, NFATC1, STAT1, ANXA6, SLIT2, and IGF1 were identified as hub genes in the network. The proportional hazards regression model constructed by 16 immune genes shows a good predictive ability for the prognosis of bladder urothelial carcinoma.
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Li Q, Xi J, Li B, Li N. MiR‐16, as a potential NF‐κB‐related miRNA, exerts anti‐inflammatory effects on LPS‐induced myocarditis via mediating CD40 expression: A preliminary study. J Biochem Mol Toxicol 2019; 34:e22426. [PMID: 31777165 DOI: 10.1002/jbt.22426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/10/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Qiang‐Qiang Li
- Department of Cardiology of Integrated Traditional Chinese and Western MedicineAnqiu People's Hospital Weifang Shandong China
| | - Jing Xi
- Department of CardiologyAnqiu People's Hospital Weifang Shandong China
| | - Bing‐Qiang Li
- Department of CardiologyAnqiu People's Hospital Weifang Shandong China
| | - Ning Li
- Department of CardiologyAnqiu People's Hospital Weifang Shandong China
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