Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites
Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncodi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2018.00139/full |
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| author | Rodrigo C. de Almeida Rodrigo C. de Almeida Vinícius S. Chagas Mauro A. A. Castro Maria L. Petzl-Erler |
| author_facet | Rodrigo C. de Almeida Rodrigo C. de Almeida Vinícius S. Chagas Mauro A. A. Castro Maria L. Petzl-Erler |
| author_sort | Rodrigo C. de Almeida |
| collection | DOAJ |
| description | Genome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3′ untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites. Yet, little is known about their effect on regulation by miRNA and the consequences for AID. Conversely, it is well known that two or more AID may share part of their genetic background. Here, we hypothesized that miRSNPs could be associated with more than one AID. To identify miRSNPs associated with AID, we integrated results from three different prediction tools (Polymirts, miRSNP, and miRSNPscore) using a naïve Bayes classifier approach to identify miRSNPs predicted to affect binding sites of miRNAs. Further, to detect miRSNPs associated with two or more AID, we integrated predictions with summary statistics from 12 AID studies. In addition, to prioritize miRSNPs, miRNAs and AID-associated target genes, we used public expression quantitative trait locus (eQTL) data and mRNA-seq and small RNA-seq data. We identified 34 miRNSPs associated with at least two AID. Furthermore, we found 86 miRNAs predicted to target 18 of the associated gene's mRNAs. Our integrative approach revealed new insights into miRNAs and AID associated target genes. Thus, it helped to prioritize AID noncoding risk SNPs that might be involved in the causal mechanisms, providing valuable information for further functional studies. |
| first_indexed | 2024-12-20T14:29:56Z |
| format | Article |
| id | doaj.art-a086b6372e514333918382f6b18c9b82 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-20T14:29:56Z |
| publishDate | 2018-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a086b6372e514333918382f6b18c9b822022-12-21T19:37:40ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-04-01910.3389/fgene.2018.00139349768Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding SitesRodrigo C. de Almeida0Rodrigo C. de Almeida1Vinícius S. Chagas2Mauro A. A. Castro3Maria L. Petzl-Erler4Human Molecular Genetics Laboratory, Department of Genetics, Federal University of Paraná, Curitiba, BrazilMolecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, NetherlandsBioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, BrazilBioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, BrazilHuman Molecular Genetics Laboratory, Department of Genetics, Federal University of Paraná, Curitiba, BrazilGenome-wide and fine mapping studies have shown that more than 90% of genetic variants associated with autoimmune diseases (AID) are located in non-coding regions of the human genome and especially in regulatory sequences, including microRNAs (miRNA) target sites. MiRNAs are small endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Single nucleotide polymorphisms (SNPs) located within the 3′ untranslated region of their target mRNAs (miRSNP) can alter miRNA binding sites. Yet, little is known about their effect on regulation by miRNA and the consequences for AID. Conversely, it is well known that two or more AID may share part of their genetic background. Here, we hypothesized that miRSNPs could be associated with more than one AID. To identify miRSNPs associated with AID, we integrated results from three different prediction tools (Polymirts, miRSNP, and miRSNPscore) using a naïve Bayes classifier approach to identify miRSNPs predicted to affect binding sites of miRNAs. Further, to detect miRSNPs associated with two or more AID, we integrated predictions with summary statistics from 12 AID studies. In addition, to prioritize miRSNPs, miRNAs and AID-associated target genes, we used public expression quantitative trait locus (eQTL) data and mRNA-seq and small RNA-seq data. We identified 34 miRNSPs associated with at least two AID. Furthermore, we found 86 miRNAs predicted to target 18 of the associated gene's mRNAs. Our integrative approach revealed new insights into miRNAs and AID associated target genes. Thus, it helped to prioritize AID noncoding risk SNPs that might be involved in the causal mechanisms, providing valuable information for further functional studies.http://journal.frontiersin.org/article/10.3389/fgene.2018.00139/fullmicroRNASNPautoimmunityeQTLGWASdata integration |
| spellingShingle | Rodrigo C. de Almeida Rodrigo C. de Almeida Vinícius S. Chagas Mauro A. A. Castro Maria L. Petzl-Erler Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites Frontiers in Genetics microRNA SNP autoimmunity eQTL GWAS data integration |
| title | Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites |
| title_full | Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites |
| title_fullStr | Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites |
| title_full_unstemmed | Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites |
| title_short | Integrative Analysis Identifies Genetic Variants Associated With Autoimmune Diseases Affecting Putative MicroRNA Binding Sites |
| title_sort | integrative analysis identifies genetic variants associated with autoimmune diseases affecting putative microrna binding sites |
| topic | microRNA SNP autoimmunity eQTL GWAS data integration |
| url | http://journal.frontiersin.org/article/10.3389/fgene.2018.00139/full |
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