A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites

Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. To analyze the effects of variants in miRNAs and their target sites, several databases storing variant impact predictions have been published. In this review, we will compare the core functionalities and features of these databases and discuss the importance of up-to-date data resources in the context of web applications. Finally, we will outline some recommendations for future developments in the field.

[1]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[2]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[3]  J. Mattick.  Non‐coding RNAs: the architects of eukaryotic complexity , 2001, EMBO reports.

[4]  A. Pasquinelli,et al.  A Cellular Function for the RNA-Interference Enzyme Dicer in the Maturation of the let-7 Small Temporal RNA , 2001, Science.

[5]  A. Caudy,et al.  Argonaute2, a Link Between Genetic and Biochemical Analyses of RNAi , 2001, Science.

[6]  Anton J. Enright,et al.  MicroRNA targets in Drosophila , 2003, Genome Biology.

[7]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[8]  V. Kim,et al.  The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.

[9]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[10]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[11]  R. Pillai.  MicroRNA function: multiple mechanisms for a tiny RNA? , 2005, RNA.

[12]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[13]  A. Hatzigeorgiou,et al.  TarBase: A comprehensive database of experimentally supported animal microRNA targets. , 2005, RNA.

[14]  Praveen Sethupathy,et al.  Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. , 2007, American journal of human genetics.

[15]  Ligang Wu,et al.  PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits , 2006, Nucleic Acids Res..

[16]  Peng Jin,et al.  Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. , 2007, Human molecular genetics.

[17]  K. Sirotkin,et al.  The NCBI dbGaP database of genotypes and phenotypes , 2007, Nature Genetics.

[18]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[19]  Joshua M. Korn,et al.  Comprehensive genomic characterization defines human glioblastoma genes and core pathways , 2008, Nature.

[20]  Gaofeng Wang,et al.  Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. , 2008, American journal of human genetics.

[21]  P. Whorwell,et al.  First evidence for an association of a functional variant in the microRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome. , 2008, Human molecular genetics.

[22]  Barbara Jarzab,et al.  Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma , 2008, Proceedings of the National Academy of Sciences.

[23]  Jian-Rong Yang,et al.  A functional polymorphism in the miR-146a gene is associated with the risk for hepatocellular carcinoma. , 2008, Carcinogenesis.

[24]  Hua Zhao,et al.  A functional polymorphism in the miR-146a gene and age of familial breast/ovarian cancer diagnosis. , 2008, Carcinogenesis.

[25]  Daniel B. Martin,et al.  Circulating microRNAs as stable blood-based markers for cancer detection , 2008, Proceedings of the National Academy of Sciences.

[26]  Michael Niepmann,et al.  microRNA-122 stimulates translation of hepatitis C virus RNA , 2008, The EMBO journal.

[27]  U. A. Ørom,et al.  MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. , 2008, Molecular cell.

[28]  John J Rossi,et al.  SNPs in human miRNA genes affect biogenesis and function. , 2009, RNA.

[29]  D. Bartel.  MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[30]  Tongbin Li,et al.  miRecords: an integrated resource for microRNA–target interactions , 2008, Nucleic Acids Res..

[31]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[32]  Tamas Dalmay,et al.  Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss , 2009, Nature Genetics.

[33]  F. Collins,et al.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits , 2009, Proceedings of the National Academy of Sciences.

[34]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[35]  J. Kappes,et al.  A Synonymous Single Nucleotide Polymorphism in ΔF508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein* , 2010, The Journal of Biological Chemistry.

[36]  Andrew E. Bruno,et al.  miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes , 2012, BMC Genomics.

[37]  Chi-Ying F. Huang,et al.  miRTarBase: a database curates experimentally validated microRNA–target interactions , 2010, Nucleic Acids Res..

[38]  D. Bartel,et al.  Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs , 2011, Nature Structural &Molecular Biology.

[39]  Bin Liu,et al.  A functional polymorphism at microRNA-629-binding site in the 3'-untranslated region of NBS1 gene confers an increased risk of lung cancer in Southern and Eastern Chinese population. , 2012, Carcinogenesis.

[40]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[41]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[42]  Hong-Mei Zhang,et al.  Genome‐wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis , 2012, Human mutation.

[43]  Dai Zhang,et al.  MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs , 2012, BMC Genomics.

[44]  Andrea Masotti,et al.  Recent Insights and Novel Bioinformatics Tools to Understand the Role of MicroRNAs Binding to 5′ Untranslated Region , 2012, International journal of molecular sciences.

[45]  Sabine C. Mueller,et al.  A blood based 12-miRNA signature of Alzheimer disease patients , 2013, Genome Biology.

[46]  Meng Li,et al.  Association of a Genetic Variation in a miR-191 Binding Site in MDM4 with Risk of Esophageal Squamous Cell Carcinoma , 2013, PloS one.

[47]  Nick C Fox,et al.  Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease , 2013, Nature Genetics.

[48]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[49]  D. Tollervey,et al.  Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.

[50]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[51]  Isidore Rigoutsos,et al.  MiR-103a-3p targets the 5′ UTR of GPRC5A in pancreatic cells , 2014, RNA.

[52]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[53]  Miryam Carecchio,et al.  Predicting Cognitive Decline in Parkinson’s Disease: Can We Ask the Genes? , 2014, Front. Neurol..

[54]  Yan Cui,et al.  PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways , 2013, Nucleic Acids Res..

[55]  Chia-Cheng Yu,et al.  Genetic variants of the autophagy pathway as prognostic indicators for prostate cancer , 2015, Scientific Reports.

[56]  Hu Chen,et al.  An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools , 2015, Database J. Biol. Databases Curation.

[57]  Amanda B. Spurdle,et al.  A genetic variant of MDM4 influences regulation by multiple microRNAs in prostate cancer. , 2015, Endocrine-related cancer.

[58]  Christina Backes,et al.  Differentially regulated miRNAs as prognostic biomarkers in the blood of primary CNS lymphoma patients. , 2015, European journal of cancer.

[59]  Li Zhang,et al.  Association of three SNPs in TOX3 and breast cancer risk: Evidence from 97275 cases and 128686 controls , 2015, Scientific Reports.

[60]  Feng Gao,et al.  A Regulatory MDM4 Genetic Variant Locating in the Binding Sequence of Multiple MicroRNAs Contributes to Susceptibility of Small Cell Lung Cancer , 2015, PloS one.

[61]  The importance of p53 pathway genetics in inherited and somatic cancer genomes , 2016, Nature Reviews Cancer.

[62]  I. Riquelme,et al.  Tools for Sequence-Based miRNA Target Prediction: What to Choose? , 2016, International journal of molecular sciences.

[63]  Robert D. Finn,et al.  The European Bioinformatics Institute in 2016: Data growth and integration , 2015, Nucleic Acids Res..

[64]  Jun Ding,et al.  TarPmiR: a new approach for microRNA target site prediction , 2016, Bioinform..

[65]  Chao Qin,et al.  A functional variant in TP63 at 3q28 associated with bladder cancer risk by creating an miR‐140‐5p binding site , 2016, International journal of cancer.

[66]  Rafał Bartoszewski,et al.  SNPs in microRNA target sites and their potential role in human disease , 2017, Open Biology.