Genome‐wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis

MicroRNAs (miRNAs) are studied as key regulators of gene expression involved in different diseases. Several single nucleotide polymorphisms (SNPs) in miRNA genes or target sites (miRNA‐related SNPs) have been proved to be associated with human diseases by affecting the miRNA‐mediated regulatory function. To systematically analyze miRNA‐related SNPs and their effects, we performed a genome‐wide scan for SNPs in human pre‐miRNAs, miRNA flanking regions, target sites, and designed a pipeline to predict the effects of them on miRNA–target interaction. As a result, we identified 48 SNPs in human miRNA seed regions and thousands of SNPs in 3′ untranslated regions with the potential to either disturb or create miRNA–target interactions. Furthermore, we experimentally confirmed seven loss‐of‐function SNPs and one gain‐of‐function SNP by luciferase assay. This is the first case of experimental validation of an SNP in an miRNA creating a novel miRNA target binding. All useful data were complied into miRNASNP, a user‐friendly free online database (http://www.bioguo.org/miRNASNP/). These data will be a useful resource for studying miRNA function, identifying disease‐associated miRNAs, and further personalized medicine. Hum Mutat 33:254–263, 2012. © 2011 Wiley Periodicals, Inc.

[1]  R B Denman,et al.  Using RNAFOLD to predict the activity of small catalytic RNAs. , 1993, BioTechniques.

[2]  Denman Rb,et al.  Using RNAFOLD to predict the activity of small catalytic RNAs. , 1993 .

[3]  E. Lai.  Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation , 2002, Nature Genetics.

[4]  S. Jayasena,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

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

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

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

[8]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

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

[10]  N. Iwai,et al.  Polymorphisms in human pre-miRNAs. , 2005, Biochemical and biophysical research communications.

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

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

[13]  Jan Krüger,et al.  RNAhybrid: microRNA target prediction easy, fast and flexible , 2006, Nucleic Acids Res..

[14]  B. Cullen,et al.  A Novel Assay for Viral MicroRNA Function Identifies a Single Nucleotide Polymorphism That Affects Drosha Processing , 2006, Journal of Virology.

[15]  Xiaoquan Wen,et al.  Correction: A Map of Recent Positive Selection in the Human Genome , 2006, PLoS Biology.

[16]  Xiaowei Wang,et al.  Systematic identification of microRNA functions by combining target prediction and expression profiling , 2006, Nucleic acids research.

[17]  J. Pritchard,et al.  A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.

[18]  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.

[19]  Baohong Zhang,et al.  MicroRNAs and their regulatory roles in animals and plants , 2007, Journal of cellular physiology.

[20]  Wen-Hsiung Li,et al.  Human polymorphism at microRNAs and microRNA target sites , 2007, Proceedings of the National Academy of Sciences.

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

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

[23]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.

[24]  Praveen Sethupathy,et al.  MicroRNA target site polymorphisms and human disease. , 2008, Trends in genetics : TIG.

[25]  Dolores Corella,et al.  Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans , 2008, Nature Genetics.

[26]  F. Slack,et al.  Cancer Risk Small Cell Lung − Untranslated Region Increases Non ′ 3 KRAS microRNA Complementary Site in the let-7 A SNP in a , 2008 .

[27]  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.

[28]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[29]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[30]  Samir K. Brahmachari,et al.  dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation , 2009, BMC Bioinformatics.

[31]  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.

[32]  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.

[33]  R. Barale,et al.  A catalog of polymorphisms falling in microRNA-binding regions of cancer genes. , 2008, DNA and cell biology.

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

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

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

[37]  Wei Zhang,et al.  Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes , 2009, RNA biology.

[38]  Rachael P. Huntley,et al.  The GOA database in 2009—an integrated Gene Ontology Annotation resource , 2008, Nucleic Acids Res..

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

[40]  Peng Liu,et al.  miR-34a, a microRNA up-regulated in a double transgenic mouse model of Alzheimer's disease, inhibits bcl2 translation , 2009, Brain Research Bulletin.

[41]  K. Jażdżewski,et al.  Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer , 2009, Proceedings of the National Academy of Sciences.

[42]  B. Shastry.  SNPs: impact on gene function and phenotype. , 2009, Methods in molecular biology.

[43]  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.

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

[45]  S. Peng,et al.  Association of MicroRNA-196a-2 Gene Polymorphism with Gastric Cancer Risk in a Chinese Population , 2010, Digestive Diseases and Sciences.

[46]  Q. Wei,et al.  Genetic variants in selected pre‐microRNA genes and the risk of squamous cell carcinoma of the head and neck , 2010, Cancer.

[47]  H. Lodish,et al.  Alteration of processing induced by a single nucleotide polymorphism in pri-miR-126. , 2010, Biochemical and biophysical research communications.

[48]  C. Harris,et al.  Genetic variation in microRNA networks: the implications for cancer research , 2010, Nature Reviews Cancer.

[49]  Y. Nakagawa,et al.  Association Study of Common Genetic Variants in Pre-microRNAs in Patients with Ulcerative Colitis , 2011, Journal of Clinical Immunology.

[50]  B. Shi,et al.  Single nucleotide polymorphism associated with nonsyndromic cleft palate influences the processing of miR‐140 , 2010, American journal of medical genetics. Part A.

[51]  Li Yang,et al.  Hsa‐mir‐27a genetic variant contributes to gastric cancer susceptibility through affecting miR‐27a and target gene expression , 2010, Cancer science.

[52]  D. Weinberger,et al.  MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets , 2010, Human mutation.

[53]  Michel Georges,et al.  Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates , 2008, Nucleic Acids Res..

[54]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[55]  Arijit Mukhopadhyay,et al.  miRvar: A comprehensive database for genomic variations in microRNAs , 2011, Human mutation.

[56]  Chu-Wen Yang,et al.  Single point mutation of microRNA may cause butterfly effect on alteration of global gene expression. , 2011, Biochemical and biophysical research communications.