Exploring genetic associations with ceRNA regulation in the human genome

Abstract Competing endogenous RNAs (ceRNAs) are RNA molecules that sequester shared microRNAs (miRNAs) thereby affecting the expression of other targets of the miRNAs. Whether genetic variants in ceRNA can affect its biological function and disease development is still an open question. Here we identified a large number of genetic variants that are associated with ceRNA's function using Geuvaids RNA-seq data for 462 individuals from the 1000 Genomes Project. We call these loci competing endogenous RNA expression quantitative trait loci or ‘cerQTL’, and found that a large number of them were unexplored in conventional eQTL mapping. We identified many cerQTLs that have undergone recent positive selection in different human populations, and showed that single nucleotide polymorphisms in gene 3΄UTRs at the miRNA seed binding regions can simultaneously regulate gene expression changes in both cis and trans by the ceRNA mechanism. We also discovered that cerQTLs are significantly enriched in traits/diseases associated variants reported from genome-wide association studies in the miRNA binding sites, suggesting that disease susceptibilities could be attributed to ceRNA regulation. Further in vitro functional experiments demonstrated that a cerQTL rs11540855 can regulate ceRNA function. These results provide a comprehensive catalog of functional non-coding regulatory variants that may be responsible for ceRNA crosstalk at the post-transcriptional level.

[1]  A. Clark,et al.  Impact of microRNA regulation on variation in human gene expression , 2012, Genome research.

[2]  L. Quintana-Murci,et al.  A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection , 2014, Genome research.

[3]  Michael Q. Zhang,et al.  MIROR: a method for cell-type specific microRNA occupancy rate prediction. , 2014, Molecular bioSystems.

[4]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[5]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[6]  P. Pandolfi,et al.  The multilayered complexity of ceRNA crosstalk and competition , 2014, Nature.

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

[8]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[9]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[10]  Y. Pawitan,et al.  A Genome‐Wide Assessment of Variability in Human Serum Metabolism , 2013, Human mutation.

[11]  C. Bouchard,et al.  Competing targets of microRNA-608 affect anxiety and hypertension , 2014, Human molecular genetics.

[12]  G. Lou,et al.  TNFAIP8 as a predictor of metastasis and a novel prognostic biomarker in patients with epithelial ovarian cancer , 2013, British Journal of Cancer.

[13]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

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

[15]  E. Stone,et al.  The genetics of quantitative traits: challenges and prospects , 2009, Nature Reviews Genetics.

[16]  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.

[17]  Kevin P. White,et al.  Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy , 2014, PLoS genetics.

[18]  Hervé Seitz,et al.  Redefining MicroRNA Targets , 2009, Current Biology.

[19]  C. Martínez-A,et al.  DIO-1 is a gene involved in onset of apoptosis in vitro, whose misexpression disrupts limb development. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Danny S. Park,et al.  Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. , 2012, American journal of human genetics.

[21]  Riccardo Zecchina,et al.  Modelling Competing Endogenous RNA Networks , 2013, PloS one.

[22]  Grace X. Y. Zheng,et al.  MicroRNAs can generate thresholds in target gene expression , 2011, Nature Genetics.

[23]  Michael Q. Zhang,et al.  Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit , 2015, Proceedings of the National Academy of Sciences.

[24]  Daniel J. Park,et al.  19p13.1 is a triple-negative-specific breast cancer susceptibility locus. , 2012, Cancer research.

[25]  C. Gieger,et al.  Genome-Wide Association Study Identifies Two Novel Regions at 11p15.5-p13 and 1p31 with Major Impact on Acute-Phase Serum Amyloid A , 2010, PLoS genetics.

[26]  Menghong Sun,et al.  Functional variants in TNFAIP8 associated with cervical cancer susceptibility and clinical outcomes. , 2013, Carcinogenesis.

[27]  R. Desnick,et al.  Warfarin pharmacogenetics: CYP2C9 and VKORC1 genotypes predict different sensitivity and resistance frequencies in the Ashkenazi and Sephardi Jewish populations. , 2008, American journal of human genetics.

[28]  Andrew D. Johnson,et al.  Genome-wide Identification of microRNA Expression Quantitative Trait Loci , 2015, Nature Communications.

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

[30]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[31]  R. Durbin,et al.  Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses , 2012, Nature Protocols.

[32]  N. Rajewsky,et al.  Natural selection on human microRNA binding sites inferred from SNP data , 2006, Nature Genetics.

[33]  M. Laakso,et al.  Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits. , 2013, Human molecular genetics.

[34]  B S Weir,et al.  Estimating F-statistics. , 2002, Annual review of genetics.

[35]  David Reich,et al.  Population differentiation as a test for selective sweeps. , 2010, Genome research.

[36]  R. Zecchina,et al.  Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments , 2013, Proceedings of the National Academy of Sciences.

[37]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[38]  Liqing Zhou,et al.  A functional lncRNA HOTAIR genetic variant contributes to gastric cancer susceptibility , 2016, Molecular carcinogenesis.

[39]  W. Iacono,et al.  A Genome-Wide Association Study of Behavioral Disinhibition , 2013, Behavior genetics.

[40]  Å. Borg,et al.  Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene. , 2011, Cancer research.

[41]  Eric S. Lander,et al.  Identifying Recent Adaptations in Large-Scale Genomic Data , 2013, Cell.

[42]  Mulin Jun Li,et al.  Current trend of annotating single nucleotide variation in humans--A case study on SNVrap. , 2015, Methods.

[43]  Yanchun Liang,et al.  3′UTR shortening identifies high-risk cancers with targeted dysregulation of the ceRNA network , 2014, Scientific Reports.

[44]  J. Berg,et al.  Genetic Variation of VKORC1 and CYP4F2 Genes Related to Warfarin Maintenance Dose in Patients with Myocardial Infarction , 2010, Journal of biomedicine & biotechnology.

[45]  Deborah A Nickerson,et al.  Effect of VKORC1 haplotypes on transcriptional regulation and warfarin dose. , 2005, The New England journal of medicine.

[46]  P. Ridker,et al.  Novel Association of ABO Histo-Blood Group Antigen with Soluble ICAM-1: Results of a Genome-Wide Association Study of 6,578 Women , 2008, PLoS genetics.

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

[48]  M. Dinger,et al.  Endogenous microRNA sponges: evidence and controversy , 2016, Nature Reviews Genetics.

[49]  Christiana Kartsonaki,et al.  A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor–negative breast cancer in the general population , 2010, Nature Genetics.

[50]  L. Liang,et al.  Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions , 2012, Nature Genetics.

[51]  Nianjun Liu,et al.  VKORC1 polymorphisms, haplotypes and haplotype groups on warfarin dose among African-Americans and European-Americans. , 2008, Pharmacogenomics.

[52]  Richard Leslie,et al.  GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database , 2014, Bioinform..

[53]  Pak Chung Sham,et al.  GWASdb: a database for human genetic variants identified by genome-wide association studies , 2011, Nucleic Acids Res..

[54]  A. Constantine.  Some Non-Central Distribution Problems in Multivariate Analysis , 1963 .

[55]  A. Naccarati,et al.  Polymorphisms in miRNA-binding sites of nucleotide excision repair genes and colorectal cancer risk. , 2012, Carcinogenesis.

[56]  Phillip A Sharp,et al.  Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. , 2014, Molecular cell.

[57]  Inês Barroso,et al.  Genetic Variants Influencing Circulating Lipid Levels and Risk of Coronary Artery Disease , 2010, Arteriosclerosis, thrombosis, and vascular biology.

[58]  Zhaolei Zhang,et al.  Evidence for Positive Selection on a Number of MicroRNA Regulatory Interactions during Recent Human Evolution , 2012, PLoS genetics.

[59]  Or Zuk,et al.  A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection , 2010, Science.

[60]  Phillip A. Sharp,et al.  Emerging Roles for Natural MicroRNA Sponges , 2010, Current Biology.

[61]  Soichiro Saito,et al.  MicroRNA-296 is enriched in cancer cells and downregulates p21WAF1 mRNA expression via interaction with its 3′ untranslated region , 2011, Nucleic acids research.

[62]  Shusheng Wang,et al.  AngiomiRs--key regulators of angiogenesis. , 2009, Current opinion in genetics & development.

[63]  Niku Oksala,et al.  Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis , 2012, PLoS genetics.

[64]  A. Pasquinelli.  MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship , 2012, Nature Reviews Genetics.

[65]  J. Flores,et al.  Dido gene expression alterations are implicated in the induction of hematological myeloid neoplasms. , 2005, The Journal of clinical investigation.

[66]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[67]  Mingxia Zhang,et al.  An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese , 2011, Scientific reports.

[68]  R. Weissleder,et al.  miR-296 regulates growth factor receptor overexpression in angiogenic endothelial cells. , 2008, Cancer cell.

[69]  T. Whiteside,et al.  Identification of a Novel Tumor Necrosis Factor-α-inducible Gene, SCC-S2, Containing the Consensus Sequence of a Death Effector Domain of Fas-associated Death Domain-like Interleukin- 1β-converting Enzyme-inhibitory Protein* , 2000, The Journal of Biological Chemistry.

[70]  Pardis C Sabeti,et al.  Genome-wide detection and characterization of positive selection in human populations , 2007, Nature.

[71]  Federico Innocenti,et al.  A genome-wide integrative study of microRNAs in human liver , 2013, BMC Genomics.

[72]  T. Hwa,et al.  Quantitative Characteristics of Gene Regulation by Small RNA , 2007, PLoS Biology.

[73]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[74]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[75]  F. Kuchenbauer,et al.  In vivo processing assay based on a dual-luciferase reporter system to evaluate DROSHA enzymatic activity. , 2014, Methods in molecular biology.

[76]  Xuerui Yang,et al.  An Extensive MicroRNA-Mediated Network of RNA-RNA Interactions Regulates Established Oncogenic Pathways in Glioblastoma , 2011, Cell.