Genome-wide identification of microRNA expression quantitative trait loci

Nature Communications

Volumn 6, Issue , 2015, Pages

  Huan, Tianxiao ^a,b   Rong, Jian ^c   Liu, Chunyu ^a,b   Zhang, Xiaoling ^a,b   Tanriverdi, Kahraman ^d   Joehanes, Roby ^a,b,e,f,g   Chen, Brian H ^a,b   Murabito, Joanne M ^a,h   Yao, Chen ^a,b   Courchesne, Paul ^a,b   Munson, Peter J ^e   O'Donnell, Christopher J ^a,b   Cox, Nancy ⁱ   Johnson, Andrew D ^a,b   Larson, Martin G ^a,c   Levy, Daniel ^a,b   Freedman, Jane E ^d  

^a FRAMINGHAM HEART STUDY   (United States)

^b NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^c Boston University   (United States)

^d UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^e NATIONAL INSTITUTES OF HEALTH   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g Hebrew Senior Life   (United States)

^h BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH DENSITY LIPOPROTEIN CHOLESTEROL; MICRORNA; MICRORNA 125B;

GENE EXPRESSION; GENOME; IDENTIFICATION METHOD; POLYMORPHISM; PROTEIN; RNA;

ARTICLE; CHILD; CPG ISLAND; EXON; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC VARIABILITY; HERITABILITY; HUMAN; HUMAN CELL; INTRON; PEDIGREE; PHENOTYPIC VARIATION; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; UNTRANSLATED REGION; ADULT; AGED; CHROMOSOMAL MAPPING; FEMALE; GENE EXPRESSION PROFILING; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPING TECHNIQUE; MALE; MIDDLE AGED; REGULATORY SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ADULT; AGED; CHROMOSOME MAPPING; FEMALE; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GENOTYPING TECHNIQUES; HUMANS; MALE; MICRORNAS; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84925275267     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms7601     Document Type: Article

References (50)

1. Lee, R., Feinbaum, R. & Ambros, V. A short history of a short RNA. Cell 116, S89-S92 (2004).
2. Lee, R. C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862-864 (2001).
3. Cordes, K. R. & Srivastava, D. MicroRNA regulation of cardiovascular development. Circ. Res. 104, 724-732 (2009).
4. Small, E. M. & Olson, E. N. Pervasive roles of microRNAs in cardiovascular biology. Nature 469, 336-342 (2011).
5. Thum, T. et al. MicroRNAs in the human heart: a clue to fetal gene reprogramming in heart failure. Circulation 116, 258-267 (2007).
6. Tijsen, A. J. et al. MiR423-5p as a circulating biomarker for heart failure. Circ. Res. 106, 1035-1039 (2010).
7. Fiedler, J. & Thum, T. MicroRNAs in myocardial infarction. Arterioscler. Thromb. Vasc. Biol. 33, 201-205 (2013).
8. Lu, J. et al. MicroRNA expression profiles classify human cancers. Nature 435, 834-838 (2005).
9. Westra, H.-J. et al. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nat. Genet. 45, 1238-1243 (2013).
10. Zhang, B. et al. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell 153, 707-720 (2013).
11. Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423-428 (2008).
12. Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008).
13. Zhang, X. et al. Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics 15, 532 (2014).
14. Borel, C. et al. Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res. 21, 68-73 (2011).
15. Gamazon, E. R. et al. Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am. J. Hum. Genet. 90, 1046-1063 (2012).
16. Civelek, M. et al. Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits. Hum. Mol. Genet. 22, 3023-3037 (2013).
17. Somel, M. et al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. Genome Res. 20, 1207-1218 (2010).
18. Siddle, K. J. et al. A genomic portrait of the genetic architecture and regulatory impact of microRNA expression in response to infection. Genome Res. 24, 850-859 (2014).
19. Abecasis, G. R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012).
20. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816 (2007).
21. Hindorff, L. A. et al. Potential etiologic and functional implications of genomewide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106, 9362-9367 (2009).
22. Leslie, R., O'Donnell, C. J. & Johnson, A. D. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics 30, i185-i194 (2014).
23. Hiard, S., Charlier, C., Coppieters, W., Georges, M. & Baurain, D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 38, D640-D651 (2010).
24. Hsu, S. D. et al. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 39, D163-D169 (2011).
25. Joehanes, R. et al. Genome-wide Expression Quantitative Trait Loci: Results from the NHLBI s SABRe CVD Initiative. in the American Society of Human Genetics (ASHG) Conference. (Boston, MA, USA, 2013).
26. Huan, T. et al. A systematic heritability analysis of the human whole blood transcriptome. Human genetics 134, 343-358 (2015).
27. Cesana, M. et al. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358-369 (2011).
28. Degner, J. F. et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482, 390-394 (2012).
29. Marsico, A. et al. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 14, R84 (2013).
30. Chen, B. H. et al. Transcriptome-wide association study of circulating lipid levels. Circulation 129, A35-A35 (2014).
31. Feinleib, M., Kannel, W. B., Garrison, R. J., McNamara, P. M. & Castelli, W. P. The Framingham Offspring Study. Design and preliminary data. Prev. Med. 4, 518-525 (1975).
32. Splansky, G. L. et al. The third generation cohort of the national heart, lung, and blood institute's Framingham heart study: design, recruitment, and initial examination. Am. J. Epidemiol. 165, 1328-1335 (2007).
33. Chen, C., Tan, R., Wong, L., Fekete, R. & Halsey, J. Quantitation of microRNAs by real-time RT-qPCR. Methods Mol. Biol. 687, 113-134 (2011).
34. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005).
35. Jensen, S. G. et al. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics 12, 435 (2011).
36. Jang, J. et al. Quantitative miRNA expression analysis using fluidigm microfluidics dynamic arrays. BMC Genomics 12, 144 (2011).
37. Levy, D. et al. Genome-wide association study of blood pressure and hypertension. Nat. Genet. 41, 677-687 (2009).
38. Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
39. Almasy, L. & Blangero, J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am. J. Hum. Genet. 62, 1198-1211 (1998).
40. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289-300 (1995).
41. Qin, Z. S., Gopalakrishnan, S. & Abecasis, G. R. An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria. Bioinformatics 22, 220-225 (2006).
42. Chen, D. et al. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res. 42, 3028-3043 (2014).
43. Chien, C. H. et al. Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 39, 9345-9356 (2011).
44. Ward, L. D. & Kellis, M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40, D930-D934 (2012).
45. Griffith, O. L. et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 36, D107-D113 (2008).
46. Cabili, M. N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
47. Vergoulis, T. et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 40, D222-D229 (2012).
48. Lawlor, D. A., Harbord, R. M., Sterne, J. A., Timpson, N. & Davey Smith, G. Mendelian randomization: using genes as instruments for making causal inferences in epidemiology. Stat. Med. 27, 1133-1163 (2008).
49. Baum, C. F., Schaffer, M. E. & Stillman, S. IVENDOG: Stata module to calculate Durbin-Wu-Hausman endogeneity test after ivreg. Statistical Software Components, Department of Economics, Boston College (2007).
50. Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707-713 (2010).