References
- Mendelson MM, Marioni RE, Joehanes R, et al. Association of body mass index with DNA methylation and gene expression in blood cells and relations to cardiometabolic disease: a mendelian randomization approach. PLoS Med. 2017;14:e1002215.
- Hedman ÅK, Mendelson MM, Marioni RE, et al. Epigenetic patterns in blood associated with lipid traits predict incident coronary heart disease events and are enriched for results from genome-wide association studies clinical perspective. Circ Cardiovasc Genet. 2017;10:e001487.
- Irvin MR, Zhi D, Joehanes R, et al. Epigenome-wide association study of fasting blood lipids in the genetics of lipid lowering drugs and diet network study. Circulation. 2014;114:009158.
- Volkmar M, Dedeurwaerder S, Cunha DA, et al. DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. Embo J. 2012;31:1405–1426.
- Ligthart S, Marzi C, Aslibekyan S, et al. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases. Genome Biol. 2016;17:255.
- Liu C, Marioni R, ÅK H, et al. A DNA methylation biomarker of alcohol consumption. Mol Psychiatry. 2016;23:422.
- Hannum G, Guinney J, Zhao L, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013;49:359–367.
- Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14:3156.
- Joehanes R, Just AC, Marioni RE, et al. Epigenetic signatures of cigarette smoking. Circ Cardiovasc Genet. 2016;9:436–447.
- Cordes KR, Srivastava D. MicroRNA regulation of cardiovascular development. Circ Res. 2009;104:724–732.
- Small EM, Olson EN. Pervasive roles of microRNAs in cardiovascular biology. Nature. 2011;469:336–342.
- Thum T, Galuppo P, Wolf C, et al. MicroRNAs in the human heart. Circulation. 2007;116:258–267.
- Huan T, Rong J, Tanriverdi K, et al. Dissecting the roles of microRNAs in coronary heart disease via integrative genomic analyses. Arterioscler Thromb Vasc Biol. 2015;ATVBAHA:114.305176.
- McManus DD, Rong J, Huan T, et al. Messenger RNA and MicroRNA transcriptomic signatures of cardiometabolic risk factors. BMC Genomics. 2017;18:139.
- Jansson MD, Lund AH. MicroRNA and cancer. Mol Oncol. 2012;6:590–610.
- Esteller M. Epigenetics in cancer. N Engl J Med. 2008;358:1148–1159.
- Loginov V, Rykov S, Fridman M, et al. Methylation of miRNA genes and oncogenesis. Biochemistry (Moscow). 2015;80:145–162.
- Chuang JC, Jones PA. Epigenetics and microRNAs. Pediatr Res. 2007;61:24R–9R.
- Ehrlich M, Gama-Sosa MA, Huang L-H, et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues or cells. Nucleic Acids Res. 1982;10:2709–2721.
- Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell. 2014;156:45–68.
- Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315–322.
- Lee R, Feinbaum R, Ambros V. A short history of a short RNA. Cell. 2004;116:S89–S92.
- Lee RC, Ambros V. An extensive class of small RNAs in caenorhabditis elegans. Science. 2001;294:862–864.
- Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42:D68–D73.
- Friedman RC, Farh KK-H, Burge CB, et al. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009;19:92–105.
- Lemire M, Zaidi SH, Ban M, et al. Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun. 2015;6:6326.
- Hannon E, Spiers H, Viana J, et al. Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci. Nat Neurosci. 2016;19:48–54.
- Bonder MJ, Luijk R, Zhernakova DV, et al. Disease variants alter transcription factor levels and methylation of their binding sites. Nat Genet. 2017;49:131.
- Shi J, Marconett C, Duan J, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nature communications. 2014;6:3365.
- Gaunt TR, Shihab HA, Hemani G, et al. Systematic identification of genetic influences on methylation across the human life course. Genome Biol. 2016;17:61.
- McClay JL, Shabalin AA, Dozmorov MG, et al. High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol. 2015;16:291.
- McRae A, Marioni RE, Shah S, et al. Identification of 55,000 replicated DNA methylation QTL. Scientific Reports. 2018;8:17605.
- Huan T, Rong J, Liu C, et al. Genome-wide identification of microRNA expression quantitative trait loci. Nat Commun. 2015;6:6601.
- Wagner JR, Busche S, Ge B, et al. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol. 2014;15:R37.
- Liu Y, Ding J, Reynolds LM, et al. Methylomics of gene expression in human monocytes. Hum Mol Genet. 2013;22:5065–5074.
- Marsico A, Huska MR, Lasserre J, et al. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. Genome Biol. 2013;14:R84.
- Chen D, Fu L-Y, Zhang Z, et al. Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res. 2014;42:3028–3043.
- Hagan JP, O’Neill BL, Stewart CL, et al. At least ten genes define the imprinted Dlk1-Dio3 cluster on mouse chromosome 12qF1. PloS One. 2009;4:e4352.
- Kagami M, Sekita Y, Nishimura G, et al. Deletions and epimutations affecting the human 14q32. 2 imprinted region in individuals with paternal and maternal upd (14)-like phenotypes. Nat Genet. 2008;40:237.
- Huan T. Genome-wide identification of DNA methylation quantitative trait loci in human whole blood highlights novel pathways for cardiovascular diseases. American Society of Human Genetics 68th Annual Meeting; San Diego; 2018.
- Perry JR, Day F, Elks CE, et al. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature. 2014;514:92.
- Kass SU, Landsberger N, Wolffe AP. DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol. 1997;7:157–165.
- Jones PA. The DNA methylation paradox. Trends Genet. 1999;15:34–37.
- MacArthur J, Bowler E, Cerezo M, et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS catalog). Nucleic acids res 2016; 45:D896–D901.
- Richardson TG, Zheng J, Smith GD, et al. Mendelian randomization analysis identifies CpG sites as putative mediators for genetic influences on cardiovascular disease risk. Am J Hum Genet. 2017;101:590–602.
- Kong A, Steinthorsdottir V, Masson G, et al. Parental origin of sequence variants associated with complex diseases. Nature. 2009;462:868.
- Wallace C, Smyth DJ, Maisuria-Armer M, et al. The imprinted DLK1-MEG3 gene region on chromosome 14q32. 2 alters susceptibility to type 1 diabetes. Nat Genet. 2010;42:68.
- Sakajiri S, O’kelly J, Yin D, et al. Dlk1 in normal and abnormal hematopoiesis. Leukemia. 2005;19:1404.
- Astuti D, Latif F, Wagner K, et al. Epigenetic alteration at the DLK1-GTL2 imprinted domain in human neoplasia: analysis of neuroblastoma, phaeochromocytoma and Wilms’ tumour. Br J Cancer. 2005;92:1574.
- Khoury H, Suarez-Saiz F, Wu S, et al. An upstream insulator regulates DLK1 imprinting in AML. Blood 2010. blood-2009-03-212746.
- Gao Y-Q, Chen X, Wang P, et al. Regulation of DLK1 by the maternally expressed miR-379/miR-544 cluster may underlie callipyge polar overdominance inheritance. Proc Nat Acad Sci. 2015;112:13627–13632.
- Day FR, Thompson DJ, Helgason H, et al. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nat Genet. 2017;49:834.
- Feinleib M, Kannel WB, Garrison RJ, et al. The Framingham offspring study. Design and preliminary data. Prev Med. 1975;4:518–525.
- Splansky GL, Corey D, Yang Q, 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. 2007;165:1328–1335.
- Pidsley R, CC YW, Volta M, et al. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics. 2013;14:293.
- Chen YA, Lemire M, Choufani S, et al. Discovery of cross-reactive probes and polymorphic CpGs in the illumina infinium HumanMethylation450 microarray. Epigenetics. 2013;8:203–209.
- Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3:e161.
- Joehanes R, Ying S, Huan T, et al. Gene expression signatures of coronary heart disease significance. Arterioscler Thromb Vasc Biol. 2013;33:1418–1426.
- Jensen SG, Lamy P, Rasmussen MH, et al. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics. 2011;12:435.
- Jang JS, Simon VA, Feddersen RM, et al. Quantitative miRNA expression analysis using fluidigm microfluidics dynamic arrays. BMC Genomics. 2011;12:144.
- Chen C, Ridzon DA, Broomer AJ, et al. Real-time quantification of microRNAs by stem–loop RT–PCR. Nucleic Acids Res. 2005;33:e179–e.
- Almasy L, Blangero J. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet. 1998;62:1198–1211.
- Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B (Methodological). 1995;57:289–300.
- Levy D, Ehret GB, Rice K, et al. Genome-wide association study of blood pressure and hypertension. Nat Genet. 2009;41:677–687.
- Li Y, Willer CJ, Ding J, et al. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol. 2010;34:816–834.
- Agarwal V, Bell GW, Nam J-W, et al. Predicting effective microRNA target sites in mammalian mRNAs. elife. 2015;4:e05005.
- Enright AJ, John B, Gaul U, et al. MicroRNA targets in Drosophila. Genome Biol. 2003;5:R1.
- Burgess S, Butterworth A, Thompson SG. Mendelian randomization analysis with multiple genetic variants using summarized data. Genet Epidemiol. 2013;37:658–665.
- Willer CJ, Schmidt EM, Sengupta S, et al. Discovery and refinement of loci associated with lipid levels. Nat Genet. 2013;45:1274.
- Hemani G, Zheng J, Elsworth, B, et al. The MR-Base platform supports systematic causal inference across the human phenome. Elife. 2018;7:e34408.
- Ernst J, Kheradpour P, Mikkelsen TS, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473:43.