Methylomics of gene expression in human monocytes

Human Molecular Genetics

Volumn 22, Issue 24, 2013, Pages 5065-5074

  Liu, Yongmei ^a   Ding, Jingzhong ^a   Reynolds, Lindsay M ^a   Lohman, Kurt ^a   Register, Thomas C ^a   De la Fuente, Alberto ^b   Howard, Timothy D ^a   Hawkins, Greg A ^a   Cui, Wei ^a   Morris, Jessica ^a   Smith, Shelly G ^a   Barr, R Graham ^c   Kaufman, Joel D ^d   Burke, Gregory L ^a   Post, Wendy ^e   Shea, Steven ^c   Mccall, Charles E ^a   Siscovick, David ^d   Jacobs, David R ^f   Tracy, Russell P ^g   Herrington, David M ^a   Hoeschele, Ina ^h   more..

^a WAKE FOREST SCHOOL OF MEDICINE   (United States)

^b LEIBNIZ INSTITUTE FOR FARM ANIMAL BIOLOGY FBN   (Germany)

^c New York Presbyterian Morgan Stanley Children's Hospital   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e JOHNS HOPKINS UNIVERSITY   (United States)

^f UNIVERSITY OF MINNESOTA   (United States)

^g UNIVERSITY OF VERMONT   (United States)

^h VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE TRANSFERASE T1; MESSENGER RNA;

3' UNTRANSLATED REGION; ADULT; AGED; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EFFECT SIZE; ENHANCER REGION; EPIGENETICS; ETHNIC DIFFERENCE; GENE EXPRESSION; GENE LOCUS; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MONOCYTE; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; SEX DIFFERENCE;

AGED; AGED, 80 AND OVER; ATHEROSCLEROSIS; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; GLUTATHIONE TRANSFERASE; HUMANS; MALE; MIDDLE AGED; MOLECULAR SEQUENCE ANNOTATION; MONOCYTES; POLYMORPHISM, SINGLE NUCLEOTIDE; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION INITIATION SITE; TRANSCRIPTOME;

EID: 84888155393     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt356     Document Type: Article

References (41)

1. Bell, A.C. and Felsenfeld, G. (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature, 405, 482-485.
2. Jaenisch, R. and Bird, A. (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet., 33 (suppl.), 245-254.
3. Esteller, M. (2007) Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum. Mol. Genet., 16 (Spec no. 1), R50-R59.
4. Portela, A. and Esteller, M. (2010) Epigenetic modifications and human disease. Nat. Biotechnol., 28, 1057-1068.
5. Thomson, J.P., Skene, P.J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A.R., Deaton, A., Andrews, R., James, K.D. et al. (2010) Cpg islands influence chromatin structure via the CpG-binding protein Cfp1. Nature, 464, 1082-1086.
6. Hui, R., Macmillan, R.D., Kenny, F.S., Musgrove, E.A., Blamey, R.W., Nicholson, R.I., Robertson, J.F. and Sutherland, R.L. (2000) INK4a gene expression and methylation in primary breast cancer: overexpression of p16INK4a messengerRNAis a marker of poor prognosis. Clin. Cancer Res., 6, 2777-2787.
7. Pike, B.L., Greiner, T.C., Wang, X., Weisenburger, D.D., Hsu, Y.H., Renaud, G., Wolfsberg, T.G., Kim, M., Weisenberger, D.J., Siegmund, K.D. et al. (2008)DNAmethylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia, 22, 1035-1043.
8. Ball, M.P., Li, J.B., Gao, Y., Lee, J.H., LeProust, E.M., Park, I.H., Xie, B., Daley, G.Q. and Church, G.M. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat. Biotechnol., 27, 361-368.
9. Li, M., Balch, C., Montgomery, J.S., Jeong, M., Chung, J.H., Yan, P., Huang, T.H., Kim, S. and Nephew, K.P. (2009) Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer. BMC Med. Genomics, 2, 34.
10. Sun, Z., Asmann, Y.W., Kalari, K.R., Bot, B., Eckel-Passow, J.E., Baker, T.R., Carr, J.M., Khrebtukova, I., Luo, S., Zhang, L. et al. (2011) Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One, 6, e17490.
11. Lee, S.T., Xiao, Y., Muench, M.O., Xiao, J., Fomin, M.E., Wiencke, J.K., Zheng, S., Dou, X., de Smith, A., Chokkalingam, A. et al. (2012) A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network. Nucleic Acids Res., 40, 11339-11351.
12. van Eijk, K.R., de Jong, S., Boks, M.P., Langeveld, T., Colas, F., Veldink, J.H., de Kovel, C.G., Janson, E., Strengman, E., Langfelder, P. et al. (2012) Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics, 13, 636.
13. Pai, A.A., Bell, J.T., Marioni, J.C., Pritchard, J.K. and Gilad, Y. (2011) A genome-wide study ofDNAmethylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet., 7, e1001316.
14. Lam, L.L., Emberly, E., Fraser, H.B., Neumann, S.M., Chen, E., Miller, G.E. and Kobor, M.S. (2012) Factors underlying variable DNA methylation in a human community cohort. Proc. Natl Acad. Sci. USA, 109 (Suppl. 2), 17253-17260.
15. Bell, J.T., Pai, A.A., Pickrell, J.K., Gaffney, D.J., Pique-Regi, R., Degner, J.F., Gilad, Y. and Pritchard, J.K. (2011) DNA Methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol., 12, R10.
16. Gibbs, J.R., van der Brug, M.P., Hernandez, D.G., Traynor, B.J., Nalls, M.A., Lai, S.L., Arepalli, S., Dillman, A., Rafferty, I.P., Troncoso, J. et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet., 6, e1000952.
17. ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
18. Schadt, E.E., Lamb, J., Yang, X., Zhu, J., Edwards, S., Guhathakurta, D., Sieberts, S.K., Monks, S., Reitman, M., Zhang, C. et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet., 37, 710-717.
19. Stranger, B.E., Nica, A.C., Forrest, M.S., Dimas, A., Bird, C.P., Beazley, C., Ingle, C.E., Dunning, M., Flicek, P., Koller, D. et al. (2007) Population genomics of human gene expression. Nat. Genet., 39, 1217-1224.
20. Cheung, V.G., Spielman, R.S., Ewens, K.G., Weber, T.M., Morley, M. and Burdick, J.T. (2005) Mapping determinants of human gene expression by regional and genome-wide association. Nature, 437, 1365-1369.
21. Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A.S., Zink, F., Zhu, J., Carlson, S., Helgason, A., Walters, G.B., Gunnarsdottir, S. et al. (2008) Genetics of gene expression and its effect on disease. Nature, 452, 423-428.
22. Zeller, T., Wild, P., Szymczak, S., Rotival, M., Schillert, A., Castagne, R., Maouche, S., Germain, M., Lackner, K., Rossmann, H. et al. (2010) Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One, 5, e10693.
23. Stadler, M.B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Scholer, A., van Nimwegan, E., Wirbelauer, C., Oakeley, E.J., Gaidatzis, D. et al. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480, 490-495.
24. Kordi-Tamandani, D.M., Hashemi, M., Birjandian, E., Bahari, A., Valizadeh, J. and Torkamanzehi, A. (2011) Lack of association of GSTT1 and GSTP1 genes methylation and their expression profiles with risk of NAFLD in a sample of Iranian patients. Clin. Res. Hepatol. Gastroenterol., 35, 387-392.
25. Bild, D.E., Bluemke, D.A., Burke, G.L., Detrano, R., Diez Roux, A.V., Folsom, A.R., Greenland, P., Jacob, D.R. Jr., Kronmal, R., Liu, K. et al. (2002) Multi-ethnic study of atherosclerosis: objectives and design. Am. J. Epidemiol., 156, 871-881.
26. Dunning, M.J., Smith, M.L., Ritchie, M.E. and Tavare, S. (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics, 23, 2183-2184.
27. Smyth, G.K., Michaud, J. and Scott, H.S. (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics, 21, 2067-2075.
28. Du, P., Kibbe, W.A. and Lin, S.M. (2008) Lumi: a pipeline for processing Illumina microarray. Bioinformatics, 24, 1547-1548.
29. Du, P., Zhang, X., Huang, C.C., Jafari, N., Kibbe, W.A., Hou, L. and Lin, S.M. (2010) Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics, 11, 587.
30. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
31. Fox, C.S., White, C.C., Lohman, K., Heard-Costa, N., Cohen, P., Zhang, Y., Johnson, A.D., Emilsson, V., Liu, C.T., Chen, Y.D. et al. (2012) Genome-wide association of pericardial fat identifies a unique locus for ectopic fat. PLoS Genet., 8, e1002705.
32. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
33. Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. and Mesirov, J.P. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
34. Abbas, A.R., Baldwin, D.,Ma,Y., Ouyang,W., Gurney, A., Martin, F., Fong, S., van Lookeren, C.M., Godowski, P., Williams, P.M. et al. (2005) Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun., 6, 319-331.
35. Henderson, A.R. (2006) Information for authors: is the advice regarding the reporting of residuals in regression analysis incomplete? Should Cook's distance be included? Clin. Chem., 52, 1848-1850.
36. Schwartzman, A. and Lin, Y. (2011) The effect of correlation in FDR estimation. Biometrika, 98, 199-214.
37. Aten, J.E., Fuller, T.F., Lusis, A.J. and Horvath, S. (2008) Using genetic markers to orient the edges in quantitative trait networks: theNEOsoftware. BMC Syst. Biol., 2, 34.
38. Rosseel, Y. (2012) Lavaan: an R package for structural equation modeling. J. Stat. Software, 48, 1-36.
39. Hooper, D., Coughlan, J. and Mullen, M. (2008) Structural equation modelling: guidelines for determining model fit. Electron. J. Bus. Res. Methods, 6, 53-60.
40. Rosenbloom, K.R., Sloan, C.A., Malladi, V.S., Dreszer, T.R., Learned, K., Kirkup, V.M., Wong, M.C., Maddren, M., Fang, R., Heitner, S.G. et al. (2013)ENCODE data in the UCSC genome browser: year 5 update. Nucleic Acids Res., 41, D56-D63.
41. Dennis, G. Jr., Sherman, B.T., Hosack, D.A., Yang, J., Gao, W., Lane, H.C. andLempicki, R.A. (2003)DAVID:Database for Annotation, Visualization, and Integrated Discovery. Genome Biol., 4, 3.