Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation

American Journal of Human Genetics

Volumn 98, Issue 5, 2016, Pages 934-955

  Do, Catherine ^a   Lang, Charles F ^a   Lin, John ^a   Darbary, Huferesh ^a   Krupska, Izabela ^a   Gaba, Aulona ^a,b   Petukhova, Lynn ^a   Vonsattel, Jean Paul ^a   Gallagher, Mary P ^a   Goland, Robin S ^c   Clynes, Raphael A ^a   Dwork, Andrew ^a   Kral, John G ^d   Monk, Catherine ^a   Christiano, Angela M ^a   Tycko, Benjamin ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIV KLIN FÜR FRAUENHEILKUNDE   (Austria)

^c NewYork Presbyterian Hospital   (United States)

^d SUNY DOWNSTATE MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CCDC155 PROTEIN; CD69 ANTIGEN; CELF2 PROTEIN; CMTM8 PROTEIN; FRMD1 PROTEIN; HLA D ANTIGEN; HLA DRB6 ANTIGEN; INTERFERON REGULATORY FACTOR 1; KBTBD11 PROTEIN; NGFR PROTEIN; PROTEIN; PROTEIN S100A PROTEIN; PTPRN2 PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; TRANSACTIVATOR PROTEIN;

ALLELE; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BINDING SITE; BRAIN DISEASE; CELLS BY BODY ANATOMY; CONTROLLED STUDY; DISEASE ASSOCIATION; DNA METHYLATION; GENOME IMPRINTING; GLIA; HAPLOTYPE; HUMAN; HUMAN CELL; HUMAN TISSUE; NERVE CELL; NEUROLOGIC DISEASE; NONHUMAN; PHENOTYPE; PLACENTA; PRIORITY JOURNAL; PROTEIN BINDING; QUANTITATIVE TRAIT LOCUS; SPECIES COMPARISON; T LYMPHOCYTE; ANIMAL; BRAIN; COMPARATIVE STUDY; FEMALE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; IMMUNOPATHOLOGY; MACACA RADIATA; METABOLISM; PATHOLOGY; PREGNANCY; RHESUS MONKEY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

ALLELES; ANIMALS; BRAIN; DNA METHYLATION; FEMALE; GENOME-WIDE ASSOCIATION STUDY; GENOMIC IMPRINTING; HAPLOTYPES; HUMANS; IMMUNE SYSTEM DISEASES; MACACA MULATTA; MACACA RADIATA; NERVOUS SYSTEM DISEASES; PLACENTA; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; QUANTITATIVE TRAIT LOCI; SPECIES SPECIFICITY; T-LYMPHOCYTES; TRANS-ACTIVATORS;

EID: 84968863271     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.03.027     Document Type: Article

References (93)

1. G.S. Barsh, G.P. Copenhaver, G. Gibson, and S.M. Williams Guidelines for genome-wide association studies PLoS Genet. 8 2012 e1002812
2. J.H. Park, M.H. Gail, C.R. Weinberg, R.J. Carroll, C.C. Chung, Z. Wang, S.J. Chanock, J.F. Fraumeni Jr., and N. Chatterjee Distribution of allele frequencies and effect sizes and their interrelationships for common genetic susceptibility variants Proc. Natl. Acad. Sci. USA 108 2011 18026 18031
3. K. Kerkel, A. Spadola, E. Yuan, J. Kosek, L. Jiang, E. Hod, K. Li, V.V. Murty, N. Schupf, E. Vilain, and et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation Nat. Genet. 40 2008 904 908
4. L.C. Schalkwyk, E.L. Meaburn, R. Smith, E.L. Dempster, A.R. Jeffries, M.N. Davies, R. Plomin, and J. Mill Allelic skewing of DNA methylation is widespread across the genome Am. J. Hum. Genet. 86 2010 196 212
5. A. Hellman, and A. Chess Extensive sequence-influenced DNA methylation polymorphism in the human genome Epigenetics Chromatin 3 2010 11
6. R. Shoemaker, J. Deng, W. Wang, and K. Zhang Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome Genome Res. 20 2010 883 889
7. J.N. Hutchinson, T. Raj, J. Fagerness, E. Stahl, F.T. Viloria, A. Gimelbrant, J. Seddon, M. Daly, A. Chess, and R. Plenge Allele-specific methylation occurs at genetic variants associated with complex disease PLoS ONE 9 2014 e98464
8. N. Plongthongkum, K.R. van Eijk, S. de Jong, T. Wang, J.H. Sul, M.P. Boks, R.S. Kahn, H.L. Fung, R.A. Ophoff, and K. Zhang Characterization of genome-methylome interactions in 22 nuclear pedigrees PLoS ONE 9 2014 e99313
9. A.K. Smith, V. Kilaru, M. Kocak, L.M. Almli, K.B. Mercer, K.J. Ressler, F.A. Tylavsky, and K.N. Conneely Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type BMC Genomics 15 2014 145
10. J.R. Gibbs, M.P. van der Brug, D.G. Hernandez, B.J. Traynor, M.A. Nalls, S.L. Lai, S. Arepalli, A. Dillman, I.P. Rafferty, J. Troncoso, and et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain PLoS Genet. 6 2010 e1000952
11. E.R. Gamazon, J.A. Badner, L. Cheng, C. Zhang, D. Zhang, N.J. Cox, E.S. Gershon, J.R. Kelsoe, T.A. Greenwood, C.M. Nievergelt, and et al. Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants Mol. Psychiatry 18 2013 340 346
12. J. Shi, C.N. Marconett, J. Duan, P.L. Hyland, P. Li, Z. Wang, W. Wheeler, B. Zhou, M. Campan, D.S. Lee, and et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Nat. Commun. 5 2014 3365
13. D. Zhang, L. Cheng, J.A. Badner, C. Chen, Q. Chen, W. Luo, D.W. Craig, M. Redman, E.S. Gershon, and C. Liu Genetic control of individual differences in gene-specific methylation in human brain Am. J. Hum. Genet. 86 2010 411 419
14. A. Paliwal, A.M. Temkin, K. Kerkel, A. Yale, I. Yotova, N. Drost, S. Lax, C.L. Nhan-Chang, C. Powell, A. Borczuk, and et al. Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation PLoS Genet. 9 2013 e1003622
15. X. Zhang, E.L. Moen, C. Liu, W. Mu, E.R. Gamazon, S.M. Delaney, C. Wing, L.A. Godley, M.E. Dolan, and W. Zhang Linking the genetic architecture of cytosine modifications with human complex traits Hum. Mol. Genet. 23 2014 5893 5905
16. B. Tycko Mapping allele-specific DNA methylation: a new tool for maximizing information from GWAS Am. J. Hum. Genet. 86 2010 109 112
17. B. Tycko Allele-specific DNA methylation: beyond imprinting Hum. Mol. Genet. 19 R2 2010 R210 R220
18. B.E. Stranger, S.B. Montgomery, A.S. Dimas, L. Parts, O. Stegle, C.E. Ingle, M. Sekowska, G.D. Smith, D. Evans, M. Gutierrez-Arcelus, and et al. Patterns of cis regulatory variation in diverse human populations PLoS Genet. 8 2012 e1002639
19. A. Matevossian, and S. Akbarian Neuronal nuclei isolation from human postmortem brain tissue J. Vis. Exp. 20 2008 914
20. F. Krueger, and S.R. Andrews Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications Bioinformatics 27 2011 1571 1572
21. Y. Liu, K.D. Siegmund, P.W. Laird, and B.P. Berman Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data Genome Biol. 13 2012 R61
22. M. Mendioroz, C. Do, X. Jiang, C. Liu, H.K. Darbary, C.F. Lang, J. Lin, A. Thomas, S. Abu-Amero, P. Stanier, and et al. Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models Genome Biol. 16 2015 263
23. P. Kheradpour, and M. Kellis Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments Nucleic Acids Res. 42 2014 2976 2987
24. M. Kellis, B. Wold, M.P. Snyder, B.E. Bernstein, A. Kundaje, G.K. Marinov, L.D. Ward, E. Birney, G.E. Crawford, J. Dekker, and et al. Defining functional DNA elements in the human genome Proc. Natl. Acad. Sci. USA 111 2014 6131 6138
25. K.B. Michels, A.M. Binder, S. Dedeurwaerder, C.B. Epstein, J.M. Greally, I. Gut, E.A. Houseman, B. Izzi, K.T. Kelsey, A. Meissner, and et al. Recommendations for the design and analysis of epigenome-wide association studies Nat. Methods 10 2013 949 955
26. X. Li, M. Ito, F. Zhou, N. Youngson, X. Zuo, P. Leder, and A.C. Ferguson-Smith A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints Dev. Cell 15 2008 547 557
27. S. Takikawa, X. Wang, C. Ray, M. Vakulenko, F.T. Bell, and X. Li Human and mouse ZFP57 proteins are functionally interchangeable in maintaining genomic imprinting at multiple imprinted regions in mouse ES cells Epigenetics 8 2013 1268 1279
28. A. Nykjaer, T.E. Willnow, and C.M. Petersen p75NTR - live or let die Curr. Opin. Neurobiol. 15 2005 49 57
29. K.M. Bakulski, D.C. Dolinoy, M.A. Sartor, H.L. Paulson, J.R. Konen, A.P. Lieberman, R.L. Albin, H. Hu, and L.S. Rozek Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex J. Alzheimers Dis. 29 2012 571 588
30. P.L. De Jager, G. Srivastava, K. Lunnon, J. Burgess, L.C. Schalkwyk, L. Yu, M.L. Eaton, B.T. Keenan, J. Ernst, C. McCabe, and et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci Nat. Neurosci. 17 2014 1156 1163
31. K. Lunnon, R. Smith, E. Hannon, P.L. De Jager, G. Srivastava, M. Volta, C. Troakes, S. Al-Sarraj, J. Burrage, R. Macdonald, and et al. Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease Nat. Neurosci. 17 2014 1164 1170
32. L. Yu, L.B. Chibnik, G.P. Srivastava, N. Pochet, J. Yang, J. Xu, J. Kozubek, N. Obholzer, S.E. Leurgans, J.A. Schneider, and et al. Association of brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease JAMA Neurol. 72 2015 15 24
33. M. Bibikova, J. Le, B. Barnes, S. Saedinia-Melnyk, L. Zhou, R. Shen, and K.L. Gunderson Genome-wide DNA methylation profiling using Infinium® assay Epigenomics 1 2009 177 200
34. F. Marabita, M. Almgren, M.E. Lindholm, S. Ruhrmann, F. Fagerström-Billai, M. Jagodic, C.J. Sundberg, T.J. Ekström, A.E. Teschendorff, J. Tegnér, and D. Gomez-Cabrero An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform Epigenetics 8 2013 333 346
35. A. Kundaje, W. Meuleman, J. Ernst, M. Bilenky, A. Yen, A. Heravi-Moussavi, P. Kheradpour, Z. Zhang, J. Wang, M.J. Ziller, et al. Roadmap Epigenomics Consortium Integrative analysis of 111 reference human epigenomes Nature 518 2015 317 330
36. B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, J. Cuff, B. Fry, A. Meissner, M. Wernig, K. Plath, and et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells Cell 125 2006 315 326
37. N.E. Banovich, X. Lan, G. McVicker, B. van de Geijn, J.F. Degner, J.D. Blischak, J. Roux, J.K. Pritchard, and Y. Gilad Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels PLoS Genet. 10 2014 e1004663
38. T.E. Reddy, J. Gertz, F. Pauli, K.S. Kucera, K.E. Varley, K.M. Newberry, G.K. Marinov, A. Mortazavi, B.A. Williams, L. Song, and et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression Genome Res. 22 2012 860 869
39. R.E. Thurman, E. Rynes, R. Humbert, J. Vierstra, M.T. Maurano, E. Haugen, N.C. Sheffield, A.B. Stergachis, H. Wang, B. Vernot, and et al. The accessible chromatin landscape of the human genome Nature 489 2012 75 82
40. G.C. Prendergast, and E.B. Ziff Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region Science 251 1991 186 189
41. C. Ogawa, Y. Tone, M. Tsuda, C. Peter, H. Waldmann, and M. Tone TGF-β-mediated Foxp3 gene expression is cooperatively regulated by Stat5, Creb, and AP-1 through CNS2 J. Immunol. 192 2014 475 483
42. T.G. Uhm, S.K. Lee, B.S. Kim, J.H. Kang, C.S. Park, T.Y. Rhim, H.S. Chang, J. Kim, and I.Y. Chung CpG methylation at GATA elements in the regulatory region of CCR3 positively correlates with CCR3 transcription Exp. Mol. Med. 44 2012 268 280
43. I.K. Mann, R. Chatterjee, J. Zhao, X. He, M.T. Weirauch, T.R. Hughes, and C. Vinson CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo Genome Res. 23 2013 988 997
44. G. Perini, D. Diolaiti, A. Porro, and G. Della Valle In vivo transcriptional regulation of N-Myc target genes is controlled by E-box methylation Proc. Natl. Acad. Sci. USA 102 2005 12117 12122
45. K. Miura, H. Mishima, A. Kinoshita, C. Hayashida, S. Abe, K. Tokunaga, H. Masuzaki, and K. Yoshiura Genome-wide association study of HPV-associated cervical cancer in Japanese women J. Med. Virol. 86 2014 1153 1158
46. J.C. Barrett, D.G. Clayton, P. Concannon, B. Akolkar, J.D. Cooper, H.A. Erlich, C. Julier, G. Morahan, J. Nerup, C. Nierras, et al. Type 1 Diabetes Genetics Consortium Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes Nat. Genet. 41 2009 703 707
47. S. Sawcer, G. Hellenthal, M. Pirinen, C.C. Spencer, N.A. Patsopoulos, L. Moutsianas, A. Dilthey, Z. Su, C. Freeman, S.E. Hunt, et al. International Multiple Sclerosis Genetics Consortium Wellcome Trust Case Control Consortium 2 Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Nature 476 2011 214 219
48. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
49. E.J. Ryan, A.J. Marshall, D. Magaletti, H. Floyd, K.E. Draves, N.E. Olson, and E.A. Clark Dendritic cell-associated lectin-1: a novel dendritic cell-associated, C-type lectin-like molecule enhances T cell secretion of IL-4 J. Immunol. 169 2002 5638 5648
50. C. Germain, F. Bihl, S. Zahn, G. Poupon, M.J. Dumaurier, H.H. Rampanarivo, S.B. Padkjær, P. Spee, and V.M. Braud Characterization of alternatively spliced transcript variants of CLEC2D gene J. Biol. Chem. 285 2010 36207 36215
51. R. González-Amaro, J.R. Cortés, F. Sánchez-Madrid, and P. Martín Is CD69 an effective brake to control inflammatory diseases? Trends Mol. Med. 19 2013 625 632
52. T. Taniguchi, K. Ogasawara, A. Takaoka, and N. Tanaka IRF family of transcription factors as regulators of host defense Annu. Rev. Immunol. 19 2001 623 655
53. J.L. Harden, J.G. Krueger, and A.M. Bowcock The immunogenetics of psoriasis: A comprehensive review J. Autoimmun. 64 2015 66 73
54. A. Franke, D.P. McGovern, J.C. Barrett, K. Wang, G.L. Radford-Smith, T. Ahmad, C.W. Lees, T. Balschun, J. Lee, R. Roberts, and et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci Nat. Genet. 42 2010 1118 1125
55. X. Li, T.D. Howard, S.L. Zheng, T. Haselkorn, S.P. Peters, D.A. Meyers, and E.R. Bleecker Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions J. Allergy Clin. Immunol. 125 2010 328 335.e11
56. J.C. Barrett, S. Hansoul, D.L. Nicolae, J.H. Cho, R.H. Duerr, J.D. Rioux, S.R. Brant, M.S. Silverberg, K.D. Taylor, M.M. Barmada, et al. NIDDK IBD Genetics Consortium Belgian-French IBD Consortium Wellcome Trust Case Control Consortium Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease Nat. Genet. 40 2008 955 962
57. L. Jostins, S. Ripke, R.K. Weersma, R.H. Duerr, D.P. McGovern, K.Y. Hui, J.C. Lee, L.P. Schumm, Y. Sharma, C.A. Anderson, et al. International IBD Genetics Consortium (IIBDGC) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease Nature 491 2012 119 124
58. D.P. McGovern, M.R. Jones, K.D. Taylor, K. Marciante, X. Yan, M. Dubinsky, A. Ippoliti, E. Vasiliauskas, D. Berel, C. Derkowski, et al. International IBD Genetics Consortium Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease Hum. Mol. Genet. 19 2010 3468 3476
59. R.B. Kennedy, I.G. Ovsyannikova, V.S. Pankratz, I.H. Haralambieva, R.A. Vierkant, and G.A. Poland Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients Hum. Genet. 131 2012 1403 1421
60. M.R. Müller, and A. Rao NFAT, immunity and cancer: a transcription factor comes of age Nat. Rev. Immunol. 10 2010 645 656
61. I.L. Mero, M.W. Gustavsen, H.S. Sæther, S.T. Flåm, P. Berg-Hansen, H.B. Søndergaard, P.E. Jensen, T. Berge, A. Bjølgerud, A. Muggerud, et al. International Multiple Sclerosis Genetics Consortium Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles PLoS ONE 8 2013 e58352
62. J.W. Han, H.F. Zheng, Y. Cui, L.D. Sun, D.Q. Ye, Z. Hu, J.H. Xu, Z.M. Cai, W. Huang, G.P. Zhao, and et al. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus Nat. Genet. 41 2009 1234 1237
63. A.H. Fanous, B. Zhou, S.H. Aggen, S.E. Bergen, R.L. Amdur, J. Duan, A.R. Sanders, J. Shi, B.J. Mowry, A. Olincy, et al. Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms Am. J. Psychiatry 169 2012 1309 1317
64. J.C. Lambert, C.A. Ibrahim-Verbaas, D. Harold, A.C. Naj, R. Sims, C. Bellenguez, A.L. DeStafano, J.C. Bis, G.W. Beecham, B. Grenier-Boley, et al. European Alzheimer's Disease Initiative (EADI) Genetic and Environmental Risk in Alzheimer's Disease Alzheimer's Disease Genetic Consortium Cohorts for Heart and Aging Research in Genomic Epidemiology Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease Nat. Genet. 45 2013 1452 1458
65. B.M. Elmer, and A.K. McAllister Major histocompatibility complex class I proteins in brain development and plasticity Trends Neurosci. 35 2012 660 670
66. H. Lee, B.K. Brott, L.A. Kirkby, J.D. Adelson, S. Cheng, M.B. Feller, A. Datwani, and C.J. Shatz Synapse elimination and learning rules co-regulated by MHC class I H2-Db Nature 509 2014 195 200
67. J.H. Lee, R. Cheng, S. Barral, C. Reitz, M. Medrano, R. Lantigua, I.Z. Jiménez-Velazquez, E. Rogaeva, P.H. St George-Hyslop, and R. Mayeux Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals Arch. Neurol. 68 2011 320 328
68. E.M. Wijsman, N.D. Pankratz, Y. Choi, J.H. Rothstein, K.M. Faber, R. Cheng, J.H. Lee, T.D. Bird, D.A. Bennett, R. Diaz-Arrastia, et al. NIA-LOAD/NCRAD Family Study Group Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE PLoS Genet. 7 2011 e1001308
69. A. Pacini, A. Toscano, V. Cesati, A. Cozzi, E. Meli, L. Di Cesare Mannelli, F. Paternostro, P. Pacini, and D.E. Pellegrini-Giampietro NAPOR-3 RNA binding protein is required for apoptosis in hippocampus Brain Res. Mol. Brain Res. 140 2005 34 44
70. S.P. Raychaudhuri, S.K. Raychaudhuri, K.R. Atkuri, L.A. Herzenberg, and L.A. Herzenberg Nerve growth factor: A key local regulator in the pathogenesis of inflammatory arthritis Arthritis Rheum. 63 2011 3243 3252
71. L.J. Scott, P. Muglia, X.Q. Kong, W. Guan, M. Flickinger, R. Upmanyu, F. Tozzi, J.Z. Li, M. Burmeister, D. Absher, and et al. Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry Proc. Natl. Acad. Sci. USA 106 2009 7501 7506
72. N. De Rocker, S. Vergult, D. Koolen, E. Jacobs, A. Hoischen, S. Zeesman, B. Bang, F. Béna, N. Bockaert, E.M. Bongers, and et al. Refinement of the critical 2p25.3 deletion region: the role of MYT1L in intellectual disability and obesity Genet. Med. 17 2015 460 466
73. D.E. Adkins, K. Aberg, J.L. McClay, J. Bukszár, Z. Zhao, P. Jia, T.S. Stroup, D. Perkins, J.P. McEvoy, J.A. Lieberman, and et al. Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs Mol. Psychiatry 16 2011 321 332
74. D. Curtis, A.E. Vine, A. McQuillin, N.J. Bass, A. Pereira, R. Kandaswamy, J. Lawrence, A. Anjorin, K. Choudhury, S.R. Datta, and et al. Case-case genome-wide association analysis shows markers differentially associated with schizophrenia and bipolar disorder and implicates calcium channel genes Psychiatr. Genet. 21 2011 1 4
75. B.Z. Yang, S. Han, H.R. Kranzler, L.A. Farrer, and J. Gelernter A genomewide linkage scan of cocaine dependence and major depressive episode in two populations Neuropsychopharmacology 36 2011 2422 2430
76. X. Zuo, J. Sheng, H.T. Lau, C.M. McDonald, M. Andrade, D.E. Cullen, F.T. Bell, M. Iacovino, M. Kyba, G. Xu, and X. Li Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain J. Biol. Chem. 287 2012 2107 2118
77. S.E. Boonen, D.J. Mackay, J.M. Hahnemann, L. Docherty, K. Grønskov, A. Lehmann, L.G. Larsen, A.P. Haemers, Y. Kockaerts, L. Dooms, and et al. Transient neonatal diabetes, ZFP57, and hypomethylation of multiple imprinted loci: a detailed follow-up Diabetes Care 36 2013 505 512
78. I. Baglivo, S. Esposito, L. De Cesare, A. Sparago, Z. Anvar, V. Riso, M. Cammisa, R. Fattorusso, G. Grimaldi, A. Riccio, and P.V. Pedone Genetic and epigenetic mutations affect the DNA binding capability of human ZFP57 in transient neonatal diabetes type 1 FEBS Lett. 587 2013 1474 1481
79. Y. Shamis, D.E. Cullen, L. Liu, G. Yang, S.F. Ng, L. Xiao, F.T. Bell, C. Ray, S. Takikawa, I.P. Moskowitz, and et al. Maternal and zygotic Zfp57 modulate NOTCH signaling in cardiac development Proc. Natl. Acad. Sci. USA 112 2015 E2020 E2029
80. B. Burgess-Beusse, C. Farrell, M. Gaszner, M. Litt, V. Mutskov, F. Recillas-Targa, M. Simpson, A. West, and G. Felsenfeld The insulation of genes from external enhancers and silencing chromatin Proc. Natl. Acad. Sci. USA 99 Suppl 4 2002 16433 16437
81. C.T. Ong, and V.G. Corces CTCF: an architectural protein bridging genome topology and function Nat. Rev. Genet. 15 2014 234 246
82. A.C. Bell, and G. Felsenfeld Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene Nature 405 2000 482 485
83. A. Feldmann, R. Ivanek, R. Murr, D. Gaidatzis, L. Burger, and D. Schübeler Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions PLoS Genet. 9 2013 e1003994
84. F. Butter, L. Davison, T. Viturawong, M. Scheibe, M. Vermeulen, J.A. Todd, and M. Mann Proteome-wide analysis of disease-associated SNPs that show allele-specific transcription factor binding PLoS Genet. 8 2012 e1002982
85. L. de la Rica, J. Rodríguez-Ubreva, M. García, A.B. Islam, J.M. Urquiza, H. Hernando, J. Christensen, K. Helin, C. Gómez-Vaquero, and E. Ballestar PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation Genome Biol. 14 2013 R99
86. M.J. Vogel, L. Guelen, E. de Wit, D. Peric-Hupkes, M. Lodén, W. Talhout, M. Feenstra, B. Abbas, A.K. Classen, and B. van Steensel Human heterochromatin proteins form large domains containing KRAB-ZNF genes Genome Res. 16 2006 1493 1504
87. A.C. Groner, S. Meylan, A. Ciuffi, N. Zangger, G. Ambrosini, N. Dénervaud, P. Bucher, and D. Trono KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading PLoS Genet. 6 2010 e1000869
88. J.A. Hagarman, M.P. Motley, K. Kristjansdottir, and P.D. Soloway Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells PLoS ONE 8 2013 e53880
89. E. Viré, C. Brenner, R. Deplus, L. Blanchon, M. Fraga, C. Didelot, L. Morey, A. Van Eynde, D. Bernard, J.M. Vanderwinden, and et al. The Polycomb group protein EZH2 directly controls DNA methylation Nature 439 2006 871 874
90. D. Umlauf, Y. Goto, R. Cao, F. Cerqueira, A. Wagschal, Y. Zhang, and R. Feil Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes Nat. Genet. 36 2004 1296 1300
91. R. Margueron, and D. Reinberg The Polycomb complex PRC2 and its mark in life Nature 469 2011 343 349
92. K.Y. Popadin, M. Gutierrez-Arcelus, T. Lappalainen, A. Buil, J. Steinberg, S.I. Nikolaev, S.W. Lukowski, G.A. Bazykin, V.B. Seplyarskiy, P. Ioannidis, and et al. Gene age predicts the strength of purifying selection acting on gene expression variation in humans Am. J. Hum. Genet. 95 2014 660 674
93. E. Hatchwell, and J.M. Greally The potential role of epigenomic dysregulation in complex human disease Trends Genet. 23 2007 588 595