Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation

References

• Elliott G, Hong C, Xing X, Zhou X, Li D, Coarfa C, Bell RJA, Maire CL, Ligon KL, Sigaroudinia M, et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun 2015; 6:6363; PMID:25691127; http://dx.doi.org/10.1038/ncomms7363
   PubMed Web of Science ®Google Scholar
• Schroeder DI, Blair JD, Lott P, Yu HOK, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, et al. The human placenta methylome. Proc Natl Acad Sci 2013; 110:6037–42; PMID:23530188; http://dx.doi.org/10.1073/pnas.1215145110
   PubMed Web of Science ®Google Scholar
• Kobayashi H, Sakurai T, Miura F, Imai M, Mochiduki K, Yanagisawa E, Sakashita A, Wakai T, Suzuki Y, Ito T, et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res 2013; 23:616–27; PMID:23410886; http://dx.doi.org/10.1101/gr.148023.112
   PubMed Web of Science ®Google Scholar
• Jenkins TG, Aston KI, Trost C, Farley J, Hotaling JM, Carrell DT. Intra-sample heterogeneity of sperm DNA methylation. Mol Hum Reprod 2015; 21:313–9; PMID:25542834; http://dx.doi.org/10.1093/molehr/gau115
   PubMed Web of Science ®Google Scholar
• Singer ZS, Yong J, Tischler J, Hackett JA, Altinok A, Surani MA, Cai L, Elowitz MB. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell 2014; 55:319–31; PMID:25038413; http://dx.doi.org/10.1016/j.molcel.2014.06.029
   PubMed Web of Science ®Google Scholar
• Shao X, Zhang C, Sun M-A, Lu X, Xie H. Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming. BMC Genomics 2014; 15:978; PMID:25404570; http://dx.doi.org/10.1186/1471-2164-15-978
   PubMed Web of Science ®Google Scholar
• Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes C, Zucknick M, Lipka DB, Weischenfeldt J, et al. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Rep 2014; 8:798–806; PMID:25066126; http://dx.doi.org/10.1016/j.celrep.2014.06.053
   PubMed Web of Science ®Google Scholar
• Hutchinson JN, Raj T, Fagerness J, Stahl E, Viloria FT, Gimelbrant A, Seddon J, Daly M, Chess A, Plenge R. Allele-specific methylation occurs at genetic variants associated with complex disease. PLoS ONE 2014; 9:e98464; PMID:24911414; http://dx.doi.org/10.1371/journal.pone.0098464
   PubMed Web of Science ®Google Scholar
• Wang Q, Jia P, Cheng F, Zhao Z. Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer. Genes Chromosomes Cancer 2015; 54:110–21; PMID:25407423; http://dx.doi.org/10.1002/gcc.22224
   PubMed Web of Science ®Google Scholar
• Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet 2012; 8:e1002440; PMID:22242016; http://dx.doi.org/10.1371/journal.pgen.1002440
   PubMed Web of Science ®Google Scholar
• Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013; 9:e1003439; PMID:23637617; http://dx.doi.org/10.1371/journal.pgen.1003439
   PubMed Web of Science ®Google Scholar
• Xu Z, Taylor JA. Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis 2014; 35:356–64; PMID:24287154; http://dx.doi.org/10.1093/carcin/bgt391
   PubMed Web of Science ®Google Scholar
• Ono R, Kobayashi S, Wagatsuma H, Aisaka K, Kohda T, Kaneko-Ishino T, Ishino F. A Retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics 2001; 73:232–7; PMID:11318613; http://dx.doi.org/10.1006/geno.2001.6494
   PubMed Web of Science ®Google Scholar
• Mancini-DiNardo D, Steele SJS, Ingram RS, Tilghman SM. A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer. Hum Mol Genet 2003; 12:283–94; PMID:12554682; http://dx.doi.org/10.1093/hmg/ddg024
   PubMed Web of Science ®Google Scholar
• Ono R, Shiura H, Aburatani H, Kohda T, Kaneko-Ishino T, Ishino F. Identification of a Large Novel Imprinted Gene Cluster on Mouse Proximal Chromosome 6. Genome Res 2003; 13:1696–705; PMID:12840045; http://dx.doi.org/10.1101/gr.906803
   PubMed Web of Science ®Google Scholar
• Lou S, Lee H-M, Qin H, Li J-W, Gao Z, Liu X, Chan LL, Lam VK, So W-Y, Wang Y, et al. Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol 2014; 15:408; PMID:25074712; http://dx.doi.org/10.1186/s13059-014-0408-0
   PubMed Web of Science ®Google Scholar
• Hahn MA, Wu X, Li AX, Hahn T, Pfeifer GP. Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS ONE 2011; 6:e18844; PMID:21526191; http://dx.doi.org/10.1371/journal.pone.0018844
   PubMed Web of Science ®Google Scholar
• Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, Popp C, Thienpont B, Dean W, Reik W. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell 2012; 48:849–62; PMID:23219530; http://dx.doi.org/10.1016/j.molcel.2012.11.001
   PubMed Web of Science ®Google Scholar
• Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 2002; 117:15–23; PMID:12204247; http://dx.doi.org/10.1016/S0925-4773(02)00181-8
   PubMed Web of Science ®Google Scholar
• Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science 2001; 293:1089–93; PMID:11498579; http://dx.doi.org/10.1126/science.1063443
   PubMed Web of Science ®Google Scholar
• Okano M, Bell DW, Haber DA, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for De novo methylation and mammalian development. Cell 1999; 99:247–57; PMID:10555141; http://dx.doi.org/10.1016/S0092-8674(00)81656-6
   PubMed Web of Science ®Google Scholar
• Morita-Fujimura Y, Tokitake Y, Matsui Y. Heterogeneity of mouse primordial germ cells reflecting the distinct status of their differentiation, proliferation and apoptosis can be classified by the expression of cell surface proteins integrin α6 and c-Kit. Dev Growth Differ 2009; 51:567–83; PMID:21314674; http://dx.doi.org/10.1111/j.1440-169X.2009.01119.x
   PubMed Web of Science ®Google Scholar
• Jeltsch A, Jurkowska RZ. New concepts in DNA methylation. Trends Biochem Sci 2014; 39:310–8; PMID:24947342; http://dx.doi.org/10.1016/j.tibs.2014.05.002
   PubMed Web of Science ®Google Scholar
• Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 2011; 27:1571–2; PMID:21493656; http://dx.doi.org/10.1093/bioinformatics/btr167
   PubMed Web of Science ®Google Scholar