1,173
Views
62
CrossRef citations to date
0
Altmetric
Research Paper

Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues

, , , , &
Pages 652-663 | Published online: 01 Jun 2012

References

  • Yang AS, Estécio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004; 32:e38; http://dx.doi.org/10.1093/nar/gnh032; PMID: 14973332
  • Fryer AA, Nafee TM, Ismail KMK, Carroll WD, Emes RD, Farrell WE. LINE-1 DNA methylation is inversely correlated with cord plasma homocysteine in man: a preliminary study. Epigenetics 2009; 4:394 - 8; http://dx.doi.org/10.4161/epi.4.6.9766; PMID: 19755846
  • Baccarelli A, Wright RO, Bollati V, Tarantini L, Litonjua AA, Suh HH, et al. Rapid DNA methylation changes after exposure to traffic particles. Am J Respir Crit Care Med 2009; 179:572 - 8; http://dx.doi.org/10.1164/rccm.200807-1097OC; PMID: 19136372
  • Rusiecki JA, Baccarelli A, Bollati V, Tarantini L, Moore LE, Bonefeld-Jorgensen EC. Global DNA hypomethylation is associated with high serum-persistent organic pollutants in Greenlandic Inuit. Environ Health Perspect 2008; 116:1547 - 52; http://dx.doi.org/10.1289/ehp.11338; PMID: 19057709
  • Wright RO, Schwartz J, Wright RJ, Bollati V, Tarantini L, Park SK, et al. Biomarkers of lead exposure and DNA methylation within retrotransposons. Environ Health Perspect 2010; 118:790 - 5; http://dx.doi.org/10.1289/ehp.0901429; PMID: 20064768
  • Ramsahoye BH. Measurement of genome wide DNA methylation by reversed-phase high-performance liquid chromatography. Methods 2002; 27:156 - 61; http://dx.doi.org/10.1016/S1046-2023(02)00069-5; PMID: 12095275
  • Li W, Liu M. Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids 2011; 2011:870726; http://dx.doi.org/10.4061/2011/870726; PMID: 21772996
  • Chen X, Guo J, Lei Y, Zou J, Lu X, Bao Y, et al. Global DNA hypomethylation is associated with NTD-affected pregnancy: A case-control study. Birth Defects Res A Clin Mol Teratol 2010; 88:575 - 81; http://dx.doi.org/10.1002/bdra.20670; PMID: 20641100
  • Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 2007; 39:457 - 66; http://dx.doi.org/10.1038/ng1990; PMID: 17334365
  • Bibikova M, Le J, Barnes B, Saedinia-Melnyk S, Zhou L, Shen R, et al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics 2009; 1:177 - 200; http://dx.doi.org/10.2217/epi.09.14; PMID: 22122642
  • Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009; 10:691 - 703; http://dx.doi.org/10.1038/nrg2640; PMID: 19763152
  • Schmid CW. Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. Prog Nucleic Acid Res Mol Biol 1996; 53:283 - 319; http://dx.doi.org/10.1016/S0079-6603(08)60148-8; PMID: 8650306
  • Xie H, Wang M, Bonaldo MdeF, Smith C, Rajaram V, Goldman S, et al. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res 2009; 37:4331 - 40; http://dx.doi.org/10.1093/nar/gkp393; PMID: 19458156
  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al, International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409:860 - 921; http://dx.doi.org/10.1038/35057062; PMID: 11237011
  • Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002; 3:370 - 9; http://dx.doi.org/10.1038/nrg798; PMID: 11988762
  • Buzdin A, Ustyugova S, Gogvadze E, Lebedev Y, Hunsmann G, Sverdlov E. Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum Genet 2003; 112:527 - 33; PMID: 12601470
  • Schmid CW. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res 1991; 19:5613 - 7; http://dx.doi.org/10.1093/nar/19.20.5613; PMID: 1945838
  • Smit AF, Tóth G, Riggs AD, Jurka J. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 1995; 246:401 - 17; http://dx.doi.org/10.1006/jmbi.1994.0095; PMID: 7877164
  • Kazazian HH Jr.. Mobile elements: drivers of genome evolution. Science 2004; 303:1626 - 32; http://dx.doi.org/10.1126/science.1089670; PMID: 15016989
  • Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, et al. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet 2009; 41:563 - 71; http://dx.doi.org/10.1038/ng.368; PMID: 19377475
  • Mätlik K, Redik K, Speek M. L1 antisense promoter drives tissue-specific transcription of human genes. J Biomed Biotechnol 2006; 2006:71753; http://dx.doi.org/10.1155/JBB/2006/71753; PMID: 16877819
  • Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37:853 - 62; http://dx.doi.org/10.1038/ng1598; PMID: 16007088
  • Szpakowski S, Sun X, Lage JM, Dyer A, Rubinstein J, Kowalski D, et al. Loss of epigenetic silencing in tumors preferentially affects primate-specific retroelements. Gene 2009; 448:151 - 67; http://dx.doi.org/10.1016/j.gene.2009.08.006; PMID: 19699787
  • Tost J, Dunker J, Gut IG. Analysis and quantification of multiple methylation variable positions in CpG islands by Pyrosequencing. Biotechniques 2003; 35:152 - 6; PMID: 12866415
  • Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E, et al. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 2005; 33:6823 - 36; http://dx.doi.org/10.1093/nar/gki987; PMID: 16326863
  • Dolinoy DC, Huang D, Jirtle RL. Maternal nutrient supplementation counteracts bisphenol A-induced DNA hypomethylation in early development. Proc Natl Acad Sci U S A 2007; 104:13056 - 61; http://dx.doi.org/10.1073/pnas.0703739104; PMID: 17670942
  • Wolff GL, Kodell RL, Moore SR, Cooney CA. Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB J 1998; 12:949 - 57; PMID: 9707167
  • Bollati V, Baccarelli A, Hou L, Bonzini M, Fustinoni S, Cavallo D, et al. Changes in DNA methylation patterns in subjects exposed to low-dose benzene. Cancer Res 2007; 67:876 - 80; http://dx.doi.org/10.1158/0008-5472.CAN-06-2995; PMID: 17283117
  • Tarantini L, Bonzini M, Apostoli P, Pegoraro V, Bollati V, Marinelli B, et al. Effects of particulate matter on genomic DNA methylation content and iNOS promoter methylation. Environ Health Perspect 2009; 117:217 - 22; PMID: 19270791
  • Wang L, Wang F, Guan J, Le J, Wu L, Zou J, et al. Relation between hypomethylation of long interspersed nucleotide elements and risk of neural tube defects. Am J Clin Nutr 2010; 91:1359 - 67; http://dx.doi.org/10.3945/ajcn.2009.28858; PMID: 20164316
  • Kang MI, Rhyu MG, Kim YH, Jung YC, Hong SJ, Cho CS, et al. The length of CpG islands is associated with the distribution of Alu and L1 retroelements. Genomics 2006; 87:580 - 90; http://dx.doi.org/10.1016/j.ygeno.2006.01.002; PMID: 16488573
  • Baccarelli A, Wright R, Bollati V, Litonjua A, Zanobetti A, Tarantini L, et al. Ischemic heart disease and stroke in relation to blood DNA methylation. Epidemiology 2010; 21:819 - 28; http://dx.doi.org/10.1097/EDE.0b013e3181f20457; PMID: 20805753
  • Ewing AD, Kazazian HH Jr.. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 2010; 20:1262 - 70; http://dx.doi.org/10.1101/gr.106419.110; PMID: 20488934
  • Yuen RK, Peñaherrera MS, von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. Eur J Hum Genet 2010; 18:1006 - 12; http://dx.doi.org/10.1038/ejhg.2010.63; PMID: 20442742
  • Novakovic B, Yuen RK, Gordon L, Penaherrera MS, Sharkey A, Moffett A, et al. Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors. BMC Genomics 2011; 12:529; http://dx.doi.org/10.1186/1471-2164-12-529; PMID: 22032438
  • Fuke C, Shimabukuro M, Petronis A, Sugimoto J, Oda T, Miura K, et al. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann Hum Genet 2004; 68:196 - 204; http://dx.doi.org/10.1046/j.1529-8817.2004.00081.x; PMID: 15180700
  • Chavan-Gautam P, Sundrani D, Pisal H, Nimbargi V, Mehendale S, Joshi S. Gestation-dependent changes in human placental global DNA methylation levels. Mol Reprod Dev 2011; 78:150; http://dx.doi.org/10.1002/mrd.21296; PMID: 21425205
  • Choi IS, Estecio MR, Nagano Y, Kim H, White JA, Yao JC, et al. Hypomethylation of LINE-1 and Alu in well-differentiated neuroendocrine tumors (pancreatic endocrine tumors and carcinoid tumors). Mod Pathol 2007; 20:802 - 10; http://dx.doi.org/10.1038/modpathol.3800825; PMID: 17483816
  • Cho NY, Kim BH, Choi M, Yoo EJ, Moon KC, Cho YM, et al. Hypermethylation of CpG island loci and hypomethylation of LINE-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinicopathological features. J Pathol 2007; 211:269 - 77; http://dx.doi.org/10.1002/path.2106; PMID: 17139617
  • Richards KL, Zhang B, Baggerly KA, Colella S, Lang JC, Schuller DE, et al. Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability. PLoS One 2009; 4:e4941; http://dx.doi.org/10.1371/journal.pone.0004941; PMID: 19293934
  • Medstrand P, van de Lagemaat LN, Mager DL. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 2002; 12:1483 - 95; http://dx.doi.org/10.1101/gr.388902; PMID: 12368240
  • Turker MS. Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene 2002; 21:5388 - 93; http://dx.doi.org/10.1038/sj.onc.1205599; PMID: 12154401
  • Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, et al. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 1982; 10:2709 - 21; http://dx.doi.org/10.1093/nar/10.8.2709; PMID: 7079182
  • Novakovic B, Wong NC, Sibson M, Ng HK, Morley R, Manuelpillai U, et al. DNA methylation-mediated down-regulation of DNA methyltransferase-1 (DNMT1) is coincident with, but not essential for, global hypomethylation in human placenta. J Biol Chem 2010; 285:9583 - 93; http://dx.doi.org/10.1074/jbc.M109.064956; PMID: 20071334
  • Hellmann-Blumberg U, Hintz MF, Gatewood JM, Schmid CW. Developmental differences in methylation of human Alu repeats. Mol Cell Biol 1993; 13:4523 - 30; PMID: 8336699
  • Cotton AM, Avila L, Penaherrera MS, Affleck JG, Robinson WP, Brown CJ. Inactive X chromosome-specific reduction in placental DNA methylation. Hum Mol Genet 2009; 18:3544 - 52; http://dx.doi.org/10.1093/hmg/ddp299; PMID: 19586922
  • Macaulay EC, Weeks RJ, Andrews S, Morison IM. Hypomethylation of functional retrotransposon-derived genes in the human placenta. Mamm Genome 2011; 22:722 - 35; http://dx.doi.org/10.1007/s00335-011-9355-1; PMID: 21874386
  • Okahara G, Matsubara S, Oda T, Sugimoto J, Jinno Y, Kanaya F. Expression analyses of human endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Genomics 2004; 84:982 - 90; http://dx.doi.org/10.1016/j.ygeno.2004.09.004; PMID: 15533715
  • Frendo JL, Olivier D, Cheynet V, Blond JL, Bouton O, Vidaud M, et al. Direct involvement of HERV-W Env glycoprotein in human trophoblast cell fusion and differentiation. Mol Cell Biol 2003; 23:3566 - 74; http://dx.doi.org/10.1128/MCB.23.10.3566-3574.2003; PMID: 12724415
  • Yuen RK, Neumann SM, Fok AK, Peñaherrera MS, McFadden DE, Robinson WP, et al. Extensive epigenetic reprogramming in human somatic tissues between fetus and adult. Epigenetics Chromatin 2011; 4:7; http://dx.doi.org/10.1186/1756-8935-4-7; PMID: 21545704
  • Yuen RK, Jiang R, Peñaherrera MS, McFadden DE, Robinson WP. Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies. Epigenetics Chromatin 2011; 4:10; http://dx.doi.org/10.1186/1756-8935-4-10; PMID: 21749726
  • Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 2010; 11:587; http://dx.doi.org/10.1186/1471-2105-11-587; PMID: 21118553
  • Wang Y, Leung FC. An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics 2004; 20:1170 - 7; http://dx.doi.org/10.1093/bioinformatics/bth059; PMID: 14764558
  • Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res 2004; 14:2245 - 52; http://dx.doi.org/10.1101/gr.2693004; PMID: 15520288