REsEa Rch papER Epigenetics 7:6, 652-663; June 2012; © 2012 Landes Bioscience Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues E. Magda price,1-3 a llison M. c otton,2 Maria s . peñaherrera,2,3 Deborah E. McFadden,2,4 Michael s . Kobor2,3,5 and Wendy p. Robinson2,3,* 1Department of Obstetrics and Gynaecology; University of British c olumbia; Vancouver, Bc c anada; 2Department of Medical Genetics; University of British c olumbia; Vancouver, Bc c anada; 3c hild and Family Research Institute; British c olumbia; Vancouver, Bc c anada; 4Department of pathology; University of British c olumbia; Vancouver, Bc c anada; 5c entre for Molecular Medicine and Therapeutics; c hild and Family Research Institute; Vancouver, Bc c anada Keywords: LINE-1, Alu, DNA methylation, CpG island, placenta, repetitive elements, epigenetics Abbreviations: Villi, placental chorionic villi; LINE-1, long interspersed nuclear element; 5mC, 5-methylcyotsine; RE, repetitive element; ReDS, representative dispersed sequences; TSS, transcription start site DNa methylation of c pGs located in two types of repetitive elements—LINE-1 and a lu—is used to assess “global” changes in DNa methylation in studies of human disease and environmental exposure. LINE-1 and a lu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNa methylation. Few studies have investigated whether repetitive element DNa methylation is associated with DNa methylation at other genomic regions, or the biological and technical factors that influence potential associations. h ere, we assess LINE-1 and a lu DNa methylation by ©pyrose2que0nc1ing 2of coLnsaensnus dseqeuesnces Bandi ousinsg csubiseetsnof cpreobe.s included in the Illumina Infinium h umanMethylation27 Beadc hip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNa methylation. a dditionally, we compare pyrosequencing results for repetitive elements to average DNa methylation of c pG islaDndso,as asseossetd n bdyarray is tprrobiebscluassifieed t .into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNa methylation. c orrelation of DNa methylation suggests an association between LINE-1 and weak c pG island DNa methylation in some of the tissues examined. We caution, however, that LINE-1, a lu and c pG island DNa methylation are distinct measures of dispersed DNa methylation and one should not be used in lieu of another. a nalysis of DNa methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways. Introduction The theory that the environment can affect gene expression has gained much attention in recent years. This has led to widespread interest in assessing the effects of environmental exposures on epi- genetic changes, including DNA methylation, at targeted loci as well as across the genome. Repetitive elements (REs) have been used as a surrogate to measure “global” changes in DNA meth- ylation1 associated with diverse factors including nutrition,2 pol- lutants3,4 and toxin exposure.5 Several approaches can be used to study the same families of REs, and each method may yield varying results depending on the population of elements that is analyzed. The degree to which RE DNA methylation relates to DNA methylation at other genomic sequences and how differ- ent measures are influenced by biological and technical variables remains unclear. Although there are numerous methods for measuring DNA methylation across the genome, one of the most widely used is high *Correspondence to: Wendy P. Robinson; Email: wrobinson@cfri.ca Submitted: 02/22/12; Revised: 03/27/12; Accepted: 03/30/12 http://dx.doi.org/10.4161/epi.20221 performance liquid chromatography (HPLC). Using HPLC, indi- vidual nucleotides are counted and a total measure of 5-methyl- cytosine (5-mC) content is obtained.6 5-mC-specific antibody kits have been developed as a less expensive and less labor intensive alternative to HPLC.7, 8 While both HPLC and antibody kits pro- vide a measure of average global methylation, the distribution of 5-mCs within the genome cannot be determined with these meth- ods. Alternatively, array-based methods sacrifice some genomic coverage for the ability to detect the specific location of 5-mCs. Methylated DNA immunoprecipitation (MeDIP) captures meth- ylated fragments of DNA with a 5-mC-specific antibody and is used in combination with a microarray for comparison against a differentially labeled control.9 Another array-based method, the Illumina Infinium HumanMethylation27 BeadChip array, allows single-nucleotide resolution of the DNA methylation status of 27578 CpG sites in over 14,000 gene promoters.10 DNA methylation of two RE families, LINE-1 and Alu, has recently been used to assess genome-wide DNA methylation 652 Epigenetics Volume 7 Issue 6