RRC ID 64108
著者 Taniguchi I, Iwaya C, Ohnaka K, Shibata H, Yamamoto K.
タイトル Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines.
ジャーナル Hum Genomics
Abstract BACKGROUND:Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types of commonly used DNA bioresources, peripheral blood cells (PBCs) and EBV-transformed lymphoblastoid cell lines (LCLs), which are available for genetic epidemiological studies. Therefore, to extend our knowledge of the difference in DNA methylation status between LCLs and PBCs is important in human population studies that use these DNA sources to elucidate the epigenetic risks for multifactorial diseases. We analyzed the methylation status of the autosomes for 192 and 92 DNA samples that were obtained from PBCs and LCLs, respectively, using a human methylation 450 K array. After excluding SNP-associated methylation sites and low-call sites, 400,240 sites were subjected to analysis using a generalized linear model with cell type, sex, and age as the independent variables.
RESULTS:We found that the large proportion of sites showed lower methylation levels in LCLs compared with PBCs, which is consistent with previous reports. We also found that significantly different methylation sites tend to be located on the outside of the CpG island and in a region relatively far from the transcription start site. Additionally, we observed that the methylation change of the sites in the low-CpG promoter region was remarkable. Finally, it was shown that the correlation between the chronological age and ageing-associated methylation sites in ELOVL2 and FHL2 in the LCLs was weaker than that in the PBCs.
CONCLUSIONS:The methylation levels of highly methylated sites of the low-CpG-density promoters in PBCs decreased in the LCLs, suggesting that the methylation sites located in low-CpG-density promoters could be sensitive to demethylation in LCLs. Despite being generated from a single cell type, LCLs may not always be a proxy for DNA from PBCs in studies of epigenome-wide analysis attempting to elucidate the role of epigenetic change in disease risks.
巻・号 11(1)
ページ 8
公開日 2017-5-12
DOI 10.1186/s40246-017-0106-6
PII 10.1186/s40246-017-0106-6
PMID 28499412
PMC PMC5429538
MeSH Acetyltransferases / genetics Aging* Blood Cells / metabolism Cell Line, Transformed CpG Islands* DNA Methylation* Fatty Acid Elongases Genome-Wide Association Study* Humans LIM-Homeodomain Proteins / genetics Lymphocyte Activation Muscle Proteins / genetics Transcription Factors / genetics
IF 3.351
リソース情報
ヒト・動物細胞 HEV0011 HEV0012 HEV0013 HEV0019 HEV0022 HEV0023 HEV0024 HEV0031 HEV0032 HEV0035 HEV0036 HEV0037 HEV0038 HEV0039 HEV0040 HEV0041 HEV0042 HEV0043 HEV0045 HEV0048 HEV0049 HEV0050 HEV0051 HEV0052 HEV0058 HEV0063 HEV0067 HEV0073 HEV0034 HEV0496 HEV0455 HEV0370 HEV0315 HEV0288 HEV0230 HEV0224 HEV0091 HEV0070 HEV0068 HEV0066 HEV0057 HEV0055 HEV0047 HEV0046