Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines

Human Genomics
Itsuki TaniguchiKen Yamamoto

Abstract

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. 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 islan...Continue Reading

References

Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
May 13, 2008·The American Journal of Clinical Nutrition·Akiko NanriSuminori Kono
May 15, 2009·Epigenetics : Official Journal of the DNA Methylation Society·Eoin P BrennanDavid A Savage
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Feb 10, 2011·Epigenetics : Official Journal of the DNA Methylation Society·Hiroko SugawaraTadafumi Kato
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Methods Mentioned

BETA
chip
PCA

Software Mentioned

GenomeStudio
Power
glm

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