Ancestry dependent DNA methylation and influence of maternal nutrition

PloS One
Khyobeni MozhuiFrances A Tylavsky

Abstract

There is extensive variation in DNA methylation between individuals and ethnic groups. These differences arise from a combination of genetic and non-genetic influences and potential modifiers include nutritional cues, early life experience, and social and physical environments. Here we compare genome-wide DNA methylation in neonatal cord blood from African American (AA; N = 112) and European American (EA; N = 91) participants of the CANDLE Study (Conditions Affecting Neurocognitive Development and Learning in Early Childhood). Our goal is to determine if there are replicable ancestry-specific methylation patterns that may implicate risk factors for diseases that have differential prevalence between populations. To identify the most robust ancestry-specific CpG sites, we replicate our results in lymphoblastoid cell lines from Yoruba African and CEPH European panels of HapMap. We also evaluate the influence of maternal nutrition--specifically, plasma levels of vitamin D and folate during pregnancy--on methylation in newborns. We define stable ancestry-dependent methylation of genes that include tumor suppressors and cell cycle regulators (e.g., APC, BRCA1, MCC). Overall, there is lower global methylation in African ancestral grou...Continue Reading

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Citations

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Datasets Mentioned

BETA
GSE64940
GSE35069

Methods Mentioned

BETA
nucleic acid purification

Software Mentioned

WGCNA R package
COMBAT R package
DAVID
R
WGCNA
Illumina GenomeStudio
CANDLE
JMP Statistics ( JMP Pro
GenomeStudio

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