Uncovering the DNA methylation landscape in key regulatory regions within the FADS cluster.

Elaheh Rahbar,Carl D Langefeld,Timothy D Howard,James E Hixson,David M Herrington,Floyd H Chilton,Hannah C Ainsworth,Gregory A Hawkins,Rasika Mathias,Michael C Seeds,Susan Sergeant,Ingo Ruczinski,Ludmila Prokunina-Olsson

doi:10.1371/journal.pone.0180903

Abstract

Genetic variants near and within the fatty acid desaturase (FADS) cluster are associated with polyunsaturated fatty acid (PUFA) biosynthesis, levels of several disease biomarkers and risk of human disease. However, determining the functional mechanisms by which these genetic variants impact PUFA levels remains a challenge. Utilizing an Illumina 450K array, we previously reported strong allele-specific methylation (ASM) associations (p = 2.69×10−29) between a single nucleotide polymorphism (SNP) rs174537 and DNA methylation of CpG sites located in the putative enhancer region between FADS1 and FADS2, in human liver tissue. However, this array only featured 20 CpG sites within this 12kb region. To better understand the methylation landscape within this region, we conducted bisulfite sequencing of the region between FADS1 and FADS2. Liver tissues from 50 male subjects (27 European Americans, 23 African Americans) were obtained from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study, and used to ascertain the genotype at rs174537 and methylation status across the region of interest. Associations between rs174537 genotype and methylation status of 136 CpG sites were determined. Age-adjusted linear regressions were used to assess ASM associations with rs174537 genotype. The majority of CpG sites (117 out of 136, 86%) exhibited high levels of methylation with the greatest variability observed at three key regulatory regions–the promoter regions for FADS1 and FADS2 and a putative enhancer site between the two genes. Eight CpG sites within the putative enhancer region displayed significant (FDR p <0.05) ASM associations with rs174537. These data support the concept that both genetic and epigenetic factors regulate PUFA biosynthesis, and raise fundamental questions as to how genetic variants such as rs174537 impact DNA methylation in distant regulatory regions, and ultimately the capacity of tissues to synthesize PUFAs.

Highlights

Polyunsaturated fatty acids (PUFAs) are vital for normal growth and development, serving as key structural components of biological membranes and modulating critical signal transduction events
It is encouraging that the CpG site we identified in the FADS2 promoter region using allele-specific methylation (ASM), for the European American population, was identified by Hoile et al [42] from whole blood samples, suggesting that there is overlap between DNA methylation in liver tissue and circulating blood cells for these specific CpG sites
This in-depth characterization of the region between FADS1 and FADS2 genes revealed eight key CpG sites that were associated with genotype at rs174537

Summary

Introduction

Polyunsaturated fatty acids (PUFAs) are vital for normal growth and development, serving as key structural components of biological membranes and modulating critical signal transduction events. Several common polymorphisms within the FADS gene cluster, including the single nucleotide polymorphism (SNP) rs174537, have been shown to be highly associated with circulating and tissue PUFA levels and PUFA product-to-precursor ratios [9,10,11, 28, 29]. In light of these studies, the conventional paradigm of slow, inefficient and uniform LC-PUFA biosynthesis in humans has been challenged

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