Open Access Research

Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants

Hyang-Min Byun1*, Valeria Motta12, Tommaso Panni3, Pier Alberto Bertazzi2, Pietro Apostoli4, Lifang Hou5 and Andrea A Baccarelli1

Author Affiliations

1 Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA

2 Department of Environmental and Occupational Health, Università degli Studi di Milano and IRCCS Ca’ Granda Maggiore Policlinico Hospital, Milan, Italy

3 Department of Statistics, University of Milano‒Bicocca, Milan, Italy

4 Department of Experimental and Applied Medicine, Occupational Medicine and Industrial Hygiene, University of Brescia, Brescia, Italy

5 Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago 60611, USA

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Particle and Fibre Toxicology 2013, 10:28  doi:10.1186/1743-8977-10-28

Published: 15 July 2013

Abstract

Background

Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants.

Methods

We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies.

Results

High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose–response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‒interaction=0.003) and benzene (p‒interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02).

Conclusions

The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation to airborne pollutants.

Keywords:
Environment; Exposures; DNA methylation; Repetitive elements; Subfamily