Research

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

Nicole YP Souren^123*, Pavlo Lutsik¹, Gilles Gasparoni¹, Sascha Tierling¹, Jasmin Gries¹, Matthias Riemenschneider⁴, Jean-Pierre Fryns⁵, Catherine Derom⁵, Maurice P Zeegers²³⁶ and Jörn Walter^1*

• * Corresponding authors: Nicole YP Souren nicole.souren@uni-saarland.de - Jörn Walter j.walter@mx.uni-saarland.de

Author Affiliations

¹ Laboratory of EpiGenetics, FR 8.3 Life Sciences, Saarland University, Saarbrücken, 66123, Saarland, Germany

² Department of Genetics and Cell Biology, Maastricht University, Maastricht, 6200 MD, Limburg, The Netherlands

³ Nutrition and Toxicology Research Institute Maastricht (NUTRIM), Maastricht University, Maastricht, 6200 MD, Limburg, The Netherlands

⁴ Department of Psychiatry and Psychotherapy, Saarland University Hospital, Homburg, 66424, Saarland, Germany

⁵ Department of Human Genetics, University Hospital Gasthuisberg, Katholieke Universiteit Leuven, Leuven, B-3000, Vlaams-Brabant, Belgium

⁶ Unit of Urologic and Genetic Epidemiology, Department of Public Health and Epidemiology, University of Birmingham, Birmingham, B15 2TT, West Midlands, UK

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Genome Biology 2013, 14:R44 doi:10.1186/gb-2013-14-5-r44

Published: 26 May 2013

Abstract

Background

Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes.

Results

Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences.

Conclusions

Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.