Passive and active DNA methylation and the interplay with genetic variation in gene regulation

Year: 2013

Type: article

Abstract: DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence and environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, DNA methylation and transcriptome sequencing data in three different cell-types of the GenCord human population cohort. We find that the association between DNA methylation and gene expression variation among individuals are likely due to different mechanisms from those establishing methylation-expression patterns during differentiation. Furthermore, cell-type differential DNA methylation may delineate a platform in which local inter-individual changes may respond to or act in gene regulation. We show that unlike genetic regulatory variation, DNA methylation alone does not significantly drive allele specific expression. Finally, inferred mechanistic relationships using genetic variation as well as correlations with TF abundance reveal both a passive and active role of DNA methylation to regulatory interactions influencing gene expression. DOI:http://dx.doi.org/10.7554/eLife.00523.001.

Source: eLife

DOI: 10.7554/elife.00523

Institutions: University of Geneva, SIB Swiss Institute of Bioinformatics, Institute of Genetics and Genomics in Geneva, Stanford University

Language: English

Topic: Epigenetics and DNA Methylation

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,500

Funders: Louis-Jeantet Foundation, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Université de Genève, European Research Council

OpenAlex ID: W2148187752