DNA methylation and evolution of duplicate genes.

Bibliographic Collection: 
APE
Publication Type: Journal Article
Authors: Keller, Thomas E; Yi, Soojin V
Year of Publication: 2014
Journal: Proc Natl Acad Sci U S A
Volume: 111
Issue: 16
Pagination: 5932-7
Date Published: 2014 Apr 22
Publication Language: eng
ISSN: 1091-6490
Keywords: Chromatin, DNA Methylation, Evolution, Molecular, Gene Expression Regulation, Genes, Duplicate, Genetic Variation, Humans, Nucleotide Motifs, Promoter Regions, Genetic, Time Factors
Abstract:

The evolutionary mechanisms underlying duplicate gene maintenance and divergence remain highly debated. Epigenetic modifications, such as DNA methylation, may contribute to duplicate gene evolution by facilitating tissue-specific regulation. However, the role of epigenetic divergence on duplicate gene evolution remains little understood. Here we show, using comprehensive data across 10 diverse human tissues, that DNA methylation plays critical roles in several aspects of duplicate gene evolution. We first demonstrate that duplicate genes are initially heavily methylated, before gradually losing DNA methylation as they age. Within each pair, DNA methylation divergence between duplicate partners increases with evolutionary age. Importantly, tissue-specific DNA methylation of duplicates correlates with tissue-specific expression, implicating DNA methylation as a causative factor for functional divergence of duplicate genes. These patterns are apparent in promoters but not in gene bodies, in accord with the complex relationship between gene-body DNA methylation and transcription. Remarkably, many duplicate gene pairs exhibit consistent division of DNA methylation across multiple, divergent tissues: For the majority (73%) of duplicate gene pairs, one partner is always hypermethylated compared with the other. This is indicative of a common underlying determinant of DNA methylation. The division of DNA methylation is also consistent with their chromatin accessibility profiles. Moreover, at least two sequence motifs known to interact with the Sp1 transcription factor mark promoters of more hypomethylated duplicate partners. These results demonstrate critical roles of DNA methylation, as well as complex interaction between genome and epigenome, on duplicate gene evolution.

DOI: 10.1073/pnas.1321420111
Alternate Journal: Proc. Natl. Acad. Sci. U.S.A.