Gene body methylation patterns in Daphnia are associated with gene family size

Environmental factors including chemicals can induce changes that can affect the offspring of exposed animals for multiple generations. These effects are referred to as transgenerational effects and are often the consequence of changes in DNA methylation. Within this paper, we have focused on understanding the role of DNA methylation by studying the patterns of methylation at the genomic level in two Daphnia species. We observed that these patterns are not random but are associated with the size of the gene family. This suggest that DNA methylation may help regulate the function and size of gene families which in turn may play an important role in stress response.

Scientific abstract

The relation between gene body methylation and gene function remains elusive. Yet, our understanding of this relationship can contribute significant knowledge on how and why organisms target specific gene bodies for methylation. Here, we studied gene body methylation patterns in two Daphnia species. We observed both highly methylated genes and genes devoid of methylation in a background of low global methylation levels. A small but highly significant number of genes was highly methylated in both species. Remarkably, functional analyses indicate that variation in methylation within and between Daphnia species is primarily targeted to small gene families whereas large gene families tend to lack variation. The degree of sequence similarity could not explain the observed pattern. Furthermore, a significant negative correlation between gene family size and the degree of methylation suggests that gene body methylation may help regulate gene family expansion and functional diversification of gene families leading to phenotypic variation.

Full reference (link)

Asselman J, De Coninck DIM, Pfrender ME, De Schamphelaere KAC. 2016. Gene body methylation patterns in Daphnia are associated with gene family size. Genome Biology and Evolution 8 (4), Accepted article.