Genomics

Dataset Information

158

Genome-wide DNA methylation profiling reveals epigenetic adaptation of stickleback to sea and freshwater conditions


ABSTRACT: Three-spined stickleback (Gasterosteus aculeatus) represents a convenient model to study microevolution - adaptation  to freshwater environment. While genetic adaptations to freshwater are well-studied, epigenetic adaptations attracted little attention. In this work, we investigated the role of DNA methylation in the adaptation of marine stickleback population to freshwater conditions. DNA methylation profiling was performed in marine and freshwater populations of sticklebacks, as well as in marine sticklebacks placed into freshwater environment and freshwater sticklebacks placed into seawater. For the first time, we demonstrated that genes encoding ion channels kcnd3, cacna1fb, gja3 are differentially methylated between marine and freshwater populations. We also showed that after placing marine stickleback into fresh water, its DNA methylation profile partially converges to the one of a freshwater stickleback. This suggests that immediate epigenetic response to freshwater conditions can be maintained in freshwater population. Interestingly, we observed enhanced epigenetic plasticity in freshwater sticklebacks that may serve as a compensatory regulatory mechanism for the lack of genetic variation in the freshwater population. Some of the regions that were reported previously to be under selection in freshwater populations also show differential methylation. Thus, epigenetic changes might represent a parallel mechanism of adaptation along with genetic selection in freshwater environment. Overall design: The following sample groups were studied: 1) marine sticklebacks kept in marine water, their natural habitat (M@M); 2) freshwater sticklebacks kept in freshwater (F@F); 3) marine sticklebacks incubated in fresh water for 4 days (M@F); 4) freshwater sticklebacks incubated in marine water for 4 days (F@M). In each gruop, 3 individual fish were profiled.

INSTRUMENT(S): Illumina HiSeq 2500 (Gasterosteus aculeatus)

SUBMITTER: Artem V Artemov 

PROVIDER: GSE82310 | GEO | 2017-05-30

SECONDARY ACCESSION(S): PRJNA324599

REPOSITORIES: GEO

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