Abstract
BackgroundFollowing gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, including protein function. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is gene-specific. Because of this and a well-annotated recent whole-genome duplication, Arabidopsis thaliana is uniquely suited for studying the potential association of H3K27me3 with the evolutionary fate of genes.ResultsParalogous pairs with H3K27me3 show the highest coding sequence divergence, which can be explained by their low expression levels. Interestingly, they also show the highest similarity in expression patterns and upstream regulatory regions, while paralogous pairs where only one gene is an H3K27me3 target show the highest divergence in expression patterns and upstream regulatory sequence. These trends in divergence of expression and upstream regions are especially pronounced for transcription factors.ConclusionsAfter duplication, a histone modification can be associated with a particular fate of paralogs: H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence. Our results show that H3K27me3 constrains expression divergence after duplication. Moreover, its association with higher conservation of upstream regions provides a potential mechanism for the conserved H3K27me3 targeting of the paralogs.
Highlights
Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns
After a whole-genome duplication (WGD), a histone modification is associated with slower divergence of expression patterns
Rate of expression divergence is associated with H3K27me3 To examine the correlation of H3K27me3 with the evolutionary fate of genes, we focused on paralogs arising from the most recent (3R or a) A. thaliana WGD
Summary
Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is genespecific. H3K27me marks long multi-gene regions of DNA while in plants it exhibits gene-specific positioning, starting at promoters and extending to the 3’ end of the transcribed region, with a bias towards the 5’ end of the gene [3] It is deposited by Polycomb Repressive Complex 2 (PRC2) [4]. Plants have several PRC2 complexes [5] that share
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