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Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis
- Source :
- Genome Biology, Genome Biology, 13(10), Genome Biology 13 (2012) 10
- Publication Year :
- 2012
-
Abstract
- Background: Following 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. Results: Paralogous 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. Conclusions: After 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.
- Subjects :
- Epigenomics
Arabidopsis
macromolecular substances
Biology
yeast
embryonic stem-cells
developmental regulators
Epigenesis, Genetic
Evolution, Molecular
Histones
BIOS Applied Bioinformatics
Gene Expression Regulation, Plant
Gene Duplication
Gene duplication
evolution
Coding region
thaliana
Epigenetics
Gene
Plant Proteins
Genetics
phylogenetic analysis
Research
fungi
DNA Methylation
gene-expression
proteins
histone h3
Regulatory sequence
DNA methylation
polycomb
Functional divergence
Genome, Plant
Subjects
Details
- ISSN :
- 1474760X and 14747596
- Volume :
- 13
- Issue :
- 10
- Database :
- OpenAIRE
- Journal :
- Genome biology
- Accession number :
- edsair.doi.dedup.....ea8183bf4eedfb0a0b2123b181c0ad40