Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification
- Robert K. Arthur1,2,
- Lijia Ma2,3,
- Matthew Slattery2,3,4,
- Rebecca F. Spokony2,3,5,
- Alexander Ostapenko2,3,
- Nicolas Nègre2,3,6 and
- Kevin P. White1,2,3,7
- 1Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA;
- 2Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, Illinois 60637, USA;
- 3Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA;
- 4Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, Minnesota 55455, USA;
- 5Department of Natural Sciences, Baruch College, City University of New York, New York 10010, USA;
- 6Université de Montpellier 2 and INRA, UMR1333 DGIMI, F-34095 Montpellier, France
Abstract
Histone modifications are critical for the regulation of gene expression, cell type specification, and differentiation. However, evolutionary patterns of key modifications that regulate gene expression in differentiating organisms have not been examined. Here we mapped the genomic locations of the repressive mark histone 3 lysine 27 trimethylation (H3K27me3) in four species of Drosophila, and compared these patterns to those in C. elegans. We found that patterns of H3K27me3 are highly conserved across species, but conservation is substantially weaker among duplicated genes. We further discovered that retropositions are associated with greater evolutionary changes in H3K27me3 and gene expression than tandem duplications, indicating that local chromatin constraints influence duplicated gene evolution. These changes are also associated with concomitant evolution of gene expression. Our findings reveal the strong conservation of genomic architecture governed by an epigenetic mark across distantly related species and the importance of gene duplication in generating novel H3K27me3 profiles.
Footnotes
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↵7 Corresponding author
E-mail kpwhite{at}uchicago.edu
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.162008.113.
Freely available online through the Genome Research Open Access option.
- Received June 12, 2013.
- Accepted January 17, 2014.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0.
