Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species.

Autor:	Devens HR; Department of Biology, Duke University, Durham, NC, USA., Davidson PL; Department of Biology, Duke University, Durham, NC, USA., Byrne M; School of Medical Science, The University of Sydney, Sydney, New South Wales, Australia.; School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales, Australia., Wray GA; Department of Biology, Duke University, Durham, NC, USA.; Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
Jazyk:	angličtina
Zdroj:	Molecular biology and evolution [Mol Biol Evol] 2023 Nov 03; Vol. 40 (11).
DOI:	10.1093/molbev/msad222
Abstrakt:	Chromatin accessibility plays an important role in shaping gene expression, yet little is known about the genetic and molecular mechanisms that influence the evolution of chromatin configuration. Both local (cis) and distant (trans) genetic influences can in principle influence chromatin accessibility and are based on distinct molecular mechanisms. We, therefore, sought to characterize the role that each of these plays in altering chromatin accessibility in 2 closely related sea urchin species. Using hybrids of Heliocidaris erythrogramma and Heliocidaris tuberculata, and adapting a statistical framework previously developed for the analysis of cis and trans influences on the transcriptome, we examined how these mechanisms shape the regulatory landscape at 3 important developmental stages, and compared our results to similar analyses of the transcriptome. We found extensive cis- and trans-based influences on evolutionary changes in chromatin, with cis effects generally larger in effect. Evolutionary changes in accessibility and gene expression are correlated, especially when expression has a local genetic basis. Maternal influences appear to have more of an effect on chromatin accessibility than on gene expression, persisting well past the maternal-to-zygotic transition. Chromatin accessibility near gene regulatory network genes appears to be distinctly regulated, with trans factors appearing to play an outsized role in the configuration of chromatin near these genes. Together, our results represent the first attempt to quantify cis and trans influences on evolutionary divergence in chromatin configuration in an outbred natural study system and suggest that chromatin regulation is more genetically complex than was previously appreciated. Competing Interests: Conflict of interest statement. None declared. (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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