Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians

被引:24
|
作者
Madgwick, Alicia [1 ]
Silvia Magri, Marta [2 ]
Dantec, Christelle [1 ]
Gailly, Damien [1 ]
Fiuza, Ulla-Maj [1 ,4 ]
Guignard, Leo [3 ]
Hettinger, Sabrina [1 ]
Luis Gomez-Skarmeta, Jose [2 ]
Lemaire, Patrick [1 ]
机构
[1] Univ Montpellier, Ctr Rech Biol Cellulaire Montpellier CRBM, CNRS, Montpellier, France
[2] Univ Pablo de Olavide, CSIC, CABD, Seville, Spain
[3] Howard Hughes Med Inst, Janelia Res Campus,19700 Helix Dr, Ashburn, VA USA
[4] European Mol Biol Lab, Cell Biol & Biophys Unit, Heidelberg, Germany
基金
欧洲研究理事会;
关键词
Ascidians; Embryo; Chromatin; Enhancer; Transcription; Evolution; DEVELOPMENTAL BIOLOGY; FUNCTIONAL-ANALYSIS; SHADOW ENHANCERS; GENE-EXPRESSION; OPEN CHROMATIN; BETA-CATENIN; TISSUE; ROBUSTNESS; SPECIFICATION; FLEXIBILITY;
D O I
10.1016/j.ydbio.2019.01.003
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.
引用
收藏
页码:71 / 87
页数:17
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