ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Brozovic, Matija; Dantec, Christelle Le; Dardaillon, Justine; Dauga, Delphine; Faure, Emmanuel; Gineste, Mathieu; Louis, Alexandra; Naville, Magali; Nitta, Kazuhiro R.; Piette, Jacques; Reeves, Wendy; Scornavacca, Céline; Simion, Paul; Vincentelli, Renaud; Bellec, Maëlle; Aicha, Sameh Ben; Fagotto, Marie; Guéroult-Bellone, Marion; Haeussler, Maximilian; Jacox, Edwin; Lowe, Elijah K.; Mendez, Mickaël; Roberge, Alexis; Stolfi, Alberto; Yokomori, Rui; Brown, C. Titus; Cambillau, Christian; Christiaen, Lionel; Delsuc, Frédéric; Douzery, Emmanuel J. P.; Dumollard, Rémi; Kusakabe, Takehiro; Nakai, Katsunori; Nishida, Hiroki; Satou, Yutaka; Swalla, Billie J.; Veeman, Michael; Volff, Jean‐Nicolas; Lemaire, Patrick

doi:10.1093/nar/gkx1108

Cited by 103 publications

(111 citation statements)

References 56 publications

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“…We associated annotated genes with ATAC-seq peaks located within 10 kb of the TSS or transcription termination site (TTS) ( Fig. S3) 33 , thus assigning median values of 11 peaks per gene, and 3 genes per peak, owing to the compact Ciona genome ( Fig. S3).…”

Section: A Reference Accessome For Cardiopharyngeal Developmentmentioning

confidence: 99%

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Racioppi

Wiechecki

Christiaen

2019

Preprint

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In embryos, lineage-specific profiles of chromatin accessibility control gene expression by modulating transcription, and thus impact multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors’ competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. Combinations of cis-regulatory elements with distinct chromatin accessibility profiles are required to activate of Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that this higher order combinatorial logic increases the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity, thus fostering spatially and temporally accurate fate choices.

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Section: A Reference Accessome For Cardiopharyngeal Developmentmentioning

confidence: 99%

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Racioppi

Wiechecki

Christiaen

2019

Preprint

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“…In light of this exceptional morphogenetic conservation, ascidian genomes are surprisingly divergent (Tsagkogeorga et al, 2012;Stolfi et al, 2014;Brozovic et al, 2018). Both coding and non-coding sequences evolve rapidly within the group.…”

Section: Introductionmentioning

confidence: 99%

“…B) View of the chromatin accessibility (normalized ATAC-seq signal) and RNA expression (normalized RNA-seq signal) around the Matrilin-like gene (Phmamm.CG.MTP2014.S242.g06002). ChIP-seq results H3 K4me3 mark are from(Brozovic et al, 2018). The Conservation track shows the local sequence conservation between Phallusia mammillata and fumigata.…”

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confidence: 99%

“…Relationship between chromatin accessibility and cis-regulatory activity in Ciona andPhallusia. A) Position of previously published Ciona robusta regulatory sequences for Otx(Bertrand et al., 2003) with respect to ATAC-seq signal (orange) at the 64-cell stage, of Gata.a ChIP-seq signal (yellow) at the 32-cell stage(Oda-Ishii et al, 2016) and of H3K4me3 ChIP-seq signal (green) at the early gastrula stage(Brozovic et al, 2018). Published pictures of representative embryos are shown next to the tested constructs.…”

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confidence: 99%

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

Madgwick

Magri

Dantec

et al. 2018

Preprint

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Open chromatin regions are highly enriched for cis-regulatory elements in ascidian early embryos.• Ascidian Clusters of Open Regulatory Elements (COREs) are found next to regulatory genes.• The spatio-temporal dynamics of chromatin accessibility and closest-gene expression are correlated.• Regulatory gene expression, the trans-regulatory code, is conserved between distantly-related Ciona and Phallusia ascidians. • Ascidians show pervasive use of "shadow" enhancers • The position of homologous enhancers can be conserved, despite extensive genome divergence. ABSTRACT 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. Openchromatin 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 transregulatory 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. of chromatin accessibility landscapes and cis-regulatory logic between these species despite extreme sequence divergence.

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“…On these embryos, thanks to their invariant lineage, cells over several generations can be unambiguously named [39,40]. At the 64cell stage, symmetric pairs of cells a7.11, a7.12, a7.13, a7.14, a7.15, a7.16, b7.11, b7.12, b7.13, b7.14, b7.15 and b7.16 were selected, corresponding to cells who will give rise to the embryonic epidermis after fate determination (green cells in Fig.…”

Section: Appendix B: P Mammillata Embryonic Epidermal Cells and Analmentioning

confidence: 99%

Multiscale mechanical model for cell division orientation in developing biological systems

Leggio¹,

Laussu²,

Faure³

et al. 2019

Preprint

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Developing biological structures are highly complex systems, within which a robust and efficient information transfer must happen to coordinate several dynamical processes. Through a reformulation of cytokinesis in terms of its energetic cost, we propose that oriented cell divisions are one mechanism by which cells can read and react to mechanical forces propagating in a tissue even in the absence of cellular strain. This view can at once account for the standard geometrical rules for cell division, as much as the known systematic deviations from them. Our results suggest the existence of a shape-dynamics to cell-division feedback loop, consisting in the competition between local and long-range mechanical signals. The consequences of this competition are explored in simulated tissues and confirmed in vivo during the epidermal morphogenesis of ascidian embryos.

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ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets

Cited by 103 publications

References 56 publications

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

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

Multiscale mechanical model for cell division orientation in developing biological systems

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