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

Madgwick, Alicia; Magri, Marta Silvia; Dantec, Christelle Le; Gailly, Damien; Fiúza, Ulla-Maj; Guignard, Léo; Hettinger, Sabrina; Gómez-Skármeta, José Luis; Lemaire, Patrick

doi:10.1016/j.ydbio.2019.01.003

Cited by 33 publications

(46 citation statements)

References 71 publications

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“…We also provide an example of using ATAC-seq for the identification of CREs controlled by the Wnt signaling pathway. For that, we used recently generated ATAC-seq libraries from Ciona embryos at the 112-cell stage as a control and embryos treated with 4 µM CHIR-99021, a GSK3 inhibitor acting as an activator of the canonical Wnt pathway (Madgwick et al, 2019). Here, we showed further bioinformatic analysis that allows the identification of differential ATAC-seq peaks between control and treated embryos, the TFBMs enrichment in those peaks, and the GO of the associated genes.…”

Section: Anticipated Resultsmentioning

confidence: 99%

“…Among the new available techniques, we selected the Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq; Buenrostro et al, 2013). ATAC-seq is a simple, easy-to-use, and efficient technique for identification of CREs actively bound by TFs in most tissues and organs of different species (Bogdanović et al, 2016;Sebé-Pedrós et al, 2016;Kittelmann et al, 2018;Marlétaz et al, 2018;Ruiz et al, 2018;Madgwick et al, 2019). The assay is based on the hyperactive Tn5 transposase, which preferentially integrates into open chromatin regions, where it cuts DNA into fragments and simultaneously attaches sequencing Illumina adapters to the fragment ends, facilitating the direct construction of the sequencing library ( Figure 1A).…”

Section: Introductionmentioning

confidence: 99%

“…Here, we provide a step-by-step protocol with the aim of unifying species-specific procedures recently published (Marlétaz et al, 2018;Madgwick et al, 2019). We also provide detailed information about the handling of embryos, such as in vitro fertilization, and about how to obtain the optimal cell lysates specific for each organism.…”

Section: Introductionmentioning

confidence: 99%

“…pathways. To demonstrate the robustness of our analysis, we used recently published ATAC-seq data from wild-type (wt) Ciona embryos at the 112-cell stage and embryos treated with CHIR-99021 (Madgwick et al, 2019), a pharmacological activator of the Wnt/β-catenin pathway (Naujok et al, 2014;Wu et al, 2015). This pathway has an ancestral function during primary body axis formation in both bilaterians and non-bilaterians (Petersen and Reddien, 2009;Imai et al, 2000;Creyghton et al, 2010;Loh et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos

Magri

Jiménez-Gancedo

Bertrand

et al. 2020

Front. Cell Dev. Biol.

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Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatiotemporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to understand how evolution operates through development. The Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq) is a powerful technique for the study of CREs that takes advantage of Tn5 transposase activity. Starting from fewer than 10 5 cells, in a 1-day procedure, it is possible to detect, at a genome-wide level, CREs located in open chromatin regions with high resolution. Here, we describe a detailed step-by-step ATAC-seq protocol for invertebrate chordate marine embryos. We have successfully applied this technique to amphioxus and two species of tunicate embryos. We also show an easy workflow to analyze data generated with this technique. Moreover, we point out that this method and our bioinformatic pipeline are efficient to detect CREs associated with Wnt signaling pathway by simply using embryos treated with a drug that perturbs this pathway. This approach can be extended to other signaling pathways and also to embryo mutants for critical genes. Our results therefore demonstrate the power of ATAC-seq for the identification of CREs that play essential functions during animal development in a wide range of invertebrate or vertebrate animals.

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Section: Anticipated Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos

Magri

Jiménez-Gancedo

Bertrand

et al. 2020

Front. Cell Dev. Biol.

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“…In this respect, ascidians are one of the most studied biological systems due to their phylogenetic position, which makes them a particularly useful model for studying the evolutionary events which occurred during the invertebrate-vertebrate transition, leading to the appearance of adaptive immunity characterized by receptor diversification through somatic recombination [3]. Furthermore, the ascidian Ciona robusta (formerly Ciona intestinalis type A) [4] was the first invertebrate chordate to have its genome sequenced, allowing for the analysis of developmental mechanisms, genome-wide gene regulatory networks, epigenetic regulatory mechanisms and gene expression profiles at single-cell resolution [5][6][7][8]. In this scenario, Ciona robusta has been extensively utilized to study inflammatory response after challenge with foreign agents, such as the injection of erythrocytes [9,10], proteins [11] and LPS [12] into the tunic and, in particular, into the pharynx, which is considered the immunocompetent organ [13].…”

Section: Introductionmentioning

confidence: 99%

Identification of an LPS-Induced Chemo-Attractive Peptide from Ciona robusta

Longo

Martorana

et al. 2020

Marine Drugs

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Background: Previously published work has demonstrated that the LPS injection of Ciona robusta leads to the overexpression of a truncated form of an immune-related mRNA (C8short) by means of Ciona robusta (CR) alternative polyadenylation (APA) (CR-APA). Methods: The 3D structure of the C8short-derived Ciona robusta chemo-attractive peptide (CrCP) was evaluated by homology modeling. The biological activity of the CrCP was studied in vitro using a primary human dermal cell line (HuDe). Real-Time PCR was used to investigate the expression levels of genes involved in cell motility. NF-κB signaling was studied by western blotting. Results: In silico modeling showed that CrCP displayed structural characteristics already reported for a short domain of the vertebrate CRK gene, suggesting its possible involvement in cell migration mechanisms. In vitro assays demonstrated that CrCP was capable of inducing the motility of HuDe cells in both wound healing and chemo-attractive experiments. qPCR demonstrated the capability of CrCP to modulate the expression of the matrix metalloproteinase-7 (MMP-7) and E-cadherin genes. Finally, western blot analysis demonstrated that treatment with CrCP induced activation of the NF-κB signaling pathway. Conclusion: Our results describe the characterization of the 3D structure and chemo-attractive activity of an LPS-induced CrCP peptide from Ciona robusta.

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