Guidelines for the nomenclature of genetic elements in tunicate genomes

Stolfi, Alberto; Sasakura, Yasunori; Chalopin, Domitille; Satou, Yutaka; Christiaen, Lionel; Dantec, Christelle Le; Endo, Toshinori; Naville, Magali; Nishida, Hiroki; Swalla, Billie J.; Volff, Jean Nicolas; Voskoboynik, Ayelet; Dauga, Delphine; Lemaire, Patrick

doi:10.1002/dvg.22822

Cited by 62 publications

(73 citation statements)

References 28 publications

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“…Whole-mount in situ hybridization was performed as previously described (Ikuta and Saiga, 2007;Satou, 1999). Gene identifiers are shown in Table S1, according to the nomenclature rule of this animal (Stolfi et al, 2015b).…”

Section: Methodsmentioning

confidence: 99%

“…As explained above, there are two neural lineages in the Ciona embryo. The anterior neural lineage produces the brain and palps, in which sensory neurons are differentiated; Zic-r.b (formerly ZicL, renamed according to a recently published nomenclature rule; Stolfi et al, 2015b) and Six3/6 mark the brain lineage, and Foxc marks the palp lineages Imai et al, 2006;Wagner and Levine, 2012). In late gastrulae injected with the lacZ MO, Zic-r.b and Six3/6 were expressed normally in cells with the brain fate ( Fig.…”

Section: Introductionmentioning

confidence: 99%

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Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

et al. 2016

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Epidermis and neural tissues differentiate from the ectoderm in animal embryos. Although epidermal fate is thought to be induced in vertebrate embryos, embryological evidence has indicated that no intercellular interactions during early stages are required for epidermal fate in ascidian embryos. To test this hypothesis, we determined the gene regulatory circuits for epidermal and neural specification in the ascidian embryo. These circuits started with Tfap2-r.b and Sox1/2/3, which are expressed in the ectodermal lineage immediately after zygotic genome activation. Tfap2-r.b expression was diminished in the neural lineages upon activation of fibroblast growth factor signaling, which is known to induce neural fate, and sustained only in the epidermal lineage. Tfap2-r. b specified the epidermal fate cooperatively with Dlx

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

et al. 2016

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“…1B). ASMFs give rise to Mrf+ differentiating muscle cells as well as Bhlh-tun1+/Mrf-stem-like muscle precursors, which activate the orphan and tunicate-specific helix-loop-helix transcription factor Bhlh-tun1 (renamed after orphan-bhlh-1 following Stolfi et al, 2015), and cease to express Mrf in response to Notch-mediated activation of the conserved transcriptional repressor of the Hairy/Enhancer-of-split family, Hes-b (Fig. 1B).…”

Section: Introductionmentioning

confidence: 99%

Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages

Tolkin

Christiaen

2016

Development

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Skeletal muscles arise from diverse embryonic origins in vertebrates, yet converge on extensively shared regulatory programs that require muscle regulatory factor (MRF)-family genes. Myogenesis in the tail of the simple chordate Ciona exhibits a similar reliance on its single MRF-family gene, and diverse mechanisms activate Ci-Mrf. Here, we show that myogenesis in the atrial siphon muscles (ASMs) and oral siphon muscles (OSMs), which control the exhalant and inhalant siphons, respectively, also requires Mrf. We characterize the ontogeny of OSM progenitors and compare the molecular basis of Mrf activation in OSM versus ASM. In both muscle types, Ebf and Tbx1/10 are expressed and function upstream of Mrf. However, we demonstrate that regulatory relationships between Tbx1/10, Ebf and Mrf differ between the OSM and ASM lineages. We propose that Tbx1, Ebf and Mrf homologs form an ancient conserved regulatory state for pharyngeal muscle specification, whereas their regulatory relationships might be more evolutionarily variable.

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“…In embryos of the invertebrate chordate Ciona intestinalis, Foxa.a, Zic-r.b (formerly ZicL, renamed according to a recently published nomenclature rule; Stolfi et al, 2015) and Fgf signaling are used for specifying the developmental fates of the notochord and the brain. In the anterior (A-line) notochord lineage, Foxa.a and Zicr.b are expressed simultaneously in the same cells from the 32-cell to the gastrula stage (Imai et al, 2002a(Imai et al, , 2004.…”

Section: Introductionmentioning

confidence: 99%

Differential temporal control of Foxa.a and Zic-r.b specifies brain versus notochord fate in the ascidian embryo

Ikeda

Satou

2016

Development

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In embryos of an invertebrate chordate, Ciona intestinalis, two transcription factors, Foxa.a and Zic-r.b, are required for specification of the brain and the notochord, which are derived from distinct cell lineages. In the brain lineage, Foxa.a and Zic-r.b are expressed with no temporal overlap. In the notochord lineage, Foxa.a and Zic-r.b are expressed simultaneously. In the present study, we found that the temporally non-overlapping expression of Foxa.a and Zic-r.b in the brain lineage was regulated by three repressors: Prdm1-r.a (formerly called BZ1), Prdm1-r.b (BZ2) and Hes.a. In morphant embryos of these three repressor genes, Foxa.a expression was not terminated at the normal time, and Zic-r.b was precociously expressed. Consequently, Foxa.a and Zic-r.b were expressed simultaneously, which led to ectopic activation of Brachyury and its downstream pathways for notochord differentiation. Thus, temporal controls by transcriptional repressors are essential for specification of the two distinct fates of brain and notochord by Foxa.a and Zic-r.b. Such a mechanism might enable the repeated use of a limited repertoire of transcription factors in developmental gene regulatory networks.

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Guidelines for the nomenclature of genetic elements in tunicate genomes

Cited by 62 publications

References 28 publications

Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages

Differential temporal control of Foxa.a and Zic-r.b specifies brain versus notochord fate in the ascidian embryo

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