Nodal coordinates the anterior-posterior patterning of germ layers and induces head formation in zebrafish explants.
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ABSTRACT:
PROVIDER: PRJNA913420 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22797023_1.fastq.gz | Fastqsanger.gz | |||
| SRR22797023_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To investingate cell types in wild-type zebrafish explants. Methods: Wild-type explants (injected with phenol red) were harvested at 10hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 9,968 single-cell transcriptomes were collected after stringent quality control measures. Conclusions: 6 Cell types were identified, wild-type explants mainly contains the anterior neural ectoderm and epidermis at 10 hpf.
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Project description:Purpose: To construct cell landscape of graded Nodal signaling in zebrafish explants. Methods: Nodal injected explants (injected with 10pg ndr2 mRNA) were harvested at 4hpf, 5hpf, 6hpf, 8hpf, 10hpf, 24hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v2 (10x Genomics, PN-120237) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 42,317 single-cell transcriptomes were collected after stringent quality control measures. Conclusions: 19 Cell types from 6 developmental stages were identified, Nodal explant mainly contains the axial mesoderm (prechordal plate and notochord) and anterior-posterior patterned head structures.
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Project description:Purpose: To identify nodal downsream target genes Methods: 0pg, 2pg, 6pg or 10pg ndr2 mRNA injected explants and 10 pg ndr2 mRNA injected plus Cycloheximide (CHX) treated explants were collected at 4hpf, 5hpf and 6hpf for bulk RNA-seq Results: We found 105 Nodal targets (p_value <0.05, padj < 0.1, log2 fold change >= 1) Conclusions: 105 Nodal targets were identified
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Project description:We report RNA-sequencing from zebrafish explants generated from embryos injected with mRNA encoding the Nodal ligand ndr2 (N), constitutively active Nodal receptor CA-acvr1b* (T), and uninjected (U) controls. Explants of all 3 conditions were compared at each of 7 developmental stages: sphere (SR), 30% epiboly (30), 50% epiboly (50), shield (SH), 75% epiboly (75), 90% epiboly (90), and 2-somite (2S) (corresponding to 4, 4.7, 5.3, 6, 8, 9, and 11 hours post fertilization, respectively).
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Project description:Single cell response landscape of graded Nodal signaling in zebrafish explants
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Project description:The anterior-posterior axis of the mammalian embryo is laid down by the anterior visceral endoderm (AVE), an extraembryonic signaling center that is specified within the visceral endoderm. Current models posit that AVE differentiation is promoted globally by epiblast-derived Nodal signals, and spatially restricted by a BMP gradient established by the extraembryonic ectoderm. Here, we report spatially restricted AVE differentiation in bilayered embryo-like aggregates made from mouse embryonic stem cells that lack an extraembryonic ectoderm. Notably, clusters of AVE cells also form in pure visceral endoderm cultures upon activation of Nodal signaling, indicating that tissue-intrinsic factors can restrict AVE differentiation. We identify β-catenin activity as a tissue-intrinsic factor that antagonizes AVE-inducing Nodal signals. Together, our results show how an AVE-like population can arise through interactions between epiblast and visceral endoderm alone. This mechanism may be a flexible solution for axis patterning in a wide range of embryo geometries, and provide robustness to axis patterning when coupled with signal gradients.
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Project description:Mammalian primordial germ cells (PGCs) migrate asynchronously through the embryonic hindgut and dorsal mesentery to reach the gonads. To characterize transcriptional heterogeneity of migrating PGCs and their niches, we performed single-cell RNA sequencing of 13,262 mouse PGCs and 7,868 surrounding somatic cells during migration (E9.5, E10.5, E11.5) and in anterior versus posterior locations to enrich for leading and lagging migrants. Analysis of PGCs by position revealed dynamic gene expression changes between faster or earlier migrants in the anterior and slower or later migrants in the posterior at E9.5. At E10.5, we found that anterior PGCs upregulate Nodal transcriptional targets including Lefty1/2 and validated this LEFTY1/2 upregulation via whole-mount immunofluorescence staining. This positional and temporal atlas of mouse PGCs supports the idea that niche interactions along the migratory route elicit changes in proliferation, actin dynamics, pluripotency and epigenetic reprogramming.
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Project description:In Xenopus, establishment of the anterior-posterior axis involves two key signalling pathways, canonical Wnt and Nodal-related TGF-β. There are also a number of transcription factors that feedback upon these pathways. The homeodomain protein Hex, an early marker of anterior positional information, acts as a transcriptional repressor suppressing induction and propagation of the Spemman organiser while specifying anterior identity. We show that Hex promotes anterior identity by amplifying the activity of canonical Wnt signalling. Hex exerts this activity by inhibiting the expression of Tle-4, a member of the Groucho family of transcriptional co-repressors that we identified as a Hex target in embryonic stem (ES) cells and Xenopus embryos. This Hex-mediated enhancement of Wnt signalling results in the up-regulation of the Nieuwkoop centre genes Siamois and Xnr-3 and the subsequent increased expression of the anterior endodermal marker Cerberus and other mesendodermal genes downstream of Wnt signalling. We also identified Nodal as a Hex target in ES cells. We demonstrate that in Xenopus, the Nodal-related genes Xnr-1 and 2, but not 5 and 6, are regulated directly by Hex. The identification of Nodal-related genes as Hex targets explains the ability of Hex to suppress induction and propagation of the organiser. Together these results support a model in which Hex acts early in development to reinforce a Wnt-mediated, Nieuwkoop-like signal to induce anterior endoderm, and later in this tissue to block further propagation of Nodal-related signals. The ability of Hex to regulate the same targets in both Xenopus and mouse implies this model is conserved. Experiment Overall Design: Identification of Hex target genes In Xenopus, the establishment of the anterior-posterior axis involves two key signalling pathways, the canonical Wnt and the Nodal-related TGF-β and a number of transcription factors that feedback upon these pathways. The homeodomain protein Hex, an early marker of anterior positional information, is a transcriptional repressor that suppresses the induction and propagation of the Spemman organiser while specifying anterior identity. Using microarray expression profiling we identified mouse Tle-4 as a Hex target in Embryonic Stem (ES) cells and showed that Tle-4 expression is directly regulated by Hex in Xenopus embryos. We also identified Nodal as a Hex target in ES cells. Taken together these results support a model in which Hex acts early in development to reinforce a Wnt-mediated, Nieuwkoop-like signal to induce anterior endoderm and later in this tissue to block further propagation of Nodal-related signals. The ability of Hex to regulate the same targets in both frog and mouse suggests that this model is conserved.
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