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Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

ABSTRACT: Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

PROVIDER: PRJNA913002 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22764300_1.fastq.gz	Fastqsanger.gz
	SRR22764300_2.fastq.gz	Fastqsanger.gz
	SRR22764301_1.fastq.gz	Fastqsanger.gz
	SRR22764301_2.fastq.gz	Fastqsanger.gz
	SRR22764302_1.fastq.gz	Fastqsanger.gz

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Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation [bulk_RNASeq]

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Here we show maintenance of pluripotency-signature (Nanog/Oct4-PouV/Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-signature is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

2023-03-02 | GSE221125 | GEO

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

Project description:Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

| PRJNA971972 | ENA

Maintenance of pluripotency signature in the entire ectoderm enables potential for neural crest formation

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

2023-08-28 | GSE232432 | GEO

Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

Project description:Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

| PRJNA913168 | ENA

Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

Project description:Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

| PRJNA913169 | ENA

Maintenance of pluripotency in the entire ectoderm enables neural crest formation and challenges dogmatic viewpoints of gastrulation

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like cells is obtained. We monitored transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. Unexpectedly, we find maintenance of undecided Nanog/Oct4-PouV/Klf4-positive pluripotent-like pan-ectodermal stem-cells spanning the entire ectoderm late in the neurulation process with ectodermal patterning completed only at the end of neurulation when pluripotency becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency is found at all axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond “ectodermal-capacity” in chick and mouse embryos.

2023-03-02 | GSE221188 | GEO

Single cell chromatin accessibility profiles of the chick embryonic ectoderm

Project description:The embryonic ectoderm gives rise to four fates: neural, neural crest, placodal and epidermal. The derivatives of these fates give rise to the entire vertebrate nervous system and skin. To explore how these cell fates emerge, we profiled single cell chromatin accessibility in the chick embryonic ectoderm at five developmental timepoints.

2025-12-02 | GSE271424 | GEO

A Molecular Atlas of the Developing Ectoderm Defines Neural, Neural Crest, Placode and Non-Neural Progenitor Identity in Vertebrates.

Project description:During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer, and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal Component Analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes, directly from its transcriptome. In parallel, we use Non-Negative Matrix Factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g. Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.

2017-10-25 | GSE103240 | GEO

MicroRNA miR-196a controls neural crest patterning by repressing immature neural ectoderm programs in Xenopus embryos.

Project description:Neural crest (NC) cells form a multipotent stem cell population specified during neurulation, which undergoes an epithelial-to-mesenchymal transition (EMT) and migrate extensively in the developing embryo, to generate numerous tissues and cell types including the craniofacial skeleton, the peripheral nervous system and pigment cells. The genetic and molecular details of neural crest specification are governed by a complex, yet still partially understood gene regulatory network (NC-GRN). In particular, the precise function of microRNAs in this network remains poorly known. MicroRNAs are short non-coding 20-22 nucleotides long RNAs which control gene expression through post-transcriptional repression. Since miRNA-196a is expressed in the developing neural and neural crest cells of Xenopus laevis embryos we here investigated miR-196a function in the NC-GRN, by knocking-down its expression using antisense morpholinos. Depletion of miR-196a revealed major neural crest and craniofacial phenotypes. These defects were preceded by the perturbed expression of key neural, neural border and neural crest markers such as sox2/3, zic1/3, pax3, sox10 and snail2. Using RNA sequencing of individual neural border and neural crest explants, we have identified a signature of genes up- and down-regulated by miR-196a and validate these with rescue experiments using a miR mimic. We show that Sox10, a predicted target of miR-196a, is lost following morpholino knockdown and rescued upon miR 196a mimic expression. Our study identifies miR-196a as a key actor of early patterning in the dorsal ectoderm, balancing the extent of immature neural plate progenitors with neural crest and placode specification, while also promoting neuron differentiation within the neural plate.

2025-10-13 | GSE289705 | GEO

Maintenance of pluripotency-like signature in the entire ectoderm leads to neural crest stem cell potential.

Project description:The ability of the pluripotent epiblast to contribute progeny to all three germ layers is thought to be lost after gastrulation. The later-forming neural crest (NC) rises from ectoderm and it remains poorly understood how its exceptionally high stem-cell potential to generate mesodermal- and endodermal-like derivatives is obtained. Here, we monitor transcriptional changes from gastrulation to neurulation using single-cell-Multiplex-Spatial-Transcriptomics (scMST) complemented with RNA-sequencing. We show maintenance of pluripotency-like signature (Nanog, Oct4/PouV, Klf4-positive) in undecided pan-ectodermal stem-cells spanning the entire ectoderm late during neurulation with ectodermal patterning completed only at the end of neurulation when the pluripotency-like signature becomes restricted to NC, challenging our understanding of gastrulation. Furthermore, broad ectodermal pluripotency-like signature is found at multiple axial levels unrelated to the NC lineage the cells later commit to, suggesting a general role in stemness enhancement and proposing a mechanism by which the NC acquires its ability to form derivatives beyond "ectodermal-capacity" in chick and mouse embryos.

| S-EPMC10518019 | biostudies-literature

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