Targets of Pax3 and Zic1 in neural crest and cranial placode progenitors
Ontology highlight
ABSTRACT:
ORGANISM(S): Xenopus laevis
PROVIDER: GSE68546 | GEO | 2015/05/06
SECONDARY ACCESSION(S): PRJNA283107
REPOSITORIES: GEO
Similar Datasets
Project description:The transcription factors Pax3 and Zic1 are among the earliest genes activated at the neural plate border. Pax3 and Zic1 in combination promote neural crest fate, while Zic1 alone regulate cranial placode progenitor formation. We used microarrays to identify the global repertoire of genes activated by these facors individually or in combination to gain insights into the molecular mechanisms underlying cell fate decision at the neural plate border. Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding Pax3GR and Zic1GR , the hormone-inducible version of Pax3 and Zic1, alone or in combination. At the blastula stage (stage 9), animal cap explants were dissected and cultured for 8 hours in the presence of dexamethasone. A glucocorticoid receptor (GR) mRNA was also injected as negative control.
2015-05-06 | E-GEOD-68546 | biostudies-arrayexpress
Project description:Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network. The transcriptomes of neural border samples (stage 14 and 18) were compared to the transcriptome of anterior neural fold (stage 18), early neural plate (stage 12), and animal cap explants (stage14) to identify genes expressed specifically in neural border samples. Tissue samples from Xenopus laevis embryos were dissected, then total RNA was extracted and hybridized on Affymetrix microarrays. Selected tissue samples encompass the neural crest at different stages of its induction (early neural plate at stage 12, neural border at stage 14, neural border at stage 18), as well as reference tissues (anterior neural fold at stage 18, a tissue that belongs to the neural border but does not produce neural crest, and animal cap grown until stage 14 that differentiates into epidermis).
2013-12-28 | E-GEOD-53678 | biostudies-arrayexpress
Project description:Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network. The transcriptomes of neural border samples (stage 14 and 18) were compared to the transcriptome of anterior neural fold (stage 18), early neural plate (stage 12), and animal cap explants (stage14) to identify genes expressed specifically in neural border samples.
2013-12-28 | GSE53678 | GEO
Project description:Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network. Transcriptomes of animal caps overexpressing Pax3+/-Zic1 in the presence/absence of cycloheximide, a translation inhibitor, were compared to control animal caps to identify direct Pax3 and Zic1 targets 2-4 cells stage embryos were injected with inducible Pax3-GR+/-Zic1-GR constructs. Animal caps were cut at stage 9. Cycloheximide (Chx, 0.1mg/ml) was then applied to the healed animal caps, from stage 10 to 10.5 (i.e. for 30 min at 23*C), then dexamethasone (Dex) was added at stage 10.5 to the cycloheximide-containing medium. Explants were rinced and lysed after two additional hours at 23*C, i.e. when sibling embryos reached stage 11.5-12. Total RNA was then extracted and hybridized on Affymetrix microarrays. Transcriptomes were compared to determine Pax3 and Zic1 targets.
2013-12-28 | E-GEOD-53677 | biostudies-arrayexpress
Project description:Neural crest development is orchestrated by a complex and still poorly understood gene regulatory network. Premigratory neural crest is induced at the lateral border of the neural plate by the combined action of signaling molecules and transcription factors such as AP2, Gbx2, Pax3 and Zic1. Among them, Pax3 and Zic1 are both necessary and sufficient to trigger a complete neural crest developmental program. However, their gene targets in the neural crest regulatory network remain unknown. Here, through a transcriptome analysis of frog microdissected neural border, we identified an extended gene signature for the premigratory neural crest, and we defined novel potential members of the regulatory network. This signature includes 34 novel genes, as well as 44 known genes expressed at the neural border. Using another microarray analysis which combined Pax3 and Zic1 gain-of-function and protein translation blockade, we uncovered 25 Pax3 and Zic1 direct targets within this signature. We demonstrated that the neural border specifiers Pax3 and Zic1 are direct upstream regulators of neural crest specifiers Snail1/2, Foxd3, Twist1, and Tfap2b. In addition, they may modulate the transcriptional output of multiple signaling pathways involved in neural crest development (Wnt, Retinoic Acid) through the induction of key pathway regulators (Axin2 and Cyp26c1). We also found that Pax3 could maintain its own expression through a positive autoregulatory feedback loop. These hierarchical inductions, feedback loops, and pathway modulation provide novel tools to understand the neural crest induction network. Transcriptomes of animal caps overexpressing Pax3+/-Zic1 in the presence/absence of cycloheximide, a translation inhibitor, were compared to control animal caps to identify direct Pax3 and Zic1 targets
2013-12-28 | GSE53677 | GEO
Project description:Cell intrinsic factors that control neuroectoderm specification of early embryonic cells include the nucleoprotein Geminin (Gmnn) and the Zic family of zinc finger transcription factors. Gmnn modulates chromatin state to activate neural gene expression during neural cell fate acquisition, while Gmnn deficiency in the forming neural plate disrupts transcriptional programs that control neural cell specification, neural plate patterning and neurogenesis, resulting in neural tube defects. Likewise, Zic1 over-expression promotes neural gene expression, while heterozygous deletion of Zic1/4 leads to Dandy-Walker malformation, the most common congenital cerebellar malformation. During embryonic development, Geminin and Zic1 expression is enriched in neuroectoderm from gastrula stages, with broad expression in the forming CNS during post-gastrula stages, when neural tube closure and neurogenesis are initiated. To gain a greater understanding of the molecular events that regulate neural cell specification, here we used ChIP-seq to define genome-wide chromatin binding profiles for Gmnn in embryonic stem cells (ESCs) and for Gmnn and Zic1 during specification of ESCs into neuroectoderm.
2016-12-01 | GSE77246 | GEO
Project description:The epiblast of vertebrate embryos is comprised of neural and non-neural ectoderm, with the border territory at their intersection harbouring neural crest and cranial placode progenitors. Here we profile avian epiblast cells as a function of time using single-cell RNA-seq to define transcriptional changes in the emerging ‘neural plate border’. The results reveal gradual establishment of heterogeneous neural plate border signatures, including novel genes that we validate by fluorescent in situ hybridization. Developmental trajectory analysis shows that segregation of neural plate border lineages only commences at early neurulation, rather than at gastrulation as previously predicted. We find that cells expressing the prospective neural crest marker Pax7 contribute to multiple lineages, and a subset of premigratory neural crest cells shares a transcriptional signature with their border precursors. Together, our results suggest that cells at the neural plate border remain heterogeneous until early neurulation, at which time progenitors become progressively allocated toward defined lineages.
2021-12-31 | GSE181577 | GEO
Project description:Targets of Pax3 and Zic1 in neural crest and cranial placode progenitors
| PRJNA283107 | ENA
Project description:Neural induction by the node and placode induction by head mesoderm share an initial state resembling neural plate border
| PRJNA416341 | ENA
Project description:The vertebrate ectoderm gives rise to a variety of cell lineages, including neural, neural crest, placodal and non-neural cell fates. How cell fates are specified at the neural plate border (the region surrounding the neural plate) is not fully understood. We therefore carried out 10x scRNAseq of the chick epiblast to investigate cell fate specification at the neural plate border. Embryos were dissected and pooled according to stage. The tissue was then dissociated and FAC sorted to remove dead cells and remaining doublets before cells were stored in MeOH. Due to the time required to dissect embryos, multiple rounds of collections were carried out, with collections from the same stage pooled prior to 10x sequencing. Libraries were sequenced using an Illumina HiSeq 4000 at the Francis Crick Institute, London. This collection was a follow up to E-MTAB-10408.
2023-08-25 | E-MTAB-11444 | biostudies-arrayexpress