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Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA-seq]

ABSTRACT: Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA-seq]

PROVIDER: PRJNA507426 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8257200.fastq.gz	Fastqsanger.gz
	SRR8257201.fastq.gz	Fastqsanger.gz
	SRR8257202.fastq.gz	Fastqsanger.gz
	SRR8257203.fastq.gz	Fastqsanger.gz
	SRR8257204.fastq.gz	Fastqsanger.gz

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Pioneer and repressive functions of p63 during embryonic ectoderm specification

Project description:Pioneer and repressive functions of p63 during embryonic ectoderm specification

| PRJNA507423 | ENA

Pioneer and repressive functions of p63 during embryonic ectoderm specification [RNA-seq]

Project description:The transcription factor p63 is a master regulator of ectoderm development essential for epidermal specification. Although previous studies have highlighted the role of p63 triggering the epidermal transcriptomic program, its precise mechanism of target gene regulation in the complex context of a developing embryo remains poorly understood. Here, we used zebrafish embryos to analyze in vivo how p63 regulates the expression of its target genes during development. We generated tp63-knock-out mutants that recapitulate human phenotypes and show down-regulated epidermal gene expression. Following p63-binding dynamics during development, we found two distinct functions clearly separated in space and time. During early development, p63 binds enhancers associated to neural genes, where it limits Sox3 binding and reduces the expression of these neural genes. Indeed, we show that p63 and Sox3 are co-expressed in the neural plate border. Later in development, p63 binds enhancers associated to epidermal genes and promotes their expression, acting as a pioneer factor, as it binds to non-accessible chromatin and is required for its opening. Therefore, our results suggest that p63 is an important regulator of cell fate decisions during ectoderm specification, promoting the epidermal fate and inhibiting the neural program.

2019-06-06 | GSE123058 | GEO

Pioneer and repressive functions of p63 during embryonic ectoderm specification [ChIP-Seq]

2019-06-06 | GSE123057 | GEO

Pioneer and repressive functions of p63 during embryonic ectoderm specification [ATAC-seq]

2019-06-06 | GSE123056 | GEO

Pioneer and repressive functions of p63 during embryonic ectoderm specification [ChIP-Seq]

Project description:Pioneer and repressive functions of p63 during embryonic ectoderm specification [ChIP-Seq]

| PRJNA507427 | ENA

Pioneer and repressive functions of p63 during embryonic ectoderm specification [ATAC-seq]

Project description:Pioneer and repressive functions of p63 during embryonic ectoderm specification [ATAC-seq]

| PRJNA507428 | ENA

Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification.

Project description:The transcription factor p63 is a master regulator of ectoderm development. Although previous studies show that p63 triggers epidermal differentiation in vitro, the roles of p63 in developing embryos remain poorly understood. Here, we use zebrafish embryos to analyze in vivo how p63 regulates gene expression during development. We generate tp63-knock-out mutants that recapitulate human phenotypes and show down-regulated epidermal gene expression. Following p63-binding dynamics, we find two distinct functions clearly separated in space and time. During early development, p63 binds enhancers associated to neural genes, limiting Sox3 binding and reducing neural gene expression. Indeed, we show that p63 and Sox3 are co-expressed in the neural plate border. On the other hand, p63 acts as a pioneer factor by binding non-accessible chromatin at epidermal enhancers, promoting their opening and epidermal gene expression in later developmental stages. Therefore, our results suggest that p63 regulates cell fate decisions during vertebrate ectoderm specification.

| S-EPMC6624255 | biostudies-literature

Cohesin HiChIP datasets of pluripotent and surface ectoderm cells with and without p63

Project description:Purpose: Assess changes in the three-dimensional (3D) chromatin architecture during surface ectoderm commitment and evaluate changes in 3D chromatin architecture in human embryonic stem cells and surface ectoderm cells with and without p63. Methods: Cohesin HiChIP profiles for human embryonic stem cells and surface ectoderm cells with and without p63 were generated in triplicate with deep sequencing on the Illumina HiSeq 4000 sequencer. Using HiC-Pro, paired end reads were aligned to hg19, duplicate reads were removed, and then were assigned to MboI restriction fragments, filtered for valid interactions, and used to generate binned interaction matrices of 10 kb resolution. Contacts were called using FitHiC and filtered for counts >= 10 and FDR < 0.001. Results: The greatest change in 3D chromatin architecture was observed between human embryonic stem cells and surface ectoderm cells, while moderate changes were observed in human embryonic stem cells with and without p63, and limited changes were observed in surface ectoderm cells with and without p63. Conclusion: Both p63 and the surface ectoderm morphogens direct changes in chromatin folding to establish the 3D chromatin landscape in the surface ectoderm.

2018-11-06 | GSE120294 | GEO

RNA-seq profiles of pluripotent and surface ectoderm cells with and without p63

Project description:Purpose: Evaluate p63 regulation of gene expression in human embryonic stem cells and the surface ectoderm Methods: RNA profiles for human embyronic stem cells and surface ectoderm cells with and without p63 using deep sequencing, in duplicate, on Illumina NextSeq 500 sequencer. Quality of reads were checked by fastqc. Reads were aligned to hg19 genome using tophat and FPKM values were generated using Homer. Results: p63 is largely unable to regulate gene expression in pluripotent cells, but acts primarily as a repressor in the surface ectoderm. Conclusion: p63 regulation of gene expression is dependent on the changes the cell undergoes during surface ectoderm commitment

2018-11-06 | GSE121994 | GEO

Pioneer and repressive functions of p63 during embryonic ectoderm specification

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-06-06 | GSE123059 | GEO