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Comparative chromatin accessibility profiling of wildtype and supt16h-/- zebrafish using ATAC-sequencing

ABSTRACT: Comparative chromatin accessibility profiling of wildtype and supt16h-/- zebrafish using ATAC-sequencing

PROVIDER: PRJNA416338 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6235060_1.fastq.gz	Fastqsanger.gz
	SRR6235060_2.fastq.gz	Fastqsanger.gz
	SRR6235061_1.fastq.gz	Fastqsanger.gz
	SRR6235061_2.fastq.gz	Fastqsanger.gz
	SRR6235062_1.fastq.gz	Fastqsanger.gz

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Comparative chromatin accessibility profiling of wildtype and supt16h-/- zebrafish using ATAC-sequencing

Project description:Chromatin organization and accessibility are fundamental to how genes are transcriptionally controlled. We identify the first vertebrate mutant for supt16h, a component of the FACT (FAcilitates Chromatin Transcription) complex along with Ssrp1 known to reorganize nucleosomes and assist in transcriptional elongation. We demonstrate its importance in hematopoietic stem cell (HSC) specification by regulating the elongation of Notch genes. Unexpectedly, Assay for Transposase Accessible Chromatin (ATAC) sequencing revealed that loss of supt16h does not affect histone accessibility on a Notch-specific or global level. Although the majority of genes are unaffected, loss of supt16h alters chromatin accessibility significantly at the p53 locus, leading to its overexpression in mutants. Upon downregulation of p53, both loss of Notch and loss of HSC phenotypes are rescued. Notably, ssrp1 mutants possessed normal elongation of Notch genes, levels of P53, and specification of HSCs. Our results highlight the discrete effects of Supt16h and Ssrp1 during HSC specification. Additionally, we demonstrate the relationship between supt16h and p53 during transcriptional elongation to specify HSC fate via modulation of Notch signaling.

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P53 based ChIP-sequencing of wildtype and mutant supt16h-/- zebrafish

Project description:Hematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signaling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signaling components, genes essential for HSC development, due to abrogated transcription. Classically, Supt16h regulates transcription and nucleosome reorganization. Whereas global chromatin accessibility in supt16h mutants is unaffected, we observe a specific increase in accessibility at the p53 locus, causing an accumulation of p53 mRNA and protein. We further demonstrate that P53 levels directly influence expression of the Polycomb Group protein, phc1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues both loss of Notch and loss of HSC phenotypes in supt16h mutants. Taken together, our results highlight a previously uncharacterized relationship between supt16h, p53, and phc1 to specify HSCs via modulation of Notch signaling.

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RNA-sequencing analysis of differential expression in supt16h mutants

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