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SALL4 Occupany in mESCs by Cut & Run

ABSTRACT: SALL4 Occupany in mESCs by Cut & Run

PROVIDER: PRJNA839388 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19270837_1.fastq.gz	Fastqsanger.gz
	SRR19270837_2.fastq.gz	Fastqsanger.gz
	SRR19270838_1.fastq.gz	Fastqsanger.gz
	SRR19270838_2.fastq.gz	Fastqsanger.gz
	SRR19270839_1.fastq.gz	Fastqsanger.gz

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SALL4 Occupany in mESCs by Cut & Run

Project description:High confidence SALL4 targets were identified in mESCs by performing Cut&Run on SALL4 Flox/Flox and SALL4 -/- cells. We validated a commercially available antibody that specifically recognizes SALL4 protein.

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CUT&RUN Targeting SALL4 and HDAC2 in human melanoma cells

Project description:SALL4 builds a complex with histone deacetylases, and is thought to confer its effects epigenetically. Both loss of Sall4 and inhibition of HDAC2 leads to an invasiveness in human melanoma cells. To study co-occupancy of SALL4 and HDAC2, we employed CUT&RUN targeting SALL4 and HDAC2 in human melanoma cells (M010817).

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Project description:The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, down-regulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive target for designing therapeutic strategies. However, whether SALL4 binds DNA directly to regulate gene expression is unclear and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) experiments, we identified and validated the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA-seq analyses after SALL4 knockdown, we discovered hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of Histone 3 Lysine 9-specific Demethylases (KDMs). Taken together, these results elucidated the mechanism of SALL4 DNA binding and revealed novel pathways and molecules to target in SALL4-dependent tumors.

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Project description:Enrichment of DPPA2 was assessed by CUT&RUN-sequencing in wildtype Esg1-tdTomato reporter mESC line.

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Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

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2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

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