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Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer

ABSTRACT: Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer

PROVIDER: PRJNA768764 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13067816.fastq.gz	Fastqsanger.gz
	SRR13067817.fastq.gz	Fastqsanger.gz
	SRR13067818.fastq.gz	Fastqsanger.gz
	SRR13067819.fastq.gz	Fastqsanger.gz
	SRR16203774_1.fastq.gz	Fastqsanger.gz

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Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer [ChIP-seq]

Project description:We interrogated global super-enhancer landscape and sought to discover master regulators governing the liver metastasis of colorectal cancer (CRC). Using de novo analysis, we predicted motif enrichment of master transcription factor in super-enhancers. We show that transcription factor-binding sites of hepatocyte nuclear factor 1 (HNF1) family are enriched at super-enhancers identified in cell lines derived from liver metastases, but not those derived from primary tumors. Using ChIP-Seq of acetylated H3K27, the enrichment of HNF1 binding motifs in super enhancers was found in a cell line derived from xenografted liver metastasis but not the parental cell line. The prediction method was further extended to pancreatic cancer where liver metastasis is also a common finding, and a similar enrichment of HNF1 family motif in super-enhancers was found. We subsequently showed that HNF1A was prominently expressed and significantly upregulated in metastatic cell lines and clinical specimens of liver metastases. Collectively, our study implicates HNF1A as a master transcription factor involved in shaping global super-enhancer landscape in CRC liver metastasis.

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super-ehancer landscape shaped by master regulator in liver metastasis of colorectal cancer [RNA-seq]

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super-ehancer landscape shaped by master regulator in liver metastasis of colorectal cancer [RNA-seq]

Project description:super-ehancer landscape shaped by master regulator in liver metastasis of colorectal cancer [RNA-seq]

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Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer [ChIP-seq]

Project description:Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer [ChIP-seq]

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Super-enhancer landscape shaped by master regulator in liver metastasis of colorectal cancer

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

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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes [ChIP-Seq]

Project description:The master transcription factors Oct4, Sox2 and Nanog bind enhancer elements and recruit the Mediator co-activator to activate much of the gene expression program of embryonic stem cells (ESCs). We report here that the ESC master transcription factors and Mediator form “super-enhancers” at most genes known to control the pluripotent state, including those encoding the master transcription factors themselves. These super-enhancers consist of extraordinarily large genomic domains occupied by exceptional amounts of Oct4, Sox2, Nanog, Klf4, Esrrb and Mediator. Super-enhancers stimulate considerably higher transcription than typical enhancers in vivo and in reporter vectors. Reduced levels of Oct4 or Mediator cause preferential loss of expression of super-enhancer-associated genes relative to other genes, suggesting how changes in gene expression programs might be accomplished during development. In other more differentiated cells, super-enhancers containing cell-type-specific master transcription factors are also found at genes that define cell identity. These results implicate super-enhancers in the control of mammalian cell identity and differentiation. ChIP-Seq and controls associated with Super-Enhancers in murine cell types

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