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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [Perturb-seq]

ABSTRACT: MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [Perturb-seq]

PROVIDER: PRJNA989650 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25100740.fastq.gz	Fastqsanger.gz
	SRR25100741.fastq.gz	Fastqsanger.gz
	SRR25100742.fastq.gz	Fastqsanger.gz
	SRR25100743.fastq.gz	Fastqsanger.gz
	SRR25100744.fastq.gz	Fastqsanger.gz

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [Perturb-seq]

Project description:We present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies highly ranked CREs, referred to as ‘hubs’, which contribute to the regulation of multiple genes and strongly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet represents a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer

Project description:MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [pcHiC]

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [pcHiC]

Project description:MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [pcHiC]

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer.

Project description:Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connecting them with their target genes remains challenging. Here, we present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies clusters of highly ranked CREs, referred to as 'hubs', which contribute to the regulation of multiple genes and significantly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet-identified CREs represent a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.

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MethNet: a robust approach to identify regulatory hubs and their distal targets from cancer data.

Project description:Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connecting them with their target genes remains challenging. Here, we present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover cis regulatory elements (CREs) in a 1 Mb region around every promoter in the genome. MethNet identifies clusters of highly ranked CREs, referred to as 'hubs', which contribute to the regulation of multiple genes and significantly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPR interference based single-cell RNA Perturb-seq validated the functional impact of CREs. Thus, MethNet-identified CREs represent a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.

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MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer

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

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