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High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

ABSTRACT: High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

PROVIDER: PRJNA657630 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12463569_1.fastq.gz	Fastqsanger.gz
	SRR12463569_2.fastq.gz	Fastqsanger.gz
	SRR12463570_1.fastq.gz	Fastqsanger.gz
	SRR12463570_2.fastq.gz	Fastqsanger.gz
	SRR12463571_1.fastq.gz	Fastqsanger.gz

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High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.

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High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

Project description:We developed an adaptation to Split-Pool Recognition of Interactions by Tag Extension (SPRITE) called SPRITE-immunoprecipitation (SIP), which enables us to map genome-wide higher-order interactions that are coupled with the protein of interest. In this study we generated SIP data fo H3K4me3 and pan-promoter mark. We generated SIP maps in two mammalian cell types – mouse embryonic stem cells (mES) and mouse bone marrow derived dendritic cells.

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Project description:The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.

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Project description:Although the locations of promoters and enhancers have been identified in several cell types, we have yet limited information on their connectivity. We developed HiCap, which combines Hi-C with promoter sequence capture, to enable genome-wide identification of regulatory interactions with single-enhancer resolution. HiCap analyses of mouse embryonic stem cells (mESC) identified promoter-enhancer interactions predictive of gene expression change upon perturbation, opening up for genomic analyses of long-range gene regulation. HiCap was designed by combining Hi-C with with sequence capture (for all promoters) and carried out in mouse embryonic stem cells (mESC)

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