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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiChIP]

ABSTRACT: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiChIP]

PROVIDER: PRJNA965792 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24386290_1.fastq.gz	Fastqsanger.gz
	SRR24386290_2.fastq.gz	Fastqsanger.gz
	SRR24386291_1.fastq.gz	Fastqsanger.gz
	SRR24386291_2.fastq.gz	Fastqsanger.gz
	SRR24386292_1.fastq.gz	Fastqsanger.gz

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC

Project description:Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIPmentation]

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiC]

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIP-seq]

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiChIP]

Project description:Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate their differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - has been shown to bind to regulatory elements in bulk CD34+ HSPCs. However, whether specific combinations of these TFs have distinct roles in regulating hematopoietic differentiation remained unknown. In this study, we mapped the genome-wide binding profiles of these TFs and other chromatin-associated markers in distinct HSPC subsets (HSC, CMP, GMP, MEP). We found that the heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type specific gene expression. Moreover, we observed distinct regulatory elements that were enriched with specific combinations of TFs, such as stem-cell specific elements with ERG, and myeloid and megakaryocyte-erythroid specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific combinations of TFs play critical roles in the regulation of hematopoietic differentiation, and provide a valuable resource for the development of targeted therapies to manipulate specific HSPC subsets.

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MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

Project description:Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.

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Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIPmentation]

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