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Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [Hi-C]

ABSTRACT: Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [Hi-C]

PROVIDER: PRJNA1040947 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26846477_1.fastq.gz	Fastqsanger.gz
	SRR26846477_2.fastq.gz	Fastqsanger.gz
	SRR26846478_1.fastq.gz	Fastqsanger.gz
	SRR26846478_2.fastq.gz	Fastqsanger.gz
	SRR26846479_1.fastq.gz	Fastqsanger.gz

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Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [Hi-C]

Project description:3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of how rapid transcriptional responses, transcriptional memory, and integration of different environmental signals are orchestrated in the 3D genome is limited. Here, we study various aspects of the inflammatory response in macrophages using transcriptomic, epigenomic, and genome conformation mapping technologies, including high-resolution Micro-Capture C. We report that interleukine-4 (IL-4) stably rewires the 3D genome conformation of macrophages and juxtaposes endotoxin-, interferon-gamma-, and dexamethasone-activated enhancers to cognate gene promoters to support enhanced gene expression. IL-4-driven conformational change is indispensable for the integration of IL-4- and endotoxin-induced enhanced and synergistic transcriptional responses, provides short-term transcriptional memory, and can occur in the absence of IL-4-induced epigenetic and transcriptional changes. Our work reveals that IL-4-driven 3D genome conformation is required to shape macrophage plasticity to subsequent immunological responses, integrate distinct inflammatory signals, and provides memory.

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Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation

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Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [MCC]

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Regulation of transcriptional signal integration and memory by inflammation-induced chromosome conformation [ChIP-Seq]

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Systematic evaluation of chromosome conformation capture assays [Hi-C]

Project description:Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of crosslinkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthening compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results in multiple cell states such as pluripotent and differentiated cells as well as cell cycle stages; Mitosis and G1. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using in situ Hi-C, Micro-C and Hi-C 3.0 for commonly cell lines in the 4D Nucleome Project.

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Regulation of immune signal integration and memory by inflammation-induced chromosome conformation.

Project description:3-dimensional (3D) genome conformation is central to gene expression regulation, yet our understanding of its contribution to rapid transcriptional responses, signal integration, and memory in immune cells is limited. Here, we study the molecular regulation of the inflammatory response in primary macrophages using integrated transcriptomic, epigenomic, and chromosome conformation data, including base pair-resolution Micro-Capture C. We demonstrate that interleukin-4 (IL-4) primes the inflammatory response in macrophages by stably rewiring 3D genome conformation, juxtaposing endotoxin-, interferon-gamma-, and dexamethasone-responsive enhancers in close proximity to their cognate gene promoters. CRISPR-based perturbations of enhancer-promoter contacts or CCCTC-binding factor (CTCF) boundary elements demonstrated that IL-4-driven conformation changes are indispensable for enhanced and synergistic endotoxin-induced transcriptional responses, as well as transcriptional memory following stimulus removal. Moreover, transcriptional memory mediated by changes in chromosome conformation often occurred in the absence of changes in chromatin accessibility or histone modifications. Collectively, these findings demonstrate that rapid and memory transcriptional responses to immunological stimuli are encoded in the 3D genome.

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