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Accessible chromatin profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages

ABSTRACT: Accessible chromatin profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages

PROVIDER: PRJNA477289 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7405950_1.fastq.gz	Fastqsanger.gz
	SRR7405950_2.fastq.gz	Fastqsanger.gz
	SRR7405960_1.fastq.gz	Fastqsanger.gz
	SRR7405960_2.fastq.gz	Fastqsanger.gz
	SRR7405970_1.fastq.gz	Fastqsanger.gz

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Accessible chromatin profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages

Project description:Interleukin-4 (IL-4) activates macrophages to adopt a distinct phenotype important for tissue repair and helminth infection, but the molecular basis of chromatin remodeling in response to IL-4 stimulation is not understood. We find that IL-4 activation of terminally differentiated macrophages in mice is accompanied by cell-type-specific chromatin remodeling in regions enriched with binding motifs of the pioneer transcription factor PU.1. Mutation studies based on natural genetic variation between C57BL/6 and BALB/c mouse strains demonstrate that accessibility of these IL-4 induced regions can be regulated through differences in DNA shape, without disruption of pioneer factor motifs. We propose a model whereby DNA shape features of stimulation-dependent genomic elements contribute to differences in the accessible chromatin landscape of alternatively activated macrophages on different genetic backgrounds.

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Project description:Setdb1 is one of the H3K9 methyltransferases and represses gene expression by H3K9 methylation. In an attempt to elucidate the role of Setdb1 in the TLR4-mediated inflammatory responses, we performed DNA microarray analysis using lipid A (the active component of LPS)-stimulated peritoneal macrophages from macrophage specific Setdb1 KO (KO) and WT mice. The genes upregulated by lipid A treatment in WT macrophages and further increased in KO macrophages contain many genes associated with interleukins and chemokines. Peritoneal macrophages from WT and KO mice were stimulated with lipid A 10 ng/ml or vehicle for 4 h. Microarray analysis was performed using Affymetrix Mouse 430 2.0.

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