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Genome-wide profiles of IRF8 and PU.1 bindings, and H3K4me1 and H3K27ac histone marks in wild-type and IRF8-knockout microglia [CHIP-seq]

ABSTRACT: The role of the lineage-determining transcription factor Interferon regulatory factor 8 (IRF8) in microglia remains elucidated. Here we report the genome-wide IRF8 binding profiles in microglia at various ages. CUT&RUN methodology revealed that IRF8 starts to bind to the genome around postnatal day 9 (P9), and its number increases with age. In comparison to peritoneal macrophages, microglia IRF8 showed a cell-intrinsic binding pattern. By co-occurrence analysis, most IRF8 was H3K4me1/H3K27ac-marked enhancers, and many of them bind to the H3K27ac(high) super-enhancer regions. In IRF8KO microglia, H3K4me1 and H3K27ac profiles were altered and deposited aberrantly on the genome. This study provides a novel insight into understanding epigenetic regulation in microglia.

ORGANISM(S): Mus musculus

PROVIDER: GSE231402 | GEO | 2023/06/01

REPOSITORIES: GEO

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Transcriptome profiles of wild-type, IRF8KO, IRF8cKO, Batf3KO, 5xFAD, and 5xFAD/IRF8KO microglia [RNA-seq]

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Project description:To understand the differentiation program in monocyte/macrophage differentiation, we performed ChIP-seq for IRF8 and H3K4me1 together with gene expression profiling during IRF8-induced monocyte differentiation. Both promoter-proximal and -distal binding of IRF8 associated with induction of the genes especially those related to monocytes/macrophages and immunity. DNA motif analysis for cis-regulatory elements of indirect IRF8 target genes predicted KLF4, essential for Ly6C+ monocyte development, to be a downstream transcription factor regulating the indirect target gene expression. Introduction of KLF4 into an Irf8-/- myeloid progenitor cell line induced a subset of IRF8 target genes and partially induced monocyte/macrophage differentiation. Together, this study revealed the genome-wide behavior of IRF8 and the IRF8-KLF4 axis during monocyte differentiation. Gene expressions in monocyte-like cells differentiated by IRF8 or KLF4 were measured at day 4 after retroviral transductions to myeloid progenitor cell line, Tot2. Two independent experiments were performed.

2013-01-24 | E-GEOD-38810 | biostudies-arrayexpress

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2013-01-24 | E-GEOD-38824 | biostudies-arrayexpress

Analysis of TF binding sites and histone modification in IRF8-induced monocyte differentiation

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