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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [ATAC-seq]

ABSTRACT: To determine the molecular regulation of ILC3s by Brg1, small intestinal ILC3s (Lin-Thy1highCD45low) from Brg1-deficient and control ILC3s were subjected to assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq).

ORGANISM(S): Mus musculus

PROVIDER: GSE148078 | GEO | 2020/07/01

REPOSITORIES: GEO

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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [RNA-seq]

Project description:In order to search for cell-intrinsic targets for Brg1 in ILC3s, Brg1-deficient and control ILC3s were sorted from bone marrow chimeric mice, generated by transfering mixed bone marrow cells of Thy1.1/Thy1.2Rag1-/-Smarca4f/f and Thy1.2Rag1-/-Smarca4f/fRorc-cre donors at 1:1 ratio to sub-lethally irriadiated Rag2-/-Il2rg-/- recipients.

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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity.

Project description:Group 3 innate lymphoid cells (ILC3s), a subset of the innate lymphoid cells, are abundantly present in the intestine and are crucial regulators of intestinal inflammation. Brg1 (Brahma-related gene 1), a catalytic subunit of the mammalian SWI-SNF-like chromatin-remodeling BAF complex, regulates the development and function of various immune cells. Here, by genetic deletion of Brg1 in ILC3s (Smarca4ΔILC3), we prove that Brg1 supports the differentiation of NKp46+ILC3s by promoting the T-bet expression in NKp46-ILC3s, which facilitates the conversion of NKp46-ILC3s to NKp46+ILC3s. Strikingly, Smarca4ΔILC3 mice of the Rag1-/- background develop spontaneous colitis accompanied with increased GM-CSF production in ILC3s. By construction of a mixed bone marrow chimeric system, we demonstrate that Brg1 enhances T-bet and inhibits GM-CSF expression in ILC3s through a cell-intrinsic manner. Blockade of GM-CSF ameliorates colitis in Rag1-/-Smarca4ΔILC3 mice, suggesting that the suppression of GM-CSF production from ILC3s by Brg1 serves as a critical mechanism for Brg1 to restrain intestinal inflammation. We have further demonstrated that Brg1 binds to the Tbx21 and Csf2 gene locus in ILC3s, and favors the active and repressive histones modifications on gene locus of Tbx21 and Csf2 respectively. Our work reveals the essential role of Brg1 in intestinal immunity by regulating ILC3s.

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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [ATAC-seq]

Project description:Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [ATAC-seq]

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Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [RNA-seq]

Project description:Brg1 restrains the pro-inflammatory properties of ILC3s and modulates intestinal immunity [RNA-seq]

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Comparison of transcriptional profiles of cultured intestinal ILC3s to freshly isolated splenic and intestinal ILC3s

Project description:ILC3s from the spleen (SP) and small intestine (SI) have been shown to be phenotypically and functional different. Intestinal factors are likely to regulate transcriptional profiles and thereby function of ILC3s. The goal of this study is to analyze if SI ILC3s acquire a SP-similar transcriptional profile after in vitro culture. Therefore transcriptional profiles of cultured SI ILC3s were compared to freshly isolated ILC3s of the murine SP and the SI by RNA seq technology. Cell suspension were generated from both organs and ILC3s (CD117+, Thy1.2+, KLRG1-, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1)) were sort purified. SI ILC3 were cultured for 7 days in vitro with IL-2, IL-7 and SCF. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological replicates. We show that intestinal ILC3 acquire a splenic-similar transcriptional profile after in vitro culture.

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Project description:Splenic and intestinal NCR- ILC3s have been shown to be phenotypically and functional different. The goal of this study is to compare transcriptional profiles of NCR- ILC3s isolated of the murine spleen (SP) and the small intestine (SI) by RNA seq technology. Cell suspension were generated from both organs and NCR- ILC3s (CD117+, Thy1.2+, eYFP+, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1, NKp46)) were sort purified. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological triplicates. We provide the first comparison of transcriptional profiles of intestinal and splenic NCR- ILC3s.

2020-03-17 | GSE114749 | GEO

Protein-protein interactions of BRG1 or BRG1-HSA in SW13 cells

Project description:The SWI/SNF complex remodels chromatin in an ATP-dependent manner through the ATPase subunits BRG1 and BRM. Chromatin remodeling alters nucleosome structure to change gene expression, however aberrant remodeling and gene expression can result in cancer. The function and localization on chromatin of the SWI/SNF complex depends on the protein makeup of the complex. Here we report the protein-protein interactions of wild-type BRG1 or mutant BRG1 in which the HSA domain has been deleted (BRG1-HSA). We demonstrate the interaction of BRG1 with most SWI/SNF complex members and a failure of a number of these members to interact with BRG1-HSA. These results demonstrate that the HSA domain of BRG1 is a critical interaction platform for the correct formation of SWI/SNF remodeling complexes.

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Comparison of transcriptional profiles of (1) intestinal ILC3s isolated from WT and IL-17D-deficient mice; (2) CD93+ILC3s and CD93-ILC3s from WT mice

Project description:IL-17D/CD93 axis was essential for ILC3s hemostasis. In order to further understand how IL-17D-CD93 axis regulate ILC3s function, we conducted RNA-seq analysis of ILC3s.

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Brg1 Modulates Enhancer Activation and Polycomb-mediated Repression in Mesoderm Differentiation [ChIP-exo]

Project description:We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications. ChIP exo for BRG1 in 2 conditions: Day4 THF (Control) and Day4 4OHT (Brg1-deleted). 1-2 replicates per condition.

2015-03-01 | E-GEOD-63976 | biostudies-arrayexpress

Analyses of ILC3s from the mesenteric lymph nodes (LN)

Project description:Analyses of ILC3s in Rorc floxed control and Id2iÎ?RORÎ³t mice following daily treatments of tamoxifen for two weeks. Cells were sort purified as lineage negative, CD127+ CD90.2+ CCR6+ ST2- CCR6+ ILCs were sorted from the mesenteric LN of Rorc floxed control and Id2iÎ?RORÎ³t mice following daily treatments of tamoxifen for two weeks.

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