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Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis

ABSTRACT: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis

PROVIDER: PRJNA353630 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3669970.fastq.gz	Fastqsanger.gz
	SRR3669971.fastq.gz	Fastqsanger.gz
	SRR3669972.fastq.gz	Fastqsanger.gz
	SRR3669963.fastq.gz	Fastqsanger.gz
	SRR3669973.fastq.gz	Fastqsanger.gz

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Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [array]

Project description:Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restricted expression, and single nucleotide polymorphisms (SNPs) within SP140 associate with Crohn’s disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unknown. Results: Individuals carrying CD-associated SNPs within SP140 had defective SP140 mRNA splicing, diminished SP140 protein, and severely suppressed innate immune signatures that stratified them from other CD patients. Conclusion: SP140 is a critical orchestrator of macrophage identity, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by suppressed innate immunity.

2017-05-03 | GSE89870 | GEO

Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-seq]

2017-05-03 | GSE83381 | GEO

Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [ChIP-seq]

2017-05-03 | GSE90126 | GEO

Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [ATAC-Seq]

2017-05-03 | GSE89177 | GEO

Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-05-03 | GSE89876 | GEO

ChIP-seq analysis done for MBD3 before and after SP140 knockout in Ramos cells

Project description:Sp140 is a lymphocytic-restricted protein, an epigenetic reader working as a corepressor of genes implicated in inflammation and orchestrating macrophage transcriptional programs to maintain cellular identity. Reduced Sp140 expression is associated both to autoimmune diseases and blood cancer. However, the molecular mechanisms that link Sp140 altered protein levels to detrimental effects on the immune response and cellular growth, as well as the interactors through which Sp140 promotes gene silencing, remain elusive. In this work, we have applied a multi-omics approach (i.e. interactomics, ChIP-seq and proteomics) in two Burkitt lymphoma cell lines to identify both interactors and target genes of endogenous Sp140. We found that Sp140 interacts with the PRC2 and NuRD complexes and we demonstrated that Sp140 interaction with PRC2 is functional and directs H3K27me3 deposition on a set of target genes related to cellular growth and leukaemia progression.

2024-11-21 | GSE208134 | GEO

H3K27me3 ChIP-seq in Burkitt lymphoma cells (Ramos cell line), wild type and SP140 knockout

2024-11-21 | GSE218453 | GEO

An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140 [CUT&RUN]

Project description:Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn’s disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.

2024-02-20 | GSE256010 | GEO

An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140 [RNA-seq]

2024-02-20 | GSE256003 | GEO

The antiviral nuclear body protein SP140 represses Ifnb1 transcript stabilization by the novel regulator RESIST [WT and SP140 KO RNA-seq]

Project description:Negative regulation of the antiviral cytokine IFN-I is critical to prevent host pathology, but is not fully understood. The highly conserved but understudied epigenetic reader and nuclear body protein SP140 represses IFN-I by an unknown mechanism. We describe the mechanism by which SP140 negatively regulates IFN-I, and include RNA-seq data of WT (B6) and SP140 KO BMMs untreated or treated with 100 ug/mL DMXAA for 8 hours in this dataset. We found that SP140 represses the expression of a novel positive regulator of IFN-I previously annotated as an annexin II receptor, which we rename RESIST (REgulated Stimulator of IFN-I via Stabilization of Transcript). RESIST promotes IFN-I mRNA stability by binding the CCR4-NOT mRNA deadenylase complex and blocking recruitment of the TTP family of RNA-binding proteins, which negatively regulate IFN-I mRNA stability, to CCR4-NOT. Mechanistically, RESIST uses N and C-terminal alpha-helices respectively to either dock to the CCR4-NOT complex or block TTP family binding. Our work reveals a new regulator of IFN-I and a new mechanism regulating IFN-I mRNA stability.

2024-08-28 | GSE269808 | GEO

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