LncRNA CARINH regulates expression and function of innate transcription factor IRF1 in macrophages [RNA-Seq]
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ABSTRACT:
PROVIDER: PRJNA1039021 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The antisense lncRNA CARINH acts as an additional regulatory layer of antiviral immunity through coordinated regulation of the transcription factor IRF1 and downstream interferon-stimulated genes.
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Project description:The antisense lncRNA CARINH acts as an additional regulatory layer of antiviral immunity through coordinated regulation of the transcription factor IRF1 and downstream interferon-stimulated genes.
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Project description:LncRNA CARINH regulates expression and function of innate transcription factor IRF1 in macrophages [RNA-Seq 2]
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Project description:Inflammasomes are critical for mounting host defense against pathogens. The molecular mechanisms that control activation of the AIM2 inflammasome in response to different cytosolic pathogens remain unclear. Here we found that the transcription factor IRF1 was required for the activation of the AIM2 inflammasome during infection with the Francisella tularensis subspecies novicida (F. novicida), whereas engagement of the AIM2 inflammasome by mouse cytomegalovirus (MCMV) or transfected double-stranded DNA did not require IRF1. Infection of F. novicida detected by the DNA sensor cGAS and its adaptor STING induced type I interferon-dependent expression of IRF1, which drove the expression of guanylate-binding proteins (GBPs); this led to intracellular killing of bacteria and DNA release. Our results reveal a specific requirement for IRF1 and GBPs in the liberation of DNA for AIM2 sensing depending on the pathogen encountered by the cell. We used microarrays to explore the gene expression profiles differentially expressed in Francisella-infected bone marrow-derived macrophages (BMDMs) isolated from Irf1-/-, Ifnar1-/-, Aim2-/- and wild-type mice.
2015-03-04 | E-GEOD-66461 | biostudies-arrayexpress
Project description:Exposure of macrophages to cytokines and pathogen-associated molecular patterns (PAMPs) can alter their subsequent stimulus responses, in part by epigenetic reprogramming. Our previous studies identified dynamic control of NFκB as a specificity mechanism for inducing hundreds of de novo enhancers in murine macrophages. A second set of hundreds of de novo enhancers are associated with the ISRE DNA binding element of the family of interferon regulatory factors (IRFs). In this project, we have dissected the roles of three endotoxin-responsive IRFs in macrophage de novo enhancer formation. While IRF3 was previously hypothesized to be a chromatin remodeling transcription factor, we found that its genetic requirement for enhancer formation (H3K4me1) is indirect, mediated by its role in type I IFN expression which activates the IRF9-containing ISGF3 transcription factor. However, our analysis shows that ISGF3 is unable to trigger enhancer formation on its own – it must cooperate with IRF1. Timecourse analysis of chromatin accessibility by ATAC-seq reveals that IRF1 plays a major role in the early steps of nucleosome eviction, while its partner ISGF3 then reinforces eviction and H3K4me1 deposition on neighboring nucleosomes. Further studies revealed that IRF1 can also cooperate with the type II IFN-induced GAF transcription factor, generating an additional set of IRF1-GAF-specific enhancers. Finally, global gene expression analysis by RNA-seq reveals that these IRF1-dependent enhancers are associated with potentiated expression of nearby genes in response to secondary immune threat exposure. Together our results reveal unexpected combinatorial coordination of IRF transcription factors in epigenomic reprograming to provide innate immune memory in a manner that is restricted to direct pathogen exposure or type II IFN-associated T-cell immunity, but not secondary innate immune stimulation via type I IFN.
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Project description:Exposure of macrophages to cytokines and pathogen-associated molecular patterns (PAMPs) can alter their subsequent stimulus responses, in part by epigenetic reprogramming. Our previous studies identified dynamic control of NFκB as a specificity mechanism for inducing hundreds of de novo enhancers in murine macrophages. A second set of hundreds of de novo enhancers are associated with the ISRE DNA binding element of the family of interferon regulatory factors (IRFs). In this project, we have dissected the roles of three endotoxin-responsive IRFs in macrophage de novo enhancer formation. While IRF3 was previously hypothesized to be a chromatin remodeling transcription factor, we found that its genetic requirement for enhancer formation (H3K4me1) is indirect, mediated by its role in type I IFN expression which activates the IRF9-containing ISGF3 transcription factor. However, our analysis shows that ISGF3 is unable to trigger enhancer formation on its own – it must cooperate with IRF1. Timecourse analysis of chromatin accessibility by ATAC-seq reveals that IRF1 plays a major role in the early steps of nucleosome eviction, while its partner ISGF3 then reinforces eviction and H3K4me1 deposition on neighboring nucleosomes. Further studies revealed that IRF1 can also cooperate with the type II IFN-induced GAF transcription factor, generating an additional set of IRF1-GAF-specific enhancers. Finally, global gene expression analysis by RNA-seq reveals that these IRF1-dependent enhancers are associated with potentiated expression of nearby genes in response to secondary immune threat exposure. Together our results reveal unexpected combinatorial coordination of IRF transcription factors in epigenomic reprograming to provide innate immune memory in a manner that is restricted to direct pathogen exposure or type II IFN-associated T-cell immunity, but not secondary innate immune stimulation via type I IFN.
2024-02-14 | GSE241818 | GEO
Project description:Exposure of macrophages to cytokines and pathogen-associated molecular patterns (PAMPs) can alter their subsequent stimulus responses, in part by epigenetic reprogramming. Our previous studies identified dynamic control of NFκB as a specificity mechanism for inducing hundreds of de novo enhancers in murine macrophages. A second set of hundreds of de novo enhancers are associated with the ISRE DNA binding element of the family of interferon regulatory factors (IRFs). In this project, we have dissected the roles of three endotoxin-responsive IRFs in macrophage de novo enhancer formation. While IRF3 was previously hypothesized to be a chromatin remodeling transcription factor, we found that its genetic requirement for enhancer formation (H3K4me1) is indirect, mediated by its role in type I IFN expression which activates the IRF9-containing ISGF3 transcription factor. However, our analysis shows that ISGF3 is unable to trigger enhancer formation on its own – it must cooperate with IRF1. Timecourse analysis of chromatin accessibility by ATAC-seq reveals that IRF1 plays a major role in the early steps of nucleosome eviction, while its partner ISGF3 then reinforces eviction and H3K4me1 deposition on neighboring nucleosomes. Further studies revealed that IRF1 can also cooperate with the type II IFN-induced GAF transcription factor, generating an additional set of IRF1-GAF-specific enhancers. Finally, global gene expression analysis by RNA-seq reveals that these IRF1-dependent enhancers are associated with potentiated expression of nearby genes in response to secondary immune threat exposure. Together our results reveal unexpected combinatorial coordination of IRF transcription factors in epigenomic reprograming to provide innate immune memory in a manner that is restricted to direct pathogen exposure or type II IFN-associated T-cell immunity, but not secondary innate immune stimulation via type I IFN.
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Project description:Myeloid lineage cells use TLRs to recognize and respond to diverse microbial ligands. Although unique transcription factors dictate the outcome of specific TLR signaling, whether lineage-specific differences exist to further modulate the quality of TLR-induced inflammation remains unclear. Comprehensive analysis of global gene transcription in human monocytes, monocyte-derived macrophages and monocyte-derived dendritic cells stimulated with various TLR ligands identifies multiple lineage-specific, TLR-responsive gene programs. Monocytes are hyperresponsive to TLR7/8 stimulation that correlates with higher expression of the receptors. While macrophages and monocytes express similar levels of TLR4, macrophages, but not monocytes, upregulate Interferon-Stimulated Genes (ISGs) in response to TLR4 stimulation. We find that TLR4 signaling in macrophages uniquely engages transcription factor IRF1, which facilitates opening of ISG loci for transcription. This study provides a critical mechanistic basis for lineage-specific TLR responses and uncovers IRF1 as a master epigenetic regulator for the ISG transcriptional program in human macrophages.
2021-03-16 | GSE147308 | GEO
Project description:Inborn errors of human IFN-γ immunity underlie mycobacterial diseases, whereas inborn errors of IFN-a/b immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe two unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-a/b immunity. The IRF1-dependent cellular responses to IFN-γ are, both quantitatively and qualitatively, much greater than those to IFN-a/b in vitro. Monocyte- and iPSC-derived macrophages from the two patients show no upregulation of at least 20% of the target genes normally induced by IFN-γ. By contrast, cell-intrinsic IFN-a/b immunity to diverse viruses, including SARS-CoV-2, is intact. Human IRF1 is, thus, largely redundant for antiviral IFN-a/b immunity. By contrast, human IRF1 is essential for IFN-γ immunity to mycobacteria in myeloid cells.
2023-01-19 | PXD037759 | Pride