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Functional analysis of chicken IRF7 in response to dsRNA analog poly(I:C) by integrating overexpression and knockdown

ABSTRACT: In this study, an integrative high-throughput functional genomics approach was applied by combining overexpression and knockdown assays with RNA-seq; this side-by-side approach was taken in an effort to obtain corroboration and complementary support in the identification of potential genes that are under the control of IRF7.

ORGANISM(S): Gallus gallus

PROVIDER: GSE70105 | GEO | 2015/06/25

SECONDARY ACCESSION(S): PRJNA287667

REPOSITORIES: GEO

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Functional analysis of chicken IRF7 in response to dsRNA analog poly(I:C) by integrating overexpression and knockdown

Project description:In this study, an integrative high-throughput functional genomics approach was applied by combining overexpression and knockdown assays with RNA-seq; this side-by-side approach was taken in an effort to obtain corroboration and complementary support in the identification of potential genes that are under the control of IRF7. Transcriptiome analysis of Poly(I:C) induced IRF7 overexpression & knockdown DF-1 cell lines and their respective controls

2015-06-25 | E-GEOD-70105 | biostudies-arrayexpress

Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown.

Project description:In order to develop novel strategies to protect against increasingly virulent bird-linked pathogens, a better understanding of the avian antiviral response mechanism is essential. Type I interferons (IFNs) are recognized as the first line of defense in a host's antiviral response; and it has been suggested that IRF7, a member of the IFN regulatory factor (IRF) family, plays an important role in modulating the immune response to avian influenza virus infection in chickens. The objective of this study was to identify candidate genes and pathways associated with IRF7 regulation at the transcriptome level as a first step towards elucidating the underlying cellular mechanisms of IRF7 modulation in the chicken antiviral response. IRF7 overexpression and knockdown DF-1 cell lines were established and stimulated by various pathogen-associated molecular patterns. Significant IRF7 and type I IFN expression changes were observed in both the IRF7 overexpression cell line and the IRF7 knockdown cell line upon exposure to the double stranded RNA (dsRNA) analog poly(I:C). Using RNA-seq based transcriptome analysis, we identified potential novel genes that IRF7 may help regulate as part of the host immune response to dsRNA; potential biomarkers and therapeutic targets revealed as a result of this study warrant further investigation. Based on our results, we suggest that IRF7 may have conserved functional activity in the avian antiviral response, and plays a crucial role in type I IFN regulation.

| S-EPMC4505898 | biostudies-literature

ChIP-seq for IRF7

Project description:We performed ChiP-Seq for IRF7 in GM-CSF induced bone-marrow cells. IRF7 ChIP-Seq in myeloid cells

2014-12-03 | E-GEOD-62697 | biostudies-arrayexpress

Chicken IRF7 knockout by CRISPR-Cas9 in DF-1 and in vitro H6N2 infection followed by RNA-seq

Project description:To elucidate the functional role of chicken IRF7 against avian influenza virus (AIV) infection, we generated inducible IRF7 knockout DF-1 cell lines and performed in vitro infection using low pathogenic AIVs (LPAIVs) followed by RNA-seq.

2018-10-01 | GSE119590 | GEO

Exploration of GFP-IRF7 neddylation sites

Project description:To explore the possible neddylation sites, GFP-IRF7 and His-NEDD8 were co-overexpressed in HEK293 cell line and GFP was immunoprecipitated, followed by SDS-PAGE and silver staining. The band detected was subjected to LC–MS/MS.

2021-08-19 | PXD024052 | Pride

Overexpression of chicken IRF7 increased viral replication and programmed cell death to the avian influenza virus infection through TGF-beta/FoxO signaling axis in DF-1

Project description:To elucidate the functional role of chicken IRF7 against avian influenza virus (AIV) infection, we generated inducible IRF7 overexpression DF-1 cell lines that could fine control the IRF7 expression level and performed in vitro infection using low pathogenic AIVs (LPAIVs) followed by RNA-seq.

2018-06-01 | GSE115131 | GEO

ChIP-seq for IRF7

Project description:We performed ChiP-Seq for IRF7 in GM-CSF induced bone-marrow cells.

2014-12-03 | GSE62697 | GEO

Aguilera2017 - Model for IRF7 circuit

Project description:Model destription: The model describes the dynamics of murine IRF7 gene expression upon IFN stimulation. The present model comprises known key components and feedback mechanisms. The overall system describes the active IRF7 promoter (Pa) by the binding of IRF7 dimer and ISGF3 to the DNA binding sites ISRE and IRFE, respectively, the transcription and translation of IRF7, and its subsequent phosphorylation and dimerization. IRF7 protein binding to the IRFE binding site in the promoter results in the production of more IRF7 protein, constituting a positive feedback loop. Publication: A New Efficient Approach to Fit Stochastic Models on the Basis of High-throughput Experimental Data Using a Model of IRF7 Gene Expression as Case Study Authors Luis U. Aguilera, Christoph Zimmer and Ursula Kummer.

2017-03-17 | MODEL1608100001 | BioModels

Gene expression signatures in IRF7 overexpressed 3T3-L1 adipocytes

Project description:To identify the genes that are regulated by IRF7, we have performed DNA microarray in 3T3-L1 adipocytes differentiated from precursor cells infected with retrovirus empty or carrying IRF7. Plasmids (Empty- and IRF7-pMSCV) were kindly provided from Dr. Eguchi at the Okayama University Graduate School of Medicine, Okayama, Japan [Cell Metab. 2008;7: 86-94.]. Infected 3T3-L1 preadipocytes were selected by puromycin treatment and differentiated into adipocytes. 7 days after the induction of adipogenesis, total RNA was isolated.

2020-04-01 | GSE147857 | GEO

RNA profiling of IRF7 knockout acute myeloid leukemia (AML) cells

Project description:Acute myeloid leukemia (AML) is an aggressive hematopoietic malignant. In our study, we found that knockout of IRF7 in AML cells accelerates the AML progression and shorten the mice survival, which is medicated by LSC level. The goals of this study aim to reveal the mechanism mediated by IRF7 knockout, we performed the RNAseq profiling of WT c-kit-, WT c-kit+ and IRF7-/- c-kit+ AML cells

2021-06-30 | GSE178560 | GEO

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