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Gene expression in HeLa cells expressing GFP-IRF3 (non-targeting control and clonal knockouts of DDX58, MAVS, ATP13A1, CAPN15, TADA2B, MED16, and MED24) following Sendai virus (SeV) infection or hpRNA transfection

ABSTRACT: IRF3 translocates from the cytoplasm to the nucleus upon recognition of a cytoplasmic RNA stimulus by RIG-I or MDA5. Using an optical pooled CRISPR knockout screen in HeLa-Cas9 cells, we identified ATP13A1, CAPN15, TADA2B, MED16, and MED24 as novel genes affecting the translocation of IRF3 upon Sendai virus infection. We generated isogenic clonal knockout HeLa-Cas9 lines and confirmed that loss of these five novel genes results in either decreased (ATP13A1 and CAPN15) or increased (TADA2B, MED16, and MED24) translocation of IRF3 upon Sendai virus or synthetic hpRNA stimulation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179288 | GEO | 2023/03/05

REPOSITORIES: GEO

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Gene expression in HeLa cells expressing GFP-IRF3 (non-targeting control and clonal knockouts of DDX58, MAVS, ATP13A1, CAPN15, TADA2B, MED16, and MED24) following Sendai virus (SeV) infection or hpRNA transfection

Project description:Gene expression in HeLa cells expressing GFP-IRF3 (non-targeting control and clonal knockouts of DDX58, MAVS, ATP13A1, CAPN15, TADA2B, MED16, and MED24) following Sendai virus (SeV) infection or hpRNA transfection

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Timecourse of gene expression in HeLa cells (parental cells and clonal knockouts of MED12 and MED24) following induction by TNFa or IL-1b

Project description:Activation of nuclear factor kappa B (NF-kB) by inflammatory signals results in nuclear translocation of the transcription factor p65 and induction of gene expression. We identified MED12 and MED24 in an optical pooled CRISPR knockout screen in HeLa-Cas9 cells for genes affecting the activation and/or relaxation of p65 to the cytoplasm following induction by either TNFa or IL-1b. We generated isogenic clonal knockout HeLa-Cas9 lines using crRNA transfection and confirmed that loss of MED12 or MED24 results in delayed relaxation of p65, assayed by live-cell imaging of a p65-mNeonGreen fluorescent fusion.

2019-10-01 | GSE132704 | GEO

Genome-wide gene expression analysis of FAF1 silencing in HeLa cells

Project description:This study is designed to examine the cellular functions of human Fas-associated factor 1 (FAF1) containing multiple ubiquitin-related domains. Microarray analyses revealed that interferon stimulated genes related to antiviral response are significantly increased in FAF1 knocked down HeLa cells. Silencing FAF1 enhanced the poly I:C and respiratory syncytial virus (RSV) induced productions of type I interferons (IFNs), the target gene of interferon regulator factor 3 (IRF3). IRF3 is a key transcription factor in IFNβ signaling responsible for host innate immune response. This study also found that FAF1 and IRF3 physically associate with IPO5/importin-β3 and that overexpression of FAF1 reduces the interaction between IRF3 and IPO5/importin-β3. These findings suggest that FAF1 negatively regulates IRF3-mediated IFNβ production and antiviral innate immune response via regulating nuclear translocation of IRF3. We conclude that FAF1 plays a novel role negatively regulating virus-induced IFNβ production and antiviral response by inhibiting the translocation of active phosphorylated IRF3 from cytosol to nucleus.

2016-01-29 | GSE71665 | GEO

Microarray analysis of med14, med16, npr1, and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

2013-05-18 | GSE45214 | GEO

Microarray analysis of At-med16-1 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

2012-06-30 | GSE38999 | GEO

Connection of core and and tail Mediator modules restrains transcription from TFIID-dependent promoters [ChEC-seq Med16-AID]

Project description:The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

2021-07-30 | GSE179765 | GEO

Microarray analysis of med16, med8, elp2, and wild type (Col-0) infected with the necrotrophic fungal pathogen Sclerotinia sclerotiorum

Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutants med16, med8, elp2, wild type in response to infection of the necrotrophic fungal pathogen Sclerotinia sclerotiorum. Results indicated that, compared with the wild type, the jasmonic acid (JA) biosynthesis genes LOX3, AOC3, and OPR3, ethylene (ET) biosynthesis genes ACS2 and ACS8, as well as salicylic acid (SA) biosynthesis genes ICS1 and EDS5 were up-regulated in med16 in local tissues at 1 day post-inoculation (dpi) and/or systemic tissues at 4 dpi. Surprisingly, however, while a number of SA pathway genes (EDS1, PAD4, NPR1, WRKY18, WRKY38, WRKY53, PR1, and PR2) and several JA-regulated wound-responsive genes (MYC2, JAR1, VSP1, and VSP2) were up-regulated in med16, a group of JA/ET-regulated defense genes (ORA59, ERF1, ERF14, PDF1.2, PDF1.2b, PDF1.2c, PDF1.3, PR4, and ChiB) and PR5 were down-regulated. On the other hand, only a few of these genes were differentially expressed between med8 or elp2 and the wild type.

2015-01-22 | GSE65165 | GEO

Microarray analysis of med14, med16, npr1, and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to identify genes that are differentially expressed among the Arabidopsis mutant med14, med16, npr1, and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that the induction of a large group of defense genes was suppressed in the med14 mutant compared with both med16 and the wild type. Three biological replicates with leaves from 8 plants per sample were collected at 0 and 4 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each replicate was used as one sample for microarray analysis.

2013-05-18 | E-GEOD-45214 | biostudies-arrayexpress

Microarray analysis of At-med16-1 and wild type (Col-0) infected with the avirulent bacterial pathogen Pst DC3000/avrRpt2

Project description:The goal of the microarray experiment was to identify defense genes that were differentially expressed in the Arabidopsis mutant At-med16-1 and wild type in response to infection of the avirulent bacterial pathogen Pst DC3000/avrRpt2. Results indicated that, compared with the wild type, several positive regulators of SAR (systemic acquired resistance) were downregulated and a group of SAR negative regulators were upregulated in At-med16-1. Three biological replicates with leaves from 8 plants per sample were collected at 0, 4, 8, and 24 hours after inoculation with the avirulent bacterial pathogen Pst DC3000/avrRpt2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the 3 biological replicates were pooled as one sample for microarray analysis.

2012-06-29 | E-GEOD-38999 | biostudies-arrayexpress

Whole genome RNA-sequencing from root tips of Arabidopsis thaliana med16-2 mutant under High and Low phosphate conditions

Project description:Total mRNA was extracted from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and med16-2 mutants grown under low and high phosphate conditions 4 days after germination, using and sequenced by RNA-seq methodology.

2020-10-07 | GSE135778 | GEO

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