Journal: Cell

Article Title: Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response.

doi: 10.1016/j.cell.2018.03.064

Figure Lengend Snippet: Figure 2. lnc-Lsm3b Inhibits RIG-I-Mediated Signaling in RNA Virus-Infected Macrophages (A–C) ELISA of IFN-a (A), IFN-b (B), and IL-6 (C) in the supernatants of peritoneal macrophages transfected with si-ctrl or si-lnc-Lsm3b for 48 hr before VSV, SeV, or HSV-1 infection for 16 hr. (D–F) ELISA of IFN-a (D), IFN-b (E), and IL-6 (F) in supernatants of lnc-Lsm3b+/+ and lnc-Lsm3b/ cells infected with VSV for indicated hours. (G and H) IFN-b (G) and NF-kB (H) promoter activity in HEK293T cells transfected with lnc-Lsm3b and RIG-I vectors upon VSV infection. (I) VSV titers by TCID50 assay in supernatants of lnc-Lsm3b+/+ and lnc-Lsm3b/ cells infected with VSV for 12 hr and 24 hr. (J) Immunoblot analysis of RIG-I signaling pathways in lnc-Lsm3b+/+ and lnc-Lsm3b/ cells infected with VSV for indicated hours. Data are shown as mean ± SD (n = 4) or typical photographs of one representative experiment. Similar results were obtained in three independent experiments. *p < 0.05; **p < 0.01. See also Figure S3.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER poly(I:C) HMW Biotin InvivoGen Cat #tlrl-picb TRIzol reagent Invitrogen Cat #15596-018 Mouse IFN-a Miltenyi Biotec Cat #130-093-130 Mouse IFN-b R&D Systems Cat #8234-MB-010 RNA FISH probe Biosearch technologies N/A GST-RIG-I This paper N/A His-RIG-I This paper N/A GST-CTD This paper N/A GST-CARD This paper N/A His-deltaCARD This paper N/A Critical Commercial Assays NorthernMax kit Thermo Fisher Scientific Cat #AM1940 RNeasy Mini Kit QIAGEN Cat #74104 miRNeasy Serum/Plasma Spike-In Control QIAGEN Cat #219610 MAXIscript SP6/T7 Kit Ambion Cat #AM1320 Streptavidin beads Thermo Fisher Scientific Cat #11206D Mouse IFN-a ELISA kit PBL Biomedical Laboratories Cat #42120-1 Mouse IFN-b ELISA kit PBL Biomedical Laboratories Cat #42400-1 Mouse IL-6 ELISA kit R&D Systems Cat #VAL604 Dual-Luciferase assay kit Promega Cat #TM040 SMARTer RACE 50/30 kit Clontech Cat #634858 ATPase/GTPase Activity Assay Kit Sigma Cat #MAK113 Deposited Data RIP-seq data This paper GEO: GSE106254 iCLIP data This paper GEO: GSE106254 Experimental Models: Cell Lines HEK293T cells American Type Culture Collection N/A L929 cells American Type Culture Collection N/A RAW264.7 cells American Type Culture Collection N/A lnc-Lsm3b / RAW264.7 cells This paper N/A Experimental Models: Organisms/Strains lnc-Lsm3b / mice This paper N/A IFNabR / mice The Jackson Laboratory JAX stock 000819 Recombinant DNA Plasmid: pSIF vector Provided by Dr. Qian Zhang from Second Military Medical University, Shanghai, China N/A Plasmid: pGEM-3zf vector Provided by Dr. Xiaozhong Peng from Peking Union Medical College, Beijing, China N/A cDNA lnc-Lsm3b This paper N/A cDNA lnc-Lsm3b mutants This paper N/A Software and Algorithms FastQC 0.11.5 Babraham Bioinfomatics http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ Samtools 0.1.19 John Marshall and Petr Danecek http://www.htslib.org/ HISAT2 2.0.4 The Center for Computational Biology http://ccb.jhu.edu/software/hisat2/index.shtml StringTie v1.3.3b The Center for Computational Biology http://ccb.jhu.edu/software/stringtie/ (Continued on next page) e2 Cell 173, 1–14.e1–e6, May 3, 2018 Please cite this article in press as: Jiang et al., Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response, Cell (2018), https://doi.org/10.1016/j.cell.2018.03.064

Techniques: Virus, Infection, Enzyme-linked Immunosorbent Assay, Transfection, Activity Assay, TCID50 Assay, Western Blot, Protein-Protein interactions

Journal: Cell

Article Title: Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response.

doi: 10.1016/j.cell.2018.03.064

Figure Lengend Snippet: Figure 3. lnc-Lsm3-Deficient Mice Produce More Type I IFNs (A) Survival of 6-week-old lnc-Lsm3b+/+ and lnc-Lsm3b/ mice given VSV (1 3 108 pfu/g body weight) via tail intravenous injection (i.v.) (n = 10). Kaplan-Meier method was used to evaluate survival curves. (B) ELISA of type I IFNs (IFN-a and IFN-b) production in sera from lnc-Lsm3b+/+ and lnc-Lsm3b/ mice (n = 5) at 18 hr and 24 hr after i.v. injection with VSV (5 3 107 pfu/g). (C) VSV loads by TCID50 assay and qPCR assay of VSV RNA copies in organs and peritoneal macrophages from mice in (B) (n = 4). (D) Pathology of lnc-Lsm3b+/+ and lnc-Lsm3b/ mice in response to VSV. H&E staining of lung sections from mice in (B). Scale bar, 80 mm. (E and F) qPCR analysis of Ifn-b (E) and lnc-Lsm3b (F) expression in organs and peritoneal macrophages from mice in (B) (n = 5). Data are shown as mean ± SD or typical photographs of one representative experiment. Similar results were obtained in three independent experiments. *p < 0.05; **p < 0.01. See also Figures S3 and S4.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER poly(I:C) HMW Biotin InvivoGen Cat #tlrl-picb TRIzol reagent Invitrogen Cat #15596-018 Mouse IFN-a Miltenyi Biotec Cat #130-093-130 Mouse IFN-b R&D Systems Cat #8234-MB-010 RNA FISH probe Biosearch technologies N/A GST-RIG-I This paper N/A His-RIG-I This paper N/A GST-CTD This paper N/A GST-CARD This paper N/A His-deltaCARD This paper N/A Critical Commercial Assays NorthernMax kit Thermo Fisher Scientific Cat #AM1940 RNeasy Mini Kit QIAGEN Cat #74104 miRNeasy Serum/Plasma Spike-In Control QIAGEN Cat #219610 MAXIscript SP6/T7 Kit Ambion Cat #AM1320 Streptavidin beads Thermo Fisher Scientific Cat #11206D Mouse IFN-a ELISA kit PBL Biomedical Laboratories Cat #42120-1 Mouse IFN-b ELISA kit PBL Biomedical Laboratories Cat #42400-1 Mouse IL-6 ELISA kit R&D Systems Cat #VAL604 Dual-Luciferase assay kit Promega Cat #TM040 SMARTer RACE 50/30 kit Clontech Cat #634858 ATPase/GTPase Activity Assay Kit Sigma Cat #MAK113 Deposited Data RIP-seq data This paper GEO: GSE106254 iCLIP data This paper GEO: GSE106254 Experimental Models: Cell Lines HEK293T cells American Type Culture Collection N/A L929 cells American Type Culture Collection N/A RAW264.7 cells American Type Culture Collection N/A lnc-Lsm3b / RAW264.7 cells This paper N/A Experimental Models: Organisms/Strains lnc-Lsm3b / mice This paper N/A IFNabR / mice The Jackson Laboratory JAX stock 000819 Recombinant DNA Plasmid: pSIF vector Provided by Dr. Qian Zhang from Second Military Medical University, Shanghai, China N/A Plasmid: pGEM-3zf vector Provided by Dr. Xiaozhong Peng from Peking Union Medical College, Beijing, China N/A cDNA lnc-Lsm3b This paper N/A cDNA lnc-Lsm3b mutants This paper N/A Software and Algorithms FastQC 0.11.5 Babraham Bioinfomatics http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/ Samtools 0.1.19 John Marshall and Petr Danecek http://www.htslib.org/ HISAT2 2.0.4 The Center for Computational Biology http://ccb.jhu.edu/software/hisat2/index.shtml StringTie v1.3.3b The Center for Computational Biology http://ccb.jhu.edu/software/stringtie/ (Continued on next page) e2 Cell 173, 1–14.e1–e6, May 3, 2018 Please cite this article in press as: Jiang et al., Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response, Cell (2018), https://doi.org/10.1016/j.cell.2018.03.064

Techniques: Injection, Enzyme-linked Immunosorbent Assay, TCID50 Assay, Staining, Expressing

Journal: EMBO Reports

Article Title: RNF144B negatively regulates antiviral immunity by targeting MDA5 for autophagic degradation

doi: 10.1038/s44319-024-00256-w

Figure Lengend Snippet: ( A ) Rnf144b +/+ and Rnf144b −/− MEFs were infected with EMCV (MOI = 1) for indicated time points, and then cell lysates were analyzed for EMCV replication level by qPCR. n = 3 biological replicates. Statistical significance was determined by two-tailed unpaired Student’s t-test. **** P = 0.000039 (4 h), *** P = 0.00050 (8 h), **** P = 0.000040 (12 h). ( B ) Rnf144b +/+ and Rnf144b −/− MEFs were infected with EMCV (MOI = 1) for indicated time points. The cell supernatant was harvested and analyzed by TCID 50 assay. n = 3 biological replicates. Statistical significance was determined by two-tailed unpaired Student’s t-test. ** P = 0.00540 (8 h), ** P = 0.00820 (12 h). ( C ) Western blot analysis of the indicated signaling proteins in MEFs from Rnf144b +/+ or Rnf144b −/− mice infected with EMCV (MOI = 1) for the indicated time periods. ( D ) Rnf144b +/+ and Rnf144b −/− MEFs were infected with EMCV (MOI = 1). After 12 h, cell lysates were analyzed for Ifnb1, TNF-α, IL-6 mRNA level by qPCR. n = 3 biological replicates. Statistical significance was determined by two-tailed unpaired Student’s t-test. **** P = 0.000009 (Ifnb1), *** P = 0.00090 (TNF-α), *** P = 0.00030 (IL-6). ( E ) Rnf144b +/+ and Rnf144b −/− MEFs were infected with EMCV (MOI = 1). 12 h post-infection, cells were treated by CHX (30 μM) for indicated time points. Protein extracts were used for immunoblot analysis of the endogenous MDA5 protein level. ( F , G ) Rnf144b +/+ and Rnf144b −/ − mice were intraperitoneally injected EMCV (5 × 10 6 PFU) for 48 h ( n = 5 per group). qPCR analysis of EMCV replication level in heart and brain, and mRNA level of Ifnb1, TNF-α, IL-6 in brain ( G ). Statistical significance was determined by two-tailed unpaired Student’s t-test. ** P = 0.00530 (heart), * P = 0.02620 (brain), *** P = 0.00030 (Ifnb1), ** P = 0.00170 (TNF-α), *** P = 0.00030 (IL-6). ( H ) ELISA of IFN-β production in serum of Rnf144b +/+ and Rnf144b −/− mice that were intraperitoneally injected with EMCV (5 × 10 6 PFU) for 12 h ( n = 3 per group). Statistical significance was determined by two-tailed unpaired Student’s t-test. **** P = 0.000020. ( I ) Survival of Rnf144b +/+ and Rnf144b −/− mice ( n = 20 per group) intraperitoneally infected with EMCV (6 × 10 7 PFU). Significance was tested using log-rank (Mantel-Cox) test, *** P = 0.00030. Data information: Data shown are representative of at least three biological replicates, with each data point representing a biological experiment. Error bars are presented as mean ± SD. Statistical significance was determined by Student’s t-test. .

Article Snippet: Mouse Interferon β (IFN-β/IFNB) ELISA Kit , CUSABIO , Cat#E04945m.

Techniques: Infection, Two Tailed Test, Western Blot, Injection, Enzyme-linked Immunosorbent Assay

Journal: EMBO Reports

Article Title: RNF144B negatively regulates antiviral immunity by targeting MDA5 for autophagic degradation

doi: 10.1038/s44319-024-00256-w

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Mouse Interferon β (IFN-β/IFNB) ELISA Kit , CUSABIO , Cat#E04945m.

Techniques: Recombinant, Sequencing, shRNA, Mutagenesis, RNA Extraction, Plasmid Preparation, Enzyme-linked Immunosorbent Assay