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R. David, Mathilde Guerbois Galla 1 ? , Philippe Despres 5 , Fré dé ric Tangy 1 *, Anastassia V Komarova 1 *, vol.3

E. Transcriptome, B. Pole, and ;. Deddouche, Unité Interactions Hô te-Agents Pathogens, Institut de Recherche Biomé dicale des Armé es, Bré tigny-sur-Orge, France; 5 Technology Platform CYROI, University of Reunion Island, Saint-Clotilde, France detects members of the Picornaviridae, Caliciviridae, and Coronaviridae. Flaviviridae, Reoviridae, and Arenaviridae are detected by both MDA5 and RIG-I. LGP2 can act both positively or negatively upon activation by different viruses (Moresco and Beutler, Biothé rapies, Biologie Molé culaire et Infectiologie (B3MI), vol.3, 2009.

. Liehl, Although human RLRs have recently received considerable attention, to our knowledge, nobody has yet simultaneously explored viral RNA partners that bind the three known RLRs under the same experimental conditions. In addition, only few studies characterised molecular features of the RLR ligands in the presence of viral infection, 2010.

(. Komarova, In addition, a stable cell line (assigned ST-CH) analysed the functional profiles of the ST-RLR cell lines upon transfection with RIG-I and MDA5 agonists by using a classical IFN-b promoter activity assay (Figure 1G). We observed that transfection of ST-MDA5 and ST-LGP2 cells with MDA5 agonist poly(I:C) elicited an increased IFN-I response. In contrast, transfection of ST-LGP2 cells with the RIG-I agonist 5'triphosphate-RNA (5'3P) masked the IFN-I response (Figure 1G). These observations are in accordance with previous studies showing that over-expression of MDA5 or simultaneous co-expression of MDA5 and LGP2 synergize type I IFN response upon activation with MDA-specific agonists or upon infection, Thus, it is difficult from existing observations to get a clear picture of i) the biological ligands for each of the RLRs and ii) the functional differences between RLRs. To study virus-host RNA-protein interactions during viral infection, we previously developed and validated a high-throughput riboproteomic approach based on One-STrEP-tagged protein affinity purification and next-generation sequencing (NGS), 2009.

S. David, , vol.5, p.27, 2016.

A. , B. , C. Content-of-rlr-specific, and R. Ligands, Significantly enriched reads/positions are represented in orange and non-significantly enriched reads are coloured in blue. (A) MDA5, (B) LGP2, (C) RIG-I NGS data. (D) Secondary structure analysis of the MV genome. Either 250 (red) or 500 (blue) nucleotide long MV genome fragments were analysed. DG (free energy) vs. position on the MV genome is shown, Figure 8. In silico analysis of NGS data

S. David, , vol.5, p.27, 2016.

. Bruns, These data suggest that, upon MV infection, LGP2 and MDA5 specifically interact with the same RNA agonist and that LGP2 could be involved in stabilizing short MDA5 filaments formed on secondary structures localized at the 5'-end of the MV-N mRNA. In summary, using One-STrEP-RLRs affinity chromatography purification and NGS we provide the first simultaneous visualisation of specific RNA ligands for RIG-I, MDA5 and LGP2 in living cells and in the presence of different RNA viruses. Our results show that each of these cytosolic sensors has its individual RNA profile upon infection with different RNA viruses, our results show that MDA5 recognizes the integrity of the MV-N mRNA, certainly through the recognition of stem loop structures. Further, our in silico (Mfold) prediction of RNA secondary structures within the different parts of the MV genome suggested that MV-N mRNA had a potential to form stem loop structures (Figure 8D), 2008.

, To establish clonal stable cell lines expressing One-ST-RLR, we used a modified pEXPR-IBA105 plasmid carrying GW cassette (pEXPR-IBA105GW) kindly provided by Dr. Yves Jacob (Unité de Gé né tique Molé culaire des Virus ARN, Institut Pasteur). First, the RLR sequences (LGP2, MDA5 or RIG-I) were amplified by standard PCR from a human spleen cDNA library (Invitrogen) using specific primers with AttB1 and AttB2 sequences included (Supplementary file 2). The corresponding DNA fragments were cloned by in vitro recombination into pDONR207 entry vector (BP reaction, Gateway, Invitrogen). RLR genes (MDA5: AF095844; LGP2: AAH14949 RIG-I: CCDS6526.1) were finally recombined from pDONR207 to One-STrEP-tag pEXPR-IBA105GW by in vitro recombination (LR reaction), Cells, plasmids and recombinant viruses HEK-293 (human embryonic kidney, ATCC CRL-1573), Hela (human cervix adenocarcinoma epithelial, ATCC CCL-2) and A549 cells (human lung adenocarcinoma epithelial, ATCC CCL-185) were maintained in DMEM-Glutamax, pp.114-129

S. David, Transfected cells were amplified and subsequently cloned by serial limit dilution. At least 5 clones were screened for each RLR to detect the tagged protein expression by qPCR and Western Blot. For STING37shRLR cell lines, we generated lentiviral vectors using the canonical triple transfection of HEK293T cells by a VSVg envelope, vol.5, 2016.

P. Charneau and ;. Zufferey, To prevent V protein expression from MV, a two-step PCR strategy was used to generate MVDV virus. Two PCR fragments were amplified using MV2313 (5'-ATCTGCTCCCATCTCTATGG) and MV2504 (5'-TCTGTGCCCTTCTTAATGGG) for the first fragment and MV2485 (5'-CCCATTAA-GAAGGGCACAGA) and MV3385 (5'-AGGTTGTACTAGTTGGGTCG) second PCR reaction using MV2313 and MV3385 primers. The produced mutated HindIII-SpeI MV fragment was moved into the pTM-MVSchwarz plasmid after digestion with the corresponding restriction enzymes, ) expressing either an shRNA with no target (RHS4346, shNeg), or targeting LGP2 (shLGP2, RHS4430-99166661-V2LHS_116526), MDA5(RHS4430-101128286-V3LHS_300657, shMDA5) or RIG-I (RHS4430-99619609-V2LHS_197176, shRIG-I), 1997.

L. Ge-healthcare, A. Chalfont-;-and, and . Enzolifescience-;-bréhin, HRP-coupled anti-mouse (NA9310V, GE Healthcare) or anti-rabbit (RPN4301, GE Healthcare) were used as secondary antibodies. Peroxidase activity was visualized with an ECL Plus Western Blotting Detection System (#RPN2132, GE Healthcare). MV intracellular staining was performed with mouse anti-N mAb (clone 25, Antibodies, western blot and intracellular staining Protein extracts were resolved by SDS-polyacrylamide gel electrophoresis on 4-12% Criterion gels, vol.5321, p.5, 1981.

, and luciferase activity was measured with Bright-Glow Luciferase assay system (E2650, Promega) or Renilla Glow Luciferase Assay System (E2720, Promega), correspondingly. For immunostaining, cells were washed twice with phosphate-buffered saline (PBS) and 2% foetal calf serum (FCS) and then fixed in PBS containing 4% paraformaldehyde, MOIs. For rMV2-Fluc or CHIKV-Rluc infection, at each time point cells were lysed by Passive Lysis buffer (E1941, Promega

S. David, , vol.5, p.27, 2016.

, RNA purification was performed using TRI reagent LS (T3934, SIGMA). RNA was dissolved in 80 ml of DNase-free and RNase-free ultrapure water. Extracted RNAs were analyzed using Nanovue (GE Healthcare) and Bioanalyser RNA nano kit, KCl, 0.5% Igepal, 2 mM b-Mercaptoethanol), supplemented with 200 unit/ml RNasin (#N2515, pp.5067-1511

. Langmead, according to manufacturer's instruction. To analyze all RNA species present, the initial poly(A) RNA isolation step was omitted. Briefly, the fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. aligned to the MV Schwarz strain reference genome, Next generation sequencing (NGS) RNA molecules isolated from ST-RLR/RNA complexes were treated for library preparation using the Truseq Stranded mRNA sample preparation kit (Illumina, vol.10, 2009.

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, In silico analysis of NGS data AU content was calculated in a sliding window of 200 nts (step size=1) and compared to the mean count within the 200 nt window and to the sum of sequenced reads (extended to 200 nt). Viral RNA sequences were subjected to secondary structure prediction using Mfold software (version 3.6, MAX=1) using standard parameters to all sliding windows (window size= (250 and 500)

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