Alphavirus infection triggers selective cytoplasmic translocation of nuclear RBPs with moonlighting antiviral roles

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1. Version published to 10.1016/j.molcel.2024.11.015

   Dec 1, 2024
2. 

   Version published to 10.1101/2021.10.06.463336v2 on bioRxiv

   Aug 25, 2024
3. 

   ScreenIT

   Oct 12, 2021

   SciScore for 10.1101/2021.10.06.463336: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   At 18 hpi, cells were fixed and treated for immunofluorescence with α-SINV C antibody at 1:200 dilution and GFP-Booster_Atto488 (ChromoTek GmbH, #gba488-100) at 1:500 dilution following the procedure described in (Garcia-Moreno et al., 2019).	α-SINV C suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   BHK21 and HEK293T cells, for growing virus stocks, were maintained in same conditions.	BHK21 suggested: None HEK293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
   Viral RNA interactome capture: HEK293 cells were grown in sets of 4x15 cm dishes.	HEK293 suggested: None
   Immunofluorescence: 1.5x105 …

   SciScore for 10.1101/2021.10.06.463336: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   At 18 hpi, cells were fixed and treated for immunofluorescence with α-SINV C antibody at 1:200 dilution and GFP-Booster_Atto488 (ChromoTek GmbH, #gba488-100) at 1:500 dilution following the procedure described in (Garcia-Moreno et al., 2019).	α-SINV C suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   BHK21 and HEK293T cells, for growing virus stocks, were maintained in same conditions.	BHK21 suggested: None HEK293T suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
   Viral RNA interactome capture: HEK293 cells were grown in sets of 4x15 cm dishes.	HEK293 suggested: None
   Immunofluorescence: 1.5x105 HeLa FlpIn/TRex GFP, DDX1-GFP, RTCB-GFP or FAM98A-GFP cells were seeded on pre-washed High Precision Coverslips (Merienfeld, #0107052) and incubated in DMEM with 10% FBS supplemented with 1ug/ml doxycycline for 16 h.	HeLa suggested: None
   Recombinant DNA
   Sentences	Resources
   Viruses: Alphaviruses used were Sindbis virus that was produced by in vitro transcription from the plasmid pT7svwt (Castello et al., 2006).	pT7svwt suggested: None
   pNL4-3.R-E-Nef-mCherry).	pNL4-3.R-E-Nef-mCherry suggested: None
   DDX1 mutagenesis: The plasmid expressing DDX1-K52A was generated by site-directed mutagenesis using pcDNA5-FRT-TO-eGFP-DDX1 (Garcia-Moreno et al., 2019) as a template.	pcDNA5-FRT-TO-eGFP-DDX1 suggested: None
   Peptides were searched against reference Uniport datasets: human proteome (Uniprot_id: UP000005640, downloaded Nov2016) and SINV proteome derived from pT7-SVwt plasmid.	pT7-SVwt suggested: None
   Software and Algorithms
   Sentences	Resources
   MaxQuant search was performed with “match between run” only activated in the search of cytoplasmic and nuclear fractions samples.	MaxQuant suggested: (MaxQuant, RRID:SCR_014485)
   Analysis of RBP binding preferences with ENCODE eCLIP data: eCLIP bed files were downloaded from the ENCODE database use ENCODExplorer on 07/04/21.	ENCODE suggested: (Encode, RRID:SCR_015482)
   This was achieved using the findOverlaps function from the genomicRanges package to align coordinates of eCLIP hits with genome annotations.	genomicRanges suggested: (GenomicRanges, RRID:SCR_000025)
   Intrinsically disordered regions and Pfam RNA-binding domains analysis: Prediction of intrinsically disordered regions were obtained from MobiDB done by MobiDB-lite method (Piovesan et al., 2021).	MobiDB suggested: (MobiDB, RRID:SCR_014542)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   Results from rtransparent:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
   • No protocol registration statement was detected.

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   Results from scite Reference Check: We found no unreliable references.

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4. 

   Version published to 10.1101/2021.10.06.463336v1 on bioRxiv

   Oct 8, 2021