SARS-CoV-2 RNA elements share human sequence identity and upregulate hyaluronan via NamiRNA-enhancer network

  1. Wei Li
  2. Shuai Yang
  3. Peng Xu
  4. Dapeng Zhang
  5. Ying Tong
  6. Lu Chen
  7. Ben Jia
  8. Ang Li
  9. Cheng Lian
  10. Daoping Ru
  11. Baolong Zhang
  12. Mengxing Liu
  13. Cancan Chen
  14. Weihui Fu
  15. Songhua Yuan
  16. Chenjian Gu
  17. Lu Wang
  18. Wenxuan Li
  19. Ying Liang
  20. Zhicong Yang
  21. Xiaoguang Ren
  22. Shaoxuan Wang
  23. Xiaoyan Zhang
  24. Yuanlin Song
  25. Youhua Xie
  26. Hongzhou Lu
  27. Jianqing Xu
  28. Hailin Wang
  29. Wenqiang Yu

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Abstract

No abstract available

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  1. Version published to 10.1016/j.ebiom.2022.103861
  2. ScreenIT

    SciScore for 10.1101/2020.11.04.361576: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    After sonication, sheared chromatin was immunoprecipitated with H3K27ac antibody (Abcam, ab177178) and Protein A magnetic beads (Invitrogen, 10002D) overnight at 4°C.
    H3K27ac
    suggested: (Abcam Cat# ab177178, RRID:AB_2828007)
    Experimental Models: Cell Lines
    SentencesResources
    Also, the antagomirs for HIS-SARS2-1, HIS-SARS2-2, HIS-SARS2-3, HIS-SARS2-4, HIS-SARS2-5, and HIS-SARS-1 were purchased from Guangzhou RiboBio Co., Ltd.
    HIS-SARS-1
    suggested: None
    Lentivirus Package and Cell Screening: We co-transfected pCDH-pre-HIS, pSPAX2, and pMD2G plasmids into HEK293T cells in a ratio of 4:3:1.2 and collected the virus supernatant by filtering cell culture supernatant with 0.45 filters at 48 hours after changing the serum-containing medium.
    HEK293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Viral Genome and Human Genome Blast: Human reference genome (hg38) was obtained from GenBank using Blastn (Chen et al., 2015) with SARS-CoV-2 as a query.
    Blastn
    suggested: (BLASTN, RRID:SCR_001598)
    The detail parameters were chosen as follow: 1) The Maximum number of hits to report:500; 2) Maximum E-value for reported alignments: 10; 3) Word size for seeding alignments: 11; 4) the match/Mismatch scores: 1,-3; 5) Gap penalties: Openging:2, Extension:2; 6) Filter low complexity regions; 7) Filter query sequences using RepeatMasker.
    RepeatMasker
    suggested: (RepeatMasker, RRID:SCR_012954)
    Gene Function Annotation: KEGG (Kyoto Encyclopedia of Genes and Genomes) and Gene Ontology analysis on the surrounding (±500kb) genes of the identical sequences of HIS in human genome were performed using DAVID (Huang da et al., 2009).
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    DAVID
    suggested: (DAVID, RRID:SCR_001881)

    Results from OddPub: Thank you for sharing your data.

    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.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

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

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

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.11.04.361576v1 on bioRxiv