Global mapping of RNA homodimers in living cells

  1. Marta M Gabryelska
  2. Grzegorz Kudla

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Abstract

RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding of RNA homodimerization has been hampered by the lack of systematic in vivo detection methods. Here we show that PARIS, COMRADES, and other RNA proximity ligation methods can detect RNA homodimers transcriptome-wide as “overlapping” chimeric reads that contain more than one copy of the same sequence. Analysing published proximity ligation datasets, we show that RNA:RNA homodimers mediated by direct base-pairing interactions are rare across the transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA and a subset of tRNAs. Analysis of data from virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N protein in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.

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    SciScore for 10.1101/2021.05.13.444021: (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

    Software and Algorithms
    SentencesResources
    We then called chimeras in the overlapping and non-overlapping datasets using hyb and STAR, using the following commands: hyb (bowtie2 mapping): hyb analyse in=input
    bowtie2
    suggested: (Bowtie 2, RRID:SCR_016368)
    : STAR --genomeDir. --readFilesIn input.fasta --outFileNamePrefix 06 -- outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.05 -- outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 -- outFilterMatchNminOverLread 0 --clip3pAdapterMMp 0.1 –chimSegmentMin 15 --scoreGapNoncan -4 --scoreGapATAC -4 --chimJunctionOverhangMin 15 We used the ua.hyb files from hyb and Chimeric.out.junction files from STAR for downstream analysis.
    STAR
    suggested: (STAR, RRID:SCR_004463)
    Overlap statistics across experimental datasets were visualized in R using the ggplot2 and ggforce libraries (facet_zoom function).
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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

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  2. Version published to 10.1101/2021.05.13.444021v1 on bioRxiv