Coronavirus Disease Research Community - COVID-19
Published May 27, 2020 | Version 1.0
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Data sets for Perspective: SARS-CoV-2's potential mechanism of regulating cellular responses through depletion of specific host miRNAs

Creators

  • 1. Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
  • 2. Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
  • 3. Jagiellonian University Medical College, Dept of Medicine, Krakow, Poland
  • 4. Department of Anesthesiology, University of Alabama at Birmingham, Birmingham, AL
  • 5. Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL

Description

Using a bioinformatic analysis of human miRNA potential interactions with the SARS-CoV-2’s genome, we examined the potential miRNA target sites in 7 coronavirus genomes that include SARS-CoV-2, MERS-CoV, SARS-CoV, and 4 non-pathogenic coronaviruses. (Data Set 1).

Our approach was to examine and compare 3 pathogenic and 4 non-pathogenic strains of HCoVs. The HCoVs' RNA genomes of pathogenic strains were SARS-CoV-2 (NC_045512.2), SARS-CoV (NC_004718.3), MERS-CoV (NC_019843.3). The non-pathogenic strains were HCoV-OC43 (KU131570.1), HCoV-229E (NC_002645.1), HCoV-HKU1 (KF686346.1), and HCoV-NL63 (NC_005831.2). These coronaviruses were tested against the set of 896 confident mature human miRNA sequences that were obtained from the miRBbase v2.21 using the RNA22 v2 microRNA target discovery tool web-server. In order to reduce the false discovery rate of the MTS predictions, the most strict parameters were applied to the default computation workflow using a specificity of 92% versus a sensitivity of 22%.

In Data set 2, using the miRDIP database with only top 1% of the most probable targets considered, we analyzed the potential targets of miRNA that could be bound to either the pathogenic, the non-pathogenic or both groups of HCoVs.

In Data set 3, using miRNAFold webserver  we identified 10 pre-miRNA sequences in the SARS-CoV-2 RNA sequence that could potentially enter the human RNAi pathway.

The graphical summary of our working hypothesis is provided in the graphical abstract.

 

 

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