Predicting GELN miRNA potential targeting to SARS-CoV-2 mRNA

After downloading SARS-CoV-2 genomes (NCBI: NC_045512.2) from the NCBI Nucleotide database, viral mRNAs potentially targeted by GELN miRNAs were identified by mapping the reverse complement of the miRNA seed sequence to the SARS-CoV-2 whole genome with the full-length 29,903 bp. Although 6 nt are the minimum requirement, and the 6- to 8-nt-long seed sequence of the miRNA is sufficient to bind the target mRNA,²³ the enrichment analysis with 9-nt seed subsequences included an adopted framework that utilizes the first-order Markov model (MM).⁴² In this framework, the observed k-mer count in the 300-bp region of each bacterial mRNA was compared against the background count derived from the first-order Markov model. A p value was then calculated for each miRNA-mRNA pair to estimate the likelihood of having a functional pair. Once all p values were calculated, the false discovery rate (FDR) was obtained using the Benjamini-Hochberg method⁴³ for multiple comparisons. The plots of miRNA distribution in SARS-CoV-2 genome were generated using a R4.0 programming environment. To determine whether the seed sequences were present in human or mouse miRNA sequences, we downloaded all of the human and mouse microRNA mature sequences (reference sequences) from miRBase database v22.¹ Then, we searched for reference sequences that have a perfect match (no mismatches were allowed) of a seed sequence.