Abstract

Endogenous oligonucleotides of miRNA (mRNA-inhibited RNA) and piRNA (PIWI-interacting RNA) are involved in the regulation of the expression of protein-coding genes at the level of mRNA translation. The biological role of miRNAs and piRNAs due to a number of misconceptions has remained insufficiently studied for more than 20 years, which is reflected in their insignificant use in biology and medicine. We found that the binding sites (BS) of many piRNAs in the 5'UTR, CDS, and 3'UTR are located with overlapping nucleotide sequences. Such complexes of BSs in mRNA, known as clusters, contain BSs for a number or even dozens of piRNAs. Such clusters significantly reduce the total length of piRNA BSs and create competition between piRNAs for the binding to mRNA. In the mRNA of many genes, more than 100–200 piRNA BSs located in the 5'UTR, CDS, or 3'UTR can be found. These piRNA BSs are located only in a limited region from 150 nt to 250 nt in length, usually with overlapping nucleotides of their BSs. Groups of piRNA BSs were found in mRNA of different genes located in clusters of BSs identical in length. We have identified piRNA BS clusters in the genome of the SARS-CoV-2 Omicron strain. The RNA regions encoding nsp3, nsp7, endoRNAse, S surface glycoprotein, ORF7a, N protein, and RNA-dependent RNA polymerase contain BS clusters for binding from 4 to 29 piRNAs. We assume that such a number of piRNA BS clusters of these regions can significantly inhibit the synthesis of proteins encoded by the coronavirus RNA. Another feature of the antiviral activity of piRNAs is that they can prevent RNA replication from 3'UTR to 5'UTR by binding to coronavirus RNA. Thus, endogenous piRNAs can be protective against coronavirus. Synthetic piRNAs may thus be a fast and effective treatment for coronavirus.