Interaction of piRNA-like sequences from the 3′-UTR of SARS-CoV-2 with mRNA regions

Piwi-interacting RNAs (piRNAs of 26e32 nt in length) regulate gene expression, epigenetics, and transcriptional and post-transcriptional processes. In humans, piRNAs are expressed in germline and somatic tissues, and generally have a uracil at the 50-end (position þ1), an adenine at the þ10 position, and are 20-O methylated at the 30-end.2 Onice piRNAs form the RNA-induced silencing complex (RISC) with PIWI proteins, they serve as guides to find their complementary sequences of the target mRNA, thus initiating their degradation. The Wuhan patient’s genome is approximately 265 nucleotides (nts) in its 30-UTR; piRNAs-like sequences have been reported in this region. Our objective was to search, through bioinformatics, for mRNA sequences that were homologous to the reverse complementary of the previously reported piRNA-like sequences from the 30-UTR of SARS-CoV-2, and identify the possible interaction between them. Considering that piRNAs bind to their target sequence in a reverse complementary manner, we used the reported piRNA-like sequences as templates and translated them into their reverse complementary sequences: 29757e29784, 29792e29819, 29692e29719, 29667e29694, 29684e29711, 29841e29868, and 29828e29855. We searched for homologous mRNA sequences in NCBI using BLASTN with the following criteria: i) eukaryotic cell gene mRNA and ii) at least 10 nt of identity to the reverse complementary sequences. Using the Nucleic Acid Builder (NAB) from AMBERTOOLS 20 (https://ambermd.org/), we designed the threedimensional structures of piRNA-like sequences of the 30-UTR of SARS-CoV-2 and its corresponding reverse complementary homologs (50 to 30 single-stranded). We also designed a double-stranded structure (sequence 29757e29784) with its reverse complementary sequence (cr-29784-29757), used as a control. The 3D structures in PDB format were docked with

Piwi-interacting RNAs (piRNAs of 26e32 nt in length) regulate gene expression, epigenetics, and transcriptional and post-transcriptional processes. 1In humans, piRNAs are expressed in germline and somatic tissues, and generally have a uracil at the 5 0 -end (position þ1), an adenine at the þ10 position, and are 2 0 -O methylated at the 3 0 -end. 2 Onice piRNAs form the RNA-induced silencing complex (RISC) with PIWI proteins, they serve as guides to find their complementary sequences of the target mRNA, thus initiating their degradation.The Wuhan patient's genome is approximately 265 nucleotides (nts) in its 3 0 -UTR; piRNAs-like sequences have been reported in this region. 3Our objective was to search, through bioinformatics, for mRNA sequences that were homologous to the reverse complementary of the previously reported piRNA-like sequences from the 3 0 -UTR of SARS-CoV-2, 3 and identify the possible interaction between them.
Considering that piRNAs bind to their target sequence in a reverse complementary manner, we used the reported piRNA-like sequences as templates and translated them into their reverse complementary sequences: 29757e29784, 29792e29819, 29692e29719, 29667e29694, 29684e29711, 29841e29868, and 29828e29855.We searched for homologous mRNA sequences in NCBI using BLASTN with the following criteria: i) eukaryotic cell gene mRNA and ii) at least 10 nt of identity to the reverse complementary sequences.Using the Nucleic Acid Builder (NAB) from AMBER-TOOLS 20 (https://ambermd.org/),we designed the threedimensional structures of piRNA-like sequences of the 3 0 -UTR of SARS-CoV-2 and its corresponding reverse complementary homologs (5 0 to 3 0 single-stranded).We also designed a double-stranded structure (sequence 29757e29784) with its reverse complementary sequence (cr-29784-29757), used as a control.The 3D structures in PDB format were docked with HEX 6.3, taking care that the resulting complexes were oriented 5 0 e3 0 for receptors and 3 0 e5 0 for ligands.Using the coupled structures from the previous stage with the best orientation, 26 ns (ns) of molecular dynamics (MD) were performed using AMBER 20 cuda code.Visualization of trajectories was performed using VMD 1.9.3.The distances of the coupled structures were calculated with RasMol for Linux.The pucker conformations, RMDS, and the distances between the nts of the trajectory were calculated by cpptraj.S1).
Nuclear receptor coactivator 1 (NCOA1) serves as a coactivator of different nuclear steroid receptors (SR), retinoid receptors (RR), prostanoid receptors (PR), and thyroid hormone; in turn, initiates the transcriptional process of genes such as interleukins (IL-12p40).While IGSF9B encodes a 763 amino acid protein that contains a fibronectin-like type III domain, suggesting its involvement in cell signaling.IGSF9B is mainly present in the brain and is associated with psychiatric illnesses and seizures, Parkinson's disease, and breast cancer where its presence is associated with a best prognosis. 5Whether SARS-CoV-2 infection impacts these genes would be important to correlate with phenotype; however, both genes (NCOA1 and IGSF9B) have not yet been studied in COVID-19 patients, thus suggesting a new topic for further study.
Although these results have the limitation that they correspond to an in-silico analysis, they are novel.Therefore, they could be significant for the secondary manifestations of SARS-CoV-2 infections, such as in long COVID.
In summary, two piRNA-mRNA complexes were found, 29757-29784-NCOA1 and 29828-29855-IGSF9B, whose results of the homologous sequences of the complementary reverse sequences from the 3 0 -UTR of SARS-CoV-2 could serve as guides for the RISC and initiates the degradation process of the target mRNA.This finding must be confirmed experimentally.