SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease (COVID-19), continues to be a pressing health concern. In this study, we investigated the impact of SARS-CoV-2 infection on host microRNA (miRNA) populations in three human lung-derived cell lines, as well as in nasopharyngeal swabs from SARS-CoV-2 infected individuals. We did not detect any major and consistent differences in host miRNA levels after SARS-CoV-2 infection. However, we unexpectedly discovered a viral miRNA-like small RNA, named vmiR-5p (for viral miRNA), derived from the SARS-CoV-2 ORF7a transcript. Its abundance ranges from low to moderate as compared to host miRNAs. vmiR-5p functionally associates with Argonaute proteins (core components of the RNA interference pathway) leading to downregulation of host transcripts. One such host messenger RNA encodes Basic Leucine Zipper ATF-Like Transcription Factor 2 (BATF2), which is linked to interferon signaling. We demonstrate that vmiR-5p production relies on cellular machinery, yet is independent of Drosha protein, and is enhanced by the presence of a strong and evolutionarily conserved hairpin formed within the ORF7a sequence.

Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP

“…However, the limited yield of non-PCR duplicate fragments, coupled with the low number of chimeric reads outside of the most abundant miRNAs, has hindered the widescale adoption of this powerful approach. With the ever-increasing catalog of miRNAs associated with human disease, coupled with the characterization of small RNAs produced by RNA viruses including SARS-CoV-2 that appear to utilize the host miRNA regulatory machinery (Pawlica et al, 2021), the ability to deeply profile targets for individual miRNAs of particular interest represents a novel opportunity to better understand the biological regulatory networks driven by individual microRNAs in a variety of context.…”

Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs

“…Generation of small RNA species from viral RNA genomes has been shown for multiple pathogens [Perez et al, 2010, Parameswaran et al, 2010 including coronaviruses [Morales et al, 2017]. However, previous studies investigating small RNA transcriptomes from SARS-CoV-1 and SARS-CoV-2 infected cells utilized ligationbased library preparation protocols for deep sequencing that captured predominantly 5'-Phosporylated/3'-OH RNA molecules such as microRNA [Pawlica et al, 2021;Singh et al, 2022;Zhao et al, 2022]. In contrast, one recent publication used a ligation-independent technique [Wyler et al, 2021] but limited analysis to the Argonaute-associated small RNAs including miRNA and vault RNA.…”

“…Several groups have previously reported putative SARS-CoV-2-derived endogenous miRNAs [Pawlica et al, 2021;Singh et al, 2022;Zhao et al, 2022]. Specifically, using deep sequencing of small RNAs carrying 5'-phosphate and 3'-OH isolated from infected Calu-3, A549 and PC-9 cells, Pawlica and co-authors identified "CoV2-miR-O7a," encoded in the SARS-CoV-2 ORF7 [Pawlica et al, 2021]. These results were confirmed by Singh et al, who detected CoV2-miR-O7a.1 and its isoform CoV2-miR-O7a.2 in infected Caco-2 and A549-ACE2 cells [Singh et al, 2022].…”

The role of microRNAs in solving COVID-19 puzzle from infection to therapeutics: A mini-review

“…In fact, the Northern blot technique has allowed researchers to validate the occurrence of viral miRNA-like RNA structures in different viruses, including the H5N1 influenza virus (miR-HA-3p) and the Ebola virus (miR-VP-3p) ( Chen et al, 2016 ; Li et al, 2018 ). Intriguingly, a recent Northern blot assay-based study confirmed that the SARS-CoV-2 could encode the viral miRNA-like small RNA vmiR-5p from its ORF7a, which might be involved in the pathogenesis of the virus at issue ( Pawlica et al, 2021 ). Moreover, deep sequencing of infected Calu-3 and Vero E6 cells revealed that the nucleocapsid gene (N) of SARS-CoV-2, which critically regulates pro-inflammatory cytokines and lung pathology, may encode miRNAs, being the top three v-miRNA-N-28612, v-miRNA-N-29094, and v-miRNA-N-29443.…”