AGO CLIP-based imputation of potent siRNA sequences targeting SARS-CoV-2 with antifibrotic miRNA-like activity
| Autor: | Yongjun Koh, Sung Wook Chi, Hye-Sook Lee, Seung Hyun Ahn, Dowoon Gu |
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| Rok vydání: | 2021 |
| Předmět: |
2019-20 coronavirus outbreak
RNAi therapy Coronavirus disease 2019 (COVID-19) Science Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Pulmonary Fibrosis RNA-Seq Computational biology Biology Article Cell Line RNA interference Sequence Homology Nucleic Acid microRNA Humans Base sequence RNA Small Interfering Multidisciplinary Binding Sites Coronavirus RNA-Dependent RNA Polymerase Base Sequence SARS-CoV-2 Gene Expression Profiling COVID-19 MicroRNAs Sequence annotation A549 Cells Argonaute Proteins Medicine RNA Interference Imputation (genetics) HeLa Cells |
| Zdroj: | Scientific Reports Scientific Reports, Vol 11, Iss 1, Pp 1-15 (2021) |
| ISSN: | 2045-2322 |
| Popis: | Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is associated with fatal pulmonary fibrosis. Small interfering RNAs (siRNAs) can be developed to induce RNA interference against SARS-CoV-2, and their susceptible target sites can be inferred by Argonaute crosslinking immunoprecipitation sequencing (AGO CLIP). Here, by reanalysing AGO CLIP data in RNA viruses, we delineated putative AGO binding in the conserved non-structural protein 12 (nsp12) region encoding RNA-dependent RNA polymerase (RdRP) in SARS-CoV-2. We utilised the inferred AGO binding to optimise the local RNA folding parameter to calculate target accessibility and predict all potent siRNA target sites in the SARS-CoV-2 genome, avoiding sequence variants. siRNAs loaded onto AGO also repressed seed (positions 2–8)-matched transcripts by acting as microRNAs (miRNAs). To utilise this, we further screened 13 potential siRNAs whose seed sequences were matched to known antifibrotic miRNAs and confirmed their miRNA-like activity. A miR-27-mimicking siRNA designed to target the nsp12 region (27/RdRP) was validated to silence a synthesised nsp12 RNA mimic in lung cell lines and function as an antifibrotic miR-27 in regulating target transcriptomes related to TGF-β signalling. siRNA sequences with an antifibrotic miRNA-like activity that could synergistically treat COVID-19 are available online (http://clip.korea.ac.kr/covid19). |
| Databáze: | OpenAIRE |
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