RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells.
SARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomi...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-03-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1010130 |
| _version_ | 1818208988504784896 |
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| author | Xinxin Peng Yikai Luo Hongyue Li Xuejiao Guo Hu Chen Xuwo Ji Han Liang |
| author_facet | Xinxin Peng Yikai Luo Hongyue Li Xuejiao Guo Hu Chen Xuwo Ji Han Liang |
| author_sort | Xinxin Peng |
| collection | DOAJ |
| description | SARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomic data from multiple bronchoalveolar lavage fluid samples of COVID-19 patients, revealing an appreciable number of A-to-I RNA editing candidate sites in SARS-CoV-2. We confirm the enrichment of A-to-I RNA editing signals at these candidate sites through evaluating four characteristics specific to RNA editing: the inferred RNA editing sites exhibit (i) stronger ADAR1 binding affinity predicted by a deep-learning model built from ADAR1 CLIP-seq data, (ii) decreased editing levels in ADAR1-inhibited human lung cells, (iii) local clustering patterns, and (iv) higher RNA secondary structure propensity. Our results have critical implications in understanding the evolution of SARS-CoV-2 as well as in COVID-19 research, such as phylogenetic analysis and vaccine development. |
| first_indexed | 2024-12-12T04:53:34Z |
| format | Article |
| id | doaj.art-c1cfe67035ef4058a9c6fc0769dad153 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-12T04:53:34Z |
| publishDate | 2022-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-c1cfe67035ef4058a9c6fc0769dad1532022-12-22T00:37:25ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042022-03-01183e101013010.1371/journal.pgen.1010130RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells.Xinxin PengYikai LuoHongyue LiXuejiao GuoHu ChenXuwo JiHan LiangSARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomic data from multiple bronchoalveolar lavage fluid samples of COVID-19 patients, revealing an appreciable number of A-to-I RNA editing candidate sites in SARS-CoV-2. We confirm the enrichment of A-to-I RNA editing signals at these candidate sites through evaluating four characteristics specific to RNA editing: the inferred RNA editing sites exhibit (i) stronger ADAR1 binding affinity predicted by a deep-learning model built from ADAR1 CLIP-seq data, (ii) decreased editing levels in ADAR1-inhibited human lung cells, (iii) local clustering patterns, and (iv) higher RNA secondary structure propensity. Our results have critical implications in understanding the evolution of SARS-CoV-2 as well as in COVID-19 research, such as phylogenetic analysis and vaccine development.https://doi.org/10.1371/journal.pgen.1010130 |
| spellingShingle | Xinxin Peng Yikai Luo Hongyue Li Xuejiao Guo Hu Chen Xuwo Ji Han Liang RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. PLoS Genetics |
| title | RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. |
| title_full | RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. |
| title_fullStr | RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. |
| title_full_unstemmed | RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. |
| title_short | RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells. |
| title_sort | rna editing increases the nucleotide diversity of sars cov 2 in human host cells |
| url | https://doi.org/10.1371/journal.pgen.1010130 |
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