Cargando…
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...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9000099/ https://www.ncbi.nlm.nih.gov/pubmed/35353808 http://dx.doi.org/10.1371/journal.pgen.1010130 |
_version_ | 1784685351081607168 |
---|---|
author | Peng, Xinxin Luo, Yikai Li, Hongyue Guo, Xuejiao Chen, Hu Ji, Xuwo Liang, Han |
author_facet | Peng, Xinxin Luo, Yikai Li, Hongyue Guo, Xuejiao Chen, Hu Ji, Xuwo Liang, Han |
author_sort | Peng, Xinxin |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-9000099 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-90000992022-04-12 RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells Peng, Xinxin Luo, Yikai Li, Hongyue Guo, Xuejiao Chen, Hu Ji, Xuwo Liang, Han PLoS Genet Research Article 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. Public Library of Science 2022-03-30 /pmc/articles/PMC9000099/ /pubmed/35353808 http://dx.doi.org/10.1371/journal.pgen.1010130 Text en © 2022 Peng et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Peng, Xinxin Luo, Yikai Li, Hongyue Guo, Xuejiao Chen, Hu Ji, Xuwo Liang, Han RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells |
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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9000099/ https://www.ncbi.nlm.nih.gov/pubmed/35353808 http://dx.doi.org/10.1371/journal.pgen.1010130 |
work_keys_str_mv | AT pengxinxin rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT luoyikai rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT lihongyue rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT guoxuejiao rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT chenhu rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT jixuwo rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells AT lianghan rnaeditingincreasesthenucleotidediversityofsarscov2inhumanhostcells |