The Architecture of SARS-CoV-2 Transcriptome

Cell - Tập 181 Số 4 - Trang 914-921.e10 - 2020
Dong-Wan Kim1,2, Joo-Yeon Lee3, Jong-Won Yang3, Jun Won Kim3, V. Narry Kim1,2, Hyeshik Chang1,2
1Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
2School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
3Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Osong 28159, Republic of Korea

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Tài liệu tham khảo

Courtney, 2017, Epitranscriptomic Enhancement of Influenza A Virus Gene Expression and Replication, Cell Host Microbe, 22, 377, 10.1016/j.chom.2017.08.004

Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635

Furuya, 1993, Three different cellular proteins bind to complementary sites on the 5′-end-positive and 3′-end-negative strands of mouse hepatitis virus RNA, J. Virol., 67, 7215, 10.1128/jvi.67.12.7215-7222.1993

Garalde, 2018, Highly parallel direct RNA sequencing on an array of nanopores, Nat. Methods, 15, 201, 10.1038/nmeth.4577

Gokhale, 2017, RNA modifications go viral, PLoS Pathog., 13, e1006188, 10.1371/journal.ppat.1006188

Gokhale, 2016, N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection, Cell Host Microbe, 20, 654, 10.1016/j.chom.2016.09.015

Irigoyen, 2016, High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling, PLoS Pathog., 12, e1005473, 10.1371/journal.ppat.1005473

Karikó, 2005, Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA, Immunity, 23, 165, 10.1016/j.immuni.2005.06.008

Kim, 2020, Identification of Coronavirus Isolated from a Patient in Korea with COVID-19, Osong Public Health Res. Perspect., 11, 3, 10.24171/j.phrp.2020.11.1.02

Krug, 1976, Influenza viral mRNA contains internal N6-methyladenosine and 5′-terminal 7-methylguanosine in cap structures, J. Virol., 20, 45, 10.1128/jvi.20.1.45-53.1976

Lai, 1981, Comparative analysis of RNA genomes of mouse hepatitis viruses, J. Virol., 38, 661, 10.1128/jvi.38.2.661-670.1981

Li, 2018, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, 34, 3094, 10.1093/bioinformatics/bty191

Liao, 1992, RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments, J. Virol., 66, 6117, 10.1128/jvi.66.10.6117-6124.1992

Lichinchi, 2016, Dynamics of Human and Viral RNA Methylation during Zika Virus Infection, Cell Host Microbe, 20, 666, 10.1016/j.chom.2016.10.002

Luytjes, 1996, Replication of synthetic defective interfering RNAs derived from coronavirus mouse hepatitis virus-A59, Virology, 216, 174, 10.1006/viro.1996.0044

Menachery, 2017, Jumping species-a mechanism for coronavirus persistence and survival, Curr. Opin. Virol., 23, 1, 10.1016/j.coviro.2017.01.002

Narayan, 1987, Unequal distribution of N6-methyladenosine in influenza virus mRNAs, Mol. Cell. Biol., 7, 1572

Pathak, 2009, Defective Interfering RNAs: Foes of Viruses and Friends of Virologists, Viruses, 1, 895, 10.3390/v1030895

Snijder, 2016, The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing, Adv. Virus Res., 96, 59, 10.1016/bs.aivir.2016.08.008

Sola, 2015, Continuous and Discontinuous RNA Synthesis in Coronaviruses, Annu. Rev. Virol., 2, 265, 10.1146/annurev-virology-100114-055218

Stewart, 2018, Transcriptional and Translational Landscape of Equine Torovirus, J. Virol., 92, 10.1128/JVI.00589-18

Stoiber, 2017, De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing, bioRxiv

Tomecki, 2004, Identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase, Nucleic Acids Res., 32, 6001, 10.1093/nar/gkh923

Tvarogová, 2019, Identification and Characterization of a Human Coronavirus 229E Nonstructural Protein 8-Associated RNA 3′-Terminal Adenylyltransferase Activity, J. Virol., 93, e00291-19, 10.1128/JVI.00291-19

Viehweger, 2019, Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis, Genome Res., 29, 1545, 10.1101/gr.247064.118

Virtanen, 2020, SciPy 1.0: fundamental algorithms for scientific computing in Python, Nat. Methods, 17, 261, 10.1038/s41592-019-0686-2

Warkocki, 2018, Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism, Philos. Trans. R. Soc. Lond. B Biol. Sci., 373, 20180162, 10.1098/rstb.2018.0162

Williams, 2019, Regulation of Viral Infection by the RNA Modification N6-Methyladenosine, Annu. Rev. Virol., 6, 235, 10.1146/annurev-virology-092818-015559

Wu, 2013, Regulation of coronaviral poly(A) tail length during infection, PLoS ONE, 8, e70548, 10.1371/journal.pone.0070548

Yogo, 1977, Polyadenylate in the virion RNA of mouse hepatitis virus, J. Biochem., 82, 1103, 10.1093/oxfordjournals.jbchem.a131782

Zhou, 2020, A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, 579, 270, 10.1038/s41586-020-2012-7

Zhu, 2020, A Novel Coronavirus from Patients with Pneumonia in China, 2019, N. Engl. J. Med., 382, 727, 10.1056/NEJMoa2001017