概要: Global analysis of protein-RNA interactions in SARS-CoV-2 infected cells reveals key regulators of infection
项目整体设计: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
Cells were maintained in DMEM supplemented with 10%FBS
处理方案:
Knockdown was induced by treatment with 1ug/ml Doxycyclin; Cells were seeded into 2.5x10^5/well into 24well plates and infected at MOI=0.1 for 24hpi
提取方案:
24hpi cells were detached and lysed in Trizol LS, total RNA extraction was performed following manufacturers recommendation
RNA sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturers guidelines. Briefly, 100ng of total RNA was first depleted of the abundant ribosomal RNA present in the samples by rRNA targeted DNA probe capture followed by enzymatic digestion. Samples were then purified by Beckman Coulter RNAClean XP beads (Cat #A63987). Obtained rRNA-depleted RNA was fragmented, reverse transcribed, converted to dsDNA, end repaired and A-tailed. The A-tailed DNA fragments were ligated to anchors allowing for PCR amplification with Illumina dual indexing primers (Cat#20040553)
建库方案:
Libraries were pooled in equimolar concentrations and sequenced on an Illumina NextSeq 500 sequencer using a high-output cartridge (Cat# 20024907), generating single 150bp long reads.
测序信息
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rRNA- RNA
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SINGLE
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Forward
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ILLUMINA
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Illumina NextSeq 500
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specific
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文章
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