Fig. 1

SARS-CoV-2 infection decreases ACTN4 expression in an epitranscriptomic manner. a Flow chart of Nanopore direct RNA sequencing. A549-ACE2 and Huh7 cells were infected with WT SARS-CoV-2 at MOI = 1, RNA was then collected at 48 h post-infection (hpi). After purification using oligo (dT), sequencing libraries were prepared and sequenced using a MinION device. b Overlap of differential gene expression in A549-ACE2 and Huh7 cells. c Map of differentially expressed genes. Sequencing data were statistically analyzed. Red dots represent up-regulated genes, green dots represent down-regulated genes. Dot size represents the degree of change. Log fold change based on the abundance of differential host genes. d Comparison of the relative abundance of ACTN4 in Huh7 cells infected with WT SARS-CoV-2 at MOI = 1 at different time points within 24 h was analyzed by RT-qPCR. Data are means ± SEMs (n = 3). **P ≤ 0.01, ***P < 0.001, one-way ANOVA. e Western blot (WB) assays of ACTN4 expression in Huh7 cells at 48 hpi with SARS-CoV-2. GAPDH was used as the loading control. f Variation and distribution of m6A modifications on ACTN4 mRNA. After performing MeRIP-seq via anti-m6A antibodies (Abs) and normalizing the m6A coverage from IP with the m6A coverage from Input, changes in m6A modification levels on ACTN4 mRNAs in Huh7 cells with SARS-CoV-2 infection or not were presented. The top two panels presented normal cells ‘Mock’, the lower two panels presented infected cells ‘Virus’. g, h MeRIP-qPCR. RNAs from SARS-CoV-2-infected or mock cells were incubated with IgG or anti-m6A Abs, followed with immunoprecipitation and RT-qPCR. Data are means ± SEMs (n = 3). ***P < 0.001, unpaired Student’s t-test