The outbreak of a novel coronavirus SARS-CoV-2 responsible for the COVID-19 pandemic has caused a worldwide public health emergency. Due to the constantly evolving nature of the coronaviruses, SARS-CoV-2-mediated alterations on post-transcriptional gene regulations across human tissues remain elusive. In this study, we analyzed publicly available genomic datasets to systematically dissect the crosstalk and dysregulation of the human post-transcriptional regulatory networks governed by RNA-binding proteins (RBPs) and micro-RNAs (miRs) due to SARS-CoV-2 infection. We uncovered that 13 out of 29 SARS-CoV-2-encoded proteins directly interacted with 51 human RBPs, of which the majority of them were abundantly expressed in gonadal tissues and immune cells. We further performed a functional analysis of differentially expressed genes in mock-treated versus SARS-CoV-2-infected lung cells that revealed enrichment for the immune response, cytokine-mediated signaling, and metabolism-associated genes. This study also characterized the alternative splicing events in SARS-CoV-2-infected cells compared to the control, demonstrating that skipped exons and mutually exclusive exons were the most abundant events that potentially contributed to differential outcomes in response to the viral infection. A motif enrichment analysis on the RNA genomic sequence of SARS-CoV-2 clearly revealed the enrichment for RBPs such as SRSFs, PCBPs, ELAVs, and HNRNPs, suggesting the sponging of RBPs by the SARS-CoV-2 genome.
Figure 1. Protein-protein interaction network analysis suggests a direct interaction of human RNA-binding proteins (RBPs) with SARS-CoV-2 viral proteins (A) An integrated SARS-CoV-2—human RBP interaction network. We obtained the mass spectrometry (MS)-based SARS-CoV-2 viral protein to the human protein interaction network established in HEK293 cells and integrated with first-neighbor-interacting RBPs (obtained from BioGRID—https://thebiogrid.org). (B) Protein abundance of SARS-CoV-2-interacting RBPs across human tissues. Expression data was obtained from the human protein map and row normalized. SARS-CoV-2 proteins were color-coded and highlighted in the network.
Figure 2. Differential expression analysis of mock-treated vs. SARS-CoV-2-infected primary human lung epithelial cells. (A) Bar plot illustrating the significant pathways obtained from the Gene Ontology (GO) term-based functional grouping of Differentially Expressed Genes (DEGs) at 5% False Discovery Rate (FDR) using ClueGO analysis (Cytoscape plugin) (B) Row normalized expression profile of differentially expressed RBPs in mock-treated and SARS-CoV-2-infected primary human lung epithelial cells (in biological triplicates). NHBE: normal vs. SARS-CoV-2-infected human bronchial epithelial cells.
Figure 3. Alternative splicing events during SARS-CoV-2 infection. (A) Bar plot showing the genes (RBP-encoding genes in blue) exhibiting alternative splicing during SARS-CoV-2 infection in primary human lung epithelial cells (at 5% FDR). (B) Clustered GO term network obtained from the function annotation analysis and grouping of the GO term for the genes exhibiting alternative splicing using ClueGO (Cytoscape plugin). Significant clustering (adj. p < 1 × 10−5) of functional groups were color-coded by functional annotation of the enriched GO biological processes, with the size of the nodes indicating the level of significant association of genes per GO term were shown.
Figure 4. Motif enrichment analysis reveals potential human RBPs titrated by the SARS-CoV-2 viral genome. (A) Violin plot shows the statistically significant (p < 1 × 10−5) preferential binding profile of the RBP motifs (sorted by frequency of binding and greater than 10 sites) across the SARS-CoV-2 viral genome (length normalized) identified using FIMO. (B) Hierarchically clustered heatmap showing the protein abundance (row normalized) of RBPs across tissues.
Figure 5. SARS-CoV-2 genome titrates the abundance of functionally important micro-RNAs (miRs) in human tissue. (A) Violin plot shows the statistically significant (p < 1 × 10−5) preferential binding profile of miR motifs (sorted by frequency of binding >15 sites) across the SARS-CoV-2 viral genome (length normalized) identified using FIMO. (B) Hierarchically clustered heatmap showing the log10 expression (Copies Per Million mapped reads (CPM), row normalized) of miRs across the tissues. (C) Bar plot illustrating the significant biological processes obtained from the gene ontology enrichment-based functional grouping of miR target genes (obtained from miRNet). Significant clustering (adj. p < 1 × 10−10) of genes enriched in GO biological processes generated by ClueGO analysis (Cytoscape plugin).