The accessible promoter-mediated supplementary effect of host factors provides new insight into the tropism of SARS-CoV-2

Abstract

In the past year, the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resulted in the worldwide coronavirus disease 2019 (COVID-19) pandemic. Yet our understanding of the SARS-CoV-2 tropism mechanism is still insufficient. In this study, we examined the chromatin accessibility at the promoters of host factor genes (ACE2, TMPRSS2, NRP1, BSG, CTSL, and FURIN) in 14 tissue types, 23 tumor types, and 189 cell lines. We showed that the promoters of ACE2 and TMPRSS2 were accessible in a tissue- and cell-specific pattern, which is accordant with previous clinical research on SARS-CoV-2 tropism. We were able to further verify that type I interferon (IFN) could induce angiotensin-converting enzyme 2 (ACE2) expression in Caco-2 cells by enhancing the binding of HNF1A, the transcription factor of ACE2, to ACE2 promoter without changing chromatin accessibility. We then performed transcription factor (TF)-gene interactions network and pathway analyses and discovered that the TFs regulating host factor genes are enriched in pathways associated with viral infection. Finally, we established a novel model that suggests that open chromatin at the promoter mediates the host factors' supplementary effect and ensures SARS-CoV-2 entry. Our work uncovers the relationship between epigenetic regulation and SARS-CoV-2 tropism and provides clues for further investigation of COVID-19 pathogenesis.

Keywords: ACE2; MT: Bioinformatics; SARS-CoV-2; TMPRSS2; chromatin accessibility; host factors.

Graphical abstract

Figure 1

The chromatin accessibility of host factors promoter in human tissues (A) Heatmaps are showing the distribution of ATAC-seq peaks and DHSs in the binned genome regions, which cover the promoters of ACE2, TMPRSS2, NRP1, BSG, CTSL, and FURIN. Promoter regions of these host factors are highlighted within red box. (B) Data of ATAC-seq peaks and DHSs from the ENCODE project are shown. Donut pie chart shows the proportions of samples in each tissue type group. (C and D) Donut pie chart shows the proportions of tissue samples in which the promoter region of ACE2 (TMPRSS2) was accessible. (E and F) Schematic representation of the chromatin accessibility of ACE2 (TMPRSS2) loci in the human lung and brain tissues.

Figure 2

The chromatin accessibility of host factors promoter in different cell types within human lung tissue (A) Heatmaps show the distribution of ATAC-seq peaks and DHSs in the binned genome regions, which cover the promoters of ACE2, TMPRSS2, NRP1, BSG, CTSL, and FURIN. Promoter regions of these host factors are highlighted within a red box. (B and C) Schematic representation of the chromatin accessibility of ACE2 (TMPRSS2) loci in the AT2 and macrophages cells of human lungs is shown.

Figure 3

The accessibility and transcription factors binding in ACE2/TMPRSS2 promoter and SARS-CoV-2 tropism in Caco-2 and A549 cells (A and B) Schematic chromatin accessibility of ACE2 (TMPRSS2) loci in the Caco-2 and A549 cell lines. (C) Representative images of SARS-CoV-2 pseudovirus infectivity in Caco-2 and A549 cell lines are shown. Scale bars, 200 μm. (D) Western blot of ACE2 and GAPDH in Caco-2 and A549 cells with or without IFN-α treatment is shown. (E) mRNA level of ACE2 in Caco-2 and A549 with or without IFN-α treatment is shown. ∗∗p<0.01, NS, not significant, t test. (F) Schematic chromatin accessibility of ACE2 loci in the Caco-2 and A549 cell lines with or without IFN-α treatment is shown. (G) Schematic HNF1A binding signal of ACE2 loci in the Caco-2 and A549 cell lines with or without IFN-α treatment is shown. (H) ATAC-qPCR of ACE2 promoter in Caco-2 and A549 with or without IFN-α treatment is shown. ∗∗p<0.01, t test. (I) CUT&Tag-qPCR of HNF1A in ACE2 promoter loci in Caco-2 and A549 with or without IFN-α treatment is shown. ∗p<0.05, t test.

Figure 4

Transcription factors regulating host factor genes are enriched in pathways associated with viral infection (A) TF-gene interaction network of host factor genes. Host factors are shown as red nodes, and transcription factors are shown as gray nodes. (B) KEGG pathways of transcription factors regulating host factor genes are shown. Pathways related to viral infection are shown as red bars. (C and D) Protein-protein interaction network of transcription factors regulating ACE2 (TMPRSS2) is shown. Transcription factors regulating host factors are shown as blue nodes, and protein interactions with transcription factors are shown as gray nodes. (E and F) KEGG pathways of PPI network in (C) and (D) are shown. Pathways related to viral infection are shown as blue bars.

Figure 5

Hypothetical model in which open chromatin at the promoter mediates entry genes supplementation and ensures the entry of SARS-CoV-2 Type I IFNs induce the transcription factors binding to ACE2 promoter without changing chromatin accessibility and promote the ACE2 expression in susceptible cells.