Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis

Abstract

Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients. The functional role and mechanism (s) of transcriptional regulation of deregulated genes in COVID-19 remain largely unknown. In the present communication, reanalyzing publicly available gene expression data, we observed that 66 lncRNA and 5491 PCG were deregulated in more than one experimental condition. Combining our earlier published results and using different publicly available resources, it was observed that 72 deregulated lncRNA interacted with 3228 genes/proteins. Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection. The majority of the deregulated lncRNA and PCG were targets of at least one of the transcription factors (TFs), interferon responsive factors (IRFs), signal transducer, and activator of transcription (STATs), NFκB, MYC, and RELA/p65. Deregulated 1069 PCG was joint targets of lncRNA and TF. These joint targets are significantly enriched with pathways relevant for SARS-CoV-2 infection indicating that joint regulation of PCG could be one of the mechanisms for deregulation. Over all this manuscript showed possible involvement of lncRNA and mechanisms of deregulation of PCG in the pathogenesis of COVID-19.

Exosomal miR-145 and miR-885 Regulate Thrombosis in COVID-19

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Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2

“… 82 By analyzing publicly available SARS-CoV-2-infected transcriptome data, several studies recovered lncRNAs that were dysregulated upon infection of human lung epithelial cell lines, primary normal human bronchial epithelial cells, and BALF. 84 , 85 , 86 , 87 However, no lncRNA with a direct and specific action on the life cycle of SARS-CoV-2 has been identified yet.…”

Long Non-Coding RNAs as Cellular Metabolism and Haematopoiesis Regulators

“…MALAT1 and NEAT1 lncRNAs do seem to be strongly linked to immunological responses and may play a role in the inflammatory course of SARS-CoV-2 infected cells according to the latest reports (Agwa SHA et al,2021;Henzinger H et al, 2020). Elevated levels of LINC02207 and LINC01127 were known to be correlated to severe COVID-19, whilst LINC02084, LINC02446, LINC00861, LINC01871, and ANKRD44-AS1 were discovered to be correlated to mild COVID-19 (Saha C et al, 2021).…”