Journal Article Epublish 7 citations
PubMed: 34940755 DOI: 10.3390/ncrna7040074
Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis.
Noncoding RNA 7(4)
Authors: Chinmay Saha, Sayantan Laha, Raghunath Chatterjee, Nitai P Bhattacharyya
Affiliations
- Department of Genome Science, School of Interdisciplinary Studies, University of Kalyani, Nadia 741235, India.
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, India.
- Department of Endocrinology and Metabolism, Institute of Post Graduate Medical Education & Research and Seth Sukhlal Karnani Memorial Hospital, Kolkata 700020, India.
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.
MeSH
Infections, Transcription Factors, Cells, Genes, Sars Virus, Rna, Untranslated, Rna, Long Noncoding, Covid-19, Sars-Cov-2
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- Transcriptomic Analysis of Long Non-Coding RNA during Infection. Genes (Basel), 2023
- Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience, 2024
- LncRNAs Ride the Storm of Epigenetic Marks. Genes (Basel), 2025
- COVID-19: Mechanisms, risk factors, genetics, non-coding RNAs and neurologic impairments. Noncoding RNA Res, 2023