Long noncoding RNAs in viral infections

Abstract

Viral infections induce strong modifications in the cell transcriptome. Among the RNAs whose expression is altered by infection are long noncoding RNAs (lncRNAs). LncRNAs are transcripts with potential to function as RNA molecules. Infected cells may express viral lncRNAs, cellular lncRNAs and chimeric lncRNAs formed by viral and cellular sequences. Some viruses express viral lncRNAs whose function is essential for viral viability. They are transcribed by polymerase II or III and some of them can be processed by unique maturation steps performed by host cell machineries. Some viral lncRNAs control transcription, stability or translation of cellular and viral genes. Surprisingly, similar functions can be exerted by cellular lncRNAs induced by infection. Expression of cellular lncRNAs may be altered in response to viral replication or viral protein expression. However, many cellular lncRNAs respond to the antiviral pathways induced by infection. In fact, many lncRNAs function as positive or negative regulators of the innate antiviral response. Our current knowledge about the identity and function of lncRNAs in infected cells is very limited. However, research into this field has already helped in the identification of novel cellular pathways and may help in the development of therapeutic tools for the treatment of viral infections, autoimmune diseases, neurological disorders and cancer.

Long non‐coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution

“…The size of the minimal ensemble was varied from 1 to 20 (1,2,3,4,6,8,20) to test the effect of ensemble size on the quality of the fitting. Starting from the atomic models of the respective full-length sfRNAs, which were assembled with the available atomic models of individual subdomains as template in Rosetta, conformational pools were generated for the respective sfRNAs using the Xplor-NIH package, which follows a simulated annealing protocol driven by molecular dynamic simulation in torsion angle space that is subject to a target function comprising of bond length, bond angles, improper dihedral angles which specify chirality and planarity of functional groups, a quartic van der Waals repulsion, and R g terms to prevent atomic overlap, a multidimensional torsion angle database potential to improve backbone and sidechain conformation.…”

“…Long non-coding RNAs (lncRNAs) are an expanding group of cellular transcripts that range from 200 nt to over 100 kb in length and possess no protein-coding potential [1]. Like their host cells, many if not all viruses can make their own lncRNAs with multiple biological functions, including the regulation of viral replication, viral persistence, host immune evasion, and pathogenesis [2,3]. These diverse roles of lncRNAs are dictated by their propensities to form stable and complex secondary and higher-order structures, as evidenced by the recent research on Kaposi's sarcoma-associated herpesvirus (KSHV) polyadenylated nuclear (PAN) RNA which a viral lncRNA consists of complex structures [4].…”

Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands

“…[1] Indeed, functional non-coding RNAs have been implicated in diseases ranging from bacterial [2] and viral infections [3] to metastatic cancer. [4] At the same time, methods for the molecular characterization of these RNAs are more difficult and/or lacking compared to those for proteins.…”

HULC and 7SL RNA expression levels in patients with Crimean‐Congo hemorrhagic fever

“…Numerous data obtained to date suggest that altered lncRNA expression plays an important role in metabolic diseases, neurodegenerative and psychiatric disorders, cardiovascular diseases, and immune system dysfunctions . In addition, several lncRNAs have also been implicated in viral infections and antiviral responses …”

“…4 In addition, several lncRNAs have also been implicated in viral infections and antiviral responses. 5 Hepatocellular carcinoma upregulated long non-coding RNA (HULC) is a novel mRNA-like lncRNAm, which is increased in hepatocellular carcinoma (HCC). 6 HULC, 500 nt lncRNA, has a very high expression in the liver.…”