HumanViCe: host ceRNA network in virus infected cells in human

Abstract

Host-virus interaction via host cellular components has been an important field of research in recent times. RNA interference mediated by short interfering RNAs and microRNAs (miRNA), is a widespread anti-viral defense strategy. Importantly, viruses also encode their own miRNAs. In recent times miRNAs were identified as key players in host-virus interaction. Furthermore, viruses were shown to exploit the host miRNA networks to suite their own need. The complex cross-talk between host and viral miRNAs and their cellular and viral targets forms the environment for viral pathogenesis. Apart from protein-coding mRNAs, non-coding RNAs may also be targeted by host or viral miRNAs in virus infected cells, and viruses can exploit the host miRNA mediated gene regulatory network via the competing endogenous RNA effect. A recent report showed that viral U-rich non-coding RNAs called HSUR, expressed in primate virus herpesvirus saimiri (HVS) infected T cells, were able to bind to three host miRNAs, causing significant alteration in cellular level for one of the miRNAs. We have predicted protein coding and non protein-coding targets for viral and human miRNAs in virus infected cells. We identified viral miRNA targets within host non-coding RNA loci from AGO interacting regions in three different virus infected cells. Gene ontology (GO) and pathway enrichment analysis of the genes comprising the ceRNA networks in the virus infected cells revealed enrichment of key cellular signaling pathways related to cell fate decisions and gene transcription, like Notch and Wnt signaling pathways, as well as pathways related to viral entry, replication and virulence. We identified a vast number of non-coding transcripts playing as potential ceRNAs to the immune response associated genes; e.g., APOBEC family genes, in some virus infected cells. All these information are compiled in HumanViCe (http://gyanxet-beta.com/humanvice), a comprehensive database that provides the potential ceRNA networks in virus infected human cells.

Cigarette smoke extract alters genome‐wide profiles of circular RNAs and mRNAs in primary human small airway epithelial cells

“…CircRNAs were reported to serve as miRNA sponges and keep miRNA away from its target genes through ceRNA network, suggesting that they might also play important roles in the development of COPD associated with smoke inhalation, considering the close linkage between miRNA and COPD. The circRNA‐mediated ceRNA networks were predicted in several types of human cells . In the present study, we also constructed a putative circRNA‐mediated ceRNA network in HSAECs under cigarette smoke stimulation.…”

lncRNA CERS6‐AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR‐125a‐5p to upregulate BAP1 expression

“…Moreover, they show the ability to combine the same miRNA varies with each other, thus constructing multiplex RNA regulatory networks centered on miRNA. This network regulates RNA expression level, allow them to influence each other, and eventually affect the function of cells, which is called competitive endogenous RNA (ceRNA) mechanism 9,10 . Long noncoding RNA (lncRNA) is a noncoding protein‐nucleic acid sequence with a length of more than 200 bp, which is critical for the incidence and progression of cancers including BC 11,12 .…”

Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells

“…For prediction of deregulated host miRNA targets on JEV genome, we used a custom algorithm developed by our group. This custom algorithm for seed-matched miRNA target finding was used in our previous works 25 46 . The custom algorithm used seed matched target searching coupled with favorable duplex stability.…”