Frequently Asked Questions

  • What is ceRNA? Why is it important?

    In recent years it has been discovered that endogenous RNAs (mRNAs, pseudogenes, long noncoding RNAs or circular RNAs) can compete with each other for a limited pool of cellular microRNAs (miRNAs) and thus affect the competing RNAís level. This class of RNAs competing for common miRNA(s) are called competing endogenous RNA or ceRNA. CeRNAs play a critical role in fine-tuning the level of miRNA mediated regulation of gene expression by sequestering the miRNAs.

  • Are there evidences of ceRNA effects in host virus interaction?

    In evidence of the viral strategy of exploiting host gene regulatory circuit by ceRNA effect, Cazalla and his group have reported that viral U-rich noncoding RNAs called HSUR expressed in primate virus herpesvirus saimiri (HVS) infected T cells are able to bind to three host miRNAs. They also noted that this activity resulted in striking alteration of the cellular levels of one of these miRNAs, miRNA-27. This phenomenon leads to the regulation of expression of the host-cell genes targeted by this miRNA.

  • Is it possible that viral miRNAs can target cellular non-coding transcripts?

    As viral miRNAs have already been reported to interact with host cellular factors, the viral miRNAs could have potential interaction with cellular non coding RNAs. In the present work, we have identified potential lncRNA and circRNA targets for both host and viral miRNAs from AGO PAR-CLIP datasets in some virus infected cells including Epstein-Barr virus (EBV) infected lymphoblastoid cell lines (LCLs), Human cytomegalovirus (HCMV) infected primary human fibroblast cells and two latently Kaposiís sarcoma associated herpesvirus (KSHV) infected primary effusion lymphoma (PEL) cell lines, BCBL-1 and BC-3.

  • How can I search for potential ceRNAs of a transcript in virus infected cells

    Users can browse for viral miRNA targets on host protein-coding and non-coding genes by choosing a particular virus. The resulting page lists miRNAs encoded by the chosen virus along with its mRNA, lncRNA and circRNA targets in host cells. Users can view details of the targets by choosing a particular viral miRNA. There is also provision for checking the host cellular miRNA targets on a particular viral miRNA target transcript. The users can check the potential ceRNAs for a chosen transcript. The resulting page shows the potential ceRNA candidates that share one or more common cellular or viral miRNA(s), sorted by their probability (p-value) to act as ceRNA to the chosen transcript.