MicroRNA (miRNA) is short non-coding RNA with approximately 22 nucleotides in length, which plays a post-transcriptional regulatory role in gene expression.
When associated with an Argonaute (AGO) protein, the miRNA induces mRNA degradation or represses its translation by complementary binding to the 3’ untranslated region (3’-UTR) of the target mRNA.
Since cellular miRNAs were known to be important regulators for gene expression in cells, it was predicted that viruses could encode their own miRNAs. Researchers indeed have found virus-encoded miRNAs which play an important role in viral infection and survival. Thus, in vivo miRNA detection is expected to bring a significant breakthrough in the diagnosis of virus infections. However, the existing RNA-seq method is not suitable to accurately discover the features of short RNAs like miRNA, and there has been no temporal analysis of miRNA targetomes during acute virus infections. The IBS Center for RNA Research (Director V. Narry Kim) employed human cytomegalovirus (HCMV), a member of the viral family known as Herpesviruses, to conduct temporal analysis of viral miRNA targetomes during acute infections. As a result, they observed that the expression of 22 HCMV miRNAs increased exceptionally during acute infections and identified approximately 4,000 human target genes

In this study, the research team developed a new bioinformatic quantitation method called ACEscoring (AGO-CLIP-Seq enrichment-scoring) to complement AGO-CLIP-Seq. AGO-CLIP-Seq is a method to identify miRNAs that are bound to AGO proteins and target mRNAs. It is based on CLIP-Seq, a method to identify RNA molecules that are bound to specific RNA-binding proteins at the genome-wide level and to find the precise location of target sites. In the previous studies, quantitative analysis was challenging only with AGO-CLIP-Seq, so the research team developed and adopted this ACE-scoring method to identify target mRNAs and to quantify the suppression efficacy of miRNAs. They discovered that their suppression efficacy correlated with ACEscores. Moreover, they identified which viral miRNAs interacted with which target mRNAs and exhibited the maximum suppression efficacy at which time points after infected. Three figures on the right side represent miRNA-target interactions correlated with ACE-scores. Red refers to miRNA sequence and blue refers to target mRNA sequence.

Published paper
Sungchul Kim et al., “Temporal Landscape of MicroRNA-Mediated Host-Virus Crosstalk during Productive Human Cytomegalovirus Infection”, Cell Host & Microbe, Vol. 17, Issue 6, pp. 838–851 (2015)