e. convergent transcription and local stem-loop structures within longer single-stranded transcripts (Sabin and Cherry, unpublished observations). Therefore, future work in shrimp and other arthropods is needed to clarify the identity of the viral transcripts targeted by the antiviral Obeticholic Acid research buy RNAi pathway. In the case of WSSV and vp28-siRNA, strand-specific RT-PCR of the region of VP28 from which the siRNA derives may aid in determining whether its dsRNA precursor is produced in trans or in cis. Another important question raised by the study of Huang and Zhang [20] is how, mechanistically,

the RNAi pathway restricts DNA virus infection. Since RNaseIII enzymes such as the Dicer proteins specifically cleave RNA, it is probable that the shrimp Dicers act on the viral RNA transcripts rather than the DNA

genome, which likely reduces the levels of these transcripts and hence their encoded proteins. Moreover, there are two straightforward mechanisms by which the vsiRNAs could interfere with viral replication: by suppressing gene expression at either the transcriptional or posttranscriptional level. We favor a posttranscriptional silencing mechanism, whereby an antiviral RISC targets viral mRNAs for degradation, which inhibits the expression of essential viral genes, leading to the suppression of viral replication. Quantification Caspase phosphorylation of the stability of viral transcripts in the presence or absence of an intact RNAi response may provide further evidence supporting posttranscriptional gene silencing as the mechanism of suppression

of DNA virus infection. Transcriptional gene silencing is a mechanism by which many organisms, including Drosophila, silence mobile genetic elements in germline and somatic tissues [21, 22]. In plants, virus-derived siRNAs can direct epigenetic silencing of DNA viruses such as ssDNA geminiviruses; Dicer-like 3-derived small RNAs direct DNA methylation and repressive H3K9 methylation of viral genomes [23]. While DNA methylation has been lost in several evolutionary lineages, including invertebrates such as Drosophila, these organisms utilize most histone modifications to modulate gene expression at the chromatin level. Indeed, recent work has demonstrated that transposon-derived piwi-interacting RNAs (piRNAs) direct the deposition of repressive histone modifications at the promoters of active transposons in Drosophila [22]. Therefore, it is possible that virus-derived siRNAs direct repressive modifications onto chromatinized viral genomes to silence gene expression in shrimp. Chromatin immunoprecipitation studies in the presence and absence of a functional RNA-silencing pathway will be essential to investigate this possibility. Of course, these mechanisms are not mutually exclusive, and both transcriptional and posttranscriptional mechanisms may be directed by the antiviral silencing pathway.