Location of miRNA genes within herpesvirus genomes. Genomes are represented for alphaherpesviruses (HSV-1, HSV-2, MDV-1, MDV-2), a betaherpesvirus (HCMV), and gammaherpesviruses (EBV, LCV, RRV, KSHV, MHV-68). MDV-1 and MDV-2 were drawn as one complete genome with the respective miRNA encoding regions depicted in more detail. Genomes are not drawn to scale. Figure was compiled from data published in Refs. [14, 16, 22-24, 27, 32, 34, 35, 37, 38]. Abbreviations: U_S, unique short; U_L, unique long; LAT, latency associated transcript.

Themes of herpesvirus miRNA regulation. Both viral and host cellular genes are targeted. (a) One main theme is the tight control of latency by inhibition of immediate early or early genes as shown for ICP0, ICP4, ICP34.5, and IE72. Additionally, EBV LMP1 expression is fine tuned by viral miRNAs to enhance cell survival during latency. Targeting of BCLAF1, a cellular gene, contributes to latent/lytic replication by sensitizing cells to reactivation. (b) Targeting of antiviral responses (MICB and CXCL11). (c) Modulation of cellular proliferation and survival. Target genes have anti-angiogenic (THBS1), or pro-apoptotic activity (BCLAF-1, PUMA, and Bach-1). (d) Impairing host cellular miRNA function. Seed sequence-independent modes of viral miRNA function have also been suggested. One alternative model is based on de novo infection experiments with MCMV, which demonstrated that early after infection viral miRNA synthesis completely overtakes host cellular miRNA production [73]. As a consequence host miRNA function might be impaired leading to a global de-repression of the cell transcriptome. This could be due to hijacking of either Drosha/DGCR8 processing or RISC loading.

Biogenesis of miRNAs. Genes encoding miRNAs are generally transcribed from polII promoters. The majority of miRNAs are encoded in introns, but a small percentage are encoded in exons of protein coding genes. MicroRNA genes can occur either as (i) clusters of multiple hairpins or as (ii) a single hairpin structure. The hairpins in primary transcripts (pri-miRNAs) are recognized by Drosha/DGCR8, a RNase III type endonuclease that cleaves off the 5′ and 3′ ends, leaving a two-nucleotide 3′ overhang. The 60-80 nt hairpin, termed pre-miRNA, is rapidly exported from the nucleus to the cytoplasm via the Exportin5/RAN-GTPase pathway. The pre-miRNA is now recognized by a cytoplasmic RNase III type endonuclease, Dicer, which is also known to cleave dsRNA to create siRNA. Dicer cleaves off the bulged end of the hairpin now forming a short dsRNA with each end having a two nucleotide 3′ overhang. The final step in miRNA biogenesis is the incorporation of one strand of the short RNA duplex into the RNA Induced Silencing Complex (RISC) to form a mature miRNA. Both strands can be incorporated into RISC and as a consequence many miRNA genes encode two mature miRNAs. Once the mature miRNA is incorporated into RISC, it targets the 3′ UTR of mRNAs that contain complementary sequences. It has been observed that positions 2-8 of the miRNA are most important for targeting of mRNAs; this site is referred to as the miRNA seed sequence (for review see [8, 9]).