Cellular versus viral microRNAs in host-virus interaction

MicroRNAs (miRNAs) mark a new paradigm of RNA-directed gene expression regulation in a wide spectrum of biological systems. These small non-coding RNAs can contribute to the repertoire of host-pathogen interactions during viral infection. This interplay has important consequences, both for the virus and the host. There have been reported evidences of host-cellular miRNAs modulating the expression of various viral genes, thereby playing a pivotal role in the host-pathogen interaction network. In the hide-and-seek game between the pathogens and the infected host, viruses have evolved highly sophisticated gene-silencing mechanisms to evade host-immune response. Recent reports indicate that virus too encode miRNAs that protect them against cellular antiviral response. Furthermore, they may exploit the cellular miRNA pathway to their own advantage. Nevertheless, our increasing knowledge of the host-virus interaction at the molecular level should lead us toward possible explanations to viral tropism, latency and oncogenesis along with the development of an effective, durable and nontoxic antiviral therapy. Here, we summarize the recent updates on miRNA-induced gene-silencing mechanism, modulating host-virus interactions with a glimpse of the miRNA-based antiviral therapy for near future.

The properties and functions of virus encoded microRNA, siRNA, and other small noncoding RNAs

microRNAs (miRNAs) represent a class of noncoding RNA species, believed to be regulating gene expression by binding to complementary sites in the 3'UTRs of target mRNAs. They play important regulatory roles in various metabolic pathways in most eukaryotes. The recent discovery of virus encoded miRNAs suggests that viruses may be using them to regulate host and viral gene expression. Another class of closely related small interfering RNAs (siRNAs) also has been found within the HIV-1 genome and shown to be exerting a limited impact on virus reproduction. Additionally, an additional type of viral noncoding RNAs named small noncoding RNAs (sncRNAs) ranging from a few tens to a few hundred nucleotides in length, has also been identified. sncRNAs have a wide phylogenesis and high levels of expression, suggesting they may play an important roles in different species. Here we discuss the genomic organization, expression, conservation as well as potential function of virally encoded miRNA, siRNA, and sncRNAs.

Trypanosome spliced-leader-associated RNA (SLA1) localization and implications for spliced-leader RNA biogenesis

Spliced-leader-associated RNA (SLA1) guides the pseudouridylation at position -12 (relative to the 5' splice site) of the spliced-leader (SL) RNA in all trypanosomatid species. Nevertheless, the exact role of this RNA is currently unknown. Here, we demonstrate that the absence of pseudouridine on Leptomonas collosoma SL RNA has only a minor effect on the ability of this RNA to function in trans splicing in vivo. To investigate the possible role of SLA1 during SL RNA biogenesis, the structure of the SL RNA was examined in permeable Trypanosoma brucei cells depleted for CBF5, the H/ACA pseudouridine synthase, lacking SLA1. Our results suggest that in the absence of SLA1, the SL RNA secondary structure is changed, as was detected by differential sensitivity to oligonucleotide-directed RNase H cleavage, suggesting that the association of SLA1 maintains the SL RNA in a structural form which is distinct from the structure of the SL RNA in the steady state. In T. brucei cells depleted for the SL RNA core protein SmD1, SL RNA first accumulates in large amounts in the nucleus and then is expelled to the cytoplasm. Here, we demonstrate by in vivo aminomethyltrimethyl UV cross-linking studies that under SmD1 depletion, SLA1 remains bound to SL RNA and escorts the SL RNA to the cytoplasm. In situ hybridization with SLA1 and SL RNA demonstrates colocalization between SLA1 and the SL RNA transcription factor tSNAP42, as well as with Sm proteins, suggesting that SLA1 associates with SL RNA early in its biogenesis. These results demonstrate that SLA1 is a unique chaperonic RNA that functions during the early biogenesis of SL RNA to maintain a structure that is most probably suitable for cap 4 modification.

The assembly of a spliceosomal small nuclear ribonucleoprotein particle

The U1, U2, U4, U5 and U6 small nuclear ribonucleoprotein particles (snRNPs) are essential elements of the spliceosome, the enzyme that catalyzes the excision of introns and the ligation of exons to form a mature mRNA. Since their discovery over a quarter century ago, the structure, assembly and function of spliceosomal snRNPs have been extensively studied. Accordingly, the functions of splicing snRNPs and the role of various nuclear organelles, such as Cajal bodies (CBs), in their nuclear maturation phase have already been excellently reviewed elsewhere. The aim of this review is, then, to briefly outline the structure of snRNPs and to synthesize new and exciting developments in the snRNP biogenesis pathways.

Progress in the therapeutic applications of siRNAs against HIV-1

Therapeutic options against the human immunodeficiency virus type 1 (HIV-1) continue to expand with the development of new drugs and new therapeutic strategies. Nevertheless, management of HIV-1 infected individuals has become increasingly complex. The emergence of drug-resistant variants, the growing recognition of the long-term toxicity of antiretroviral therapies and the persistence of viral reservoirs justify the continued efforts to develop new anti-HIV-1 strategies. Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Here, the recent advances in siRNA-based therapies are reviewed.

An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival

Epstein-Barr virus (EBV) is a herpesvirus associated with nasopharyngeal carcinoma (NPC), gastric carcinoma (GC), and other malignancies. EBV is the first human virus found to express microRNAs (miRNAs), the functions of which remain largely unknown. We report on the regulation of a cellular protein named p53 up-regulated modulator of apoptosis (PUMA) by an EBV miRNA known as miR-BART5, which is abundantly expressed in NPC and EBV-GC cells. Modulation of PUMA expression by miR-BART5 and anti–miR-BART5 oligonucleotide was demonstrated in EBV-positive cells. In addition, PUMA was found to be significantly underexpressed in ∼60% of human NPC tissues. Although expression of miR-BART5 rendered NPC and EBV-GC cells less sensitive to proapoptotic agents, apoptosis can be triggered by depleting miR-BART5 or inducing the expression of PUMA. Collectively, our findings suggest that EBV encodes an miRNA to facilitate the establishment of latent infection by promoting host cell survival.

Signal peptide-dependent inhibition of MHC class I heavy chain translation by rhesus cytomegalovirus

The US2-11 region of human and rhesus cytomegalovirus encodes a conserved family of glycoproteins that inhibit MHC-I assembly with viral peptides, thus preventing cytotoxic T cell recognition. Since HCMV lacking US2-11 is no longer able to block assembly and transport of MHC-I, we examined whether this is also observed for RhCMV lacking the corresponding region. Unexpectedly, recombinant RhCMV lacking US2-11 was still able to inhibit MHC-I expression in infected fibroblasts, suggesting the presence of an additional MHC-I evasion mechanism. Progressive deletion analysis of RhCMV-specific genomic regions revealed that MHC-I expression is fully restored upon additional deletion of rh178. The protein encoded by this RhCMV-specific open reading frame is anchored in the endoplasmic reticulum membrane. In the presence of rh178, RhCMV prevented MHC-I heavy chain (HC) expression, but did not inhibit mRNA transcription or association of HC mRNA with translating ribosomes. Proteasome inhibitors stabilized a HC degradation intermediate in the absence of rh178, but not in its presence, suggesting that rh178 prevents completion of HC translation. This interference was signal sequence-dependent since replacing the signal peptide with that of CD4 or murine HC rendered human HCs resistant to rh178. We have identified an inhibitor of antigen presentation encoded by rhesus cytomegalovirus unique in both its lack of homology to any other known protein and in its mechanism of action. By preventing signal sequence-dependent HC translocation, rh178 acts prior to US2, US3 and US11 which attack MHC-I proteins after protein synthesis is completed. Rh178 is the first viral protein known to interfere at this step of the MHC-I pathway, thus taking advantage of the conserved nature of HC leader peptides, and represents a new mechanism of translational interference.

To avoid immune detection by cytotoxic T lymphocytes, viruses interfere with antigen presentation by major histocompatibility complex class I (MHC-I) molecules. We have discovered a unique cytomegaloviral protein that interferes with the biosynthesis of MHC-I heavy chains and was thus termed viral inhibitor of heavy chain expression (VIHCE). We show that VIHCE does not affect transcription of MHC-I mRNA or the formation of poly-ribosomes. Surprisingly, however, very little MHC-I protein is detected, even when proteasomal protein degradation is inhibited, suggesting incomplete protein translation. Interestingly, VIHCE requires the proper MHC-I signal peptide, suggesting that CMV takes advantage of the high conservation of MHC-I signal peptides and interferes with protein translation by inhibiting signal sequence-dependent protein translocation. This is the first description of a viral protein that specifically targets the translation of a cellular immuno-stimulatory protein.

Interfering RNA and HIV: reciprocal interferences

In this review, a quick presentation of what interfering RNA (iRNA) are—small RNA able to exert an inhibition on gene expression at a posttranscriptional level, based on sequence homology between the iRNA and the mRNA—will be given. The many faces of the interrelations between iRNA and viruses, particularly HIV, will be reviewed. Four kinds of interactions have been described: i) iRNA of viral origin blocking viral RNA, ii) iRNA of viral origin downregulating cellular mRNA, iii) iRNA of cellular origin (microRNA) targeting viral RNA, and iv) microRNA downregulating cellular mRNA encoding cell proteins used by the virus for its replication. Next, HIV strategies to manipulate these interrelations will be considered: suppression of iRNA biosynthesis by Tat, trapping by the HIV TAR sequence of a cell component, TRBP, necessary for iRNA production and action, and induction by the virus of some microRNA together with suppression of others. Then, we will discuss the putative effects of these mutual influences on viral replication as well as on viral latency, immune response, and viral cytopathogenicity. Finally, the potential consequences on the human infection of genetic polymorphisms in microRNA genes and the therapeutic potential of iRNA will be presented.

Role of protein translocation pathways across the endoplasmic reticulum in Trypanosoma brucei

The translocation of secretory and membrane proteins across the endoplasmic reticulum (ER) membrane is mediated by co-translational (via the signal recognition particle (SRP)) and post-translational mechanisms. In this study, we investigated the relative contributions of these two pathways in trypanosomes. A homologue of SEC71, which functions in the post-translocation chaperone pathway in yeast, was identified and silenced by RNA interference. This factor is essential for parasite viability. In SEC71-silenced cells, signal peptide (SP)-containing proteins traversed the ER, but several were mislocalized, whereas polytopic membrane protein biogenesis was unaffected. Surprisingly trypanosomes can interchangeably utilize two of the pathways to translocate SP-containing proteins except for glycosylphosphatidylinositol-anchored proteins, whose level was reduced in SEC71-silenced cells but not in cells depleted for SRP68, an SRP-binding protein. Entry of SP-containing proteins to the ER was significantly blocked only in cells co-silenced for the two translocation pathways (SEC71 and SRP68). SEC63, a factor essential for both translocation pathways in yeast, was identified and silenced by RNA interference. SEC63 silencing affected entry to the ER of both SP-containing proteins and polytopic membrane proteins, suggesting that, as in yeast, this factor is essential for both translocation pathways in vivo. This study suggests that, unlike bacteria or other eukaryotes, trypanosomes are generally promiscuous in their choice of mechanism for translocating SP-containing proteins to the ER, although the SRP-independent pathway is favored for glycosylphosphatidylinositol-anchored proteins, which are the most abundant surface proteins in these parasites.

MicroRNAs, the immune system and rheumatic disease

MicroRNAs (miRNAs) are short noncoding RNA molecules that modulate the expression of multiple target genes at the post-transcriptional level and are implicated in a wide array of cellular and developmental processes. In hematopoietic cells, miRNA levels are dynamically regulated during lineage differentiation and also during the course of the immune response. Mouse models have provided good evidence for miRNAs being key players in the establishment of hematopoietic lineages. Furthermore, miRNA-dependent alterations in gene expression in hematopoietic cells are critical for mounting an appropriate immune response to a wide range of pathogens, spontaneously emerging tumors, and autoimmune cells. Deregulation of hematopoietic-specific miRNA expression results in defects in both central and peripheral tolerance, hematopoietic malignancies, and sometimes both. Abnormal expression of miRNAs-which is implicated in inflammation-has also been found in patients with rheumatoid arthritis. These findings identify miRNAs as critical targets for immunomodulatory drug development.

Microfluidic-based enzymatic on-chip labeling of miRNAs

Small noncoding RNAs (sncRNAs) have moved from oddity to recognized important players in gene regulation. Next generation sequencing approaches discover more and more such molecules from a variety of different groups, but flexible tools translating this sequence information into affordable high-throughput assays are missing. Here we describe a microfluidic primer extension assay (MPEA) for the detection of sncRNAs on highly flexible microfluidic microarrays which combines several beneficial parameters: it can effortless incorporate any new sequence information; it is sensitive enough to work with as little as 20ng of total RNA and has a high level of specificity owing to a combination of a conventional hybridization assay and an enzymatic elongation step. Importantly, no labeling step is needed before hybridization and - because of its high sensitivity - no amplification is required. Both aspects ensure that no bias is introduced by such processes. Although the assay is exemplified with miRNAs, the flexibility of the technology platform allows the analysis of any type of sncRNA, such as piRNAs.

MicroRNA epigenetic alterations: predicting biomarkers and therapeutic targets in human diseases

MicroRNAs (miRNAs) consist of a class of evolutionarily conserved small non-coding RNA that regulates target messenger RNAs by mechanisms such as incomplete base pairing and post-transcriptional gene silencing. Recent studies have shown that aberrant miRNA expression is a common feature of many human disorders including aging, heart diseases, cancer, autoimmune diseases and others. It seems likely that miRNA expression levels can be used as novel diagnostic markers. MiRNAs may also provide a new strategy for therapeutic interventions. In this review, we focus on recent advances in understanding how miRNA changes contribute to disease development and their potential as novel biomarkers and therapeutic targets for human diseases.

MicroRNAs in the immune response

MicroRNAs (miRs) were only discovered little more than a decade ago, yet it has become rapidly clear that they are crucial posttranscriptional regulators of gene expression by decreasing the abundance or translational efficiency of mRNAs [Maroney PA, Yu Y, Nilsen TW. MicroRNAs, mRNAs, and translation. Cold Spring Harb Symp Quant Biol 2006;71: 531-5; Nilsen TW. Mechanisms of microRNA-mediated gene regulation in animal cells. Trends Genet 2007;23: 243-9], [1,2]. While the role of miRs in cell fate decisions linked to proliferation, differentiation and apoptosis was recognized early on, the importance of these noncoding small RNAs on immune system development and response has only recently become evident. In addition to facilitating cell fate decisions of immune cells (e.g. miR-181a and miR-223), miRs also regulate central elements of the adaptive immune response such as antigen presentation (e.g. miR-155) and T cell receptor signaling (mir-181a). Furthermore, miRs are involved in innate immunity through regulation of Toll-like receptor signaling and cytokine responses (e.g. miR-146). Intriguingly, cellular miRs not only alter immune cell development and function, but are also able to directly affect viral replication. Conversely, virus-encoded miRs shape the host-virus interactions and regulate the viral life cycle. Here, we provide a brief overview on the role of cellular and viral miRs in the development and function of the immune system.

Evolutionary diversification of the Sm family of RNA-associated proteins

The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Archaea typically carry one or two forms of Sm proteins and assemble one homomorphic ring per Sm protein. Eukaryotes typically carry 16 or more Sm proteins that assemble to form heteromorphic rings which lie at the center of a number of critical RNA-associated small nuclear ribonucleoproteins (snRNPs). High Sm protein diversity and heteromorphic Sm rings are features stretching back to the origin of eukaryotes; very deep phylogenetic divisions among existing Sm proteins indicate simultaneous evolution across essentially all existing eukaryotic life. Two basic forms of heteromorphic Sm rings are found in eukaryotes. Fixed Sm rings are highly stable and static and are assembled around an RNA cofactor. Flexible Sm rings also stabilize and chaperone RNA but assemble in the absence of an RNA substrate and, more significantly, associate with and dissociate from RNA substrates more freely than fixed rings. This suggests that the conformation of flexible Sm rings might be modified in some specific manner to facilitate association and dissociation with RNA. Diversification of eukaryotic Sm proteins may have been initiated by gene transfers and/or genome clashes that accompanied the origin of the eukaryotic cell itself, with further diversification driven by a greater need for steric specificity within increasingly complex snRNPs.

MicroRNA prediction with a novel ranking algorithm based on random walks

MicroRNA (miRNAs) play essential roles in post-transcriptional gene regulation in animals and plants. Several existing computational approaches have been developed to complement experimental methods in discovery of miRNAs that express restrictively in specific environmental conditions or cell types. These computational methods require a sufficient number of characterized miRNAs as training samples, and rely on genome annotation to reduce the number of predicted putative miRNAs. However, most sequenced genomes have not been well annotated and many of them have a very few experimentally characterized miRNAs. As a result, the existing methods are not effective or even feasible for identifying miRNAs in these genomes.

Aiming at identifying miRNAs from genomes with a few known miRNA and/or little annotation, we propose and develop a novel miRNA prediction method, miRank, based on our new random walks- based ranking algorithm. We first tested our method on Homo sapiens genome; using a very few known human miRNAs as samples, our method achieved a prediction accuracy greater than 95%. We then applied our method to predict 200 miRNAs in Anopheles gambiae, which is the most important vector of malaria in Africa. Our further study showed that 78 out of the 200 putative miRNA precursors encode mature miRNAs that are conserved in at least one other animal species. These conserved putative miRNAs are good candidates for further experimental study to understand malaria infection.

Availability: MiRank is programmed in Matlab on Windows platform. The source code is available upon request.

Contact:zhang@cse.wustl.edu

Viral and cellular microRNAs as determinants of viral pathogenesis and immunity

MicroRNAs (miRNAs) have recently emerged as key posttranscriptional regulators of gene expression in multicellular eukaryotes. It is increasingly clear that miRNAs of both viral and cellular origin can positively or negatively influence viral replication. Viral miRNAs can directly alter host physiology, including components of the immune system, and host miRNAs can directly alter the virus life cycle. Here, we discuss what is known about how viral and cellular miRNAs influence viral replication and pathogenic potential through their regulation of viral mRNAs or by reshaping cellular gene expression.

Parasites lead to evolution of robustness against gene loss in host signaling networks

Many biological networks can maintain their function against single gene loss. However, the evolutionary mechanisms responsible for such robustness remain unclear. Here, we demonstrate that antagonistic host–parasite interactions can act as a selective pressure driving the emergence of robustness against gene loss. Using a model of host signaling networks and simulating their coevolution with parasites that interfere with network function, we find that networks evolve both redundancy and specific architectures that allow them to maintain their response despite removal of proteins. We show that when the parasite pressure is removed, subsequent evolution can lead to loss of redundancy while architecture-based robustness is retained. Contrary to intuition, increased parasite virulence hampers evolution of robustness by limiting the generation of population level diversity in the host. However, when robustness emerges under high virulence, it tends to be stronger. These findings predict an increased presence of robustness mechanisms in biological networks operating under parasite interference. Conversely, the presence of such mechanisms could indicate current or past parasite interference.

NKG2D ligands: key targets of the immune response

NKG2D is an activating receptor expressed by NK and T cells. NKG2D ligands show a restricted expression in normal tissues, but they are frequently overexpressed in cancer and infected cells. The binding of NKG2D to its ligands activates NK and T cells and promotes cytotoxic lysis of the cells expressing these molecules. The mechanisms involved in the expression of the ligands of NKG2D play a key role in the recognition of stressed cells by the immune system and represent a promising therapeutic target for improving the immune response against cancer or autoimmune disease. In this review, we analyse the recent advances in understanding the regulation of NKG2D ligand expression and their therapeutic implications.

Human cytomegalovirus infection alters the expression of cellular microRNA species that affect its replication

The human genome encodes over 500 microRNAs (miRNAs), small RNAs (19 to 26 nucleotides [nt]) that regulate the expressions of diverse cellular genes. Many cellular processes are altered through a variety of mechanisms by human cytomegalovirus (HCMV) infection. We asked whether HCMV infection leads to changes in the expression of cellular miRNAs and whether HCMV-regulated miRNAs are important for HCMV replication. Levels of most miRNAs did not change markedly during infection, but some were positively or negatively regulated. Patterns of miRNA expression were linked to the time course of infection. Some similarly reregulated miRNAs share identical or similar seed sequences, suggesting coordinated regulation of miRNA species that have shared targets. miRNAs miR-100 and miR-101 were chosen for further analyses based on their reproducible changes in expression after infection and on the basis of having predicted targets in the 3' untranslated regions (3'-UTR) of genes encoding components of the mammalian target of rapamycin (mTOR) pathway, which is important during HCMV infection. Reporter genes that contain the 3'-UTR of mTOR (predicted targets for miR-100 and miR-101) or raptor (a component of the mTOR pathway; predicted site for miR-100) were constructed. Mimics of miR-100 and miR-101 inhibited expression from the mTOR construct, while only miR-100 inhibited the raptor construct. Together, miR-100 and miR-101 reduced mTOR protein levels. While the miR-100 and miR-101 mimics individually modestly inhibited production of infectious progeny, much greater inhibition was achieved with a combination of both (33-fold). Our key finding is that HCMV selectively manipulates the expression of some cellular miRNAs to help its own replication.

Small RNAs in viral infection and host defense

Small RNAs are the key mediators of RNA silencing and related pathways in plants and other eukaryotic organisms. Silencing pathways couple the destruction of double-stranded RNA with the use of the resulting small RNAs to target other nucleic acid molecules that contain the complementary sequence. This discovery has revolutionized our ideas about host defense and genetic regulatory mechanisms in eukaryotes. Small RNAs can direct the degradation of mRNAs and single-stranded viral RNAs, the modification of DNA and histones, and the inhibition of translation. Viruses might even use small RNAs to do some targeting of their own to manipulate host gene expression. This review highlights the current understanding and new insights concerning the roles of small RNAs in virus infection and host defense in plants.

MicroRNA miR-328 regulates zonation morphogenesis by targeting CD44 expression

Morphogenesis is crucial to initiate physiological development and tumor invasion. Here we show that a microRNA controls zonation morphogenesis by targeting hyaluronan receptor CD44. We have developed a novel system to study microRNA functions by generating constructs expressing pre-miRNAs and mature miRNAs. Using this system, we have demonstrated that expression of miR-328 reduced cell adhesion, aggregation, and migration, and regulated formation of capillary structure. Protein analysis indicated that miR-328 repressed CD44 expression. Activities of luciferase constructs harboring the target site in CD44, but not the one containing mutation, were repressed by miR-328. Zonation morphogenesis appeared in cells transfected by miR-328: miR-328-transfected cells were present on the surface of zonating structures while the control cells stayed in the middle. MiR-328-mediated CD44 actions was validated by anti-CD44 antibody, hyaluronidase, CD44 siRNA, and CD44 expression constructs. In vivo experiments showed that CD44-silencing cells appeared as layers on the surfaces of nodules or zonating structures. Immuno-histochemistry also exhibited CD44-negative cells on the surface layers of normal rat livers and the internal zones of Portal veins. Our results demonstrate that miR-328 targets CD44, which is essential in regulating zonation morphogenesis: silencing of CD44 expression is essential in sealing the zonation structures to facilitate their extension and to inhibit complex expansion.

Everything you wanted to know about small RNA but were afraid to ask

MicroRNAs are a class of recently discovered small RNA molecules that regulate other genes in the human genome. Studies in human cells and model organisms have begun to reveal the mechanisms of microRNA activity, and the wide range of normal physiological functions they influence. Their alteration in pathologic states from cancer to cardiovascular disease is also increasingly clear. A review of current evidence for the role of these molecules in human health and disease will be helpful to pathologists and medical researchers as the fascinating story of these small regulators continues to unfold.

New roles for large and small viral RNAs in evading host defences

It has been known for decades that some clinically important viruses encode abundant amounts of non-coding RNAs (ncRNAs) during infection. Until recently, the number of viral ncRNAs identified was few and their functions were mostly unknown. Although our understanding is still in its infancy, several recent reports have identified new functions for viral microRNAs and larger ncRNAs. These results so far show that different classes of viral ncRNAs act to autoregulate viral gene expression and evade host antiviral defences such as apoptosis and the immune response.

Modulation of natural killer cells by human cytomegalovirus

Human cytomegalovirus (HCMV) causes lifelong, persistent infections and its survival is under intense, continuous selective pressure from the immune system. A key aspect of HCMV's capacity for survival lies in immune avoidance. In this context, cells undergoing productive infection exhibit remarkable resistance to natural killer (NK) cell-mediated cytolysis in vitro. To date, six genes encoding proteins (UL16, UL18, UL40, UL83, UL141 and UL142) and one encoding a microRNA (miR-UL112) have been identified as capable of suppressing NK cell recognition. Even though HCMV infection efficiently activates expression of ligands for the NK cell activating receptor NKG2D, at least three functions (UL16, UL142 and miR-UL112) act in concert to suppress presentation of these ligands on the cell surface. Although HCMV downregulates expression of endogenous MHC-I, it encodes an MHC-I homologue (UL18) and also upregulates the expression of cellular HLA-E through the action of UL40. The disruption of normal intercellular connections exposes ligands for NK cell activating receptors on the cell surface, notably CD155. HCMV overcomes this vulnerability by encoding a function (UL141) that acts post-translationally to suppress cell surface expression of CD155. The mechanisms by which HCMV systematically evades (or, more properly, modulates) NK cell recognition constitutes an area of growing understanding that is enhancing our appreciation of the basic mechanisms of NK cell function in humans.

Identification and function of human cytomegalovirus microRNAs

microRNAs are an extensive class of non-coding genes that regulate gene expression through post-transcriptional repression. These small RNAs are evolutionarily conserved and are likely to be a basic mechanism of gene regulation present within most eukaryotic organisms. Over 100 viral miRNAs have been identified to date through a combination of bioinformatics and cloning studies. In this review we discuss the use of bioinformatics for the identification of HCMV miRNAs and also for the discovery of potential target transcripts. Such studies will enable us to define the functional role of viral miRNAs and gain a better understanding of viral gene regulation.

Immune evasion of natural killer cells by viruses

Natural killer (NK) cells are important in the host resistance to viral infections. They are among the first cells to sense the release of proinflammatory cytokines, as well as the downregulation of surface MHC class I molecules and molecules induced by viral invasion of cells. Various viral functions have evolved to counter NK cell responses illustrating the evolutionary struggles between viruses and NK cells. Ligands for NK cell receptors are primary targets for viral immunoevasion. In order to counteract NK cell activation via the 'missing self'-axis, viruses encode proteins which serve as ligands for inhibitory NK cell receptors. Viruses also downmodulate the ligands for the activating NK cell receptors and encode soluble ligands which block these receptors. In addition to viral immunoregulatory proteins, regulatory RNAs can also inhibit the expression of ligands for NK cell receptors. Improving our understanding of viral regulation of NK cell function could be essential for designing more efficient measures in the prophylaxis and treatment of virus-induced pathology.

Natural killer cells: diversity in search of a niche

Over the years, the enigmatic lifestyle of natural killer (NK) cells has fascinated immunologists. Elucidating the principles governing NK cell biology is a constant source of surprise, as these lymphocytes often break the rules of lymphocyte 'behavior' established by their T and B cell counterparts. In this Focus issue, experts address how NK cells have secured a fundamental place in the immune system, how they 'see' their targets and how they participate in and influence immune responses. We now need to understand how environmental 'niches' condition the generation and function of distinct NK cell subsets in vivo. Ultimately, we can hope that unraveling the mysteries of how these atypical lymphocytes function will have an impact on human disease therapies.

Viral miRNAs: tiny but mighty helpers for large and small DNA viruses

Recognition of the importance of noncoding RNAs has risen exponentially since the discovery that small molecules of 20–26 nucleotides in length were at the core of all RNA silencing phenomena. Among those small RNAs, miRNAs clearly represent the most prominent family and have been implicated in a wide range of biological processes. Recently, it has been recognized that even viruses encode their own miRNAs, and this finding has unveiled a new level in the study of host–virus interactions. Viral miRNAs have been mainly described in herpesviruses, including the oncogenic gammaherpesviruses, such as Epstein–Barr virus or Kaposi’s sarcoma-associated herpesvirus, and they have been shown to regulate the expression of both viral and cellular genes. We are only just starting to elucidate the function of viral miRNAs, however, the results obtained so far clearly indicate that they play a prominent role in the virus life cycle.

Human MHC architecture and evolution: implications for disease association studies

Major histocompatibility complex (MHC) variation is a key determinant of susceptibility and resistance to a large number of infectious, autoimmune and other diseases. Identification of the MHC variants conferring susceptibility to disease is problematic, due to high levels of variation and linkage disequilibrium. Recent cataloguing and analysis of variation over the complete MHC has facilitated localization of susceptibility loci for autoimmune diseases, and provided insight into the MHC's evolution. This review considers how the unusual genetic characteristics of the MHC impact on strategies to identify variants causing, or contributing to, disease phenotypes. It also considers the MHC in relation to novel mechanisms influencing gene function and regulation, such as epistasis, epigenetics and microRNAs. These developments, along with recent technological advances, shed light on genetic association in complex disease.

Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: implications for latency

A quantitative algorithm was developed and applied to predict target genes of microRNAs encoded by herpesviruses. Although there is almost no conservation among microRNAs of different herpesvirus subfamilies, a common pattern of regulation emerged. The algorithm predicts that herpes simplex virus 1, human cytomegalovirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus all employ microRNAs to suppress expression of their own genes, including their immediate-early genes. In the case of human cytomegalovirus, a virus-coded microRNA, miR-112-1, was predicted to target the viral immediate-early protein 1 mRNA. To test this prediction, mutant viruses were generated that were unable to express the microRNA, or encoded an immediate-early 1 mRNA lacking its target site. Analysis of RNA and protein within infected cells demonstrated that miR-UL112-1 inhibits expression of the major immediate-early protein. We propose that herpesviruses use microRNA-mediated suppression of immediate-early genes as part of their strategy to enter and maintain latency.

Analysis of the expression profiles of Marek's disease virus-encoded microRNAs by real-time quantitative PCR

MicroRNAs (miRNAs) are a large class of endogenous approximately 22-nucleotide long non-coding RNAs involved in post-transcriptional silencing of gene expression by translational repression or direct cleavage of the target mRNAs. Several hundreds of miRNAs have now been identified in a wide range of organisms including many viruses. Marek's disease virus serotype 1 (MDV-1) is a highly contagious oncogenic herpesvirus that induces fatal T-cell lymphomas in chickens. MDV-1 has been shown recently to encode several miRNAs clustered in the Meq and LAT region of the viral genome. The majority of these miRNAs are expressed at very high levels in infected chicken embryo fibroblasts (CEF) as well as in MDV-transformed lymphomas and lymphoblastoid cell lines derived from tumours. As part of the studies to evaluate the functions of these miRNAs, a quantitative RT-PCR to analyse the expression of three MDV-encoded miRNAs, viz. miR-4, miR-8 and miR-12 in CEF infected with oncogenic strain RB-1B and vaccine strain CVI988 was developed. The study shows that these miRNAs are expressed at very high levels in the tumour tissues compared to the non-tumour tissues from the infected birds indicating that expression levels of MDV-1 miRNAs can be used as biomarkers for transformation.

Identification of the heptameric Lsm complex that binds U6 snRNA in Trypanosoma brucei

Lsm proteins are ubiquitous, multifunctional proteins that are involved in nuclear processing and turnover of many RNAs in eukaryotes. Lsm proteins form two distinct complexes, the Lsm2-8 complex, which binds U6 snRNA, and the Lsm1-7 complex, which governs mRNA degradation. Previously, seven Lsm proteins were identified in Trypanosoma brucei. Two of these proteins were later identified as SSm proteins (specific spliceosomal Sm proteins). In this study, the Lsm proteins (Lsm2 and Lsm5) that bind to U6 snRNA were identified. RNAi silencing and protein purification of TAP-tagged Lsm proteins were used to identify all the components of the trypanosome heptameric Lsm2-8 complex. Localization studies demonstrated that these proteins are found in the nucleus, near the nucleolus. Lsm proteins were not detected in cytoplasmic bodies that were tagged with YFP-Dhh1, which may suggest that in trypanosomes, Lsm-mediated degradation is not confined to such bodies.

Evolutionary struggles between NK cells and viruses

Natural killer (NK) cells are well recognized for their ability to provide a first line of defence against viral pathogens and they are increasingly being implicated in immune responses against certain bacterial and parasitic infections. Reciprocally, viruses have devised numerous strategies to evade the activation of NK cells and have influenced the evolution of NK-cell receptors and their ligands. NK cells contribute to host defence by their ability to rapidly secrete cytokines and chemokines, as well as to directly kill infected host cells. In addition to their participation in the immediate innate immune response against infection, interactions between NK cells and dendritic cells shape the nature of the subsequent adaptive immune response to pathogens.

Human cytomegalovirus regulates surface expression of the viral protein UL18 by means of two motifs present in the cytoplasmic tail

UL18 is a trans-membrane viral protein expressed on human cytomegalovirus (HCMV)-infected cells, and its surface expression determines the interaction of infected cells with lymphocytes expressing the CD85j (LIR-1/ILT2) receptor. We previously showed that the UL18-CD85j interaction elicits activation of T lymphocytes. However, in in vitro cell models UL18 displays mostly undetectable surface expression. Thus, we asked how surface expression of UL18 is regulated. Domain-swapping experiments and construction of specific mutants demonstrated that two motifs on its cytoplasmic tail, homologous to YXXPhi and KKXX consensus sequences, respectively, are responsible for impairing UL18 surface expression. However, the presence of the whole HCMV genome, granted by HCMV infection of human fibroblasts, restored surface expression of either UL18 or chimeric proteins carrying the UL18 cytoplasmic tail, starting from the third day after infection. It is of note that the two motifs responsible for cytoplasmic retention are identical in all 17 HCMV strains examined. We disclosed a control mechanism used by the HCMV to regulate the availability of UL18 on the infected-cell surface to allow interaction with its ligand on T and NK cells.

RNA silencing suppressors: how viruses fight back

RNA silencing is a collective term that refers to diverse RNA-directed processes resulting in sequence-specific degradation of target RNA and repression of gene expression, either at transcriptional or post-transcriptional levels. In animals, fungi and plants, RNA silencing represents a mechanism guided by small RNAs against virus infection. Viruses can be inducers and targets of RNA silencing, and have evolved active and passive strategies to counter the cellular antiviral mechanism. This review discusses various approaches, including protein- and RNA-mediated silencing suppression and viral escape of RNA silencing without suppression, to highlight how viruses could fight back to survive under the universal host surveillance.

Micromanagement of the immune system by microRNAs

MicroRNAs (miRNAs) are an abundant class of evolutionarily conserved small non-coding RNAs that are thought to control gene expression by targeting mRNAs for degradation or translational repression. Emerging evidence suggests that miRNA-mediated gene regulation represents a fundamental layer of genetic programmes at the post-transcriptional level and has diverse functional roles in animals. Here, we provide an overview of the mechanisms by which miRNAs regulate gene expression, with specific focus on the role of miRNAs in regulating the development of immune cells and in modulating innate and adaptive immune responses.

Adenovirus E3/19K promotes evasion of NK cell recognition by intracellular sequestration of the NKG2D ligands major histocompatibility complex class I chain-related proteins A and B

The adenovirus (Ad) early transcription unit 3 (E3) encodes multiple immunosubversive functions that are presumed to facilitate the establishment and persistence of infection. Indeed, the capacity of E3/19K to inhibit transport of HLA class I (HLA-I) to the cell surface, thereby preventing peptide presentation to CD8(+) T cells, has long been recognized as a paradigm for viral immune evasion. However, HLA-I downregulation has the potential to render Ad-infected cells vulnerable to natural killer (NK) cell recognition. Furthermore, expression of the immediate-early Ad gene E1A is associated with efficient induction of ligands for the key NK cell-activating receptor NKG2D. Here we show that while infection with wild-type Ad enhances synthesis of the NKG2D ligands, major histocompatibility complex class I chain-related proteins A and B (MICA and MICB), their expression on the cell surface is actively suppressed. Both MICA and MICB are retained within the endoplasmic reticulum as immature endoglycosidase H-sensitive forms. By analyzing a range of cell lines and viruses carrying mutated versions of the E3 gene region, E3/19K was identified as the gene responsible for this activity. The structural requirements within E3/19K necessary to sequester MICA/B and HLA-I are similar. In functional assays, deletion of E3/19K rendered Ad-infected cells more sensitive to NK cell recognition. We report the first NK evasion function in the Adenoviridae and describe a novel function for E3/19K. Thus, E3/19K has a dual function: inhibition of T-cell recognition and NK cell activation.

Genomics and the immune system

While the hereditary information encoded in the Watson-Crick base pairing of genomes is largely static within a given individual, access to this information is controlled by dynamic mechanisms. The human genome is pervasively transcribed, but the roles played by the majority of the non-protein-coding genome sequences are still largely unknown. In this review we focus on insights to gene transcriptional regulation by placing special emphasis on genome-wide approaches, and on how non-coding RNAs, which derive from global transcription of the genome, in turn control gene expression. We review recent progress in the field with highlights on the immune system.

miRNAs: effectors of environmental influences on gene expression and disease

Discovered less than a decade ago, micro-RNAs (miRNAs) have emerged as important regulators of gene expression in mammals. They consist of short nucleic acids, on average approximately 22 nucleotides in length. The miRNAs exert their effect by binding directly to target messenger RNAs (mRNAs) and inhibiting mRNA stability and translation. Each miRNA can bind to multiple targets and many miRNAs can bind to the same target mRNA, allowing for a complex pattern of regulation of gene expression. Once bound to their targets, miRNAs can suppress translation of the mRNA by either sequestration or degradation of the message. Thus, miRNAs function as powerful and sensitive posttranscriptional regulators of gene expression. This review will summarize what is known about miRNA biogenesis, expression, regulation, function, mode of action, and role in disease processes with an emphasis on miRNAs in mammals. We discuss some of the methodology employed in miRNA research and the potential of miRNAs as therapeutic targets. The role of miRNAs in signal transduction and cellular stress is reviewed. Lastly, we identify new exciting avenues of research on the role of miRNAs in toxicogenomics and the possibility of epigenetic effects on gene expression.

MicroRNAs as targets for antisense-based therapeutics

MicroRNAs (miRNAs) are a novel class of endogenous non-coding single-stranded RNAs, which regulate gene expression post-transcriptionally by base pairing with their target mRNAs. So far > 5000 miRNA entries have been registered and miRNAs have been implicated in most, if not all, central cellular processes and several diseases. As the mechanism of action for miRNA regulation of target mRNAs is mediated by Watson-Crick base pairing, antisense oligonucleotides targeting the miRNAs appear as an obvious choice to specifically inhibit miRNA function. Indeed, miRNAs can be antagonized in vivo by oligonucleotides composed of high-affinity nucleotide mimics. Lessons learned from traditional antisense strategies and small-interfering RNA approaches, that is from potent nucleotide mimics, design rules, pharmacokinetics, administration and safety issues, are likely to pave the way for future clinical trials of miRNA-antagonizing oligonucleotides.

Murine cytomegalovirus regulation of NKG2D ligands

Human cytomegalovirus (HCMV) is a ubiquitous pathogen that causes morbidity risk in immunologically suppressed and immunodeficient patients including congenital infections. Approaches to curb the consequences of HCMV infections are restricted by a lack of complete understanding of viral pathogenesis. The infection of mice with murine cytomegalovirus (MCMV) as a model of HCMV infection has been particularly useful in elucidating the role of innate and adaptive immune response mechanisms. A large number of cytomegalovirus genes modulate the innate and the adaptive host immune response. The products of several MCMV genes are involved in subverting the natural killer (NK) cell response by down-modulating cellular ligands for the NKG2D receptor expressed on NK cells and CD8(+) T cells. Mutant viruses lacking these immunoevasion genes are attenuated with respect to virus growth in vivo. Given the importance of the NKG2D receptor in controlling both NK- and T cell-mediated immunity, it is of tremendous importance to understand the molecular mechanisms and consequences of viral regulation of the NKG2D ligands.

RNA interference: a multifaceted innate antiviral defense

The RNA interference mechanism utilizes short RNA duplexes to either suppress or induce target gene expression. Post-transcriptional regulation mediated by microRNA is an integral component of innate antiviral defense. The magnitude and the efficiency of viral restriction guided by RNA-based defenses, as well as the full physiological implication of host-pathogen engagement, constitute exciting areas of investigation in the biology of non-coding RNAs.

A human cytomegalovirus-encoded microRNA regulates expression of multiple viral genes involved in replication

Although multiple studies have documented the expression of over 70 novel virus-encoded microRNAs (miRNAs), the targets and functions of most of these regulatory RNA species are unknown. In this study a comparative bioinformatics approach was employed to identify potential human cytomegalovirus (HCMV) mRNA targets of the virus-encoded miRNA miR-UL112-1. Bioinformatics analysis of the known HCMV mRNA 3' untranslated regions (UTRs) revealed 14 potential viral transcripts that were predicted to contain functional target sites for miR-UL112-1. The potential target sites were screened using luciferase reporters that contain the HCMV 3'UTRs in co-transfection assays with miR-UL112-1. Three of the 14 HCMV miRNA targets were validated, including the major immediate early gene encoding IE72 (UL123, IE1), UL112/113, and UL120/121. Further analysis of IE72 regulation by miR-UL112-1 with clones encoding the complete major immediate early region revealed that the IE72 3'UTR target site is necessary and sufficient to direct miR-UL112-1-specific inhibition of expression in transfected cells. In addition, miR-UL112-1 regulation is mediated through translational inhibition rather than RNA degradation. Premature expression of miR-UL112-1 during HCMV infection resulted in a significant decrease in genomic viral DNA levels, suggesting a functional role for miR-UL112-1 in regulating the expression of genes involved in viral replication. This study demonstrates the ability of a viral miRNA to regulate multiple viral genes.

A viral microRNA functions as an orthologue of cellular miR-155

All metazoan eukaryotes express microRNAs (miRNAs), roughly 22-nucleotide regulatory RNAs that can repress the expression of messenger RNAs bearing complementary sequences. Several DNA viruses also express miRNAs in infected cells, suggesting a role in viral replication and pathogenesis. Although specific viral miRNAs have been shown to autoregulate viral mRNAs or downregulate cellular mRNAs, the function of most viral miRNAs remains unknown. Here we report that the miR-K12-11 miRNA encoded by Kaposi's-sarcoma-associated herpes virus (KSHV) shows significant homology to cellular miR-155, including the entire miRNA 'seed' region. Using a range of assays, we show that expression of physiological levels of miR-K12-11 or miR-155 results in the downregulation of an extensive set of common mRNA targets, including genes with known roles in cell growth regulation. Our findings indicate that viral miR-K12-11 functions as an orthologue of cellular miR-155 and probably evolved to exploit a pre-existing gene regulatory pathway in B cells. Moreover, the known aetiological role of miR-155 in B-cell transformation suggests that miR-K12-11 may contribute to the induction of KSHV-positive B-cell tumours in infected patients.

RNA interference as a genetic tool in trypanosomes

RNA interference (RNAi) is a cellular mechanism that is often exploited as a technique for quelling the expression of a specific gene. RNAi studies are carried out in vivo, making this a powerful means for the study of protein function in situ Several trypanosomatids, including those organisms responsible for human and animal diseases, naturally possess the machinery necessary for RNAi manipulations. This allows for the use of RNAi in unraveling many of the pressing questions regarding the parasite's unique biology. The completion of the Trypanosoma brucei genome sequence, coupled with several powerful genetic tools, has resulted in widespread utilization of RNAi in this organism. The key steps for RNAi-based reduction of gene expression, including parasite cell culture, DNA transfection, RNAi expression, and experimental execution, are discussed with a focus on procyclic forms of Trypanosoma brucei.