Decoding ARE-mediated decay: is microRNA part of the equation?

Messenger ribonucleic acids (mRNAs) containing adenine/uridine-rich elements (AREs) in their 3′ untranslated region are particularly labile, allowing for the regulation of expression for growth factors, oncoproteins, and cytokines. The regulators, effectors, and location of ARE-mediated decay (AMD) have been investigated by many groups in recent years, and several links have been found between AMD and microRNA-mediated decay. We highlight these similarities, along with recent advances in the field of AMD, and also mention how there is still much left unknown surrounding this specialized mode of mRNA decay

Pumilio directs deadenylation-associated translational repression of the cyclin-dependent kinase 1 activator RGC-32

Response gene to complement-32 (RGC-32) activates cyclin-dependent kinase 1, regulates the cell cycle and is deregulated in many human tumours. We previously showed that RGC-32 expression is upregulated by the cancer-associated Epstein-Barr virus (EBV) in latently infected B cells through the relief of translational repression. We now show that EBV infection of naïve primary B cells also induces RGC-32 protein translation. In EBV-immortalised cell lines, we found that RGC-32 depletion resulted in cell death, indicating a key role in B cell survival. Studying RGC-32 translational control in EBV-infected cells, we found that the RGC-32 3′untranslated region (3′UTR) mediates translational repression. Repression was dependent on a single Pumilio binding element (PBE) adjacent to the polyadenylation signal. Mutation of this PBE did not affect mRNA cleavage, but resulted in increased polyA tail length. Consistent with Pumilio-dependent recruitment of deadenylases, we found that depletion of Pumilio in EBV-infected cells increased RGC-32 protein expression and polyA tail length. The extent of Pumilio binding to the endogenous RGC-32 mRNA in EBV-infected cell lines also correlated with RGC-32 protein expression. Our data demonstrate the importance of RGC-32 for the survival of EBV-immortalised B cells and identify Pumilio as a key regulator of RGC-32 translation

Comparative Analysis of mRNA Targets for Human PUF-Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System

Genome-wide identification of mRNAs regulated by RNA-binding proteins is crucial to uncover post-transcriptional gene regulatory systems. The conserved PUF family RNA-binding proteins repress gene expression post-transcriptionally by binding to sequence elements in 3′-UTRs of mRNAs. Despite their well-studied implications for development and neurogenesis in metazoa, the mammalian PUF family members are only poorly characterized and mRNA targets are largely unknown. We have systematically identified the mRNAs associated with the two human PUF proteins, PUM1 and PUM2, by the recovery of endogenously formed ribonucleoprotein complexes and the analysis of associated RNAs with DNA microarrays. A largely overlapping set comprised of hundreds of mRNAs were reproducibly associated with the paralogous PUM proteins, many of them encoding functionally related proteins. A characteristic PUF-binding motif was highly enriched among PUM bound messages and validated with RNA pull-down experiments. Moreover, PUF motifs as well as surrounding sequences exhibit higher conservation in PUM bound messages as opposed to transcripts that were not found to be associated, suggesting that PUM function may be modulated by other factors that bind conserved elements. Strikingly, we found that PUF motifs are enriched around predicted miRNA binding sites and that high-confidence miRNA binding sites are significantly enriched in the 3′-UTRs of experimentally determined PUM1 and PUM2 targets, strongly suggesting an interaction of human PUM proteins with the miRNA regulatory system. Our work suggests extensive connections between the RBP and miRNA post-transcriptional regulatory systems and provides a framework for deciphering the molecular mechanism by which PUF proteins regulate their target mRNAs

Specificity factors in cytoplasmic polyadenylation

Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3′ untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man

Resolution of inflammation: a new therapeutic frontier

Dysregulated inflammation is a central pathological process in diverse disease states. Traditionally, therapeutic approaches have sought to modulate the pro- or anti-inflammatory limbs of inflammation, with mixed success. However, insight into the pathways by which inflammation is resolved has highlighted novel opportunities to pharmacologically manipulate these processes — a strategy that might represent a complementary (and perhaps even superior) therapeutic approach. This Review discusses the state of the art in the biology of resolution of inflammation, highlighting the opportunities and challenges for translational research in this field

HuR and its cleavage are key regulators of apoptotic cell death

Cells, and in fact all living organisms, are capable of responding to stimuli. Regardless of the source and purpose of the signal, when responding to varying factors, complex mechanisms ensure tight regulation of cellular processes. This is particularly true during cellular response to stress. Depending on the severity of a stress stimulus, cells may attempt to cope with and overcome the assault, or they may opt for an organized suicide, in the face of too potent a signal. To provide a tight control over cellular survival and death, numerous protein factors promote or inhibit apoptotic cell death. Intriguingly, not only does the mRNA-binding protein HuR contribute to regulating the expression of pro- and anti-apoptotic factors, but we previously discovered that in response to lethal stress, HuR is cleaved by active caspases, and that this event enhances apoptotic cell death. Given the broad spectrum of mRNAs regulated by HuR, and the well-documented overexpression of this protein in cancer development, we aimed to characterize the caspase-mediated cleavage of HuR and its implication in apoptotic progression. In doing so, we first delineated the signalling cascade that enables stress stimuli to trigger the cleavage of HuR, and confirmed that the HuR cleavage products (HuR-CPs) are capable of inducing apoptosis in non-lethal conditions. Furthermore, we clarified how one of these HuR-CPs, HuR-CP1, can further promote the cleavage of HuR. This is done by competitively binding to the HuR nuclear import factor TRN2, thus causing full-length HuR to accumulate in the cytoplasm, as has been reported to occur during apoptosis. Finally, we obtained data suggesting that the HuR-CPs may coordinate a post-transcriptional regulatory program that is distinct from that of full-length HuR. The HuR-CPs bind and stabilize the mRNA of the pro-apoptotic caspase-9 to a greater extent than does full-length HuR, and bind to a lesser degree to the HuR mRNA target Prothymosin α, which encodes an anti-apoptotic regulator of cell death. Collectively, our findings have revealed the mechanism by which HuR switches its function from promoting cell survival in normal and non-lethal conditions, to becoming a promoter of apoptotic cell death in response to lethal stress. Mechanistically, this occurs via the cleavage of HuR, through particular signalling pathways. The two HuR-CPs that are generated may exercise different functions to mediate altered post-transcriptional regulatory events, thus enhancing the progress of apoptosis. Beyond extensively characterizing the cleavage of HuR, this cumulative work brings to light previously undiscovered mechanisms of regulation of gene expression, particularly during the strictly-controlled process of cell stress response.Les cellules, ainsi que tous les êtres vivants sont capables de réagir à des stimuli. Quelque soit la source et le rôle de ces signaux, les mécanismes d'action en réponse à ces stimuli sont fortement régulés au sein de la cellule. Ceci s'avère particulièrement vrai en réponse à des stress puisque leur intensité détermine la réponse cellulaire. En effet, les cellules peuvent décider de continuer à vivre, en s'adaptant à cet assaut, ou bien elles peuvent décider d'induire leur mort si le stress est trop fort. Pour bien contrôler la balance entre la survie et la mort, plusieurs protéines activent ou inhibent la mort cellulaire par l'apoptose. Notamment, la protéine HuR, qui s'associe avec des ARN messagers (ARNms), peut réguler l'expression de facteurs activateurs et inhibiteurs de l'apoptose. De plus, nous avons découvert que de forts stress induisent un clivage de HuR par des caspases activées ainsi que l'apoptose. Malgré l'implication de HuR dans l'apoptose, ses niveaux d'expression sont élevés durant le développement de certains cancers et permettent la régulation de l'expression de divers ARNms. Nous nous sommes donc posés comme objectif de caractériser le clivage de HuR et son rôle dans l'apoptose. Premièrement, nous avons déterminé la cascade de signaux induisant le clivage de HuR. En même temps, nous avons confirmé que les produits de clivage de HuR (HuR-CPs) sont capables d'induire l'apoptose dans des conditions non toxiques. Deuxièmement, nous avons découvert comment un de ces produits de clivage, HuR-CP1, peut augmenter le clivage propre de HuR. HuR-CP1 accompli ceci en s'associant compétitivement avec le facteur TRN2, qui régule l'import nucléaire de HuR, causant ainsi une augmentation du niveau de HuR non-clivé dans le cytoplasme, comme déjà constaté durant l'apoptose. Finalement, nous avons obtenu des résultats qui suggèrent que les HuR-CPs peuvent coordonner un programme de régulation au niveau post-transcriptionel différent de celui effectué par HuR. Les produits de clivage de HuR s'associent et stabilisent l'ARNm du facteur apoptique caspase-9 plus fortement que HuR non-clivé, et ils s'associent moins fortement que HuR avec l'ARNm de Prothymosin α, qui code un facteur de survie. En résumé, nos découvertes ont dévoilé le mécanisme par lequel la fonction de HuR transite entre activateur de la survie cellulaire dans des conditions normales et non-toxiques, et inducteur de l'apoptose suite à un signal toxique. Ceci est dû au clivage de HuR induit par des voies de signalisations spécifiques. Les deux HuR-CPs qui sont produits ont des effets différents de HuR pour influencer la régulation post-transcriptionel, et en conséquence, peuvent promouvoir l'apoptose. Nos travaux ont non seulement caractérisé le clivage de HuR, mais nous avons découvert un nouveau mécanisme de régulation d'expression génétique, spécifiquement durant la réponse cellulaire aux stress