New RNA playgrounds : non-coding RNAs and RNA-binding proteins control cellular processes

Het eiwit Dead End noodzakelijk is voor het overleven van geslachtscellen. Het beschermt enkele genen tegen blokkades door microRNA__s. Dat stelt onderzoeker Martijn Kedde van het NKI-AVL in zijn proefschrift. Kedde promoveert donderdag 22 januari. MicroRNA__s, kleine stukjes RNA, blokkeren de ontwikkeling van geslachtscellen door enkele genen te remmen. Om te zorgen dat geslachtscellen zich toch kunnen ontwikkelen, is er het eiwit Dead End 1 (Dnd1). Het eiwit schermt het boodschapper-RNA van het erfelijk materiaal van de geslachtscel af zodat microRNA-430 er niet aan kan binden. In feite een doodlopende weg voor de microRNA__s. Ook heeft Kedde, onderzoeker in de groep van Reuven Agami, de rol van hTR in reactie op schade aan het DNA beschreven. hTR is onderdeel van het telomerasecomplex, een enzym dat er voor zorgt dat kankercellen ongebreideld kunnen delen. Het blijkt dat hTR de groei van kankercellen in de hand werkt doordat het schade aan het DNA negeert. De rode draad in het proefschrift van Kedde is non-coderend RNA. De functies van de verschillende non-coderende RNA__s die hij beschrijft, laten zien dat het speelveld (de __playground__) van niet-coderende RNA__s steeds maar weer groter blijkt dan eerder werd aangenomen.UBL - phd migration 201

Sexual health of people with disability and chronic illness

Dit proefschrift beschrijft vijf empirische studies, waarvan drie studies gericht zijn op het in kaart brengen van diverse aspecten van de seksuele gezondheid van mensen met een chronische ziekte of een lichamelijke beperking, en in het bijzonder van jonge vrouwen met borstkanker. Deze studies geven onder andere inzicht in de ernst en de aard van de seksuele problemen die mensen met een chronische ziekte of een lichamelijke beperking ervaren, alsook in de aandoenings- en behandelingsgerelateerde factoren die hiermee samenhangen. De overige twee studies richten zich op de effecten van een kortdurende psychoseksuele behandeling welke specifiek is ontwikkeld voor mensen met een chronische ziekte of lichamelijke beperking, en op het hulpzoekgedrag bij seksuele problemen en factoren die hiermee samenhangen. De belangrijkste bevindingen van dit proefschrift worden hieronder samengevat. Hulpzoekgedrag van mensen met een chronische ziekte of een lichamelijke beperking Mensen met een chronische ziekte of lichamelijke beperking hebben een veel grotere kans op problemen rondom seksualiteit en seksuele gezondheid dan de algemene bevolking. Diverse internationale studies hebben aangetoond dat zowel mannen als vrouwen met een lichamelijke aandoening, zoals bijvoorbeeld dwarslaesie, hersenbeschadiging, spierziekte, artritis, neurologische aandoening en spina bifida, minder tevreden zijn over hun seksueel leven en een lagere seksuele en lichamelijke zelfwaardering hebben in vergelijking met gezonde mannen en vrouwen. Dit impliceert dat deze groep ook vaker behoefte zal hebben aan hulp bij seksuele problemen. Alhoewel er diverse onderzoeken zijn uitgevoerd naar het hulpzoekgedrag bij seksuele problemen onder de algemene bevolking, is het onbekend of mensen met een ziekte of een beperking een geschikte hulpverlener weten te vinden

Verteporfin ameliorates fibrotic aspects of Dupuytren's disease nodular fibroblasts irrespective the activation state of the cells

Dupuytren's disease is a chronic, progressive fibroproliferative condition of the hand fascia which results in digital contraction. So far, treatments do not directly interfere with the (myo)fibroblasts that are responsible for the formation of the collagen-rich cords and its contraction. Here we investigated whether verteporfin (VP) is able to inhibit the activation and subsequent differentiation of DD nodular fibroblasts into myofibroblasts. Fibroblasts were isolated from nodules of 7 Dupuytren patients. Cells are treated (1) for 48 h with 5 ng/ml transforming growth factor β1 (TGF-β1) followed by 48 h with/without 250 nM VP in the absence of TGF-β1, or treated (2) for 48 h with TGF-β1 followed by 48 h with/without VP in the presence of TGF-β1. mRNA levels were measured by means of Real-Time PCR, and proteins were visualized by means of Western blotting and/or immunofluorescence. Quantitative data were statistically analyzed with GraphPad Prism using the paired t-test. We found that fibroblasts activated for 48 h with TGF-β1 show a decrease in mRNA levels of COL1A1, COL3A1, COL4A1, PLOD2, FN1EDA, CCN2 and SERPINE1 when exposed for another 48 h with VP, whereas no decrease is seen for ACTA2, YAP1, SMAD2 and SMAD3 mRNA levels. Cells exposed for an additional 48 h with TGF-β1, but now in the presence of VP, are not further activated anymore, whereas in the absence of VP the cells continue to differentiate into myofibroblasts. Collagen type I, fibronectin-extra domain A, α-smooth muscle actin, YAP1, Smad2 and Smad3 protein levels were attenuated by both VP treatments. We conclude that VP has strong anti-fibrotic properties: it is able to halt the differentiation of fibroblasts into myofibroblasts, and is also able to reverse the activation status of fibroblasts. The decreased protein levels of YAP1, Smad2 and Smad3 in the presence of VP explain in part the strong anti-fibrotic properties of VP. Verteporfin is clinically used as a photosensitizer for photodynamic therapy to eliminate abnormal blood vessels in the eye to attenuate macular degeneration. The antifibrotic properties of VP do not rely on photo-activation, as we used the molecule in its non-photoinduced state

AREsite: a database for the comprehensive investigation of AU-rich elements

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3′-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3′-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential role of the structural mRNA context in which these sequence motifs are embedded. AREsite is the first database that allows to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. Moreover, we also provide a detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite

HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA

The microRNA (miRNA)-mediated repression of protein synthesis in mammalian cells is a reversible process. Target mRNAs with regulatory AU-rich elements (AREs) in their 3′-untranslated regions (3′-UTR) can be relieved of miRNA repression under cellular stress in a process involving the embryonic lethal and altered vision family ARE-binding protein HuR. The HuR-mediated derepression occurred even when AREs were positioned at a considerable distance from the miRNA sites raising questions about the mechanism of HuR action. Here, we show that the relief of miRNA-mediated repression involving HuR can be recapitulated in different in vitro systems in the absence of stress, indicating that HuR alone is sufficient to relieve the miRNA repression upon binding to RNA ARE. Using in vitro assays with purified miRISC and recombinant HuR and its mutants, we show that HuR, likely by its property to oligomerize along RNA, leads to the dissociation of miRISC from target RNA even when miRISC and HuR binding sites are positioned at a distance. Further, we demonstrate that HuR association with AREs can also inhibit miRNA-mediated deadenylation of mRNA in the Krebs-2 ascites extract, in a manner likewise depending on the potential of HuR to oligomerize

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

MicroRNAs (miRNAs) are prevalent regulatory RNAs that mediate gene silencing and play key roles in diverse cellular processes. While synthetic RNA-based regulatory systems that integrate regulatory and sensing functions have been demonstrated, the lack of detail on miRNA structure–function relationships has limited the development of integrated control systems based on miRNA silencing. Using an elucidated relationship between Drosha processing and the single-stranded nature of the miRNA basal segments, we developed a strategy for designing ligand-responsive miRNAs. We demonstrate that ligand binding to an aptamer integrated into the miRNA basal segments inhibits Drosha processing, resulting in titratable control over gene silencing. The generality of this control strategy was shown for three aptamer–small molecule ligand pairs. The platform can be extended to the design of synthetic miRNAs clusters, cis-acting miRNAs and self-targeting miRNAs that act both in cis and trans, enabling fine-tuning of the regulatory strength and dynamics. The ability of our ligand-responsive miRNA platform to respond to user-defined inputs, undergo regulatory performance tuning and display scalable combinatorial control schemes will help advance applications in biological research and applied medicine

DAZL Relieves miRNA-Mediated Repression of Germline mRNAs by Controlling Poly(A) Tail Length in Zebrafish

BACKGROUND:During zebrafish embryogenesis, microRNA (miRNA) miR-430 contributes to restrict Nanos1 and TDRD7 to primordial germ cells (PGCs) by inducing mRNA deadenylation, mRNA degradation, and translational repression of nanos1 and tdrd7 mRNAs in somatic cells. The nanos1 and tdrd7 3'UTRs include cis-acting elements that allow activity in PGCs even in the presence of miRNA-mediated repression. METHODOLOGY/PRINCIPAL FINDINGS:Using a GFP reporter mRNA that was fused with tdrd7 3'UTR, we show that a germline-specific RNA-binding protein DAZ-like (DAZL) can relieve the miR-430-mediated repression of tdrd7 mRNA by inducing poly(A) tail elongation (polyadenylation) in zebrafish. We also show that DAZL enhances protein synthesis via the 3'UTR of dazl mRNA, another germline mRNA targeted by miR-430. CONCLUSIONS/SIGNIFICANCE:Our present study indicated that DAZL acts as an "anti-miRNA factor" during vertebrate germ cell development. Our data also suggested that miRNA-mediated regulation can be modulated on specific target mRNAs through the poly(A) tail control

Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity

MicroRNAs (miRNAs) interact with 3′-untranslated regions of messenger RNAs to restrict expression of most protein-coding genes during normal development and cancer. RNA-binding proteins (RBPs) can control the biogenesis, stability and activity of miRNAs. Here we identify RBM38 in a genetic screen for RBPs whose expression controls miRNA access to target mRNAs. RBM38 is induced by p53 and its ability to modulate miRNA-mediated repression is required for proper p53 function. In contrast, RBM38 shows lower propensity to block the action of the p53-controlled miR-34a on SIRT1. Target selectivity is determined by the interaction of RBM38 with uridine-rich regions near miRNA target sequences. Furthermore, in large cohorts of human breast cancer, reduced RBM38 expression by promoter hypermethylation correlates with wild-type p53 status. Thus, our results indicate a novel layer of p53 gene regulation, which is required for its tumour suppressive function

MiR-200c Regulates Noxa Expression and Sensitivity to Proteasomal Inhibitors

The pro-apoptotic p53 target Noxa is a BH3-only protein that antagonizes the function of selected anti-apoptotic Bcl-2 family members. While much is known regarding the transcriptional regulation of Noxa, its posttranscriptional regulation remains relatively unstudied. In this study, we therefore investigated whether Noxa is regulated by microRNAs. Using a screen combining luciferase reporters, bioinformatic target prediction analysis and microRNA expression profiling, we identified miR-200c as a negative regulator of Noxa expression. MiR-200c was shown to repress basal expression of Noxa, as well as Noxa expression induced by various stimuli, including proteasomal inhibition. Luciferase reporter experiments furthermore defined one miR-200c target site in the Noxa 3′UTR that is essential for this direct regulation. In spite of the miR-200c:Noxa interaction, miR-200c overexpression led to increased sensitivity to the clinically used proteasomal inhibitor bortezomib in several cell lines. This apparently contradictory finding was reconciled by the fact that in cells devoid of Noxa expression, miR-200c overexpression had an even more pronounced positive effect on apoptosis induced by proteasomal inhibition. Together, our data define miR-200c as a potentiator of bortezomib-induced cell death. At the same time, we show that miR-200c is a novel negative regulator of the pro-apoptotic Bcl-2 family member Noxa