TY - JOUR A1 - Kuai, Yue A1 - Gong, Xin A1 - Ding, Liya A1 - Li, Fang A1 - Lei, Lizhen A1 - Gong, Yuqi A1 - Liu, Qingmeng A1 - Tan, Huajiao A1 - Zhang, Xinxia A1 - Liu, Dongyu A1 - Ren, Guoping A1 - Pan, Hongyang A1 - Shi, Yaoyao A1 - Berberich-Siebelt, Friederike A1 - Ma, Zhengrong A1 - Zhou, Ren T1 - Wilms’ tumor 1-associating protein plays an aggressive role in diffuse large B-cell lymphoma and forms a complex with BCL6 via Hsp90 JF - Cell Communication and Signaling N2 - Background Wilms’ tumor 1-associating protein (WTAP) is a nuclear protein, which is ubiquitously expressed in many tissues. Furthermore, in various types of malignancies WTAP is overexpressed and plays a role as an oncogene. The function of WTAP in diffuse large B-cell lymphoma (DLBCL), however, remains unclear. Methods Immunohistochemistry was applied to evaluate the levels of WTAP expression in DLBCL tissues and normal lymphoid tissues. Overexpression and knock-down of WTAP in DLBCL cell lines, verified on mRNA and protein level served to analyze cell proliferation and apoptosis in DLBCL cell lines by flow cytometry. Finally, co-immunoprecipitation (Co-IP), IP, and GST-pull down assessed the interaction of WTAP with Heat shock protein 90 (Hsp90) and B-cell lymphoma 6 (BCL6) as well as determined the extend of its ubiquitinylation. Results WTAP protein levels were consistently upregulated in DLBCL tissues. WTAP promoted DLBCL cell proliferation and improved the ability to confront apoptosis, while knockdown of WTAP in DLBCL cell lines allowed a significant higher apoptosis rate after treatment with Etoposide, an anti-tumor drug. The stable expression of WTAP was depended on Hsp90. In line, we demonstrated that WTAP could form a complex with BCL6 via Hsp90 in vivo and in vitro. Conclusion WTAP is highly expressed in DLBCL, promoting growth and anti-apoptosis in DLBCL cell lines. WTAP is a client protein of Hsp90 and can appear in a complex with BCL6 and Hsp90 in DLBCL. Down-regulation of WTAP could improve the chemotherapeutic treatments in DLBCL. KW - WTAP KW - BCL6 KW - Hsp90 KW - complex KW - DLBCL Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230168 VL - 16 ER - TY - JOUR A1 - Sherif, Mohammad A. A1 - Ince, Hüseyin A1 - Maniuc, Octavian A1 - Reiter, Therese A1 - Voelker, Wolfram A1 - Ertl, Georg A1 - Öner, Alper T1 - Two-dimensional transesophageal echocardiography for aortic annular sizing in patients undergoing transcatheter aortic valve implantation JF - BMC Cardiovascular Disorders N2 - Background: Accurate preoperative assessment of the aortic annulus dimension is crucial for successful transcatheter aortic valve implantation (TAVI). In this study we examined the accuracy of a novel method using two-dimensional transesophageal echocardiography (2D-TEE) for measurement of the aortic annulus. Methods: We evaluated the theoretical impact of the measurement of the annulus diameter and area using the circumcircle of a triangle method on the decision to perform the procedure and choice of the prosthesis size. Results: Sixty-three consecutive patients were scheduled for TAVI. Mean age was 82 +/- 4 years, and 25 patients (55.6 %) were female. Mean aortic annulus diameter was 20.3 +/- 2.2 mm assessed by TEE on the mid-esophageal long-axis view and 23.9 +/- 2.3 mm using CT (p < 0.001). There was a tendency for the TEE derived areas using the new method to be higher (p < 0.001). The TEE measurements were on average 42.33 mm(2) higher than the CT measurements without an evidence of a systematic over-or under-sizing (p = 1.00). Agreement between TEE and CT chosen valve sizes was good overall (kappa = 0.67 and weighted kappa = 0.71). For patients who turned out to have no AR, the two methods agreed in 84.6 % of patients. Conclusions: CT remanis the gold standard in sizing of the aortic valve annulus. Nevertheless, sizing of the aortic valve annulus using TEE derived area may be helpful. The impact of integration of this method in the algorithm of aortic annulus sizing on the outcome of patients undergoing TAVI should be examined in future studies. KW - multicenter KW - TAVI KW - impact KW - complex KW - anatomy KW - dimensions KW - regurgitation KW - root KW - sizing KW - echocardiography KW - multidetector computed-tomography KW - replacement KW - outcomes Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-136002 VL - 15 IS - 181 ER - TY - JOUR A1 - Matos, I A1 - Machado, M. P. A1 - Schartl, M. A1 - Coelho, M. M. T1 - Gene expression dosage regulation in an allopolyploid fish JF - PLoS ONE N2 - How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional "diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression). Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5). Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock, and be an immediate evolutionary advantage of allopolyploids. KW - RNA-Seq KW - balance hypothesis KW - hybrids KW - genome KW - maize KW - Squalius alburnoides KW - cell size KW - evolution KW - heterosis KW - complex Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143565 VL - 10 IS - 3 ER - TY - JOUR A1 - Westbury, Sarah K A1 - Turro, Ernest A1 - Greene, Daniel A1 - Lentaigne, Claire A1 - Kelly, Anne M A1 - Bariana, Tadbir K A1 - Simeoni, Ilenia A1 - Pillois, Xavier A1 - Attwood, Antony A1 - Austin, Steve A1 - Jansen, Sjoert BG A1 - Bakchoul, Tamam A1 - Crisp-Hihn, Abi A1 - Erber, Wendy N A1 - Favier, Rémi A1 - Foad, Nicola A1 - Gattens, Michael A1 - Jolley, Jennifer D A1 - Liesner, Ri A1 - Meacham, Stuart A1 - Millar, Carolyn M A1 - Nurden, Alan T A1 - Peerlinck, Kathelijne A1 - Perry, David J A1 - Poudel, Pawan A1 - Schulman, Sol A1 - Schulze, Harald A1 - Stephens, Jonathan C A1 - Furie, Bruce A1 - Robinson, Peter N A1 - van Geet, Chris A1 - Rendon, Augusto A1 - Gomez, Keith A1 - Laffan, Michael A A1 - Lambert, Michele P A1 - Nurden, Paquita A1 - Ouwehand, Willem H A1 - Richardson, Sylvia A1 - Mumford, Andrew D A1 - Freson, Kathleen T1 - Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders JF - Genome Medicine N2 - Background: Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases. Methods: We report a new approach in which the clinical and laboratory characteristics of BPD cases are annotated with adapted Human Phenotype Ontology (HPO) terms. Cluster analyses are then used to characterise groups of cases with similar HPO terms and variants in the same genes. Results: We show that 60% of index cases with heritable BPD enrolled at 10 European or US centres were annotated with HPO terms indicating abnormalities in organ systems other than blood or blood-forming tissues, particularly the nervous system. Cases within pedigrees clustered closely together on the bases of their HPO-coded phenotypes, as did cases sharing several clinically suspected syndromic disorders. Cases subsequently found to harbour variants in ACTN1 also clustered closely, even though diagnosis of this recently described disorder was not possible using only the clinical and laboratory data available to the enrolling clinician. Conclusions: These findings validate our novel HPO-based phenotype clustering methodology for known BPD, thus providing a new discovery tool for BPD of unknown genetic basis. This approach will also be relevant for other rare diseases with significant genetic heterogeneity. KW - disease KW - thrombocytopenia KW - guidelines KW - complex Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-143329 VL - 7 IS - 36 ER - TY - JOUR A1 - Murakawa, Yasuhiro A1 - Hinz, Michael A1 - Mothes, Janina A1 - Schuetz, Anja A1 - Uhl, Michael A1 - Wyler, Emanuel A1 - Yasuda, Tomoharu A1 - Mastrobuoni, Guido A1 - Friedel, Caroline C. A1 - Dölken, Lars A1 - Kempa, Stefan A1 - Schmidt-Supprian, Marc A1 - Blüthgen, Nils A1 - Backofen, Rolf A1 - Heinemann, Udo A1 - Wolf, Jana A1 - Scheidereit, Claus A1 - Landthaler, Markus T1 - RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway JF - Nature Communications N2 - The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNF\(\alpha\) mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ~3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-\(\kappa\)B pathway regulators such as I\(\kappa\)B\(\alpha\) and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with I\(\kappa\)B kinase and NF-\(\kappa\)B activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-\(\kappa\)B pathway. KW - large gene lists KW - decay KW - identification KW - stress KW - binding protein KW - RQQ domain KW - autoimmunity KW - complex KW - degradation KW - motifs Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-151596 VL - 6 IS - 7367 ER - TY - JOUR A1 - Nguyen, Tu N. A1 - Müller, Laura S. M. A1 - Park, Sung Hee A1 - Siegel, T. Nicolai A1 - Günzl, Arthur T1 - Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression sites in Trypanosoma brucei JF - Nucleic Acid Research N2 - Monoallelic expression within a gene family is found in pathogens exhibiting antigenic variation and in mammalian olfactory neurons. Trypanosoma brucei, a lethal parasite living in the human bloodstream, expresses variant surface glycoprotein (VSG) from 1 of 15 bloodstream expression sites (BESs) by virtue of a multifunctional RNA polymerase I. The active BES is transcribed in an extranucleolar compartment termed the expression site body (ESB), whereas silent BESs, located elsewhere within the nucleus, are repressed epigenetically. The regulatory mechanisms, however, are poorly understood. Here we show that two essential subunits of the basal class I transcription factor A (CITFA) predominantly occupied the promoter of the active BES relative to that of a silent BES, a phenotype that was maintained after switching BESs in situ. In these experiments, high promoter occupancy of CITFA was coupled to high levels of both promoter-proximal RNA abundance and RNA polymerase I occupancy. Accordingly, fluorescently tagged CITFA-7 was concentrated in the nucleolus and the ESB. Because a ChIP-seq analysis found that along the entire BES, CITFA-7 is specifically enriched only at the promoter, our data strongly indicate that monoallelic BES transcription is activated by a mechanism that functions at the level of transcription initiation. KW - RNA-polymerase-I KW - blood-stream forms KW - acrican trypanosomes KW - gene expression KW - antigenic variation KW - ribosomal RNA KW - plasmodium falciparum KW - virulence genes KW - subunit KW - complex Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117232 SN - 1362-4962 VL - 42 IS - 5 ER - TY - JOUR A1 - Akhoon, Bashir A. A1 - Singh, Krishna P. A1 - Varshney, Megha A1 - Gupta, Shishir K. A1 - Shukla, Yogeshwar A1 - Gupta, Shailendra K. T1 - Understanding the Mechanism of Atovaquone Drug Resistance in Plasmodium falciparum Cytochrome b Mutation Y268S Using Computational Methods JF - PLOS ONE N2 - The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance. KW - molecular-dynamics simulations KW - HIV-1 protease KW - structure prediction KW - saccharomyces cerevisiae KW - I-tasser KW - inhibitors KW - binding KW - malaria KW - complex KW - protein-protein interactions Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-114882 VL - 9 IS - 10 ER - TY - JOUR A1 - Geyer, Kathrin K. A1 - Chalmers, Iain W. A1 - MacKintosh, Neil A1 - Hirst, Julie E. A1 - Geoghegan, Rory A1 - Badets, Mathieu A1 - Brophy, Peter M. A1 - Brehm, Klaus A1 - Hoffmann, Karl F. T1 - Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes JF - BMC Genomics N2 - Background: The phylum Platyhelminthes (flatworms) contains an important group of bilaterian organisms responsible for many debilitating and chronic infectious diseases of human and animal populations inhabiting the planet today. In addition to their biomedical and veterinary relevance, some platyhelminths are also frequently used models for understanding tissue regeneration and stem cell biology. Therefore, the molecular (genetic and epigenetic) characteristics that underlie trophic specialism, pathogenicity or developmental maturation are likely to be pivotal in our continued studies of this important metazoan group. Indeed, in contrast to earlier studies that failed to detect evidence of cytosine or adenine methylation in parasitic flatworm taxa, our laboratory has recently defined a critical role for cytosine methylation in Schistosoma mansoni oviposition, egg maturation and ovarian development. Thus, in order to identify whether this epigenetic modification features in other platyhelminth species or is a novelty of S. mansoni, we conducted a study simultaneously surveying for DNA methylation machinery components and DNA methylation marks throughout the phylum using both parasitic and non-parasitic representatives. Results: Firstly, using both S. mansoni DNA methyltransferase 2 (SmDNMT2) and methyl-CpG binding domain protein (SmMBD) as query sequences, we illustrate that essential DNA methylation machinery components are well conserved throughout the phylum. Secondly, using both molecular (methylation specific amplification polymorphism, MSAP) and immunological (enzyme-linked immunoabsorbent assay, ELISA) methodologies, we demonstrate that representative species (Echinococcus multilocularis, Protopolystoma xenopodis, Schistosoma haematobium, Schistosoma japonicum, Fasciola hepatica and Polycelis nigra) within all four platyhelminth classes (Cestoda, Monogenea, Trematoda and 'Turbellaria') contain methylated cytosines within their genome compartments. Conclusions: Collectively, these findings provide the first direct evidence for a functionally conserved and enzymatically active DNA methylation system throughout the Platyhelminthes. Defining how this epigenetic feature shapes phenotypic diversity and development within the phylum represents an exciting new area of metazoan biology. KW - methyltransferase homolog KW - echinococcus multilocularis KW - platyhelminthes KW - 5-methyl cytosine KW - gene KW - proteins KW - stem cells KW - maximum liklihood KW - schistoma mansoni KW - flatworm KW - CPG binding domain KW - DNA methylation KW - epgenetics KW - complex Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-121892 SN - 1471-2164 VL - 14 IS - 462 ER - TY - JOUR A1 - Zhao, Bo A1 - Zhang, Keya A1 - Bhuripanyo, Karan A1 - Choi, Chan Hee J. A1 - Villhauer, Eric B. A1 - Li, Heng A1 - Zheng, Ning A1 - Kiyokawa, Hiroaki A1 - Schindelin, Hermann A1 - Yin, Jun T1 - Profiling the Cross Reactivity of Ubiquitin with the Nedd8 Activating Enzyme by Phage Display JF - PLoS ONE N2 - The C-terminal peptides of ubiquitin (UB) and UB-like proteins (UBLs) play a key role in their recognition by the specific activating enzymes (E1s) to launch their transfer through the respective enzymatic cascades thus modifying cellular proteins. UB and Nedd8, a UBL regulating the activity of cullin-RING UB ligases, only differ by one residue at their C-termini; yet each has its specific E1 for the activation reaction. It has been reported recently that UAE can cross react with Nedd8 to enable its passage through the UB transfer cascade for protein neddylation. To elucidate differences in UB recognition by UAE and NAE, we carried out phage selection of a UB library with randomized C-terminal sequences based on the catalytic formation of UB similar to NAE thioester conjugates. Our results confirmed the previous finding that residue 72 of UB plays a "gate-keeping" role in E1 selectivity. We also found that diverse sequences flanking residue 72 at the UB C-terminus can be accommodated by NAE for activation. Furthermore heptameric peptides derived from the C-terminal sequences of UB variants selected for NAE activation can function as mimics of Nedd8 to form thioester conjugates with NAE and the downstream E2 enzyme Ubc12 in the Nedd8 transfer cascade. Once the peptides are charged onto the cascade enzymes, the full-length Nedd8 protein is effectively blocked from passing through the cascade for the critical modification of cullin. We have thus identified a new class of inhibitors of protein neddylation based on the profiles of the UB C-terminal sequences recognized by NAE. KW - protein NEDD8 KW - E1 KW - system KW - conjugation KW - pathway KW - complex KW - ligases KW - purification KW - neddylation KW - expression Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-128479 SN - 1932-6203 VL - 8 IS - e70312 ER - TY - JOUR A1 - Kato, Hiroki A1 - Lu, Qiping A1 - Rapaport, Doron A1 - Kozjak-Pavlovic, Vera T1 - Tom70 Is Essential for PINK1 Import into Mitochondria JF - PLoS ONE N2 - PTEN induced kinase 1 (PINK1) is a serine/threonine kinase in the outer membrane of mitochondria (OMM), and known as a responsible gene of Parkinson's disease (PD). The precursor of PINK1 is synthesized in the cytosol and then imported into the mitochondria via the translocase of the OMM (TOM) complex. However, a large part of PINK1 import mechanism remains unclear. In this study, we examined using cell-free system the mechanism by which PINK1 is targeted to and assembled into mitochondria. Surprisingly, the main component of the import channel, Tom40 was not necessary for PINK1 import. Furthermore, we revealed that the import receptor Tom70 is essential for PINK1 import. In addition, we observed that although PINK1 has predicted mitochondrial targeting signal, it was not processed by the mitochondrial processing peptidase. Thus, our results suggest that PINK1 is imported into mitochondria by a unique pathway that is independent of the TOM core complex but crucially depends on the import receptor Tom70. KW - binding KW - outer-membrane proteins KW - Parkinsons diesease KW - intracellular membranes KW - quality control KW - pathway KW - recruitment KW - biogenesis KW - mechanisms KW - complex Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131061 VL - 8 IS - 3 ER -