@phdthesis{Schwarz2023,
  author    = {Schwarz, Jessica Denise},
  title     = {Genome-wide reporter screens identify transcriptional regulators of ribosome biogenesis},
  doi       = {10.25972/OPUS-27901},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-279010},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {Cellular growth and proliferation are among the most important processes for cells and organisms. One of the major determinants of these processes is the amount of proteins and consequently also the amount of ribosomes. Their synthesis involves several hundred proteins and four different ribosomal RNA species, is highly coordinated and very energy-demanding. However, the molecular mechanims of transcriptional regulation of the protein-coding genes involved, is only poorly understood in mammals. In this thesis, unbiased genome-wide knockout reporter screens were performed, aiming to identify previously unknown transcriptional regulators of ribosome biogenesis factors (RiBis), which are important for the assembly and maturation of ribosomes, and ribosomal proteins (RPs), which are ribosomal components themself. With that approach and follow-up (validation) experiments, ALDOA and RBM8A among others, could be identified as regulators of ribosome biogenesis. Depletion of the glycolytic enzyme ALDOA led to a downregulation of RiBi- and RPpromoter driven reporters on protein and transcript level, as well as to a downregulation of ribosome biogenesis gene transcripts and of mRNAs of other genes important for proliferation. Reducing the amount of the exon junction complex protein RBM8A, led to a more prominent downregulation of one of the fluorescent reporters, but this regulation was independent of the promoter driving the expression of the reporter. However, acute protein depletion experiments in combination with nascent RNA sequencing (4sU-Seq) revealed, that mainly cytosolic ribosomal proteins (CRPs) were downregulated upon acute RBM8A withdrawal. ChIP experiments showed RBM8A binding to promoters of RP genes, but also to other chromatin regions. Total POL II or elongating and initiating POL II levels were not altered upon acute RBM8A depletion. These data provide a starting point for further research on the mechanisms of transcriptional regulation of RP and RiBi genes in mammals.},
  subject      = {Ribosom},
  language  = {en}
}
@phdthesis{Deng2023,
  author    = {Deng, Chunchu},
  title     = {Dynamic remodeling of endoplasmic reticulum and ribosomes in axon terminals of wildtype and Spinal Muscular Atrophy motoneurons},
  doi       = {10.25972/OPUS-26495},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-264954},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {In highly polarized neurons, endoplasmic reticulum (ER) forms a dynamic and continuous network in axons that plays important roles in lipid synthesis, Ca2+ homeostasis and the maintenance of synapses. However, the mechanisms underlying the regulation of axonal ER dynamics and its function in regulation of local translation still remain elusive. In the course of my thesis, I investigated the fast dynamic movements of ER and ribosomes in the growth cone of wildtype motoneurons as well as motoneurons from a mouse model of Spinal Muscular Atrophy (SMA), in response to Brain-derived neurotrophic factor (BDNF) stimulation. Live cell imaging data show that ER extends into axonal growth cone filopodia along actin filaments and disruption of actin cytoskeleton by cytochalasin D treatment impairs the dynamic movement of ER in the axonal filopodia. In contrast to filopodia, ER movements in the growth cone core seem to depend on coordinated actions of the actin and microtubule cytoskeleton. Myosin VI is especially required for ER movements into filopodia and drebrin A mediates actin/microtubule coordinated ER dynamics. Furthermore, we found that BDNF/TrkB signaling induces assembly of 80S ribosomes in growth cones on a time scale of seconds. Activated ribosomes relocate to the presynaptic ER and undergo local translation. These findings describe the dynamic interaction between ER and ribosomes during local translation and identify a novel potential function for the presynaptic ER in intra-axonal synthesis of transmembrane proteins such as the α-1β subunit of N-type Ca2+ channels in motoneurons. In addition, we demonstrate that in Smn-deficient motoneurons, ER dynamic movements are impaired in axonal growth cones that seems to be due to impaired actin cytoskeleton. Interestingly, ribosomes fail to undergo rapid structural changes in Smn-deficient growth cones and do not associate to ER in response to BDNF. Thus, aberrant ER dynamics and ribosome response to extracellular stimuli could affect axonal growth and presynaptic function and maintenance, thereby contributing to the pathology of SMA.},
  subject      = {Motoneuron},
  language  = {en}
}
@phdthesis{Uttinger2022,
  author    = {Uttinger, Konstantin Lukas},
  title     = {Der antiproliferative Effekt des RNA-Polymerase I Inhibitors CX-5461 in Zellen kolorektaler Karzinomzelllinien auf zellul{\"a}rer und molekularer Ebene},
  doi       = {10.25972/OPUS-26503},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-265033},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2022},
  abstract  = {Die halbmaximale (Proliferations-) inhibitorische Konzentration (IC50) vom RNA-Polymerase I-Inhibitor CX-5461 liegt f{\"u}r die getesteten sieben humanen kolorektalen Karzinomzell¬linien zwischen 0,7 und 3,1 µmol/L, f{\"u}r nicht-transformierte Fibroblasten bei 8,1 µmol/L. Der deutlich st{\"a}rkere antiproliferative Effekt von CX-5461 auf Tumorzellen l{\"a}sst somit ein m{\"o}gliches therapeutisches Fenster erkennen. CX-5461 (1 µmol/L und weniger) induziert einen persistierenden Zellzyklus-arretierten Zellph{\"a}notyp mit Seneszenz-assoziierter (SA) -Galaktosidase-Aktivit{\"a}t (SA-β-Gal). Die durch CX-5461 ausgel{\"o}ste verringerte Synthese ribosomaler RNA (rRNA)-Transkripte im Nucleolus, ein Subkompartiment des Nucleus, in dem die Transkription der ribosomalen DNA und Bildung von Pr{\"a}-Ribosomen stattfinden, hat eine St{\"o}rung der Ribosomen¬biogenese zur Folge. Diese als nucleol{\"a}rer Stress bezeichnete Situation ist mit zahlreichen Einzelph{\"a}nomen assoziiert wie der Akkumulation ribosomaler Proteine aufgrund eines durch CX-5461 verursachten Missverh{\"a}ltnisses bei der Synthese ribosomaler Proteine und rRNAs. Auch kommt es bei nucleol{\"a}rem Stress zur Aktivierung Zellzykusarrest-f{\"u}hrender Signalwege vermittelt durch DNA-Damage-Response, p53 und Retinoblastom (Rb). Die durch CX-5461 induzieren seneszenten Zellen lassen sich durch Kombination mit dem Bcl-Inhibitor und Senotlytikum Navitoclax in Apoptose {\"u}berf{\"u}hren. Das kombinierte Strategiekonzept demonstriert, dass der pro-proliferative Ph{\"a}notyp von Tumorzellen mit CX-5461 durch Induktion von Seneszenz effektiv gestoppt werden kann, um anschließend diese Zellen mit dem Bcl-Inhibitor Navitoclax gezielt in Apoptose zu {\"u}berf{\"u}hren. Der durch CX-5461 ausgel{\"o}ste seneszente Zellph{\"a}notyp zeigt sich sensitiv gegen{\"u}ber dem Apoptose-ausl{\"o}senden Effekt von Navitoclax - im Ggs. zu nicht-seneszenten Zellen. Basierend auf diesem Konzept deutet sich eine potentielle neue Strategie f{\"u}r eine Tumortherapie an, deren Grundlage die kombinierte Adressierung der beiden antiproliferativen Ph{\"a}nomene Seneszenz und Apoptose in soliden Tumorzellen wie dem kolorektalen Karzinom darstellt.},
  subject      = {Dickdarmkrebs},
  language  = {de}
}
@phdthesis{VasquezOspina2016,
  author    = {Vasquez Ospina, Juan Jose},
  title     = {Development of tools for the study of gene regulation in Trypanosoma brucei},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-133996},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {The protozoan parasite Trypanosoma brucei is the causal agent of sleeping sickness and besides its epidemiological importance it has been used as model organism for the study of many aspects of cellular and molecular biology especially the post-transcriptional control of gene expression. Several studies in the last 30 years have shown the importance of mRNA processing and stability for gene regulation. In T. brucei genes are unusually arranged in polycistronic transcription units (PTUs) and a coupled process of trans-splicing and polyadenylation produces the mature mRNAs. Both processes, mRNA processing and stability, cannot completely explain the control of gene expression in the different life cycle stages analyzed in T. brucei so far. In recent years, the relevance of expression regulation at the level of translation has become evident in other eukaryotes. Therefore, in the first part of my thesis I studied the impact of translational regulation by means of a genome-wide ribosome profiling approach. My data suggest that translational efficiencies vary between life cycle stages of the parasite as well as between genes within one life cycle stage. Furthermore, using ribosome profiling I was able to identify many new putative un-annotated coding sequences and to evaluate the coding potential of upstream open reading frames (uORF). Comparing my results with previously published proteomic and RNA interference (RNAi) target sequencing (RIT-seq) datasets allowed me to validate some of the new coding sequences and to evaluate their relevance for the fitness of the parasite. In the second part of my thesis I used the transcriptomic and translatomic profiles obtained from the ribosome profiling analysis for the identification of putative non-coding RNAs (ncRNAs). These results led to the analysis of the coding potential in the regions upstream and downstream of the expressed variant surface glycoprotein (VSG), which is outlined in the third part of the results section. The region upstream of the VSG, the co-transposed region (CTR), has been implicated in an increase of the in situ switching rate upon its deletion. The ribosome profiling results indicated moderate transcription but not translation in this region. These results raised the possibility that the CTR may be transcribed into ncRNA. Therefore, in the third part of my thesis, I performed a primary characterization of the CTR-derived transcripts based on northern blotting and RACE. The results suggested the presence of a unique transcript species of about 1,200 nucleotides (nt) and polyadenylated at the 3'-end of the sequence. The deletion of the CTR sequence promoting and increase of the in situ switching rates was performed around 20 years ago by means of inserting reporter genes. With the recent development of endonuclease-based tools for genome editing, it is now possible to delete sequences in a marker-free way. In the fourth part of my thesis, I show the results on the implementation of the highly efficient genome-editing CRISPR-Cas9 system in T. brucei using episomes. As a proof of principle, I inserted the sequence coding for the enhanced green fluorescent protein (eGFP) at the end of the SCD6 coding sequence (CDS). Fluorescent cells were observed as early as two days after transfection. Therefore, after the successful set up of the CRISPR-Cas9 system it will be possible to modify genomic regions with more relevance for the biology of the parasite, such as the substitution of codons present in gene tandem arrays. The implementation of ribosome profiling in T. brucei opens the opportunity for the study of translational regulation in a genome-wide scale, the re-annotation of the currently available genome, the search for new putative coding sequences, the detection of putative ncRNAs, the evaluation of the coding potential in uORFs and the role of unstranslated regions (UTRs) in the regulation of translation. In turn, the implementation of the CRISPR-Cas9 system offers the possibility to manipulate the genome of the parasite at a nucleotide resolution and without the need of including resistant makers. The CRISPR-Cas9 system is a powerful tool for editing ncRNAs, UTRs, multicopy gene families and CDSs keeping their endogenous UTRs. Moreover, the system can be used for the modification of both alleles after just one round of transfection and of codons coding for amino acids carrying post-translational modifications (PTMs) among other possibilities.    },
  subject      = {Trypanosoma brucei},
  language  = {en}
}
@article{SiegelVasquezHonetal.2014,
  author    = {Siegel, T. Nicolai and Vasquez, Juan-Jos{\´e} and Hon, Chung-Chau and Vanselow, Jens T. and Schlosser, Andreas},
  title     = {Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages},
  doi       = {10.1093/nar/gkt1386},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-112657},
  year      = {2014},
  abstract  = {While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and ∼100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5' UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for >200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.},
  subject      = {Ribosom},
  language  = {en}
}
@phdthesis{Fischer2010,
  author    = {Fischer, Matthias},
  title     = {Der Einfluß der Ribosomale S6 Kinase 2 (RSK2) auf das Neuriten- und Synapsenwachstum in vivo und in Zellkultur},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-48341},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {In dieser Arbeit sollte die Funktion der Ribosomalen S6 Kinase 2 (RSK2) auf neuronaler Ebene untersucht werden. Dahingehend gab es, z.B. auf Grund der Ph{\"a}notypen von Fliegen und M{\"a}usen mit Mutationen im entsprechenden Gen oder von Patienten mit Coffin-Lowry-Syndrom (CLS) nur Vermutungen. Es bestand letztlich die Hoffnung, einen Beitrag zur Aufkl{\"a}rung der Pathophysiologie des CLS zu leisten. Es stellte sich auf Grund von Experimenten sowohl in vivo als auch in vitro in verschiedenen Modellsystemen in dieser Arbeit heraus, daß RSK2 einen negativen Einfluß auf das Neuriten- und Synapsenwachstum hat. In kultivierten Motoneuronen f{\"u}hrte der KO von RSK2 zu l{\"a}ngeren Axonen und die {\"U}berexpression eines konstitutiv aktiven RSK2-Konstrukts zu k{\"u}rzeren Axonen. In PC12-Zellen f{\"u}hrte die Expression von konstitutiv aktiven RSK2 Konstrukten zur Verk{\"u}rzung der Neuriten und die Expression eines Kinase-inaktiven RSK2 Konstrukts zu l{\"a}ngeren Neuriten. In vivo war die neuromuskul{\"a}re Synapse bei RSK2-KO M{\"a}usen vergr{\"o}ßert und hatte bei Drosophila rsk Mutanten mehr Boutons. Das RSK2-Protein ist in Motoneuronen der Maus und in {\"u}berexprimierter Form in den Boutons der neuromuskul{\"a}ren Synapse bei Drosophila nachweisbar. Damit wurde zum ersten Mal die Funktion von RSK2 auf neuronaler Ebene beschrieben. Bez{\"u}glich des Mechanismus, wie RSK2 das Nervenwachstum beeinflußt gab es deutliche Hinweise, die daf{\"u}r sprechen, daß RSK2 dies {\"u}ber eine in der Literatur schon h{\"a}ufiger beschriebene Hemmung der MAPK ERK1/2 erreicht. F{\"u}r diese Hypothese spricht die Tatsache, daß die ERK-Phosphorylierung in murinen Motoneuronen und im R{\"u}ckenmark embryonaler M{\"a}use der RSK2-Mutante erh{\"o}ht ist und der Axonwachstumsdefekt durch eine Hemmung von MEK/ERK behoben werden kann. Auch ist die ERK-Phosphorylierung an der murinen Muskel-Endplatte in der Mutante erh{\"o}ht. Zudem zeigen genetische Epistasis-Experimente in Drosophila, daß RSK die Bouton-Zahl {\"u}ber ERK/RL hemmt. RSK scheint also in Drosophila von der Funktion her der RSK2-Isoform in Wirbeltieren sehr {\"a}hnlich zu sein. Ein weiteres wichtiges Ergebnis ist die Beobachtung, daß RSK2 bei Motoneuronen keinen wesentlichen Einfluß auf das {\"U}berleben der Zellen in Gegenwart neurotropher Faktoren hat. M{\"o}glicherweise spielen hier redundante Funktionen der RSK Familienmitglieder eine Rolle. Ein bislang unerkl{\"a}rter Befund ist die reduzierte Frequenz spontaner Depolarisationen bzw. damit einhergehender Ca2+ Einstr{\"o}me bei RSK2-KO Motoneuronen in Zellkultur. Die H{\"a}ufigkeit und Dichte von Ca2+-Kan{\"a}len und aktive Zonen Proteinen war in Motoneuronen nicht von der Anwesenheit des RSK2-Proteins abh{\"a}ngig. Im Hippocampus konnte außerdem das RSK2-Protein pr{\"a}synaptisch in den Moosfaser-Boutons der CA3 Region nachgewiesen werden. Es befindet sich auch in den Pyramidenzellen, aber nicht in den Pyramidenzell-Dendriten in CA3. Bez{\"u}glich der Bedeutung dieser Befunde f{\"u}r die Aufkl{\"a}rung der Pathologie des CLS ist zu folgern, daß der neuro-psychologische Ph{\"a}notyp bei CLS Patienten wahrscheinlich nicht durch reduziertes {\"U}berleben von Neuronen, sondern eher durch disinhibiertes Axonwachstum oder Synapsenwachstum bedingt ist. Dies kann grob sowohl f{\"u}r die peripheren als auch die zentralen Defekte gelten, denn die Synapsen im ZNS und am Muskel sind in ihrer molekularen Ausstattung z.B. im Bereich der Vesikel, der aktiven Zonen oder der Transmitteraussch{\"u}ttung sehr {\"a}hnlich. Weiterhin k{\"o}nnte eine ver{\"a}nderte synaptische Plastizit{\"a}t u.a. an der Moosfaser-Pyramidenzell-Synapse in der CA3 Region des Hippocampus eine Rolle bei den kognitiven und mnestischen Einschr{\"a}nkungen der Patienten spielen. Die Entdeckung, daß aktiviertes ERK bei den beobachteten Effekten eine Rolle spielt kann f{\"u}r die Entwicklung von Therapiestrategien eine wertvolle Erkenntnis sein.},
  subject      = {Ribosom},
  language  = {de}
}