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New insights into the histone variant H2A.Z incorporation pathway in \(Trypanosoma\) \(brucei\)
(2022)
The histone variant H2A.Z is a key player in transcription regulation in eukaryotes. Histone acetylations by the NuA4/TIP60 complex are required to enable proper incorporation of the histone variant and to promote the recruitment of other complexes and proteins required for transcription initiation. The second key player in H2A.Z-mediated transcription is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant. By the time this project started little was known about H2A.Z in the unicellular parasite Trypanosoma brucei. Like in other eukaryotes H2A.Z was exclusively found in the transcription start sites of the polycistronic transcription units where it keeps the chromatin in an open conformation to enable RNA-polymerase II-mediated transcription. Previous studies showed the variant colocalizing with an acetylation of lysine on histone H4 and a methylation of lysine 4 on histone H3. Data indicated that HAT2 is linked to H2A.Z since it is required for acetylation of lyinse 10 on histone H4. A SWR1-like complex and a complex homologous to the NuA4/TIP60 could not be identified yet. This study aimed at identifying a SWR1-like remodelling complex in T. brucei and at identifying a protein complex orthologous to NuA4/TIP60 as well as at answering the question whether HAT2 is part of this complex or not. To this end, I performed multiple mass spectrometry-coupled co-Immunoprecipitation assays with potential subunits of a SWR1 complex, HAT2 and a putative homolog of a NuA4/TIP60 subunit. In the course of these experiments, I was able to identify the TbSWR1 complex. Subsequent cell fractionation and chromatin immunoprecipitation-coupled sequencing analysis experiments confirmed, that this complex is responsible for the incorporation of the histone variant H2A.Z in T. brucei. In addition to this chromatin remodelling complex, I was also able to identify two histone acetyltransferase complexes assembled around HAT1 and HAT2. In the course of my study data were published by the research group of Nicolai Siegel that identified the histone acetyltransferase HAT2 as being responsible for histone H4 acetylation, in preparation to promote H2A.Z incorporation. The data also indicated that HAT1 is responsible for acetylation of H2A.Z. According to the literature, this acetylation is required for proper transcription initiation. Experimental data generated in this study indicated, that H2A.Z and therefore TbSWR1 is involved in the DNA double strand break response of T. brucei. The identification of the specific complex composition of all three complexes provided some hints about how they could interact with each other in the course of transcription regulation and the DNA double strand break response. A proximity labelling approach performed with one of the subunits of the TbSWR1 complex identified multiple transcription factors, PTM writers and proteins potentially involved in chromatin maintenance. Overall, this work will provide some interesting insights about the composition of the complexes involved in H2A.Z incorporation in T. brucei. Furthermore, it is providing valuable information to set up experiments that could shed some light on RNA-polymerase II-mediated transcription and chromatin remodelling in T. brucei in particular and Kinetoplastids in general.
The role of BRCA1 and DCP1A in the coordination of transcription and replication in neuroblastoma
(2021)
The deregulation of the MYC oncoprotein family plays a major role in tumorigenesis and tumour maintenance of many human tumours. Because of their structure and nuclear localisation, they are defined as undruggable targets which makes it difficult to find direct therapeutic approaches. An alternative approach for targeting MYC-driven tumours is the identification and targeting of partner proteins which score as essential in a synthetic lethality screen.
Neuroblastoma, an aggressive entity of MYCN-driven tumours coming along with a bad prognosis, are dependent on the tumour suppressor protein BRCA1 as synthetic lethal data showed. BRCA1 is recruited to promoter regions in a MYCN-dependent manner. The aim of this study was to characterise the role of BRCA1 in neuroblastoma with molecular biological methods.
BRCA1 prevents the accumulation of RNA Polymerase II (RNAPII) at the promoter region. Its absence results in the formation of DNA/RNA-hybrids, so called R-loops, and DNA damage. To prevent the accumulation of RNAPII, the cell uses DCP1A, a decapping factor known for its cytoplasmatic and nuclear role in mRNA decay. It is the priming factor in the removal of the protective 5’CAP of mRNA, which leads to degradation by exonucleases. BRCA1 is necessary for the chromatin recruitment of DCP1A and its proximity to RNAPII. Cells showed upon acute activation of MYCN a higher dependency on DCP1A. Its activity prevents the deregulation of transcription and leads to proper coordination of transcription and replication. The deregulation of transcription in the absence of DCP1A results in replication fork stalling and leads to activation of the Ataxia telangiectasia and Rad3 related (ATR) kinase. The result is a disturbed cell proliferation to the point of increased apoptosis. The activation of the ATR kinase pathway in the situation where DCP1A is knocked down and MYCN is activated, makes those cells more vulnerable for the treatment with ATR inhibitors.
In summary, the tumour suppressor protein BRCA1 and the decapping factor DCP1A, mainly known for its function in the cytoplasm, have a new nuclear role in a MYCN-dependent context. This study shows their essentiality in the coordination of transcription and replication which leads to an unrestrained growth of tumour cells if uncontrolled.
For cellular viability, transcription is a fundamental process. Hereby, the DNA plays the most elemental and highly versatile role. It has long been known that promoters contain conserved and often well-defined motifs, which dictate the site of transcription initiation by providing binding sites for regulatory proteins. However, research within the last decade revealed that it is promoters lacking conserved promoter motifs and transcribing constitutively expressed genes that constitute the majority of promoters in eukaryotes. While the process of transcription initiation is well studied, whether defined DNA sequence motifs are required for the transcription of constitutively expressed genes in eukaryotes remains unknown. In the highly divergent protozoan parasite Trypanosoma brucei, most of the proteincoding genes are organized in large polycistronic transcription units. The genes within one polycistronic transcription unit are generally unrelated and transcribed by a common transcription start site for which no RNA polymerase II promoter motifs have been identified so far. Thus, it is assumed that transcription initiation is not regulated but how transcription is initiated in T. brucei is not known. This study aimed to investigate the requirement of DNA sequence motifs and chromatin structures for transcription initiation in an organism lacking transcriptional regulation. To this end, I performed a systematic analysis to investigate the dependence of transcription initiation on the DNA sequence. I was able to identify GT-rich promoter elements required for directional transcription initiation and targeted deposition of the histone variant H2A.Z, a conserved component during transcription initiation. Furthermore, nucleosome positioning data in this work provide evidence that sites of transcription initiation are rather characterized by broad regions of open and more accessible chromatin than narrow nucleosome depleted regions as it is the case in other eukaryotes. These findings highlight the importance of chromatin during transcription initiation. Polycistronic RNA in T. brucei is separated by adding an independently transcribed miniexon during trans-splicing. The data in this work suggest that nucleosome occupancy plays an important role during RNA maturation by slowing down the progressing polymerase and thereby facilitating the choice of the proper splice site during trans-splicing. Overall, this work investigated the role of the DNA sequence during transcription initiation and nucleosome positioning in a highly divergent eukaryote. Furthermore, the findings shed light on the conservation of the requirement of DNA motifs during transcription initiation and the regulatory potential of chromatin during RNA maturation. The findings improve the understanding of gene expression regulation in T. brucei, a eukaryotic parasite lacking transcriptional Regulation.
Several important cellular processes, including transcription, nucleotide excision repair and cell cycle control are mediated by the multifaceted interplay of subunits within the general transcription factor II H (TFIIH).
A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these pathways. This becomes especially important in the context of severe diseases like xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy, that arise from single point mutations in some of the TFIIH subunits.
In an attempt to structurally characterize the TFIIH complex, we harnessed the qualities of the eukaryotic thermophile Chaetomium thermophilum, a remarkable fungus, which has only recently been recognized as a novel model organism. Homologues of TFIIH from C. thermophilum were expressed in E. coli, purified to homogeneity and subsequently utilized for crystallization trials and biochemical studies.
The results of the present work include the first crystal structure of the p34 subunit of TFIIH, comprising the N-terminal domain of the protein. The structure revealed a von Willebrand Factor A (vWA) like fold, which is generally known to be involved in a multitude of protein-protein interactions. Structural comparison allowed to delineate similarities as well as differences to already known vWA domains, providing insight into the role of p34 within TFIIH. These results indicate that p34 assumes the role of a structural scaffold for other TFIIH subunits via its vWA domain, while likely serving additional functions, which are mediated through its
C-terminal zinc binding domain and are so far unknown.
Within TFIIH p34 interacts strongly with the p44 subunit, a positive regulator of the XPD helicase, which is required for regulation of RNA Polymerase II mediated transcription and essential for eukaryotic nucleotide excision repair. Based on the p34 vWA structure putative protein-protein interfaces were analyzed and binding sites for the p34 p44 interaction suggested. Continuous crystallization efforts then led to the first structure of a p34 p44 minimal complex, comprising the N-terminal vWA domain of p34 and the C-terminal C4C4 RING domain of p44. The structure of the p34 p44 minimal complex verified the previous hypothesis regarding the involved binding sites. In addition, careful analysis of the complex interface allowed to identify critical residues, which were subsequently mutated and analyzed with respect to their significance in mediating the p34 p44 interaction, by analytical size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The structure of the p34 p44 complex also revealed a binding mode of the p44 C4C4 RING domain, which differed from that of other known RING domains in several aspects, supporting the hypothesis that p44 contains a novel variation of this domain.
Das Y-Box-bindende Protein 1 (YB-1) ist ein Vertreter der hochkonservierten Familie eukaryotischer Kälteschockproteine und ein DNA/RNA-bindendes Protein. In Abhängigkeit von seiner Lokalisation übernimmt es Aufgaben bei der DNA-Transkription oder mRNA-Translation. YB-1 ist ein potentielles Onkogen beim Multiplen Myelom (MM), dass in primären MM-Zellen exprimiert ist. Für die funktionellen Untersuchungen von YB-1 in der vorliegenden Arbeit wurden humane Myelomzelllinien (HMZL) verwendet, die als in vitro Modell dieser malignen B Zell-Erkrankung dienen. Aufgrund der potentiellen Expression von YB-1 im Zellkern und/oder Zytoplasma von HMZL, wurde zunächst die Lokalisation des Proteins bestimmt. Es konnte gezeigt werden, dass YB 1 in den HMZL ausschließlich im Zytoplasma lokalisiert ist. Eine Translokation von YB-1 in den Nukleus kann durch die Serin-Phosphorylierung (Aminosäure 102) in der Kälteschockdomäne induziert werden. Die analysierten Myelomzelllinien zeigen jedoch kein nukleäres YB 1 und keine S102-Phosphorylierung. Diese Ergebnisse stützen die These, dass die Regulation der mRNA-Translation im Zytoplasma die vorherrschende Funktion von YB-1 beim MM ist. YB-1 könnte über diesen Mechanismus seine anti-apoptotische Wirkung vermitteln und die MM-Zellen vor genotoxischem Stress schützen. Um YB-1-regulierte mRNAs zu identifizieren wurden YB 1-Immunpräzipitationen mit zwei HMZL, einer Maus-Plasmozytomzelllinie und einem primären Maus-Plasmazelltumor durchgeführt. Zu den YB-1-gebundenen mRNAs gehören Translationsfaktoren und ribosomale Proteine, die eine starke Beteiligung von YB-1 beim RNA-Metabolismus bestätigen. In der vorliegenden Arbeit wurden spezifisch zwei mRNA-Kandidaten untersucht, die für den malignen Phänotyp von MM-Zellen wichtig sein können: das translationell kontrollierte Tumorprotein TCTP und MYC. Sowohl TCTP als auch MYC wurden bereits in Zusammenhang mit der Proliferation und Apoptose-Resistenz von malignen Zellen beschrieben. Die immunhistochemische Untersuchung der Knochenmarkbiopsien von MM-Patienten ergab eine gute Ko-Expression von YB-1 und TCTP in intramedullären MM-Zellen, während MYC erst in extramedullärem MM-Tumormaterial verstärkt mit der hohen YB 1-Expression korreliert. Die funktionellen Analysen der Arbeit haben gezeigt, dass YB 1 für die Translation der TCTP- und MYC-mRNA essentiell ist. Es kontrolliert die Verteilung dieser mRNAs zwischen translationell aktiven und inaktiven messenger Ribonukleoprotein-Partikeln. Die shRNA-vermittelte Reduktion von YB-1 führte zur Hemmung der TCTP- und MYC-Translation in der Phase der Initiation. Um den Einfluss der Kandidaten auf das Überleben der HMZL zu untersuchen, wurden proteinspezifische Knockdown-Experimente durchgeführt. Beim shRNA-vermittelten TCTP-Knockdown konnten keine Auswirkungen auf die Proliferation oder Viabilität von MM-Zellen beobachtet werden. Im Gegensatz dazu ist MYC für das Überleben und Wachstum der HMZL ausschlaggebend, denn der MYC-Knockdown induzierte Apoptose. Wie beim YB 1-Knockdown war ein Anstieg der Caspase-Aktivität und der Zusammenbruch des mitochondrialen Membranpotentials in den HMZL nachweisbar. Da es beim MYC-Knockdown gleichzeitig zur einer Reduktion der YB 1-Protein- und mRNA-Expression kam, wurde der Einfluss von MYC auf die Transkription des YB-1-Gens untersucht. Mit Hilfe von embryonalen Mausfibroblasten, die ein induzierbares MYC als Transgen besitzen, konnte gezeigt werden, dass die Aktivierung von MYC mit einer Zunahme der YB-1-mRNA einher geht. YB-1 ist somit ein direktes Zielgen des Transkriptionsfaktors MYC. Die Ergebnisse der vorliegenden Arbeit haben zum ersten Mal ein gegenseitiges regulatorisches Netzwerk aufgezeigt, in dem YB 1 transkriptionell durch MYC reguliert wird und YB-1 für die Translation der MYC-mRNA essentiell ist. Die Ko-Expression beider Proteine trägt zum Wachstum und Überleben von malignen Plasmazellen bei.