@article{GoosDejungWehmanetal.2019, author = {Goos, Carina and Dejung, Mario and Wehman, Ann M. and M-Natus, Elisabeth and Schmidt, Johannes and Sunter, Jack and Engstler, Markus and Butter, Falk and Kramer, Susanne}, title = {Trypanosomes can initiate nuclear export co-transcriptionally}, series = {Nucleic Acids Research}, volume = {47}, journal = {Nucleic Acids Research}, number = {1}, doi = {10.1093/nar/gky1136}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177709}, pages = {266-282}, year = {2019}, abstract = {The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.}, language = {en} } @phdthesis{Herold2003, author = {Herold, Andrea}, title = {The role of human and Drosophila NXF proteins in nuclear mRNA export}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-5601}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2003}, abstract = {A distinguishing feature of eukaryotic cells is the spatial separation of the site of mRNA synthesis (nucleus) from the site of mRNA function (cytoplasm) by the nuclear envelope. As a consequence, mRNAs need to be actively exported from the nucleus to the cytoplasm. At the time when this study was initiated, both human TAP and yeast Mex67p had been proposed to play a role in this process. Work presented in this thesis (section 2.1) revealed that TAP and Mex67p belong to an evolutionarily conserved family of proteins which are characterized by a conserved modular domain organization. This family was termed nuclear export factor (NXF) family. While the yeast genome encodes only one NXF protein (Mex67p), the genomes of higher eukaryotes encode several NXF proteins. There are two nxf genes in C. elegans and A. gambiae, four in D. melanogaster, and at least four in H. sapiens and M. musculus. It was unclear whether, apart from TAP and Mex67p, other members of this family would also be involved in mRNA export. In the first part of this thesis (2.1), several human NXF members were tested for a possible function in nuclear mRNA export. They were analyzed for their interaction with RNA, nucleoporins and other known TAP partners in vitro, and tested for their ability to promote nuclear export of a reporter mRNA in vivo. Using these assays, human NXF2, NXF3 and NXF5 were all shown to interact with the known NXF partner p15. NXF2 and NXF5 were also found to bind directly to RNA, but only NXF2 was able to bind directly to nucleoporins and to promote the nuclear export of an (untethered) reporter mRNA. Thus NXF2 possesses many and NXF3 and NXF5 possess some of the features required to serve as an export receptor for cellular mRNAs. As NXF2 and NXF3 transcripts were mainly found in testis, and the closest orthologue of NXF5 in mouse has the highest levels of expression in brain, these NXF members could potentially serve as tissue-specific mRNA export receptors. In the second part of this work (2.2), the role of different Drosophila NXF proteins and other export factors in mRNA export was investigated using double-stranded RNA interference (RNAi) in Drosophila Schneider cells. Three of the four predicted Drosophila NXF members (NXF1-3) were found to be expressed in this cell line and could be targeted by RNAi. Depletion of endogenous NXF1 inhibited growth and resulted in the nuclear accumulation of polyadenylated RNA. Fluorescence in situ hybridization revealed that export of both heat shock and non-heat shock mRNAs, including intron-containing and intronless mRNAs, was inhibited. Depleting endogenous NXF2 or NXF3 had no apparent phenotype. These results suggested that NXF1 (but not NXF2-NXF4) mediates the export of bulk mRNA in Drosophila cells. We and others have shown that human NXF proteins function as heterodimers bound to the small protein p15. Accordingly, silencing of Drosophila p15 resulted in a block of mRNA export which was indistinguishable from the export inhibition seen after targeting NXF1. These observations indicated that neither NXF1 nor p15 can promote export in the absence of the other subunit of the heterodimer. NXF1:p15 heterodimers are implicated in late steps of mRNA export, i.e. in the translocation of mRNP export cargoes across the nuclear pore complex. The mechanism by which NXF1:p15 dimers are recruited to the mRNA is unclear. A protein that is thought to play a role in this process is the putative RNA helicase UAP56. Similar to NXF1 and p15, UAP56 was shown to be essential for mRNA export in Drosophila. UAP56 is recruited cotranscriptionally to nascent transcripts and was suggested to facilitate the interaction of NXF1:p15 with mRNPs. Even though both NXF1:p15 heterodimers and UAP56 had been implicated in general mRNA export, it was unclear whether there are classes of mRNAs that require NXF1:p15, but not UAP56 or vice versa. It was also unclear what fraction of cellular mRNAs is exported by NXF1:p15 dimers and UAP56, and whether mRNAs exist that reach the cytoplasm through alternative routes, i.e. by recruiting other export receptors. To address these issues we performed a genome-wide analysis of nuclear mRNA export pathways using microarray technology (2.2.2). We analyzed the relative abundance of nearly half of the Drosophila transcriptome in the cytoplasm of Drosophila Schneider cells depleted of different export factors by RNAi. We showed that the vast majority of transcripts were underrepresented in the cytoplasm of cells depleted of NXF1, p15 or UAP56 as compared to control cells. Only a small number of mRNAs were apparently not affected by the depletions. These observations, together with the wide and similar effects on mRNA levels caused by the depletion of NXF1, p15 or UAP56, indicate that these proteins define the major mRNA export pathway in these cells. We also identified a small subset of mRNAs which appeared to be exported by NXF1:p15 dimers independently of UAP56. In contrast, no significant changes in mRNA expression profiles were observed in cells depleted of NXF2 or NXF3, suggesting that neither NXF2 nor NXF3 play an essential role in mRNA export in Drosophila Schneider cells. Crm1 is a transport receptor implicated in the export of a variety of non-mRNA and protein cargoes. In addition, human Crm1 has been suggested to be involved in the export of a specific mRNA species, serving as a "specialized" mRNA export receptor. A role of human Crm1 in the export of bulk mRNA is considered unlikely. We analyzed the role of Drosophila Crm1 in mRNA export by inhibiting Crm1 with the drug leptomycin B in Schneider cells. Subsequent microarray analysis demonstrated that the inactivation of Crm1 resulted in decreased cytoplasmic levels of less than 1\% of all mRNAs, indicating that Crm1 is indeed not a major mRNA export receptor. The genome-wide analysis also revealed a feedback loop by which a block to mRNA export triggers the upregulation of genes involved in this process. This thesis also includes two sections describing projects in which I participated during my Ph.D., but which were not the main focus of this thesis. In section 2.3, the role of the different TAP/NXF1 domains in nuclear mRNA export is discussed. Section 2.4 describes results that were obtained as part of a collaboration using the RNAi technique in Schneider cells to study the function of Cdc37.}, subject = {Zellkern}, language = {en} } @article{Kramer2016, author = {Kramer, Susanne}, title = {Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution}, series = {Nucleic Acids Research}, journal = {Nucleic Acids Research}, doi = {10.1093/nar/gkw1245}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148002}, pages = {gkw1245}, year = {2016}, abstract = {The detection of mRNAs undergoing transcription or decay is challenging, because both processes are fast. However, the relative proportion of an mRNA in synthesis or decay increases with mRNA size and decreases with mRNA half-life. Based on this rationale, I have exploited a 22 200 nucleotide-long, short-lived endogenous mRNA as a reporter for mRNA metabolism in trypanosomes. The extreme 5΄ and 3΄ ends were labeled with red- and green-fluorescent Affymetrix® single mRNA FISH probes, respectively. In the resulting fluorescence images, yellow spots represent intact mRNAs; red spots are mRNAs in transcription or 3΄-5΄ decay, and green spots are mRNAs in 5΄-3΄ degradation. Most red spots were nuclear and insensitive to transcriptional inhibition and thus likely transcription intermediates. Most green spots were cytoplasmic, confirming that the majority of cytoplasmic decay in trypanosomes is 5΄-3΄. The system showed the expected changes at inhibition of transcription or translation and RNAi depletion of the trypanosome homologue to the 5΄-3΄ exoribonuclease Xrn1. The method allows to monitor changes in mRNA metabolism both on cellular and on population/tissue wide levels, but also to study the subcellular localization of mRNA transcription and decay pathways. I show that the system is applicable to mammalian cells.}, language = {en} } @article{KramerMeyerNatusStigloheretal.2021, author = {Kramer, Susanne and Meyer-Natus, Elisabeth and Stigloher, Christian and Thoma, Hanna and Schnaufer, Achim and Engstler, Markus}, title = {Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples}, series = {Nucleic Acids Research}, volume = {49}, journal = {Nucleic Acids Research}, number = {3}, doi = {10.1093/nar/gkaa1142}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230647}, year = {2021}, abstract = {Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.}, language = {en} } @phdthesis{Schmidt2007, author = {Schmidt, Doris}, title = {Blimp-1deltaexon7 : Eine nat{\"u}rlich vorkommende Blimp-1 Deletionsmutante mit autoregulativen Eigenschaften}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-24750}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2007}, abstract = {Blimp-1 (B lymphocyte induced maturation protein-1) kontrolliert die Regulation der terminalen B-Zelldifferenzierung. So ist die ektopische Expression von Blimp-1 ausreichend, damit naive B-Zellen zu antik{\"o}rpersezernierenden Zellen differenzieren k{\"o}nnen. Dabei wirkt Blimp-1 als transkriptioneller Repressor, der zusammen mit Kofaktoren die Chromatinstruktur in der Promotorregion der Zielgene modifiziert und so deren Expression steuert. Neben der urspr{\"u}nglich beschriebnen Blimp-1 mRNA existiert eine weitere mRNA, welcher das Exon 7 fehlt (Blimp-1?exon7). In diesem Exon sind die ersten zwei von insgesamt f{\"u}nf Zinkfingern kodiert, welche nachweislich essentiell f{\"u}r die sequenzspezifische DNA-Interaktion von Blimp-1 sind. In dieser Arbeit konnte gezeigt werden, dass die Blimp-1?exon7 Deletionsmutante vorwiegend in ruhenden CD19+ B-Zellen der Maus und in unstimulierten humanen B-Zellen exprimiert wird. Obwohl die Blimp-1 sequenzspezifische DNA-Bindung des Proteins (Blimp-1?Ex7) nicht mehr gegeben ist, lokalisiert es teilweise in den Kern, interagiert ebenfalls mit Korepressoren wie Histondeacetylase-2, und assoziiert mit heterochromatischen Bereichen der DNA. Die ektopische Expression von Blimp-1?Ex7 in einer murinen B-Zell-Lymphomlinie, f{\"u}hrt zu Zellzyklusarrest und Apoptose, ohne jedoch die Differenzierung zur Plasmazelle zu erm{\"o}glichen. Dar{\"u}ber hinaus ist in Gegenwart von Blimp-1?Ex7 die LPS-induzierte B-Zelldifferenzierung blockiert. Die Unterdr{\"u}ckung der Differenzierung korreliert mit einer verminderten Blimp-1 Expression. Zusammenfassend legen die Ergebnisse den Schluss nahe, dass Blimp-1?Ex7 in naiven B-Zellen exprimiert wird und eine vorzeitige Differenzierung verhindert, indem es autoregulativ die Promotoraktivit{\"a}t herabsetzt und damit Blimp-1 kontrolliert.}, subject = {B-Zelle}, language = {de} } @article{ZoltnerKrienitzFieldetal.2018, author = {Zoltner, Martin and Krienitz, Nina and Field, Mark C. and Kramer, Susanne}, title = {Comparative proteomics of the two T. brucei PABPs suggests that PABP2 controls bulk mRNA}, series = {PLoS Neglected Tropical Diseases}, volume = {12}, journal = {PLoS Neglected Tropical Diseases}, number = {7}, doi = {10.1371/journal.pntd.0006679}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177126}, pages = {e0006679}, year = {2018}, abstract = {Poly(A)-binding proteins (PABPs) regulate mRNA fate by controlling stability and translation through interactions with both the poly(A) tail and eIF4F complex. Many organisms have several paralogs of PABPs and eIF4F complex components and it is likely that different eIF4F/PABP complex combinations regulate distinct sets of mRNAs. Trypanosomes have five eIF4G paralogs, six of eIF4E and two PABPs, PABP1 and PABP2. Under starvation, polysomes dissociate and the majority of mRNAs, most translation initiation factors and PABP2 reversibly localise to starvation stress granules. To understand this more broadly we identified a protein interaction cohort for both T. brucei PABPs by cryo-mill/affinity purification-mass spectrometry. PABP1 very specifically interacts with the previously identified interactors eIF4E4 and eIF4G3 and few others. In contrast PABP2 is promiscuous, with a larger set of interactors including most translation initiation factors and most prominently eIF4G1, with its two partners TbG1-IP and TbG1-IP2. Only RBP23 was specific to PABP1, whilst 14 RNA-binding proteins were exclusively immunoprecipitated with PABP2. Significantly, PABP1 and associated proteins are largely excluded from starvation stress granules, but PABP2 and most interactors translocate to granules on starvation. We suggest that PABP1 regulates a small subpopulation of mainly small-sized mRNAs, as it interacts with a small and distinct set of proteins unable to enter the dominant pathway into starvation stress granules and localises preferentially to a subfraction of small polysomes. By contrast PABP2 likely regulates bulk mRNA translation, as it interacts with a wide range of proteins, enters stress granules and distributes over the full range of polysomes.}, language = {en} }