TY - JOUR A1 - Kramer, Susanne A1 - Meyer-Natus, Elisabeth A1 - Stigloher, Christian A1 - Thoma, Hanna A1 - Schnaufer, Achim A1 - Engstler, Markus T1 - Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples JF - Nucleic Acids Research N2 - 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. KW - mRNA Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-230647 VL - 49 IS - 3 ER - TY - JOUR A1 - Libre, Camille A1 - Seissler, Tanja A1 - Guerrero, Santiago A1 - Batisse, Julien A1 - Verriez, Cédric A1 - Stupfler, Benjamin A1 - Gilmer, Orian A1 - Cabrera-Rodriguez, Romina A1 - Weber, Melanie M. A1 - Valenzuela-Fernandez, Agustin A1 - Cimarelli, Andrea A1 - Etienne, Lucie A1 - Marquet, Roland A1 - Paillart, Jean-Christophe T1 - A conserved uORF regulates APOBEC3G translation and is targeted by HIV-1 Vif protein to repress the antiviral factor JF - Biomedicines N2 - The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation, and protein degradation) that altogether reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5′ untranslated region (5′-UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation. KW - HIV-1 KW - APOBEC3G KW - Vif KW - mRNA KW - translation KW - uORF Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-252147 SN - 2227-9059 VL - 10 IS - 1 ER - TY - JOUR A1 - Meyer, Malin Tordis A1 - Watermann, Christoph A1 - Dreyer, Thomas A1 - Wagner, Steffen A1 - Wittekindt, Claus A1 - Klussmann, Jens Peter A1 - Ergün, Süleyman A1 - Baumgart-Vogt, Eveline A1 - Karnati, Srikanth T1 - Differential expression of peroxisomal proteins in distinct types of parotid gland tumors JF - International Journal of Molecular Sciences N2 - Salivary gland cancers are rare but aggressive tumors that have poor prognosis and lack effective cure. Of those, parotid tumors constitute the majority. Functioning as metabolic machinery contributing to cellular redox balance, peroxisomes have emerged as crucial players in tumorigenesis. Studies on murine and human cells have examined the role of peroxisomes in carcinogenesis with conflicting results. These studies either examined the consequences of altered peroxisomal proliferators or compared their expression in healthy and neoplastic tissues. None, however, examined such differences exclusively in human parotid tissue or extended comparison to peroxisomal proteins and their associated gene expressions. Therefore, we examined differences in peroxisomal dynamics in parotid tumors of different morphologies. Using immunofluorescence and quantitative PCR, we compared the expression levels of key peroxisomal enzymes and proliferators in healthy and neoplastic parotid tissue samples. Three parotid tumor subtypes were examined: pleomorphic adenoma, mucoepidermoid carcinoma and acinic cell carcinoma. We observed higher expression of peroxisomal matrix proteins in neoplastic samples with exceptional down regulation of certain enzymes; however, the degree of expression varied between tumor subtypes. Our findings confirm previous experimental results on other organ tissues and suggest peroxisomes as possible therapeutic targets or markers in all or certain subtypes of parotid neoplasms. KW - peroxisomes KW - parotid gland KW - salivary KW - tumors KW - pleomorphic adenoma KW - mucoepidermoid carcinoma KW - acinic cell carcinoma KW - differential expression KW - immunohistochemistry KW - mRNA Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-261047 SN - 1422-0067 VL - 22 IS - 15 ER -