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Lewinski M, Brüggemann M, Köster T, Reichel M, Bergelt T, Meyer K, König J, Zarnack K, Staiger D. Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nat Protoc 2024; 19:1183-1234. [PMID: 38278964 DOI: 10.1038/s41596-023-00935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/20/2023] [Indexed: 01/28/2024]
Abstract
Despite crucial roles of RNA-binding proteins (RBPs) in plant physiology and development, methods for determining their transcriptome-wide binding landscape are less developed than those used in other model organisms. Cross-linking and immunoprecipitation (CLIP) methods (based on UV-mediated generation of covalent bonds between RNAs and cognate RBPs in vivo, purification of the cross-linked complexes and identification of the co-purified RNAs by high-throughput sequencing) have been applied mainly in mammalian cells growing in monolayers or in translucent tissue. We have developed plant iCLIP2, an efficient protocol for performing individual-nucleotide-resolution CLIP (iCLIP) in plants, tailored to overcome the experimental hurdles posed by plant tissue. We optimized the UV dosage to efficiently cross-link RNA and proteins in plants and expressed epitope-tagged RBPs under the control of their native promoters in loss-of-function mutants. We select epitopes for which nanobodies are available, allowing stringent conditions for immunopurification of the RNA-protein complexes to be established. To overcome the inherently high RNase content of plant cells, RNase inhibitors are added and the limited RNA fragmentation step is modified. We combine the optimized isolation of RBP-bound RNAs with iCLIP2, a streamlined protocol that greatly enhances the efficiency of library preparation for high-throughput sequencing. Plant researchers with experience in molecular biology and handling of RNA can complete this iCLIP2 protocol in ~5 d. Finally, we describe a bioinformatics workflow to determine targets of Arabidopsis RBPs from iCLIP data, covering all steps from downloading sequencing reads to identifying cross-linking events ( https://github.com/malewins/Plant-iCLIPseq ), and present the R/Bioconductor package BindingSiteFinder to extract reproducible binding sites ( https://bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html ).
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Thorsten Bergelt
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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2
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Xu M, Ito-Kureha T, Kang HS, Chernev A, Raj T, Hoefig KP, Hohn C, Giesert F, Wang Y, Pan W, Ziętara N, Straub T, Feederle R, Daniel C, Adler B, König J, Feske S, Tsokos GC, Wurst W, Urlaub H, Sattler M, Kisielow J, Wulczyn FG, Łyszkiewicz M, Heissmeyer V. The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression. Nat Commun 2024; 15:2194. [PMID: 38467629 PMCID: PMC10928157 DOI: 10.1038/s41467-024-46371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identify 642 RBPs in the thymus and focus on Arpp21, which shows selective and dynamic expression in early thymocytes. Arpp21 is downregulated in response to T cell receptor (TCR) and Ca2+ signals. Downregulation requires Stim1/Stim2 and CaMK4 expression and involves Arpp21 protein phosphorylation, polyubiquitination and proteasomal degradation. Arpp21 directly binds RNA through its R3H domain, with a preference for uridine-rich motifs, promoting the expression of target mRNAs. Analysis of the Arpp21-bound transcriptome reveals strong interactions with the Rag1 3'-UTR. Arpp21-deficient thymocytes show reduced Rag1 expression, delayed TCR rearrangement and a less diverse TCR repertoire. This phenotype is recapitulated in Rag1 3'-UTR mutant mice harboring a deletion of the Arpp21 response region. These findings show how thymocyte-specific Arpp21 promotes Rag1 expression to enable TCR repertoire diversity until signals from the TCR terminate Arpp21 and Rag1 activities.
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Affiliation(s)
- Meng Xu
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Aleksandar Chernev
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
| | - Timsse Raj
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Kai P Hoefig
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
| | - Christine Hohn
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yinhu Wang
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - Wenliang Pan
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Natalia Ziętara
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tobias Straub
- Institute for Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, German Research Center for Environmental Health, Neuherberg, Germany
| | - Carolin Daniel
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Adler
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Stefan Feske
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - George C Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) site Munich, Munich, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
- University Medical Center Göttingen, Department of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Jan Kisielow
- Institute for Molecular Health Sciences, ETH Zürich, Zürich, Switzerland.
- Repertoire Immune Medicines (Switzerland) AG, Schlieren, Switzerland.
| | - F Gregory Wulczyn
- Institute for Integrative Neuroanatomie, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Marcin Łyszkiewicz
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany.
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany.
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3
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Polo-Generelo S, Rodríguez-Mateo C, Torres B, Pintor-Tortolero J, Guerrero-Martínez JA, König J, Vázquez J, Bonzón-Kulichenco E, Padillo-Ruiz J, de la Portilla F, Reyes JC, Pintor-Toro JA. Serpine1 mRNA confers mesenchymal characteristics to the cell and promotes CD8+ T cells exclusion from colon adenocarcinomas. Cell Death Discov 2024; 10:116. [PMID: 38448406 PMCID: PMC10917750 DOI: 10.1038/s41420-024-01886-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
Serine protease inhibitor clade E member 1 (SERPINE1) inhibits extracellular matrix proteolysis and cell detachment. However, SERPINE1 expression also promotes tumor progression and plays a crucial role in metastasis. Here, we solve this apparent paradox and report that Serpine1 mRNA per se, independent of its protein-coding function, confers mesenchymal properties to the cell, promoting migration, invasiveness, and resistance to anoikis and increasing glycolytic activity by sequestering miRNAs. Expression of Serpine1 mRNA upregulates the expression of the TRA2B splicing factor without affecting its mRNA levels. Through transcriptional profiling, we found that Serpine1 mRNA expression downregulates through TRA2B the expression of genes involved in the immune response. Analysis of human colon tumor samples showed an inverse correlation between SERPINE1 mRNA expression and CD8+ T cell infiltration, unveiling the potential value of SERPINE1 mRNA as a promising therapeutic target for colon tumors.
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Affiliation(s)
- Salvador Polo-Generelo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Cristina Rodríguez-Mateo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Belén Torres
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José Pintor-Tortolero
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José A Guerrero-Martínez
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Jesús Vázquez
- Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Elena Bonzón-Kulichenco
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Javier Padillo-Ruiz
- Hepatobiliary Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - Fernando de la Portilla
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José C Reyes
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José A Pintor-Toro
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain.
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4
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Suryo Rahmanto A, Blum CJ, Scalera C, Heidelberger JB, Mesitov M, Horn-Ghetko D, Gräf JF, Mikicic I, Hobrecht R, Orekhova A, Ostermaier M, Ebersberger S, Möckel MM, Krapoth N, Da Silva Fernandes N, Mizi A, Zhu Y, Chen JX, Choudhary C, Papantonis A, Ulrich HD, Schulman BA, König J, Beli P. K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution. Mol Cell 2023; 83:4272-4289.e10. [PMID: 37951215 DOI: 10.1016/j.molcel.2023.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/17/2023] [Accepted: 10/13/2023] [Indexed: 11/13/2023]
Abstract
Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
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Affiliation(s)
- Aldwin Suryo Rahmanto
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany
| | | | | | | | | | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Anna Orekhova
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | | | | | - Nils Krapoth
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | | | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Yajie Zhu
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, 55128 Mainz, Germany.
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5
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Rücklé C, Körtel N, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI, König J. Author Correction: RNA stability controlled by m 6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol 2023; 30:1607. [PMID: 37415011 PMCID: PMC10584671 DOI: 10.1038/s41594-023-01053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Affiliation(s)
| | - Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | | | | | - Marco Bertin
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Susann Schweiger
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany.
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6
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Rücklé C, Körtel N, Basilicata MF, Busch A, Zhou Y, Hoch-Kraft P, Tretow K, Kielisch F, Bertin M, Pradhan M, Musheev M, Schweiger S, Niehrs C, Rausch O, Zarnack K, Keller Valsecchi CI, König J. RNA stability controlled by m 6A methylation contributes to X-to-autosome dosage compensation in mammals. Nat Struct Mol Biol 2023; 30:1207-1215. [PMID: 37202476 PMCID: PMC10442230 DOI: 10.1038/s41594-023-00997-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/06/2023] [Indexed: 05/20/2023]
Abstract
In mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared with two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanisms of X-to-autosome dosage compensation are still under debate. Here we show that X-chromosomal transcripts have fewer m6A modifications and are more stable than their autosomal counterparts. Acute depletion of m6A selectively stabilizes autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.
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Affiliation(s)
| | - Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | | | | | - Marco Bertin
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | - Susann Schweiger
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany.
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7
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Meindl A, Romberger M, Lehmann G, Eichner N, Kleemann L, Wu J, Danner J, Boesl M, Mesitov M, Meister G, König J, Leidel S, Medenbach J. A rapid protocol for ribosome profiling of low input samples. Nucleic Acids Res 2023; 51:e68. [PMID: 37246712 PMCID: PMC10359457 DOI: 10.1093/nar/gkad459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/04/2023] [Accepted: 05/13/2023] [Indexed: 05/30/2023] Open
Abstract
Ribosome profiling provides quantitative, comprehensive, and high-resolution snapshots of cellular translation by the high-throughput sequencing of short mRNA fragments that are protected by ribosomes from nucleolytic digestion. While the overall principle is simple, the workflow of ribosome profiling experiments is complex and challenging, and typically requires large amounts of sample, limiting its broad applicability. Here, we present a new protocol for ultra-rapid ribosome profiling from low-input samples. It features a robust strategy for sequencing library preparation within one day that employs solid phase purification of reaction intermediates, allowing to reduce the input to as little as 0.1 pmol of ∼30 nt RNA fragments. Hence, it is particularly suited for the analyses of small samples or targeted ribosome profiling. Its high sensitivity and its ease of implementation will foster the generation of higher quality data from small samples, which opens new opportunities in applying ribosome profiling.
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Affiliation(s)
- Andreas Meindl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Markus Romberger
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Norbert Eichner
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Leon Kleemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Jie Wu
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Johannes Danner
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Maria Boesl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | | | - Gunter Meister
- Biochemistry I, University of Regensburg, Regensburg, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Sebastian Andreas Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Jan Medenbach
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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8
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Ebersberger S, Hipp C, Mulorz MM, Buchbender A, Hubrich D, Kang HS, Martínez-Lumbreras S, Kristofori P, Sutandy FXR, Llacsahuanga Allcca L, Schönfeld J, Bakisoglu C, Busch A, Hänel H, Tretow K, Welzel M, Di Liddo A, Möckel MM, Zarnack K, Ebersberger I, Legewie S, Luck K, Sattler M, König J. FUBP1 is a general splicing factor facilitating 3' splice site recognition and splicing of long introns. Mol Cell 2023:S1097-2765(23)00516-6. [PMID: 37506698 DOI: 10.1016/j.molcel.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/19/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Splicing of pre-mRNAs critically contributes to gene regulation and proteome expansion in eukaryotes, but our understanding of the recognition and pairing of splice sites during spliceosome assembly lacks detail. Here, we identify the multidomain RNA-binding protein FUBP1 as a key splicing factor that binds to a hitherto unknown cis-regulatory motif. By collecting NMR, structural, and in vivo interaction data, we demonstrate that FUBP1 stabilizes U2AF2 and SF1, key components at the 3' splice site, through multivalent binding interfaces located within its disordered regions. Transcriptional profiling and kinetic modeling reveal that FUBP1 is required for efficient splicing of long introns, which is impaired in cancer patients harboring FUBP1 mutations. Notably, FUBP1 interacts with numerous U1 snRNP-associated proteins, suggesting a unique role for FUBP1 in splice site bridging for long introns. We propose a compelling model for 3' splice site recognition of long introns, which represent 80% of all human introns.
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Affiliation(s)
| | - Clara Hipp
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Dalmira Hubrich
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Santiago Martínez-Lumbreras
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany
| | - Panajot Kristofori
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany
| | | | | | - Jonas Schönfeld
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Cem Bakisoglu
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kerstin Tretow
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Mareen Welzel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | | | - Martin M Möckel
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; CardioPulmonary Institute (CPI), 35392 Gießen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Senckenberg Biodiversity and Climate Research Center (S-BIK-F), 60325 Frankfurt am Main, Germany; LOEWE Center for Translational Biodiversity Genomics (TBG), 60325 Frankfurt am Main, Germany
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, 70569 Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, 70569 Stuttgart, Germany
| | - Katja Luck
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, 85747 Garching, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB) gGmbH, 55128 Mainz, Germany.
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9
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Molitor L, Klostermann M, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck S, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K, Niessing D. Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res 2023; 51:1297-1316. [PMID: 36651277 PMCID: PMC9943675 DOI: 10.1093/nar/gkac1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular roles and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6 and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs are not affected. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study proposes PURA Syndrome as a new model to study the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.
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Affiliation(s)
| | | | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spranger
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Carolin Ketteler
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ejona Rusha
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Daniel Tews
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Anna Pertek
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Marcel Proske
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Pamela Fischer-Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Kathi Zarnack
- Correspondence may also be addressed to Kathi Zarnack. Tel: +49 69 798 42506; Fax: +49 69 798 763 42506;
| | - Dierk Niessing
- To whom correspondence should be addressed. Tel: +49 731 50 23160; Fax: +49 731 50 23169;
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10
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Ziegler N, Cortés-López M, Alt F, Sprang M, Ustjanzew A, Lehmann N, El Malki K, Wingerter A, Russo A, Beck O, Attig S, Roth L, König J, Paret C, Faber J. Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL. Oncoimmunology 2023; 12:2184143. [PMID: 36875548 PMCID: PMC9980455 DOI: 10.1080/2162402x.2023.2184143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Despite massive improvements in the treatment of B-ALL through CART-19 immunotherapy, a large number of patients suffer a relapse due to loss of the targeted epitope. Mutations in the CD19 locus and aberrant splicing events are known to account for the absence of surface antigen. However, early molecular determinants suggesting therapy resistance as well as the time point when first signs of epitope loss appear to be detectable are not enlightened so far. By deep sequencing of the CD19 locus, we identified a blast-specific 2-nucleotide deletion in intron 2 that exists in 35% of B-ALL samples at initial diagnosis. This deletion overlaps with the binding site of RNA binding proteins (RBPs) including PTBP1 and might thereby affect CD19 splicing. Moreover, we could identify a number of other RBPs that are predicted to bind to the CD19 locus being deregulated in leukemic blasts, including NONO. Their expression is highly heterogeneous across B-ALL molecular subtypes as shown by analyzing 706 B-ALL samples accessed via the St. Jude Cloud. Mechanistically, we show that downregulation of PTBP1, but not of NONO, in 697 cells reduces CD19 total protein by increasing intron 2 retention. Isoform analysis in patient samples revealed that blasts, at diagnosis, express increased amounts of CD19 intron 2 retention compared to normal B cells. Our data suggest that loss of RBP functionality by mutations altering their binding motifs or by deregulated expression might harbor the potential for the disease-associated accumulation of therapy-resistant CD19 isoforms.
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Affiliation(s)
- Nicole Ziegler
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Francesca Alt
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg University Mainz, Biozentrum I, Mainz, Germany
| | - Arsenij Ustjanzew
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nadine Lehmann
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Khalifa El Malki
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Arthur Wingerter
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alexandra Russo
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Olaf Beck
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Attig
- Department of Translational Oncology and Immunology at the Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Lea Roth
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Claudia Paret
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Faber
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Thielemann JFB, Kasparik B, König J, Unterhitzenberger J, Rosner R. A systematic review and meta-analysis of trauma-focused cognitive behavioral therapy for children and adolescents. Child Abuse Negl 2022; 134:105899. [PMID: 36155943 DOI: 10.1016/j.chiabu.2022.105899] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Among minors, posttraumatic stress symptoms (PTSS) are a common consequence of traumatic events requiring trauma-focused treatment. OBJECTIVE This meta-analysis quantified treatment effects of trauma-focused cognitive behavioral therapy (TF-CBT) with PTSS as primary outcome and symptoms of depression, anxiety, and grief as secondary outcomes. PARTICIPANTS AND SETTING Inclusion criteria for individual settings: (1) patients aged between 3 and 21, (2) at least one traumatic event, (3) minimum 8 sessions of (4) TF-CBT according to Cohen, Mannarino and Deblinger (2006, 2017), (5) a quantitative PTSS measure at pre- and post-treatment, (6) original research only. Inclusion criteria for group settings: had to involve (1) psychoeducation, (2) coping strategies, (3) exposure, (4) cognitive processing/restructuring, (5) contain some reference to the manual and no minimum session number was required. METHODS Searched databases were PsychInfo, MEDLINE, Cochrane Library, PTSDPubs, PubMed, Web of Science, and OpenGrey. RESULTS 4523 participants from 28 RCTs and 33 uncontrolled studies were included. TF-CBT showed large improvements across all outcomes from pre- to post-treatment (PTSS: g = 1.14, CI 0.97-1.30) and favorable results compared to any control condition including wait-list, treatment as usual, and active treatment at post-treatment (PTSS: g = 0.52, CI 0.31-0.73). Effects were more pronounced for group settings. We give pooled estimates adjusted for risk of bias and publication bias, which initially limited the quality of the analyzed data. CONCLUSIONS TF-CBT is an effective treatment for pediatric PTSS as well as for depressive, anxiety, and grief symptoms. It is superior to control conditions, supporting international guidelines recommending it as a first-line treatment.
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Affiliation(s)
- J F B Thielemann
- Department of Psychology, Catholic University of Eichstätt-Ingolstadt, Levelingstr. 7, 85049 Ingolstadt, Germany.
| | - B Kasparik
- Department of Psychology, Catholic University of Eichstätt-Ingolstadt, Levelingstr. 7, 85049 Ingolstadt, Germany
| | - J König
- Department of Psychology, Catholic University of Eichstätt-Ingolstadt, Levelingstr. 7, 85049 Ingolstadt, Germany
| | - J Unterhitzenberger
- Department of Psychology, Catholic University of Eichstätt-Ingolstadt, Levelingstr. 7, 85049 Ingolstadt, Germany; Centre for Children and Adolescents Inn-Salzach e.V., Department of Child and Adolescent Psychiatry, Vinzenz-von-Paul-Straße 14, 84503 Altoetting, Germany
| | - R Rosner
- Department of Psychology, Catholic University of Eichstätt-Ingolstadt, Levelingstr. 7, 85049 Ingolstadt, Germany
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12
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Kmietczyk V, Ölschläger J, Kamuf-Schenk V, Frey N, Katus H, König J, Dieterich C, Völkers M. Ythdf2-mediated post-transcriptional control of gene expression regulates cardiac remodeling. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Quesnel-Vallières M, Torres-Diz M, Unic S, Busch A, Orekhova A, Kuban M, Mesitov M, Mulorz MM, Shraim R, Kielisch F, Faber J, Barash Y, Thomas-Tikhonenko A, Zarnack K, Legewie S, König J. High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nat Commun 2022; 13:5570. [PMID: 36138008 PMCID: PMC9500061 DOI: 10.1038/s41467-022-31818-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/05/2022] [Indexed: 11/29/2022] Open
Abstract
Following CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to developing CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to pervasive CD19 mis-splicing. Our dataset represents a comprehensive resource for identifying predictive biomarkers for CART-19 therapy. Multiple alternative splicing events in CD19 mRNA have been associated with resistance/relapse to CD19 CAR-T therapy in patients with B cell malignancies. Here, by combining patient data and a high-throughput mutagenesis screen, the authors identify single point mutations and RNA-binding proteins that can control CD19 splicing and be associated with CD19 CAR-T therapy resistance.
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Affiliation(s)
| | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Claudia Paret
- Department of Pediatric Hematology/Oncology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,German Cancer Consortium (DKTK), site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Bea Spiekermann
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sebastian Unic
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anna Orekhova
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Monika Kuban
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany
| | - Mikhail Mesitov
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Miriam M Mulorz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Rawan Shraim
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Fridolin Kielisch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Jörg Faber
- Department of Pediatric Hematology/Oncology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, 55131, Mainz, Germany.,German Cancer Consortium (DKTK), site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. .,Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Allmandring 30E, 70569, Stuttgart, Germany. .,Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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14
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Bayarjargal L, Spahr D, König J, Milman V, Winkler B. Polymerization of CO 4 groups in carbonates. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322095225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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15
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Ito-Kureha T, Leoni C, Borland K, Cantini G, Bataclan M, Metzger RN, Ammann G, Krug AB, Marsico A, Kaiser S, Canzar S, Feske S, Monticelli S, König J, Heissmeyer V. The function of Wtap in N 6-adenosine methylation of mRNAs controls T cell receptor signaling and survival of T cells. Nat Immunol 2022; 23:1208-1221. [PMID: 35879451 DOI: 10.1038/s41590-022-01268-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022]
Abstract
T cell antigen-receptor (TCR) signaling controls the development, activation and survival of T cells by involving several layers and numerous mechanisms of gene regulation. N6-methyladenosine (m6A) is the most prevalent messenger RNA modification affecting splicing, translation and stability of transcripts. In the present study, we describe the Wtap protein as essential for m6A methyltransferase complex function and reveal its crucial role in TCR signaling in mouse T cells. Wtap and m6A methyltransferase functions were required for the differentiation of thymocytes, control of activation-induced death of peripheral T cells and prevention of colitis by enabling gut RORγt+ regulatory T cell function. Transcriptome and epitranscriptomic analyses reveal that m6A modification destabilizes Orai1 and Ripk1 mRNAs. Lack of post-transcriptional repression of the encoded proteins correlated with increased store-operated calcium entry activity and diminished survival of T cells with conditional genetic inactivation of Wtap. These findings uncover how m6A modification impacts on TCR signal transduction and determines activation and survival of T cells.
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Affiliation(s)
- Taku Ito-Kureha
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Cristina Leoni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Kayla Borland
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Giulia Cantini
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany.,Institute for Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marian Bataclan
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Rebecca N Metzger
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Gregor Ammann
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Anne B Krug
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Annalisa Marsico
- Institute for Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität in Munich, Munich, Germany.,Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt am Main, Germany
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Stefan Feske
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany. .,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany.
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16
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Wicke FS, Ernst M, Otten D, Werner A, Dreier M, Brähler E, Tibubos AN, Reiner I, Michal M, Wiltink J, Münzel T, Lackner KJ, Pfeiffer N, König J, Wild PS, Beutel ME. The association of depression and all-cause mortality: Explanatory factors and the influence of gender. J Affect Disord 2022; 303:315-322. [PMID: 35176339 DOI: 10.1016/j.jad.2022.02.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/29/2021] [Accepted: 02/13/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND The association of depression with mortality and the significance of explanatory factors, in particularly gender, have remained an issue of debate. We therefore aimed to estimate the effect of depression on all-cause mortality, to examine potential explanatory factors and to assess effect modification by gender. METHODS We used Cox regression models to estimate the effect of depression on mortality based on data from the Gutenberg Health Study, which is a prospective cohort study of the adult population in the districts of Mainz and Mainz-Bingen, Germany. Baseline assessment was between 2007 and 2012. Effect modification by gender was measured on both additive and multiplicative scales. RESULTS Out of 14,653 participants, 7.7% were depressed according to Patient Health Questionnaire 9 (PHQ-9), and 1,059 (7.2%) died during a median follow-up of 10.7 years. Depression elevated the risk of mortality in men and women in age-adjusted models (HR: 1.41, 95%-CI: 1.03-1.92; resp. HR: 1.96, 95%-CI: 1.43-2.69). Adjustment for social status, physical health and lifestyle covariates attenuated the effect and in the fully-adjusted model the hazard ratio was 0.96 (95%-CI: 0.69-1.33) in men and 1.53 (95%-CI: 1.10-2.12) in women. For effect modification by gender, the measure on multiplicative interaction was 0.68 (95%-CI 0.44-1.07) and on additive interaction was RERI=-0.47 (95%-CI -1.24-0.30). LIMITATIONS The PHQ-9 is a single self-report measure of depression reflecting symptoms of the past two weeks, limiting a more detailed assessment of depression and course of symptoms, which likely affects the association with mortality. CONCLUSIONS Depression elevates mortality by multifactorial pathways, which should be taken into account in the biopsychosocially informed treatment of depression. Effect modification by gender was not statistically significant.
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Affiliation(s)
- F S Wicke
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany.
| | - M Ernst
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - D Otten
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - A Werner
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - M Dreier
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - E Brähler
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - A N Tibubos
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - I Reiner
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - M Michal
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - J Wiltink
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
| | - T Münzel
- Center for Cardiology - Cardiology I, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - K J Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - N Pfeiffer
- Department of Ophthalmology, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - J König
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - P S Wild
- Preventive Cardiology and Preventive Medicine - Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - M E Beutel
- Department of Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstr. 1, Mainz 55113, Germany
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17
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Kleinherbers E, Stegmann P, Kurzmann A, Geller M, Lorke A, König J. Pushing the Limits in Real-Time Measurements of Quantum Dynamics. Phys Rev Lett 2022; 128:087701. [PMID: 35275653 DOI: 10.1103/physrevlett.128.087701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Time-resolved studies of quantum systems are the key to understanding quantum dynamics at its core. The real-time measurement of individual quantum numbers as they switch between certain discrete values, well known as a "random telegraph signal," is expected to yield maximal physical insight. However, the signal suffers from both systematic errors, such as a limited time resolution and noise from the measurement apparatus, as well as statistical errors due to a limited amount of data. Here we demonstrate that an evaluation scheme based on factorial cumulants can reduce the influence of such errors by orders of magnitude. The error resilience is supported by a general theory for the detection errors as well as experimental data of single-electron tunneling through a self-assembled quantum dot. Thus, factorial cumulants push the limits in the analysis of random telegraph data, which represent a wide class of experiments in physics, chemistry, engineering, and life sciences.
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Affiliation(s)
- E Kleinherbers
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - P Stegmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A Kurzmann
- 2nd Institute of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - M Geller
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - A Lorke
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
| | - J König
- Faculty of Physics and CENIDE, University of Duisburg-Essen, 47057 Duisburg, Germany
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18
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Siech C, Arnold H, Mattigk A, Bellut L, König J, Kluth L. Gender differences in Urologic training – results of the second GeSRU (Germany Society of Residents in Urology) training survey. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00187-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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19
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Stahl L, Struck JP, König J, Braun M, Westphal J. [Implementation of the new collective agreement in 2021 in urological clinics : Expectations and reality]. Urologe A 2021; 61:407-410. [PMID: 34935996 DOI: 10.1007/s00120-021-01736-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 10/19/2022]
Abstract
The amendment to the collective agreement is intended to significantly improve the working conditions of physicians and includes longer-term duty scheduling, work on a maximum of two weekends per month, less overtime. Smaller hospitals often have problems implementing these requirements and have to make compromises. At least the overtime is now better paid-overall, an improvement in working conditions can only be achieved by increasing the number of staff, then better and more intensive training is also possible.
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Affiliation(s)
- L Stahl
- Klinik für Urologie, Klinikum Lippe Detmold, Detmold, Deutschland. .,Urologie, Klinikum Lippe GmbH, Röntgenstr. 18, 32756, Detmold, Deutschland.
| | - J P Struck
- Klinik für Urologie, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Deutschland
| | - J König
- Abteilung für Urologie, Asklepios Stadtklinik Bad Tölz, Bad Tölz, Deutschland
| | - M Braun
- Standort Spital Männedorf, Uroviva, Männedorf, Schweiz
| | - J Westphal
- Klinik für Urologie und Kinderurologie, Krankenhaus Maria Hilf der Alexianer Krefeld GmbH, Krefeld, Deutschland
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20
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Schätzer M, Bhardwaj J, Sommer J, Miskovic R, König J, Hoppichler F. Catering situation at Austrian schools. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab165.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Due to the increase in all-day compulsory schools in Austria, it is important that students receive health-promoting meals throughout the day. The aim of the analysis was a nationwide evaluation of the current situation concerning catering at schools.
Methods
Using a nationwide representative sample of schools from the 5th grade upwards, a questionnaire was conducted as a telephone interview with 331 randomly chosen schools. In addition, 56 schools in Vienna from the 5th grade onwards were randomly selected in order to analyze the current offer at school cafeterias in detail.
Results
Lunch was offered at 72% of all schools, a school cafeteria was available at 81%, a cold drink vending machine at 66%, a hot drink vending machine at 41% and a snack vending machine at 23%. With regard to the health promoting composition of the catering offer, 18% of all schools already had a certified lunch menu, 22% a certified school cafeteria, 14% a certified cold drink vending machine and 5% a certified snack vending machine. In 79% of schools there is direct competition for school catering (93% supermarkets, 45% bakeries, 33% snack stands, 8% fast food restaurants). The results of the detailed analysis in Vienna showed that only 35% of all school cafeterias are certified. All of these locations are advised externally.
Conclusions
The majority of the schools offer catering during breaks and at lunchtime. Without external advice, the majority of the offers must be classified as not health promoting.
Key messages
The food offered at schools is an important component in the nutrition of students in Austria. Cafeteria operators in schools often need external advice in order to be able to offer a healthy selection of food and beverages.
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Affiliation(s)
- M Schätzer
- Special Institute for Preventive Cardiology and Nutrition, Elsbethen/Salzburg, Austria
| | - J Bhardwaj
- Special Institute for Preventive Cardiology and Nutrition, Elsbethen/Salzburg, Austria
| | - J Sommer
- Special Institute for Preventive Cardiology and Nutrition, Elsbethen/Salzburg, Austria
- Department for Nutritional Sciences, University of Vienna, Vienna, Austria
| | - R Miskovic
- Special Institute for Preventive Cardiology and Nutrition, Elsbethen/Salzburg, Austria
- Department for Nutritional Sciences, University of Vienna, Vienna, Austria
| | - J König
- Department for Nutritional Sciences, University of Vienna, Vienna, Austria
| | - F Hoppichler
- Special Institute for Preventive Cardiology and Nutrition, Elsbethen/Salzburg, Austria
- Department of Internal Medicine, Hospital of the Brothers of St. John of God Salzburg, Salzburg, Austria
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21
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Körtel N, Rücklé C, Zhou Y, Busch A, Hoch-Kraft P, Sutandy FXR, Haase J, Pradhan M, Musheev M, Ostareck D, Ostareck-Lederer A, Dieterich C, Hüttelmaier S, Niehrs C, Rausch O, Dominissini D, König J, Zarnack K. Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Res 2021; 49:e92. [PMID: 34157120 PMCID: PMC8450095 DOI: 10.1093/nar/gkab485] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based approach to map m6A sites with single-nucleotide resolution. However, due to broad antibody reactivity, reliable identification of m6A sites from miCLIP data remains challenging. Here, we present miCLIP2 in combination with machine learning to significantly improve m6A detection. The optimized miCLIP2 results in high-complexity libraries from less input material. Importantly, we established a robust computational pipeline to tackle the inherent issue of false positives in antibody-based m6A detection. The analyses were calibrated with Mettl3 knockout cells to learn the characteristics of m6A deposition, including m6A sites outside of DRACH motifs. To make our results universally applicable, we trained a machine learning model, m6Aboost, based on the experimental and RNA sequence features. Importantly, m6Aboost allows prediction of genuine m6A sites in miCLIP2 data without filtering for DRACH motifs or the need for Mettl3 depletion. Using m6Aboost, we identify thousands of high-confidence m6A sites in different murine and human cell lines, which provide a rich resource for future analysis. Collectively, our combined experimental and computational methodology greatly improves m6A identification.
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Affiliation(s)
- Nadine Körtel
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - F X Reymond Sutandy
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt 60590, Germany
| | - Jacob Haase
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Mihika Pradhan
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Dirk Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Antje Ostareck-Lederer
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen 52074, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg 69120, Germany
- German Centre for Cardiovascular Research (DZHK) - Partner Site Heidelberg/Mannheim, Heidelberg 69120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Sect. Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Halle 06120, Germany
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Dan Dominissini
- Cancer Research Center and Wohl Institute for Translational Medicine, Chaim Sheba Medical Center, Tel HaShomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt 60438, Germany
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22
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König J, Kneuer C, Herrmann K. Using multiple in silico models to improve robustness of predictions for bacterial mutagenicity. Toxicol Lett 2021. [DOI: 10.1016/s0378-4274(21)00440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Arnold H, Fassbach M, Mattigk A, Zehe V, Beck A, Wundrack F, Bellut L, König J, Siech C. [Training and work conditions of residents in urology in Germany : Results of the second German Society of Residents in Urology e. V. (GeSRU) residency survey from 2020]. Urologe A 2021; 60:1025-1034. [PMID: 34259878 PMCID: PMC8278189 DOI: 10.1007/s00120-021-01608-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Residency is the fundation for high-quality medical care and also for career development of young urologists. In 2015 the GeSRU (German Society of Residents in Urology) carried out the first nationwide survey among young physicians in urology and described the status quo of their residency. This revised follow-up examination draws an updated picture of the training and working conditions of residents in urology and assesses the development. METHODS In 2020 the GeSRU conducted an online-based survey of all residents in urology; therefore, the 2015 questionnaire was expanded. The model of the professional gratification crisis was used again. RESULTS A total of 332 questionnaires were analyzed. Major findings have not changed since 2015. The daily working routine is characterized by high pace and workload and economic considerations. Family- and research-friendly working conditions are largely lacking. 35% of the respondents draw professional consequences. The psychosocial strain remains very high and conveys a risk for physicians' health and patients' quality of care. CONCLUSION These results demonstrate that there are still systemically immanent burdens for residents in urology, which require adjustments to the working and training conditions. A structured, transparent curriculum for urological residency, remuneration and time for training and models which enable work-life balance should be established.
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Affiliation(s)
- H Arnold
- Facharztpraxis, Urologie Dr. Hannah Arnold, Gesundheitszentrum Senden, Hauptstraße 11 c, 89250, Senden, Deutschland.
| | - M Fassbach
- Klinik für Urologie, urologische Onkologie und Kinderurologie, Helios Klinikum Duisburg, Duisburg, Deutschland
| | - A Mattigk
- Klinik für Urologie und Kinderurologie, Universitätsklinikum Ulm, Ulm, Deutschland
| | - V Zehe
- Klinik für Urologie und Kinderurologie, Universitätsklinikum Ulm, Ulm, Deutschland
| | - A Beck
- Klinik für Urologie, Katholisches Marienkrankenhaus Hamburg, Hamburg, Deutschland
| | - F Wundrack
- Klinik für Urologie, Helios Klinikum Berlin-Buch, Berlin-Buch, Deutschland
| | - L Bellut
- Klinik für Urologie und Kinderurologie, Universitätsklinikum Erlangen, Erlangen, Deutschland
| | - J König
- Klinik für Urologie, Asklepios Stadtklinik Bad Tölz, Bad Tölz, Deutschland
| | - C Siech
- Klinik für Urologie, Universitätsklinikum Frankfurt, Frankfurt am Main, Deutschland
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24
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Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 2021; 22:190. [PMID: 34183059 PMCID: PMC8240250 DOI: 10.1186/s13059-021-02411-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
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MESH Headings
- Alternative Splicing
- Antibodies, Bispecific/pharmacology
- Antineoplastic Agents, Immunological/pharmacology
- Artifacts
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Datasets as Topic
- Exons
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Introns
- Models, Biological
- Nucleic Acid Conformation
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Reverse Transcription
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Affiliation(s)
- Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Present address: Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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25
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Michel MS, Himmler M, Necknig U, Kriegmair M, Speck T, Fichtner J, Steffens J, Borgmann H, Bolenz C, Tuellmann M, Ruppin S, Petersilie F, Rebmann U, König J, Westphal J, Goebell P, Leyh H, Borchers H. [Certified residency curriculum for the specialization training in urology from the German Society of Urology according to the 2018 Training Regulations (version of 20. September 2019)]. Urologe A 2021; 59:135-140. [PMID: 33141266 PMCID: PMC7721681 DOI: 10.1007/s00120-020-01367-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- M S Michel
- Klinik für Urologie und Urochirurgie, Universitätsmedizin Mannheim, Universität Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Deutschland.
| | - M Himmler
- Klinik für Urologie und Urochirurgie, Universitätsmedizin Mannheim, Universität Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Deutschland
| | - U Necknig
- Abteilung für Urologie und Kinderurologie, Klinikum Garmisch-Partenkirchen, Auenstraße 6, 82467, Garmisch-Partenkirchen, Deutschland
| | - M Kriegmair
- Urologische Klinik München Planegg, Germeringer Str. 32, 82152, Planegg, Deutschland
| | - T Speck
- , Treskow Allee 103, 10318, Berlin, Deutschland
| | - J Fichtner
- Klinik für Urologie, Johanniter-Krankenhaus Oberhausen, Steinbrinkstraße 96a, 46245, Oberhausen, Deutschland
| | - J Steffens
- Klinik für Urologie und Kinderurologie, St.-Antonius Hospital, Akademisches Lehrkrankenhaus der RWTH Aachen, Dechant-Deckers-Straße 8, 52249, Eschweiler, Deutschland
| | - H Borgmann
- Klinik und Poliklinik für Urologie und Kinderurologie, Universitätsmedizin Mainz, Langenbeckstr. 1, 55131, Mainz, Deutschland
| | - C Bolenz
- Klinik für Urologie und Kinderurologie, Universitätsklinikum Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Deutschland
| | - M Tuellmann
- , Dr.-Henkel-Str. 2, 85435, Erding, Deutschland
| | - S Ruppin
- , Friedrichstr. 94, 10117, Berlin, Deutschland
| | - F Petersilie
- Deutsche Gesellschaft für Urologie, Martin-Buber-Str. 10, 14163, Berlin, Deutschland
| | - U Rebmann
- , Große Nikolaistr. 1, 06108, Halle, Deutschland
| | - J König
- Abteilung für Urologie, Asklepios Stadtklinik Bad Tölz, Schützenstraße 15, 83646, Bad Tölz, Deutschland
| | - J Westphal
- Klinik für Urologie und Kinderurologie, Krankenhaus Maria Hilf der Alexianer Krefeld GmbH, Dießemer Bruch 81, 47805, Krefeld, Deutschland
| | - P Goebell
- Urologische und Kinderurologische Universitätsklinik, Malteser Waldkrankenhaus St. Marien, Rathsberger Straße 57, 91054, Erlangen, Deutschland
| | - H Leyh
- Abteilung für Urologie und Kinderurologie, Klinikum Garmisch-Partenkirchen, Auenstraße 6, 82467, Garmisch-Partenkirchen, Deutschland
| | - H Borchers
- Deutsche Gesellschaft für Urologie, Martin-Buber-Str. 10, 14163, Berlin, Deutschland
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Ott N, Harland A, Scaal M, König J, Bredow J, Eysel P, Müller LP, Meyer C. The role of the transversal ligament on the atlantoaxial complex - Bending forces at C1/2 flexion limits in the elderly. Clin Biomech (Bristol, Avon) 2021; 84:105329. [PMID: 33765570 DOI: 10.1016/j.clinbiomech.2021.105329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/16/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Biomechanical functionality as well as trauma mechanisms of the atlantoaxial complex are still an issue of controversy. The transverse atlantal ligament is the strongest stabilizator. The present study aimed to analyze the bending forces of the transverse atlantal ligament and of the base of the odontoid in elderly specimens. METHODS In this biomechanical study five cadaveric specimen with a mean age of 72 at death and bone mineral density measuring for 555.3 Hounsfield units on average were used. To analyze the strain of the transverse atlantal ligament and the dense base, strain gauges were used. A custom biomechanical setup was used to test each specimen at C1/2 flexion and the strain of the transverse atlantal ligament and the dens base (μm/m) were measured. FINDINGS In four out of five, a rupture of the transverse atlantal ligament was observed, the mean force required for the ligament to fall was 175 N (min. 99.8 N; 249.2 N; SD 64.7) by a mean strain of 2102.9 μm/m (min. 1953.5 μm/m; max. 2272.3 μm/m; SD 189.7). In one specimen with the lowest Hounsfield units (155), the dens base fractured before the transverse atlantal ligament ruptured and no strain could be measured at the transversal ligament during movement afterwards. INTERPRETATION The transverse atlantal ligament fails at an average of 175 N in the elderly, which is less than the value reported previously. In osteoporotic specimen the generated force to rupture the transverse atlantal ligament can fracture the dens itself.
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Affiliation(s)
- N Ott
- Department of Trauma and Orthopedic Surgery, University Hospital of Cologne, Cologne, Germany.
| | - A Harland
- Department of Trauma and Orthopedic Surgery, University Hospital of Cologne, Cologne, Germany
| | - Martin Scaal
- Department of Anatomy, University of Cologne, Cologne, Germany
| | - J König
- Department of Orthopedic Surgery, Division of Spine Surgery, Schön-Kliniken Düsseldorf, Düsseldorf, Germany
| | - J Bredow
- Department of Trauma and Orthopedic Surgery, University Hospital of Cologne, Cologne, Germany
| | - P Eysel
- Department of Trauma and Orthopedic Surgery, University Hospital of Cologne, Cologne, Germany
| | - L P Müller
- Department of Trauma and Orthopedic Surgery, University Hospital of Cologne, Cologne, Germany
| | - C Meyer
- Department of Orthopedic Surgery, Division of Spine Surgery, Schön-Kliniken Düsseldorf, Düsseldorf, Germany
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Werner S, Galliot A, Pichot F, Kemmer T, Marchand V, Sednev MV, Lence T, Roignant JY, König J, Höbartner C, Motorin Y, Hildebrandt A, Helm M. NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination. Nucleic Acids Res 2021; 49:e23. [PMID: 33313868 PMCID: PMC7913672 DOI: 10.1093/nar/gkaa1173] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 12/26/2022] Open
Abstract
Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully detected known m6A sites in human rRNA, and the long non-coding RNA MALAT1, and positively validated several m6A candidate sites, drawn from miCLIP data with an m6A antibody, in the transcriptome of Drosophila melanogaster. Conceptually related to bisulfite sequencing, NOseq presents a novel amplicon-based sequencing approach for the validation of m6A sites in defined sequences.
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Affiliation(s)
- Stephan Werner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Aurellia Galliot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Thomas Kemmer
- Institute of Computer Science, Johannes Gutenberg-University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and Sequencing (EpiRNA-Seq) Core Facility, UMS2008/US40 IBSLor, Biopôle UL, F-54000 Nancy, France
| | - Maksim V Sednev
- Institute of Organic Chemistry, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tina Lence
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany.,Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.,Génopode - Center for Integrative Genomics, Université de Lausanne, 1015 Lausanne, Switzerland
| | - Julian König
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Biopôle UL, F-54000 Nancy, France
| | - Andreas Hildebrandt
- Institute of Computer Science, Johannes Gutenberg-University Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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28
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Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL. The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance 2021; 4:e202000825. [PMID: 33376132 PMCID: PMC7772782 DOI: 10.26508/lsa.202000825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mirko Brüggemann
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Miguel Lopes
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Kathi Zarnack
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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29
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Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J 2021; 40:e104975. [PMID: 33428246 PMCID: PMC7883056 DOI: 10.15252/embj.2020104975] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
N6‐methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior, albeit the underlying molecular mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hans-Hermann Wessels
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department CIBIO, University of Trento, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anke Busch
- Bioinformatics Core Facility, IMB, Mainz, Germany
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michela Notarangelo
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg-Mannheim, Heidelberg, Germany
| | - Alessandro Quattrone
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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30
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Holster S, Repsilber D, Geng D, Hyötyläinen T, Salonen A, Lindqvist CM, Rajan SK, de Vos WM, Brummer RJ, König J. Correlations between microbiota and metabolites after faecal microbiota transfer in irritable bowel syndrome. Benef Microbes 2020; 12:17-30. [PMID: 33350360 DOI: 10.3920/bm2020.0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Faecal microbiota transfer (FMT) consists of the infusion of donor faecal material into the intestine of a patient with the aim to restore a disturbed gut microbiota. In this study, it was investigated whether FMT has an effect on faecal microbial composition, its functional capacity, faecal metabolite profiles and their interactions in 16 irritable bowel syndrome (IBS) patients. Faecal samples from eight different time points before and until six months after allogenic FMT (faecal material from a healthy donor) as well as autologous FMT (own faecal material) were analysed by 16S RNA gene amplicon sequencing and gas chromatography coupled to mass spectrometry (GS-MS). The results showed that the allogenic FMT resulted in alterations in the microbial composition that were detectable up to six months, whereas after autologous FMT this was not the case. Similar results were found for the functional profiles, which were predicted from the phylogenetic sequencing data. While both allogenic FMT as well as autologous FMT did not have an effect on the faecal metabolites measured in this study, correlations between the microbial composition and the metabolites showed that the microbe-metabolite interactions seemed to be disrupted after allogenic FMT compared to autologous FMT. This shows that FMT can lead to altered interactions between the gut microbiota and its metabolites in IBS patients. Further research should investigate if and how this affects efficacy of FMT treatments.
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Affiliation(s)
- S Holster
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Repsilber
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - D Geng
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - T Hyötyläinen
- Man-Technology-Environmental Research Centre, Faculty of Business, Science and Engineering, School of Science and Technology, Örebro University, Örebro, Sweden
| | - A Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - C M Lindqvist
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - S K Rajan
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Laboratory of Microbiology, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - R J Brummer
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J König
- Nutrition-Gut-Brain Interactions Research Centre, Faculty of Medicine and Health, School of Medical Sciences, Örebro University, Örebro, Sweden
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31
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Gkika E, Tanja S, Stephanie K, Schaefer-Schuler A, Mix M, Küsters A, Tosch M, Eschmann S, Bultel Y, Hass P, Fleckenstein J, Thieme A, Stockinger M, Dieckmann K, Miederer M, Holl G, Rischke C, Adebahr S, Lenz S, Broichhagen C, Binder H, König J, Grosu A, Nestle U. PD-0413: The role of different chemotherapy protocols for concurrent CRT in locally advanced NSCLC. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Weichmann F, Hett R, Schepers A, Ito-Kureha T, Flatley A, Slama K, Hastert FD, Angstman NB, Cardoso MC, König J, Hüttelmaier S, Dieterich C, Canzar S, Helm M, Heissmeyer V, Feederle R, Meister G. Validation strategies for antibodies targeting modified ribonucleotides. RNA 2020; 26:1489-1506. [PMID: 32636310 PMCID: PMC7491328 DOI: 10.1261/rna.076026.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/30/2020] [Indexed: 05/29/2023]
Abstract
Chemical modifications are found on almost all RNAs and affect their coding and noncoding functions. The identification of m6A on mRNA and its important role in gene regulation stimulated the field to investigate whether additional modifications are present on mRNAs. Indeed, modifications including m1A, m5C, m7G, 2'-OMe, and Ψ were detected. However, since their abundances are low and tools used for their corroboration are often not well characterized, their physiological relevance remains largely elusive. Antibodies targeting modified nucleotides are often used but have limitations such as low affinity or specificity. Moreover, they are not always well characterized and due to the low abundance of the modification, particularly on mRNAs, generated data sets might resemble noise rather than specific modification patterns. Therefore, it is critical that the affinity and specificity is rigorously tested using complementary approaches. Here, we provide an experimental toolbox that allows for testing antibody performance prior to their use.
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Affiliation(s)
- Franziska Weichmann
- Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Robert Hett
- Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Aloys Schepers
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center of the Ludwig-Maximilians-University München, 82152 Planegg-Martinsried, Germany
| | - Andrew Flatley
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Kaouthar Slama
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | | | - M Cristina Cardoso
- Cell Biology and Epigenetics, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Centre, 06120 Halle, Germany
| | - Christoph Dieterich
- Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, 55128 Mainz, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center of the Ludwig-Maximilians-University München, 82152 Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), 81377 Munich, Germany
| | - Regina Feederle
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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33
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König J, Zarnack K. High-throughput approaches in RNA biology. Methods 2020; 178:1-2. [DOI: 10.1016/j.ymeth.2020.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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34
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König J, Ueding J, Janoske U. Analytical Model to Characterize the Efficiency of Disk Stack Separators. CHEM-ING-TECH 2020. [DOI: 10.1002/cite.201900177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julian König
- GEA Westfalia Separator Group GmbH Werner-Habig-Straße 1 59302 Oelde Germany
- Bergische Universität Wuppertal Institut für Strömungsmechanik Gaußstraße 20 42119 Wuppertal Germany
| | - Jens Ueding
- GEA Westfalia Separator Group GmbH Werner-Habig-Straße 1 59302 Oelde Germany
| | - Uwe Janoske
- Bergische Universität Wuppertal Institut für Strömungsmechanik Gaußstraße 20 42119 Wuppertal Germany
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35
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Radermacher LK, Ponto K, Merkesdal S, Pomart V, Frommer L, Pfeiffer N, König J, Kahaly GJ. Type I Diabetes is the Main Cost Driver in Autoimmune Polyendocrinopathy. J Clin Endocrinol Metab 2020; 105:5570009. [PMID: 31529067 DOI: 10.1210/clinem/dgz021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
CONTEXT Autoimmune polyendocrinopathy (AP), a chronic complex orphan disease, encompasses at least two autoimmune-induced endocrine diseases. OBJECTIVE To estimate for the first time total, indirect and direct costs for patients with AP, as well as cost drivers. DESIGN Cross-sectional cost of illness study. SETTING Academic tertiary referral center for AP. PATIENTS 146 consecutive, unselected AP patients. INTERVENTION Interviews pertaining to patients' socioeconomic situation covered a recall period of 12 months. Both the human capital (HCA) and the friction cost approaches (FCAs) were applied as estimation methods. MAIN OUTCOME MEASURES Direct and indirect annual costs, and sick leave and medication costs. RESULTS AP markedly impacts healthcare expenses. Mean overall costs of AP in Germany ranged from €5 971 090 to €29 848 187 per year (HCA). Mean indirect costs ranged from €3 388 284 to €16 937 298 per year (HCA) while mean direct costs ranged from €2 582 247 to €12 908 095/year. Mean direct costs per year were €1851 in AP patients with type 1 diabetes (T1D, 76%) and €671 without T1D, which amounts to additional direct costs of €1209 for T1D when adjusting for concomitant autoimmune disease (95% CI = €1026-1393, P < 0.0001). Sick leave cost estimates for AP patients with T1D exceeded those without T1D by 70% (FCA) and 43% (HCA), respectively. In multiple regression analyses, T1D predicted total and direct costs, medication costs and costs for diabetic devices (all P < 0.001). Overall, AP patients with T1D were 54% (FCA) more expensive than those without T1D. CONCLUSIONS Public health socioeconomic relevance of AP was demonstrated, with T1D as main cost driver.
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Affiliation(s)
| | - Katharina Ponto
- Department of Ophthalmology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Sonja Merkesdal
- Department of Rheumatology, Hannover Medical School, Hannover, Germany
| | - Vanessa Pomart
- Department of Medicine I, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Lara Frommer
- Department of Medicine I, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Norbert Pfeiffer
- Department of Ophthalmology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - J König
- Institute of Medical Biostatistics, Epidemiology and Informatics, Johannes Gutenberg University, Medical Center, Mainz, Germany
| | - George J Kahaly
- Department of Medicine I, Johannes Gutenberg University Medical Center, Mainz, Germany
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Enculescu M, Braun S, Thonta Setty S, Busch A, Zarnack K, König J, Legewie S. Exon Definition Facilitates Reliable Control of Alternative Splicing in the RON Proto-Oncogene. Biophys J 2020; 118:2027-2041. [PMID: 32336349 DOI: 10.1016/j.bpj.2020.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 01/01/2023] Open
Abstract
Alternative splicing is a key step in eukaryotic gene expression that allows for the production of multiple transcript and protein isoforms from the same gene. Even though splicing is perturbed in many diseases, we currently lack insights into regulatory mechanisms promoting its precision and efficiency. We analyze high-throughput mutagenesis data obtained for an alternatively spliced exon in the proto-oncogene RON and determine the functional units that control this splicing event. Using mathematical modeling of distinct splicing mechanisms, we show that alternative splicing is based in RON on a so-called "exon definition" mechanism. Here, the recognition of the adjacent exons by the spliceosome is required for removal of an intron. We use our model to analyze the differences between the exon and intron definition scenarios and find that exon definition prevents the accumulation of deleterious, partially spliced retention products during alternative splicing regulation. Furthermore, it modularizes splicing control, as multiple regulatory inputs are integrated into a common net input, irrespective of the location and nature of the corresponding cis-regulatory elements in the pre-messenger RNA. Our analysis suggests that exon definition promotes robust and reliable splicing outcomes in RON splicing.
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Affiliation(s)
| | - Simon Braun
- Institute of Molecular Biology, Mainz, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anke Busch
- Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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König J, Janssen N, Janoske U. Visualization of the deposition mechanisms in disk stack centrifuges with an acrylic glass bowl top and high-speed image processing. SEP SCI TECHNOL 2020. [DOI: 10.1080/01496395.2020.1728326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Julian König
- GEA Westfalia Separator Group GmbH, Oelde, Germany
| | - Nils Janssen
- Department of Mechanical Engineering, University Wuppertal, Wuppertal, Germany
| | - Uwe Janoske
- Department of Mechanical Engineering, University Wuppertal, Wuppertal, Germany
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38
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Klepzig K, Horn U, König J, Holtz K, Wendt J, Hamm A, Lotze M. Brain imaging of chill reactions to pleasant and unpleasant sounds. Behav Brain Res 2020; 380:112417. [DOI: 10.1016/j.bbr.2019.112417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
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Dold A, Han H, Liu N, Hildebrandt A, Brüggemann M, Rücklé C, Hänel H, Busch A, Beli P, Zarnack K, König J, Roignant JY, Lasko P. Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genet 2020; 16:e1008581. [PMID: 31978041 PMCID: PMC7001992 DOI: 10.1371/journal.pgen.1008581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 02/05/2020] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila, maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar (osk). We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in a region adjacent to A-rich sequences. Using Drosophila S2R+ cultured cells we show that this binding site overlaps with a Bruno1 (Bru1) responsive element (BREs) that regulates osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR. To ensure accurate development of the Drosophila embryo, proteins and mRNAs are positioned at specific sites within the embryo. Many of these factors are produced and localized during the development of the egg in the mother. One protein essential for this process that has been heavily studied is Oskar (Osk), which is positioned at the posterior pole. During the localization of osk mRNA, its translation is repressed by the RNA-binding protein Bruno1 (Bru1), ensuring that Osk protein is not present outside of the posterior where it is harmful. At the posterior pole, osk mRNA is activated through mechanisms that are not yet understood. In this work, we show that the conserved protein Makorin 1 (Mkrn1) is a novel factor involved in the translational activation of osk. Mkrn1 binds specifically to osk mRNA, overlapping with a binding site of Bru1, thus alleviating the association of Bru1 with osk. Moreover, Mkrn1 is stabilized by poly(A) binding protein (pAbp), a translational activator that binds osk mRNA in close proximity to one Mkrn1 binding site. Our work thus helps to answer a long-standing question in the field, providing insight about the function of Mkrn1 and more generally into embryonic patterning in animals.
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Affiliation(s)
- Annabelle Dold
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Hong Han
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Niankun Liu
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andrea Hildebrandt
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany.,Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Cornelia Rücklé
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Heike Hänel
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Anke Busch
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Petra Beli
- Chromatin Biology and Proteomics, Institute of Molecular Biology, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Julian König
- Genomic Views of Splicing Regulation, Institute of Molecular Biology, Mainz, Germany
| | - Jean-Yves Roignant
- RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany.,Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Hildebrandt A, Brüggemann M, Rücklé C, Boerner S, Heidelberger JB, Busch A, Hänel H, Voigt A, Möckel MM, Ebersberger S, Scholz A, Dold A, Schmid T, Ebersberger I, Roignant JY, Zarnack K, König J, Beli P. The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biol 2019; 20:216. [PMID: 31640799 PMCID: PMC6805484 DOI: 10.1186/s13059-019-1814-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and proteins. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and decay of the truncated nascent polypeptide via ribosome-associated quality control. RESULTS Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at poly(A) sequences during ribosome-associated quality control. We show that MKRN1 directly binds to the cytoplasmic poly(A)-binding protein (PABPC1) and associates with polysomes. MKRN1 is positioned upstream of poly(A) tails in mRNAs in a PABPC1-dependent manner. Ubiquitin remnant profiling and in vitro ubiquitylation assays uncover PABPC1 and ribosomal protein RPS10 as direct ubiquitylation substrates of MKRN1. CONCLUSIONS We propose that MKRN1 mediates the recognition of poly(A) tails to prevent the production of erroneous proteins from prematurely polyadenylated transcripts, thereby maintaining proteome integrity.
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Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Cornelia Rücklé
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Heike Hänel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Martin M Möckel
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | | | - Anica Scholz
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Annabelle Dold
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Tobias Schmid
- Faculty of Medicine, Institute of Biochemistry I, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Department for Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Straße 14-16, 60325, Frankfurt am Main, Germany
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Génopode Building, CH-1015, Lausanne, Switzerland
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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41
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Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. A systems view of spliceosomal assembly and branchpoints with iCLIP. Nat Struct Mol Biol 2019; 26:930-940. [PMID: 31570875 PMCID: PMC6859068 DOI: 10.1038/s41594-019-0300-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 08/14/2019] [Indexed: 02/02/2023]
Abstract
Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small nuclear ribonucleoprotein particles and auxiliary RNA binding proteins, to map spliceosome engagement with pre-messenger RNAs in human cell lines. This revealed seven peaks of spliceosomal crosslinking around branchpoints (BPs) and splice sites. We identified RNA binding proteins that crosslink to each peak, including known and candidate splicing factors. Moreover, we detected the use of over 40,000 BPs with strong sequence consensus and structural accessibility, which align well to nearby crosslinking peaks. We show how the position and strength of BPs affect the crosslinking patterns of spliceosomal factors, which bind more efficiently upstream of strong or proximally located BPs and downstream of weak or distally located BPs. These insights exemplify spliceosome iCLIP as a broadly applicable method for transcriptomic studies of splicing mechanisms.
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Affiliation(s)
- Michael Briese
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Institute of Clinical Neurobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Nejc Haberman
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Christopher R Sibley
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh University, Edinburgh, UK
| | - Rupert Faraway
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Andrea S Elser
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK
| | - Anob M Chakrabarti
- The Francis Crick Institute, London, UK
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, London, UK
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Julian König
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Institute of Molecular Biology GmbH, Mainz, Germany
| | - David Perera
- MRC Cancer Unit at the University of Cambridge, Cambridge, UK
| | - Vihandha O Wickramasinghe
- MRC Cancer Unit at the University of Cambridge, Cambridge, UK
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Luciano Saieva
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- The Francis Crick Institute, London, UK.
- Department of Neuromuscular Disease, UCL Institute of Neurology, London, UK.
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42
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König J, Aeishen S, Cebulla A, Bellut L, Fassbach M, Westphal J, Struck JP. Qualität statt Quantität verbessert die Weiterbildung. Urologe A 2019; 58:877-880. [DOI: 10.1007/s00120-019-0987-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Klepzig K, Horn U, Holtz K, König J, Wendt J, Hamm A, Lotze M. FV 14 Brain imaging of chill reactions to pleasant and unpleasant sounds. Clin Neurophysiol 2019. [DOI: 10.1016/j.clinph.2019.04.624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Kurzmann A, Stegmann P, Kerski J, Schott R, Ludwig A, Wieck AD, König J, Lorke A, Geller M. Optical Detection of Single-Electron Tunneling into a Semiconductor Quantum Dot. Phys Rev Lett 2019; 122:247403. [PMID: 31322370 DOI: 10.1103/physrevlett.122.247403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Indexed: 06/10/2023]
Abstract
The maximum information of a dynamic quantum system is given by real-time detection of every quantum event, where the ultimate challenge is a stable, sensitive detector with high bandwidth. All physical information can then be drawn from a statistical analysis of the time traces. We demonstrate here an optical detection scheme based on the time-resolved resonance fluorescence on a single quantum dot. Single-electron resolution with high signal-to-noise ratio (4σ confidence) and high bandwidth of 10 kHz make it possible to record the individual quantum events of the transport dynamics. Full counting statistics with factorial cumulants gives access to the nonequilibrium dynamics of spin relaxation of a singly charged dot (γ_{↑↓}=3 ms^{-1}), even in an equilibrium transport measurement.
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Affiliation(s)
- A Kurzmann
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
- Solid State Physics Laboratory, ETH Zurich, 8093 Zurich, Switzerland
| | - P Stegmann
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
| | - J Kerski
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
| | - R Schott
- Chair for Applied Solid State Physics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - A Ludwig
- Chair for Applied Solid State Physics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - A D Wieck
- Chair for Applied Solid State Physics, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780 Bochum, Germany
| | - J König
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
| | - A Lorke
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
| | - M Geller
- Faculty of Physics and CENIDE, University of Duisburg-Essen, Lotharstrasse 1, 47057 Duisburg, Germany
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45
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Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Rep 2018; 20:embr.201846588. [PMID: 30552148 DOI: 10.15252/embr.201846588] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 01/09/2023] Open
Abstract
RNA-binding proteins (RBPs) determine spatiotemporal gene expression by mediating active transport and local translation of cargo mRNAs. Here, we cast a transcriptome-wide view on the transported mRNAs and cognate RBP binding sites during endosomal messenger ribonucleoprotein (mRNP) transport in Ustilago maydis Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we compare the key transport RBP Rrm4 and the newly identified endosomal mRNP component Grp1 that is crucial to coordinate hyphal growth. Both RBPs bind predominantly in the 3' untranslated region of thousands of shared cargo mRNAs, often in close proximity. Intriguingly, Rrm4 precisely binds at stop codons, which constitute landmark sites of translation, suggesting an intimate connection of mRNA transport and translation. Towards uncovering the code of recognition, we identify UAUG as specific binding motif of Rrm4 that is bound by its third RRM domain. Altogether, we provide first insights into the positional organisation of co-localising RBPs on individual cargo mRNAs.
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Affiliation(s)
- Lilli Olgeiser
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Carl Haag
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Susan Boerner
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Janine Koepke
- Medical Clinic II (Molecular Pneumology), Excellence Cluster Cardio-Pulmonary System, Justus Liebig University of Gießen, Gießen, Germany
| | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
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46
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Hertel J, Frenzel S, König J, Wittfeld K, Füllen G, Pietzner M, Völzke H, Grabe H. MEASURING BIOLOGICAL AGE AS A TASK OF INDIVIDUALIZATION: A FRAMEWORK FOR PREDICTOR SELECTION AND MODEL VALIDATION. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.3118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J Hertel
- University Medicine Greifswald, Greifswald, Mecklenburg-Vorpommern, Germany
| | - S Frenzel
- University Medicine Greifswald, Department of Psychiatry and Psychotherapy, Germany
| | - J König
- University Medicine Greifswald, Department of Psychiatry and Psychotherapy, Germany
| | - Katharina Wittfeld
- German Center for Neurodegenerative Diseases (DZNE), Partner Site Greifswald/Rostock, Germany
| | - G Füllen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Germany
| | - M Pietzner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Germany
| | - H Völzke
- Institute for Community Medicine, University Medicine Greifswald, Germany
| | - H Grabe
- University Medicine Greifswald, Department of Psychiatry and Psychotherapy, Germany
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47
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Braun S, Enculescu M, Setty ST, Cortés-López M, de Almeida BP, Sutandy FXR, Schulz L, Busch A, Seiler M, Ebersberger S, Barbosa-Morais NL, Legewie S, König J, Zarnack K. Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nat Commun 2018; 9:3315. [PMID: 30120239 PMCID: PMC6098099 DOI: 10.1038/s41467-018-05748-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 07/19/2018] [Indexed: 01/22/2023] Open
Abstract
Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.
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Affiliation(s)
- Simon Braun
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Mihaela Enculescu
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Samarth T Setty
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Bernardo P de Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal.,Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | | | - Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | | | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisboa, Portugal
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.
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Görig T, Eichinger M, Philippi H, König J, Urschitz M, De Bock F. Evaluation einer ICF-CY-basierten komplexen Versorgungsmaßnahme zur Verbesserung der partizipativen Entscheidungsfindung an Sozialpädiatrischen Zentren (SPZ) und der sozialen Teilhabe von Kindern mit chronischen Erkrankungen: Design der Studie PART-CHILD. Das Gesundheitswesen 2018. [DOI: 10.1055/s-0038-1667815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- T Görig
- Universität Heidelberg, Mannheimer Institut für Public Health, Sozial- und Präventivmedizin, Mannheim, Deutschland
| | - M Eichinger
- Universität Heidelberg, Mannheimer Institut für Public Health, Sozial- und Präventivmedizin, Mannheim, Deutschland
| | - H Philippi
- SPZ Frankfurt-Mitte, Frankfurt am Main, Deutschland
| | - J König
- Universität Mainz, Institut für Medizinische Biometrie, Epidemiologie und Informatik, Mainz, Deutschland
| | - M Urschitz
- Universität Mainz, Institut für Medizinische Biometrie, Epidemiologie und Informatik, Mainz, Deutschland
| | - F De Bock
- Universität Heidelberg, Mannheimer Institut für Public Health, Sozial- und Präventivmedizin, Mannheim, Deutschland
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Schülein S, Schoffer O, Radde K, König J, Weyer V, Blettner M, Klug S. Probability of hysterectomy in Germany. Rev Epidemiol Sante Publique 2018. [DOI: 10.1016/j.respe.2018.05.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F, Ketting RF. GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J 2018; 37:embj.201899325. [PMID: 29769402 DOI: 10.15252/embj.201899325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/09/2022] Open
Abstract
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.
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Affiliation(s)
| | - Sabrina Dietz
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Andrea Hildebrandt
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Julian König
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
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