1
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Chen YL, Jones AN, Crawford A, Sattler M, Ettinger A, Torres-Padilla ME. Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells. J Cell Biol 2024; 223:e202309027. [PMID: 38625077 PMCID: PMC11022885 DOI: 10.1083/jcb.202309027] [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: 09/05/2023] [Revised: 03/06/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
The centromere is a fundamental higher-order structure in chromosomes ensuring their faithful segregation upon cell division. Centromeric transcripts have been described in several species and suggested to participate in centromere function. However, low sequence conservation of centromeric repeats appears inconsistent with a role in recruiting highly conserved centromeric proteins. Here, we hypothesized that centromeric transcripts may function through a secondary structure rather than sequence conservation. Using mouse embryonic stem cells (ESCs), we show that an imbalance in the levels of forward or reverse minor satellite (MinSat) transcripts leads to severe chromosome segregation defects. We further show that MinSat RNA adopts a stem-loop secondary structure, which is conserved in human α-satellite transcripts. We identify an RNA binding region in CENPC and demonstrate that MinSat transcripts function through the structured region of the RNA. Importantly, mutants that disrupt MinSat secondary structure do not cause segregation defects. We propose that the conserved role of centromeric transcripts relies on their secondary RNA structure.
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Affiliation(s)
- Yung-Li Chen
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Alisha N. Jones
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
| | - Amy Crawford
- Department of Chemistry, New York University, New York, NY, USA
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, Bavarian NMR Center, School of Natural Sciences, Technical University of Munich, Garching, Germany
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Munich, München, Germany
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany
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2
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Bose E, Xiong S, Jones AN. Probing RNA Structure and Dynamics using Nanopore and Next Generation Sequencing. J Biol Chem 2024:107317. [PMID: 38677514 DOI: 10.1016/j.jbc.2024.107317] [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] [Received: 07/03/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
It has become increasingly evident that the structures RNAs adopt are conformationally dynamic; the various structured states that RNAs sample govern their interactions with other nucleic acids, proteins, and ligands to regulate a myriad of biological processes. Although several biophysical approaches have been developed and used to study the dynamic landscape of structured RNAs, technical limitations have limited their application to all classes of RNA due to variable size and flexibility. Recent advances combining chemical probing experiments with next-generation- and direct sequencing have emerged as an alternative approach to exploring the conformational dynamics of RNA. In this review, we provide a methodological overview of the sequencing-based techniques used to study RNA conformational dynamics. We discuss how different techniques have enabled us to better understand the propensity of RNAs from a variety of different classes to sample multiple conformational states. Finally, we present examples of the ways these techniques have reshaped how we think about RNA structure.
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Affiliation(s)
- Emma Bose
- Department of Chemistry, New York University, New York, New York, USA
| | - Shengwei Xiong
- Department of Chemistry, New York University, New York, New York, USA
| | - Alisha N Jones
- Department of Chemistry, New York University, New York, New York, USA.
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3
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Matsuda A, Plewka J, Rawski M, Mourão A, Zajko W, Siebenmorgen T, Kresik L, Lis K, Jones AN, Pachota M, Karim A, Hartman K, Nirwal S, Sonani R, Chykunova Y, Minia I, Mak P, Landthaler M, Nowotny M, Dubin G, Sattler M, Suder P, Popowicz GM, Pyrć K, Czarna A. Despite the odds: formation of the SARS-CoV-2 methylation complex. Nucleic Acids Res 2024:gkae165. [PMID: 38499483 DOI: 10.1093/nar/gkae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14's exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.
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Affiliation(s)
- Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-387 Kraków, Poland
| | - Jacek Plewka
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Poland
| | - Michał Rawski
- SOLARIS National Synchrotron Radiation Centre, Jagiellonian University, 30-392 Kraków, Poland
| | - André Mourão
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Weronika Zajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Leanid Kresik
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Kinga Lis
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Faculty of Chemical Engineering and Technology, Kraków University of Technology, 31-155 Kraków, Poland
| | - Alisha N Jones
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Magdalena Pachota
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Abdulkarim Karim
- Department of Biology, College of Science, Salahaddin University-Erbil, 44002 Erbil, Kurdistan Region, Iraq
- Department of Community Health, College of Health Technology, Cihan University-Erbil, 44001 Erbil, Kurdistan Region, Iraq
| | - Kinga Hartman
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Ravi Sonani
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Yuliya Chykunova
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Igor Minia
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Paweł Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Markus Landthaler
- Laboratory for RNA Biology, Berlin Institute for Medical System Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Grzegorz Dubin
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Michael Sattler
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Piotr Suder
- Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, 30-059 Kraków, Poland
| | - Grzegorz M Popowicz
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
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4
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Jones AN, Graß C, Meininger I, Geerlof A, Klostermann M, Zarnack K, Krappmann D, Sattler M. Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. Sci Adv 2022; 8:eabp9153. [PMID: 35921415 PMCID: PMC9348792 DOI: 10.1126/sciadv.abp9153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Alternative splicing plays key roles for cell type-specific regulation of protein function. It is controlled by cis-regulatory RNA elements that are recognized by RNA binding proteins (RBPs). The MALT1 paracaspase is a key factor of signaling pathways that mediate innate and adaptive immune responses. Alternative splicing of MALT1 is critical for controlling optimal T cell activation. We demonstrate that MALT1 splicing depends on RNA structural elements that sequester the splice sites of the alternatively spliced exon7. The RBPs hnRNP U and hnRNP L bind competitively to stem-loop RNA structures that involve the 5' and 3' splice sites flanking exon7. While hnRNP U stabilizes RNA stem-loop conformations that maintain exon7 skipping, hnRNP L disrupts these RNA elements to facilitate recruitment of the essential splicing factor U2AF2, thereby promoting exon7 inclusion. Our data represent a paradigm for the control of splice site selection by differential RBP binding and modulation of pre-mRNA structure.
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Affiliation(s)
- Alisha N. Jones
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, 85748 München, Germany
| | - Carina Graß
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Isabel Meininger
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Corresponding author. (D.K.); (M.S.)
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, 85764 München, Germany
- Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Garching, 85748 München, Germany
- Corresponding author. (D.K.); (M.S.)
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5
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Jones AN, Mourão A, Czarna A, Matsuda A, Fino R, Pyrc K, Sattler M, Popowicz GM. Characterization of SARS-CoV-2 replication complex elongation and proofreading activity. Sci Rep 2022; 12:9593. [PMID: 35688849 PMCID: PMC9185715 DOI: 10.1038/s41598-022-13380-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/03/2021] [Accepted: 02/14/2022] [Indexed: 01/18/2023] Open
Abstract
The replication complex (RC) of SARS-CoV-2 was recently shown to be one of the fastest RNA-dependent RNA polymerases of any known coronavirus. With this rapid elongation, the RC is more prone to incorporate mismatches during elongation, resulting in a highly variable genomic sequence. Such mutations render the design of viral protein targets difficult, as drugs optimized for a given viral protein sequence can quickly become inefficient as the genomic sequence evolves. Here, we use biochemical experiments to characterize features of RNA template recognition and elongation fidelity of the SARS-CoV-2 RdRp, and the role of the exonuclease, nsp14. Our study highlights the 2'OH group of the RNA ribose as a critical component for RdRp template recognition and elongation. We show that RdRp fidelity is reduced in the presence of the 3' deoxy-terminator nucleotide 3'dATP, which promotes the incorporation of mismatched nucleotides (leading to U:C, U:G, U:U, C:U, and A:C base pairs). We find that the nsp10-nsp14 heterodimer is unable to degrade RNA products lacking free 2'OH or 3'OH ribose groups. Our results suggest the potential use of 3' deoxy-terminator nucleotides in RNA-derived oligonucleotide inhibitors as antivirals against SARS-CoV-2.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Roberto Fino
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
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6
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Jones AN, Tikhaia E, Mourão A, Sattler M. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res 2022; 50:2350-2362. [PMID: 35166835 PMCID: PMC8887474 DOI: 10.1093/nar/gkac080] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 09/13/2021] [Revised: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The A-repeat region of the lncRNA Xist is critical for X inactivation and harbors several N6-methyladenosine (m6A) modifications. How the m6A modification affects the conformation of the conserved AUCG tetraloop hairpin of the A-repeats and how it can be recognized by the YTHDC1 reader protein is unknown. Here, we report the NMR solution structure of the (m6A)UCG hairpin, which reveals that the m6A base extends 5′ stacking of the A-form helical stem, resembling the unmethylated AUCG tetraloop. A crystal structure of YTHDC1 bound to the (m6A)UCG tetraloop shows that the (m6A)UC nucleotides are recognized by the YTH domain of YTHDC1 in a single-stranded conformation. The m6A base inserts into the aromatic cage and the U and C bases interact with a flanking charged surface region, resembling the recognition of single-stranded m6A RNA ligands. Notably, NMR and fluorescence quenching experiments show that the binding requires local unfolding of the upper stem region of the (m6A)UCG hairpin. Our data show that m6A can be readily accommodated in hairpin loop regions, but recognition by YTH readers requires local unfolding of flanking stem regions. This suggests how m6A modifications may regulate lncRNA function by modulating RNA structure.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Ekaterina Tikhaia
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85747, Garching, Germany
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7
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Heumüller AW, Jones AN, Mourão A, Klangwart M, Shi C, Wittig I, Fischer A, Muhly-Reinholz M, Buchmann GK, Dieterich C, Potente M, Braun T, Grote P, Jaé N, Sattler M, Dimmeler S. Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses. Circ Res 2022; 130:67-79. [PMID: 34789007 DOI: 10.1161/circresaha.121.320029] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/17/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) are generated by back splicing of mostly mRNAs and are gaining increasing attention as a novel class of regulatory RNAs that control various cellular functions. However, their physiological roles and functional conservation in vivo are rarely addressed, given the inherent challenges of their genetic inactivation. Here, we aimed to identify locus conserved circRNAs in mice and humans, which can be genetically deleted due to retained intronic elements not contained in the mRNA host gene to eventually address functional conservation. METHODS AND RESULTS Combining published endothelial RNA-sequencing data sets with circRNAs of the circATLAS databank, we identified locus-conserved circRNA retaining intronic elements between mice and humans. CRISPR/Cas9 mediated genetic depletion of the top expressed circRNA cZfp292 resulted in an altered endothelial morphology and aberrant flow alignment in the aorta in vivo. Consistently, depletion of cZNF292 in endothelial cells in vitro abolished laminar flow-induced alterations in cell orientation, paxillin localization and focal adhesion organization. Mechanistically, we identified the protein SDOS (syndesmos) to specifically interact with cZNF292 in endothelial cells by RNA-affinity purification and subsequent mass spectrometry analysis. Silencing of SDOS or its protein binding partner Syndecan-4, or mutation of the SDOS-cZNF292 binding site, prevented laminar flow-induced cytoskeletal reorganization thereby recapitulating cZfp292 knockout phenotypes. CONCLUSIONS Together, our data reveal a hitherto unknown role of cZNF292/cZfp292 in endothelial flow responses, which influences endothelial shape.
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Affiliation(s)
- Andreas W Heumüller
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Faculty for Biological Sciences (A.W.H.), Goethe University, Frankfurt, Germany
| | - Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - Marius Klangwart
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Chenyue Shi
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
| | - Ilka Wittig
- Functional Proteomics, Institute for Cardiovascular Physiology (I.W.), Goethe University, Frankfurt, Germany
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
| | - Ariane Fischer
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Marion Muhly-Reinholz
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Giulia K Buchmann
- Institute for Cardiovascular Physiology (G.K.B.), Goethe University, Frankfurt, Germany
| | - Christoph Dieterich
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg, Germany (C.D.)
| | - Michael Potente
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Germany (M.P.)
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany (M.P.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
| | - Phillip Grote
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Nicolas Jaé
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany (A.N.J., A.M., M.S.)
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany (A.N.J., A.M., M.S.)
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration (A.W.H., M.K., A.F., M.M.R., P.G., N.J., S.D.), Goethe University, Frankfurt, Germany
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.S., M.P., T.B.)
- German Center for Cardiovascular Research (DZHK), Frankfurt, Germany (I.W., M.P., T.B., S.D.)
- Cardio-Pulmonary Institute (CPI), Frankfurt, Germany (M.P., T.B., S.D.)
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8
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Stadler D, Kächele M, Jones AN, Hess J, Urban C, Schneider J, Xia Y, Oswald A, Nebioglu F, Bester R, Lasitschka F, Ringelhan M, Ko C, Chou W, Geerlof A, van de Klundert MA, Wettengel JM, Schirmacher P, Heikenwälder M, Schreiner S, Bartenschlager R, Pichlmair A, Sattler M, Unger K, Protzer U. Interferon-induced degradation of the persistent hepatitis B virus cccDNA form depends on ISG20. EMBO Rep 2021; 22:e49568. [PMID: 33969602 PMCID: PMC8183418 DOI: 10.15252/embr.201949568] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 10/30/2019] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B virus (HBV) persists by depositing a covalently closed circular DNA (cccDNA) in the nucleus of infected cells that cannot be targeted by available antivirals. Interferons can diminish HBV cccDNA via APOBEC3-mediated deamination. Here, we show that overexpression of APOBEC3A alone is not sufficient to reduce HBV cccDNA that requires additional treatment of cells with interferon indicating involvement of an interferon-stimulated gene (ISG) in cccDNA degradation. Transcriptome analyses identify ISG20 as the only type I and II interferon-induced, nuclear protein with annotated nuclease activity. ISG20 localizes to nucleoli of interferon-stimulated hepatocytes and is enriched on deoxyuridine-containing single-stranded DNA that mimics transcriptionally active, APOBEC3A-deaminated HBV DNA. ISG20 expression is detected in human livers in acute, self-limiting but not in chronic hepatitis B. ISG20 depletion mitigates the interferon-induced loss of cccDNA, and co-expression with APOBEC3A is sufficient to diminish cccDNA. In conclusion, non-cytolytic HBV cccDNA decline requires the concerted action of a deaminase and a nuclease. Our findings highlight that ISGs may cooperate in their antiviral activity that may be explored for therapeutic targeting.
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9
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Jones AN, Pisignano G, Pavelitz T, White J, Kinisu M, Forino N, Albin D, Varani G. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA 2020; 26:1234-1246. [PMID: 32457084 PMCID: PMC7430676 DOI: 10.1261/rna.076117.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
The wide prevalence and regulated expression of long noncoding RNAs (lncRNAs) highlight their functional roles, but the molecular basis for their activities and structure-function relationships remains to be investigated, with few exceptions. Among the relatively few lncRNAs conserved over significant evolutionary distances is the long intergenic noncoding RNA (lincRNA) Cyrano (orthologous to human OIP5-AS1), which contains a region of 300 highly conserved nucleotides within tetrapods, which in turn contains a functional stretch of 26 nt of deep conservation. This region binds to and facilitates the degradation of the microRNA miR-7, a short ncRNA with multiple cellular functions, including modulation of oncogenic expression. We probed the secondary structure of Cyrano in vitro and in cells using chemical and enzymatic probing, and validated the results using comparative sequence analysis. At the center of the functional core of Cyrano is a cloverleaf structure maintained over the >400 million years of divergent evolution that separates fish and primates. This strikingly conserved motif provides interaction sites for several RNA-binding proteins and masks a conserved recognition site for miR-7. Conservation in this region strongly suggests that the function of Cyrano depends on the formation of this RNA structure, which could modulate the rate and efficiency of degradation of miR-7.
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Affiliation(s)
- Alisha N Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Giuseppina Pisignano
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH-6500, Switzerland
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Jessica White
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Martin Kinisu
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Nicholas Forino
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Dreycey Albin
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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10
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Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol 2020; 11:845-859. [PMID: 31336384 PMCID: PMC6917512 DOI: 10.1093/jmcb/mjz086] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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] [Received: 02/11/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022] Open
Abstract
Following the discovery of numerous long non-coding RNA (lncRNA) transcripts in the human genome, their important roles in biology and human disease are emerging. Recent progress in experimental methods has enabled the identification of structural features of lncRNAs. However, determining high-resolution structures is challenging as lncRNAs are expected to be dynamic and adopt multiple conformations, which may be modulated by interaction with protein binding partners. The X-inactive specific transcript (Xist) is necessary for X inactivation during dosage compensation in female placental mammals and one of the best-studied lncRNAs. Recent progress has provided new insights into the domain organization, molecular features, and RNA binding proteins that interact with distinct regions of Xist. The A-repeats located at the 5′ end of the transcript are of particular interest as they are essential for mediating silencing of the inactive X chromosome. Here, we discuss recent progress with elucidating structural features of the Xist lncRNA, focusing on the A-repeats. We discuss the experimental and computational approaches employed that have led to distinct structural models, likely reflecting the intrinsic dynamics of this RNA. The presence of multiple dynamic conformations may also play an important role in the formation of the associated RNPs, thus influencing the molecular mechanism underlying the biological function of the Xist A-repeats. We propose that integrative approaches that combine biochemical experiments and high-resolution structural biology in vitro with chemical probing and functional studies in vivo are required to unravel the molecular mechanisms of lncRNAs.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Center for Integrated Protein Science Munich and Bavarian NMR Center at Department of Chemistry, Technical University of Munich, Garching, 85747, Germany
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11
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Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res 2019; 47:1523-1531. [PMID: 30481318 PMCID: PMC6379670 DOI: 10.1093/nar/gky1197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [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: 09/28/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Paul T Wille
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Alisha N Jones
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Jasmina Bogdanovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Eric Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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12
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von Gamm M, Schaub A, Jones AN, Wolf C, Behrens G, Lichti J, Essig K, Macht A, Pircher J, Ehrlich A, Davari K, Chauhan D, Busch B, Wurst W, Feederle R, Feuchtinger A, Tschöp MH, Friedel CC, Hauck SM, Sattler M, Geerlof A, Hornung V, Heissmeyer V, Schulz C, Heikenwalder M, Glasmacher E. Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3. J Exp Med 2019; 216:1700-1723. [PMID: 31126966 PMCID: PMC6605757 DOI: 10.1084/jem.20181762] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 09/16/2018] [Revised: 02/15/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022] Open
Abstract
The RNase Regnase-1 is a master RNA regulator in macrophages and T cells that degrades cellular and viral RNA upon NF-κB signaling. The roles of its family members, however, remain largely unknown. Here, we analyzed Regnase-3-deficient mice, which develop hypertrophic lymph nodes. We used various mice with immune cell-specific deletions of Regnase-3 to demonstrate that Regnase-3 acts specifically within myeloid cells. Regnase-3 deficiency systemically increased IFN signaling, which increased the proportion of immature B and innate immune cells, and suppressed follicle and germinal center formation. Expression analysis revealed that Regnase-3 and Regnase-1 share protein degradation pathways. Unlike Regnase-1, Regnase-3 expression is high specifically in macrophages and is transcriptionally controlled by IFN signaling. Although direct targets in macrophages remain unknown, Regnase-3 can bind, degrade, and regulate mRNAs, such as Zc3h12a (Regnase-1), in vitro. These data indicate that Regnase-3, like Regnase-1, is an RNase essential for immune homeostasis but has diverged as key regulator in the IFN pathway in macrophages.
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Affiliation(s)
- Matthias von Gamm
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annalisa Schaub
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Center for Integrated Protein Science Munich, Chemistry Department, Technical University of Munich, Garching, Germany
| | - Christine Wolf
- Institute of Environmental Medicine, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Gesine Behrens
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Johannes Lichti
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katharina Essig
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Anna Macht
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Joachim Pircher
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Ludwig-Maximilians-University, Munich, Germany
| | - Andreas Ehrlich
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Ludwig-Maximilians-University, Munich, Germany
| | | | - Dhruv Chauhan
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Benjamin Busch
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Munich, Germany.,Technische Universität München-Weihenstephan, Neuherberg-Munich, Germany.,German Center for Neurodegenerative Diseases, Munich, Germany.,Munich Cluster for Systems Neurology, Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Division of Metabolic Diseases, Department of Medicine, Technische Universität München, Munich, Germany
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Center for Integrated Protein Science Munich, Chemistry Department, Technical University of Munich, Garching, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Christian Schulz
- Medizinische Klinik und Poliklinik I, Klinikum der Universität München, Ludwig-Maximilians-University, Munich, Germany.,German Center for Cardiovascular Research, partner site Munich Heart Alliance, Munich, Germany
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer (F180), German Cancer Research Center, Heidelberg, Germany
| | - Elke Glasmacher
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany .,Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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Hinks JA, Jones AN, Theodosiou A, van den Berg JA, Donnelly SE. Transmission Electron Microscopy Study of Graphite underin situIon Irradiation. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/371/1/012046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Nansera D, Graziano FM, Friedman DJ, Bobbs MK, Jones AN, Hansen KE. Vitamin D and calcium levels in Ugandan adults with human immunodeficiency virus and tuberculosis. Int J Tuberc Lung Dis 2012; 15:1522-7, i. [PMID: 22008767 DOI: 10.5588/ijtld.10.0701] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vitamin D increases cathelicidin production, and might alter mortality due to tuberculosis (TB) in human immunodeficiency virus (HIV) coinfection. However, due to abundant sun exposure, vita min D levels might be excellent among Ugandans with HIV and TB. METHODS We measured 25(OH)D and calcium levels in 50 HIV-negative, 50 HIV-infected and 50 TB-HIV coinfected Ugandan adults. RESULTS Mean ± standard deviation 25(OH)D levels were 26 ± 7 ng/ml in HIV-negative, 28 ± 11 ng/ml in HIV-infected and 24 ± 11 ng/ml in TB-HIV co-infected adults (P > 0.05 all comparisons). Vitamin D deficiency (< 12 ng/ml) was present in 10% of the HIV-infected subjects, 12% of the TB-HIV co-infected and none of the healthy controls (P = 0.03 for healthy vs. TB, P > 0.05 for other comparisons); 20% of the healthy controls, 22% of the HIV-positive and 38% of the TB-HIV co-infected subjects (P = 0.047 for healthy vs. TB, P > 0.05 for other comparisons) had suboptimal vitamin D levels (< 20 ng/ml). No participant had hypercalcemia. Serum 25(OH)D levels correlated positively with body mass index (r = 0.22, P = 0.03) and serum calcium levels (r = 0.18, P = 0.03). CONCLUSIONS Ugandan HIV-infected adults with and without TB commonly had suboptimal vitamin D levels. Clinical trials are needed to evaluate the effect of vitamin D on health outcomes in HIV-infected patients with low vitamin D levels.
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Affiliation(s)
- D Nansera
- Mbarara University of Science and Technology/Teaching Hospital, Mbarara, Uganda.
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15
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Ni S, McGookey ME, Tinch SL, Jones AN, Jayaraman S, Tong L, Kennedy MA. The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1480-4. [PMID: 22139148 PMCID: PMC3232121 DOI: 10.1107/s1744309111037432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 08/15/2011] [Accepted: 09/14/2011] [Indexed: 01/01/2023]
Abstract
At2g44920 belongs to a diverse family (Pfam PF00805) of pentapeptide-repeat proteins (PRPs) that are present in all known organisms except yeast. PRPs contain at least eight tandem-repeating sequences of five amino acids with an approximate consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Recent crystal structures show that PRPs adopt a highly regular four-sided right-handed β-helical structure consisting mainly of type II and type IV β-turns, sometimes referred to as a repeated five-residue (or Rfr) fold. Among sequenced genomes, PRP genes are most abundant in cyanobacteria, leading to speculation that PRPs play an important role in the unique lifestyle of photosynthetic cyanobacteria. Despite the recent structural characterization of several cyanobacterial PRPs, most of their functions remain unknown. Plants, whose chloroplasts are of cyanobacterial origin, have only four PRP genes in their genomes. At2g44920 is one of three PRPs located in the thylakoid lumen. Here, the crystal structure of a double methionine mutant of residues 81-224 of At2g44920, the naturally processed fragment of one of its full-length isoforms, is reported at 1.7 Å resolution. The structure of At2g44920 consists of the characteristic Rfr fold with five uninterrupted coils made up of 25 pentapeptide repeats and α-helical elements capping both termini. A disulfide bridge links the two α-helices with a conserved loop between the helical elements at its C-terminus. This structure represents the first structure of a PRP protein whose subcellular location has been experimentally confirmed to be the thylakoid lumen in a plant species.
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Affiliation(s)
- Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Michael E. McGookey
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Stuart L. Tinch
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Alisha N. Jones
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | | | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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Abstract
UNLABELLED In one Veterans Affairs' medical center, alendronate non-adherence was more likely in male veterans who smoke or report side effects, and less likely in men undergoing bone densitometry during therapy. Providers urgently need programs to increase adherence to osteoporosis medications. Initial programs should target patients with risk factors for non-adherence. INTRODUCTION Adherence to osteoporosis therapy in men is unknown. We hypothesized that ca. 50% of men at one center would be adherent to alendronate and one or more patient-specific factors would associate with adherence. METHODS We conducted a retrospective chart review study of male veterans to determine the rates and predictors of alendronate adherence over two years. We excluded women, men who received primary care elsewhere and those who took alendronate for indications other than low bone mass. We defined adherence as a medication possession ratio > or =80% in the first 24 months of therapy. RESULTS Adherence in the first 12 and 24 months of therapy was 59% and 54%, respectively. In multivariate analyses, non-adherence was more likely in men using tobacco (OR 2.08, 95% CI 1.13, 3.84, p = 0.02) and reporting side effects (OR 2.06, 95% CI 1.14, 3.73, p = 0.02) and less likely in men undergoing bone density during therapy (OR 0.49, 95% CI 0.26, 0.90, p = 0.02). CONCLUSIONS Alendronate non-adherence is more likely in male veterans who smoke or report side effects, and less likely in men having bone densitometry during therapy. Providers urgently need programs to increase adherence to osteoporosis medications. Initial programs should target patients with risk factors for non-adherence.
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Affiliation(s)
- K E Hansen
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA.
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Zimmerman RA, Tomasek JJ, McRae J, Haaksma CJ, Schwartz RJ, Lin HK, Cowan RL, Jones AN, Kropp BP. Decreased expression of smooth muscle alpha-actin results in decreased contractile function of the mouse bladder. J Urol 2004; 172:1667-72. [PMID: 15371786 DOI: 10.1097/01.ju.0000139874.48574.1b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE Smooth muscle alpha-actin (SMalphaA) is an important actin isoform for functional contractility in the mouse bladder. Alterations in the expression of SMalphaA have been associated with a variety of bladder pathological conditions. Recently, a SMalphaA-null mouse was generated and differences in vascular tone and contractility were observed between wild-type and SMalphaA-null mice suggesting alterations in function of vascular smooth muscle. We used SMalphaA-null mice to explore the hypothesis that SMalphaA is necessary for normal bladder function. MATERIALS AND METHODS Reverse transcriptase polymerase chain reaction, Western blotting and immunohistochemical staining were used to confirm the absence of SMalphaA transcript and protein in the bladder of SMalphaA-null mice. In vitro bladder contractility compared between bladder rings harvested from wild-type and SMalphaA-null mice was determined by force measurement following electrical field stimulation (EFS), and exposure to chemical agonists and antagonists including KCl, carbachol, atropine and tetrodotoxin. Resulting force generation profiles for each tissue and agent were analyzed. RESULTS There was no detectable SMalphaA transcript and protein expression in the bladder of SMalphaA-null mice. Nine wild-type and 9 SMalphaA-null mice were used in the contractility study. Bladders from SMalphaA-null mice generated significantly less force than wild-type mice in response to EFS after KCl. Similarly, bladders from SMalphaA-null mice generated less force than wild-type mice in response to pretreatment EFS, and EFS after carbachol and atropine, although the difference was not significant. Surprisingly, the bladders in SMalphaA-null mice appeared to function normally and showed no gross or histological abnormalities. CONCLUSIONS SMalphaA appears to be necessary for the bladder to be able to generate normal levels of contractile force. No functional deficits were observed in the bladders of these animals but no stress was placed on these bladders. To our knowledge this study represents the first report to demonstrate the importance of expression of SMalphaA in force generation in the bladder.
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Affiliation(s)
- R A Zimmerman
- Department of Urology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
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18
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Halpin RA, Geer LA, Zhang KE, Marks TM, Dean DC, Jones AN, Melillo D, Doss G, Vyas KP. The absorption, distribution, metabolism and excretion of rofecoxib, a potent and selective cyclooxygenase-2 inhibitor, in rats and dogs. Drug Metab Dispos 2000; 28:1244-54. [PMID: 10997947] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Absorption, distribution, metabolism, and excretion studies were conducted in rats and dogs with rofecoxib (VIOXX, MK-0966), a potent and highly selective inhibitor of cyclooxygenase-2 (COX-2). In rats, the nonexponential decay during the terminal phase (4- to 10-h time interval) of rofecoxib plasma concentration versus time curves after i.v. or oral administration of [(14)C]rofecoxib precluded accurate determinations of half-life, AUC(0-infinity) (area under the plasma concentration versus time curve extrapolated to infinity), and hence, bioavailability. After i.v. administration of [(14)C]rofecoxib to dogs, plasma clearance, volume of distribution at steady state, and elimination half-life values of rofecoxib were 3.6 ml/min/kg, 1.0 l/kg, and 2.6 h, respectively. Oral absorption (5 mg/kg) was rapid in both species with C(max) occurring by 0.5 h (rats) and 1.5 h (dogs). Bioavailability in dogs was 26%. Systemic exposure increased with increasing dosage in rats and dogs after i.v. (1, 2, and 4 mg/kg), or oral (2, 5, and 10 mg/kg) administration, except in rats where no additional increase was observed between the 5 and 10 mg/kg doses. Radioactivity distributed rapidly to tissues, with the highest concentrations of the i.v. dose observed in most tissues by 5 min and by 30 min in liver, skin, fat, prostate, and bladder. Excretion occurred primarily by the biliary route in rats and dogs, except after i.v. administration of [(14)C]rofecoxib to dogs, where excretion was divided between biliary and renal routes. Metabolism of rofecoxib was extensive. 5-Hydroxyrofecoxib-O-beta-D-glucuronide was the major metabolite excreted by rats in urine and bile. 5-Hydroxyrofecoxib, rofecoxib-3',4'-dihydrodiol, and 4'-hydroxyrofecoxib sulfate were less abundant, whereas cis- and trans-3,4-dihydro-rofecoxib were minor. Major metabolites in dog were 5-hydroxyrofecoxib-O-beta-D-glucuronide (urine), trans-3, 4-dihydro-rofecoxib (urine), and 5-hydroxyrofecoxib (bile).
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Affiliation(s)
- R A Halpin
- Department of Drug Metabolism, Merck Research Laboratories, West Point, Pennsylvania and Rahway, New Jersey, USA
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Jones AN. Late bloomers: saving for college when your kids are teenagers. Northwest Dent 1998; 77:39-40. [PMID: 9872100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- A N Jones
- Merrill Lynch Private Client Marketing Group, USA
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Jones AN. Cover your health care costs with a medical savings account. Northwest Dent 1998; 77:47-8. [PMID: 9872095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Anderson WK, Jones AN. Synthesis and evaluation of furan, thiophene, and azole bis[(carbamoyloxy)methyl] derivatives as potential antineoplastic agents. J Med Chem 1984; 27:1559-65. [PMID: 6502590 DOI: 10.1021/jm00378a006] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A series of bis(hydroxymethyl)-substituted heterocycles were synthesized and converted to the corresponding bis(methylcarbamate) derivatives. The heterocyclic systems studied were based on 2-phenyl-3-methylfuran (2-4), 1-phenylpyrazole (5-7), 1-phenyl-5-methylpyrazole (9-11), 1-phenyl-5-methylthiophene (13), 1-phenyl-1,2,3-triazole (14), 3-phenylisoxazole (15), 3-phenylisothiazole (16), 2-phenylthiazole (17), and 2-phenyloxazole (18). None of the bis(carbamates) prepared was active against murine P388 lymphocytic leukemia. Pyrrole bis(carbamates) 20 and 21, which exhibited antileukemic activity, also showed reactivity toward 4-(p-nitrobenzyl)pyridine while the inactive bis(carbamates) were unreactive in the 4-(p-nitrobenzyl)pyridine assay.
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Anderson WK, Chang CP, Corey PF, Halat MJ, Jones AN, McPherson HL, New JS, Rich AC. Vinylogous carbinolamine tumor inhibitors. 8. Activity of bis(acyloxymethyl) derivatives of pyrroles and pyrrolizines against a panel of murine leukemias and solid tumors. Cancer Treat Rep 1982; 66:91-7. [PMID: 7053273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The activity of three pyrroles and four pyrrolizines is compared in several different experimental leukemias and solid tumors in mice. Two compounds were particularly noteworthy, the bis(N-cyclohexylcarbamate) and the bis[N-(2-propyl)] derivatives of 2,3-dihydro-5-(3,4-dichlorophenyl)-6,7-bis(hydroxymethyl)-1H-pyrrolizine. These two compounds showed a very high level of activity against B16 melanocarcinoma, CD8F1 mammary tumor, colon tumor 26, and colon tumor 38, and a significant number of "cures" were recorded. The isopropyl compound was more potent than the cyclohexyl compound, but both showed a similar profile of activity.
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Abstract
Prescribing of compound analgesics containing dextropropoxyphene was limited to consultants only in a teaching hospital. Inpatient prescribing (mainly by junior staff) fell immediately to very low levels but outpatient prescribing (by consultants) fell more slowly to about one-third of the original level, suggesting that patients and doctors find dextropropoxyphene compounds useful. Prescriptions for paracetamol increased but so did those for other compound analgesics, particularly those containing high doses of codeine, indicating a belief that compound analgesics have a role in treatment. Restrictions may produce unexpected results and monitoring is essential, but the method of audit used by pharmacies is not suitable for detailed analysis.
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Abstract
After nothing the rarity of papers describing the pathology of delayed radiation necrosis of the spinal cord, the clinical and pathological findings from four cases are presented. The main pathological features are asymmetric demyelination of the lateral columns and to a lesser degree the posterior and anterior columns of white matter, with coagulative necrosis at the level of irradiation which affected the grey matter to a lesser degree. There is ascending and descending secondary tract degeneration, and poor glial response in the lesions themselves. Vascular changes, mainly hyalilne thickening of arteriolar walls, are present, but not in degree sufficient to explain the primary lesion. The discussion of the pathogenesis of the myelopathy weighs the merits of a primary vascular lesion against those of a primary effect of the radiation on neural tissue. The latter is favoured.
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