151
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Wu G, Adachi H, Ge J, Stephenson D, Query CC, Yu YT. Pseudouridines in U2 snRNA stimulate the ATPase activity of Prp5 during spliceosome assembly. EMBO J 2016; 35:654-67. [PMID: 26873591 DOI: 10.15252/embj.201593113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/04/2016] [Indexed: 12/20/2022] Open
Abstract
Pseudouridine (Ψ) is the most abundant internal modification identified in RNA, and yet little is understood of its effects on downstream reactions. Yeast U2 snRNA contains three conserved Ψs (Ψ35, Ψ42, and Ψ44) in the branch site recognition region (BSRR), which base pairs with the pre-mRNA branch site during splicing. Here, we show that blocks to pseudouridylation at these positions reduce the efficiency of pre-mRNA splicing, leading to growth-deficient phenotypes. Restoration of pseudouridylation at these positions using designer snoRNAs results in near complete rescue of splicing and cell growth. These Ψs interact genetically with Prp5, an RNA-dependent ATPase involved in monitoring the U2 BSRR-branch site base-pairing interaction. Biochemical analysis indicates that Prp5 has reduced affinity for U2 snRNA that lacks Ψ42 and Ψ44 and that Prp5 ATPase activity is reduced when stimulated by U2 lacking Ψ42 or Ψ44 relative to wild type, resulting in inefficient spliceosome assembly. Furthermore, in vivo DMS probing analysis reveals that pseudouridylated U2, compared to U2 lacking Ψ42 and Ψ44, adopts a slightly different structure in the branch site recognition region. Taken together, our results indicate that the Ψs in U2 snRNA contribute to pre-mRNA splicing by directly altering the binding/ATPase activity of Prp5.
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Affiliation(s)
- Guowei Wu
- Department of Biochemistry and Biophysics, Center for RNA Biology, The Rochester Aging Research (RoAR) Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, The Rochester Aging Research (RoAR) Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Junhui Ge
- Department of Pathology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - David Stephenson
- Department of Biochemistry and Biophysics, Center for RNA Biology, The Rochester Aging Research (RoAR) Center, University of Rochester Medical Center, Rochester, NY, USA
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, The Rochester Aging Research (RoAR) Center, University of Rochester Medical Center, Rochester, NY, USA
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152
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Abstract
The purpose of this review is to provide an overview of the complexity of the epigenetic target space. Chemical modifications of histones and nucleic acids constitute a key epigenetic mechanism. Whereas modifications such as methylation and acetylation are well-known, there are many additional, less explored modifications described here. The writers, readers and erasers of such diverse modifications, which constitute a major portion of the potential epigenetic target space, are discussed, in addition to the various other protein families that do not fall under these three categories. Finally, disease relevance and druggability of epigenetic targets are discussed with concluding remarks about the richness and diversity they will provide for future targeted therapies.
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Affiliation(s)
- Vineet Pande
- Discovery Sciences, Janssen-Pharmaceutical Companies of Johnson & Johnson , Turnhoutseweg 30, Beerse 2340, Belgium
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153
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Huang C, Wu G, Yu YT. Purification and Functional Reconstitution of Box H/ACA Ribonucleoprotein Particles. Methods Mol Biol 2016; 1421:97-109. [PMID: 26965260 PMCID: PMC5702500 DOI: 10.1007/978-1-4939-3591-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Pseudouridylation is the most abundant and widespread RNA modification, and it plays an important role in modulating the structure and function of RNA. In eukaryotes and archaea, RNA pseudouridylation is catalyzed largely by box H/ACA ribonucleoproteins (RNPs), a distinct group of RNA-protein complexes each consisting of a unique RNA and four common proteins. The RNA component of the complex serves as a guide that base-pairs with its substrate RNA and specifies the target uridine to be modified. In order to systematically study the function and mechanism of pseudouridylation, it is desirable to have a reconstitution system in which biochemically purified/reconstituted box H/ACA RNPs are capable of introducing pseudouridines into an RNA at any target site. Here, we describe a method for the reconstitution of functional box H/ACA RNPs using designer box H/ACA guide RNAs, which in principle can be adopted to reconstitute other RNA-protein complexes as well.
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Affiliation(s)
- Chao Huang
- Process Science Downstream, Bristol-Myers Squibb Company, 6000 Thompson Road, East Syracuse, NY, 13057, USA
| | - Guowei Wu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-065, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, 14642, USA.
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154
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Yamauchi Y, Nobe Y, Izumikawa K, Higo D, Yamagishi Y, Takahashi N, Nakayama H, Isobe T, Taoka M. A mass spectrometry-based method for direct determination of pseudouridine in RNA. Nucleic Acids Res 2015; 44:e59. [PMID: 26673725 PMCID: PMC4824092 DOI: 10.1093/nar/gkv1462] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/27/2015] [Indexed: 02/01/2023] Open
Abstract
Pseudouridine (5-ribosyluracil, Ψ) is the only ‘mass-silent’ nucleoside produced by post-transcriptional RNA modification. We describe here a novel mass spectrometry (MS)-based method for direct determination of Ψ in RNA. The method assigns a Ψ-containing nucleolytic RNA fragment by an accurate measurement of a signature doubly dehydrated nucleoside anion ([C9H7N2O4]1−, m/z 207.04) produced by collision-induced dissociation MS, and it determines the Ψ-containing nucleotide sequence by pseudo-MS3, i.e. in-source fragmentation followed by MS2. By applying this method, we identified all of the known Ψs in the canonical human spliceosomal snRNAs and, unexpectedly, found two previously unknown Ψs in the U5 and U6 snRNAs. Because the method allows direct determination of Ψ in a subpicomole quantity of RNA, it will serve as a useful tool for the structure/function studies of a wide variety of non-coding RNAs.
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Affiliation(s)
- Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Keiichi Izumikawa
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific, 3-9 Moriya-cho, Kanagawa-ku, Yokohama-shi, Kanagawa 221-0022, Japan
| | - Yoko Yamagishi
- Thermo Fisher Scientific, 3-9 Moriya-cho, Kanagawa-ku, Yokohama-shi, Kanagawa 221-0022, Japan
| | - Nobuhiro Takahashi
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Department of Biotechnology, United Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Hiroshi Nakayama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
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155
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Laptev IG, Golovina AY, Sergiev PV, Dontsova OA. Posttranscriptional modification of messenger RNAs in eukaryotes. Mol Biol 2015; 49:825-836. [PMID: 32214475 PMCID: PMC7088549 DOI: 10.1134/s002689331506014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide mapping of posttranscriptional modifications in eukaryotic RNA revealed tens of thousands of modification sites. Modified nucleotides include 6-methyladenosine, 5-methylcytidine, pseudouridine, inosine, etc. Many modification sites are conserved, and many are regulated. The function is known for a minor subset of modified nucleotides, while the role of their majority is still obscure. In view of the global character of mRNA modification, RNA epigenetics arose as a new field of molecular biology. The review considers posttranscriptional modification of eukaryotic mRNA, focusing on the major modified nucleotides, the role they play in the cell, the methods to detect them, and the enzymes responsible for modification.
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Affiliation(s)
- I G Laptev
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia
| | - A Ya Golovina
- 2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
| | - P V Sergiev
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia.,2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
| | - O A Dontsova
- 1Department of Chemistry, Moscow State University, Moscow, 119991 Russia.,2Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992 Russia
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156
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Mishima E, Jinno D, Akiyama Y, Itoh K, Nankumo S, Shima H, Kikuchi K, Takeuchi Y, Elkordy A, Suzuki T, Niizuma K, Ito S, Tomioka Y, Abe T. Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides. PLoS One 2015; 10:e0143756. [PMID: 26606401 PMCID: PMC4659547 DOI: 10.1371/journal.pone.0143756] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/09/2015] [Indexed: 11/19/2022] Open
Abstract
The biological roles of RNA modifications are still largely not understood. Thus, developing a method for detecting RNA modifications is important for further clarification. We developed a method for detecting RNA modifications called immuno-northern blotting (INB) analysis and herein introduce its various capabilities. This method involves the separation of RNAs using either polyacrylamide or agarose gel electrophoresis, followed by transfer onto a nylon membrane and subsequent immunoblotting using antibodies against modified nucleosides for the detection of specific modifications. We confirmed that INB with the antibodies for 1-methyladenosine (m1A), N6-methyladenosine (m6A), pseudouridine, and 5-methylcytidine (m5C) showed different modifications in a variety of RNAs from various species and organelles. INB with the anti-m5C antibody revealed that the antibody cross-reacted with another modification on DNA, suggesting the application of this method for characterization of the antibody for modified nucleosides. Additionally, using INB with the antibody for m1A, which is a highly specific modification in eukaryotic tRNA, we detected tRNA-derived fragments known as tiRNAs under the cellular stress response, suggesting the application for tracking target RNA containing specific modifications. INB with the anti-m6A antibody confirmed the demethylation of m6A by the specific demethylases fat mass and obesity-associated protein (FTO) and ALKBH5, suggesting its application for quantifying target modifications in separated RNAs. Furthermore, INB demonstrated that the knockdown of FTO and ALKBH5 increased the m6A modification in small RNAs as well as in mRNA. The INB method has high specificity, sensitivity, and quantitative capability, and it can be employed with conventional experimental apparatus. Therefore, this method would be useful for research on RNA modifications and metabolism.
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Affiliation(s)
- Eikan Mishima
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank Organization, Sendai, Japan
| | - Daisuke Jinno
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Yasutoshi Akiyama
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Tohoku Medical Megabank Organization, Sendai, Japan
| | - Kunihiko Itoh
- Department of Clinical Pharmacology and Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Shinnosuke Nankumo
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Hisato Shima
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koichi Kikuchi
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Takeuchi
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Alaa Elkordy
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takehiro Suzuki
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Sadayoshi Ito
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Takaaki Abe
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
- * E-mail:
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157
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GSE4, a Small Dyskerin- and GSE24.2-Related Peptide, Induces Telomerase Activity, Cell Proliferation and Reduces DNA Damage, Oxidative Stress and Cell Senescence in Dyskerin Mutant Cells. PLoS One 2015; 10:e0142980. [PMID: 26571381 PMCID: PMC4646510 DOI: 10.1371/journal.pone.0142980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/29/2015] [Indexed: 02/04/2023] Open
Abstract
Dyskeratosis congenita is an inherited disease caused by mutations in genes coding for telomeric components. It was previously reported that expression of a dyskerin-derived peptide, GSE24.2, increases telomerase activity, regulates gene expression and decreases DNA damage and oxidative stress in dyskeratosis congenita patient cells. The biological activity of short peptides derived from GSE24.2 was tested and one of them, GSE4, that probed to be active, was further characterized in this article. Expression of this eleven amino acids long peptide increased telomerase activity and reduced DNA damage, oxidative stress and cell senescence in dyskerin-mutated cells. GSE4 expression also activated c-myc and TERT promoters and increase of c-myc, TERT and TERC expression. The level of biological activity of GSE4 was similar to that obtained by GSE24.2 expression. Incorporation of a dyskerin nuclear localization signal to GSE24.2 did not change its activity on promoter regulation and DNA damage protection. However, incorporation of a signal that increases the rate of nucleolar localization impaired GSE24.2 activity. Incorporation of the dyskerin nuclear localization signal to GSE4 did not alter its biological activity. Mutation of the Aspartic Acid residue that is conserved in the pseudouridine synthase domain present in GSE4 did not impair its activity, except for the repression of c-myc promoter activity and the decrease of c-myc, TERT and TERC gene expression in dyskerin-mutated cells. These results indicated that GSE4 could be of great therapeutic interest for treatment of dyskeratosis congenita patients.
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158
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Shafik A, Schumann U, Evers M, Sibbritt T, Preiss T. The emerging epitranscriptomics of long noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:59-70. [PMID: 26541084 DOI: 10.1016/j.bbagrm.2015.10.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/15/2015] [Accepted: 10/28/2015] [Indexed: 01/08/2023]
Abstract
The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Andrew Shafik
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Maurits Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst (Sydney), New South Wales 2010, Australia.
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159
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Carlile TM, Rojas-Duran MF, Gilbert WV. Transcriptome-Wide Identification of Pseudouridine Modifications Using Pseudo-seq. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2015; 112:4.25.1-4.25.24. [PMID: 26423590 PMCID: PMC8006903 DOI: 10.1002/0471142727.mb0425s112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A diverse array of post-transcriptional modifications is found in RNA molecules from all domains of life. While the locations of RNA modifications are well characterized in abundant noncoding RNAs, modified sites in less abundant mRNAs are just beginning to be discovered. Recent work has revealed hundreds of previously unknown and dynamically regulated pseudouridines (Ψ) in mRNAs from diverse organisms. This unit describes Pseudo-seq, an efficient, high-resolution method for identification of Ψs genome-wide. This unit includes methods for isolation of RNA from S. cerevisiae, preparation of Pseudo-seq libraries from RNA samples, and identification of sites of pseudouridylation from the sequencing data. Pseudo-seq is applicable to any organism or cell type, facilitating rapid identification of novel pseudouridylation events.
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Affiliation(s)
- Thomas M Carlile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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160
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Toffano-Nioche C, Gautheret D, Leclerc F. Revisiting the structure/function relationships of H/ACA(-like) RNAs: a unified model for Euryarchaea and Crenarchaea. Nucleic Acids Res 2015; 43:7744-61. [PMID: 26240384 PMCID: PMC4652768 DOI: 10.1093/nar/gkv756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/22/2023] Open
Abstract
A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.
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Affiliation(s)
- Claire Toffano-Nioche
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Daniel Gautheret
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Fabrice Leclerc
- I2BC, Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
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161
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Andries O, Mc Cafferty S, De Smedt SC, Weiss R, Sanders NN, Kitada T. N(1)-methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice. J Control Release 2015; 217:337-44. [PMID: 26342664 DOI: 10.1016/j.jconrel.2015.08.051] [Citation(s) in RCA: 341] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/17/2015] [Accepted: 08/26/2015] [Indexed: 12/26/2022]
Abstract
Messenger RNA as a therapeutic modality is becoming increasingly popular in the field of gene therapy. The realization that nucleobase modifications can greatly enhance the properties of mRNA by reducing the immunogenicity and increasing the stability of the RNA molecule (the Kariko paradigm) has been pivotal for this revolution. Here we find that mRNAs containing the N(1)-methylpseudouridine (m1Ψ) modification alone and/or in combination with 5-methylcytidine (m5C) outperformed the current state-of-the-art pseudouridine (Ψ) and/or m5C/Ψ-modified mRNA platform by providing up to ~44-fold (when comparing double modified mRNAs) or ~13-fold (when comparing single modified mRNAs) higher reporter gene expression upon transfection into cell lines or mice, respectively. We show that (m5C/)m1Ψ-modified mRNA resulted in reduced intracellular innate immunogenicity and improved cellular viability compared to (m5C/)Ψ-modified mRNA upon in vitro transfection. The enhanced capability of (m5C/)m1Ψ-modified mRNA to express proteins may at least partially be due to the increased ability of the mRNA to evade activation of endosomal Toll-like receptor 3 (TLR3) and downstream innate immune signaling. We believe that the (m5C/)m1Ψ-mRNA platform presented here may serve as a new standard in the field of modified mRNA-based therapeutics.
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Affiliation(s)
- Oliwia Andries
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Séan Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent Research Group on Nanomedicine, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, USA
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - Tasuku Kitada
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA, USA.
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162
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Li X, Zhu P, Ma S, Song J, Bai J, Sun F, Yi C. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol 2015; 11:592-7. [DOI: 10.1038/nchembio.1836] [Citation(s) in RCA: 331] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023]
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163
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Li YH, Zhang G, Cui Q. PPUS: a web server to predict PUS-specific pseudouridine sites. Bioinformatics 2015; 31:3362-4. [PMID: 26076723 DOI: 10.1093/bioinformatics/btv366] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/05/2015] [Indexed: 01/28/2023] Open
Abstract
MOTIVATION Pseudouridine (Ψ), catalyzed by pseudouridine synthase (PUS), is the most abundant RNA modification and has important cellular functions. Developing an algorithm to identify Ψ sites is an important work. And it is better if the algorithm could assign which PUS modifies the Ψ sites. Here, we developed PPUS (http://lyh.pkmu.cn/ppus/), the first web server to predict PUS-specific Ψ sites. PPUS: employed support vector machine as the classifier and used nucleotides around Ψ sites as the features. Currently, PPUS: could accurately predict new Ψ sites for PUS1, PUS4 and PUS7 in yeast and PUS4 in human. PPUS: is well designed and friendly to user. AVAILABILITY AND IMPLEMENTATION Our web server is available freely for non-commercial purposes at: http://lyh.pkmu.cn/ppus/ CONTACT liyanhui@bjmu.edu.cn or cuiqinghua@hsc.pku.edu.cn.
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Affiliation(s)
- Yan-Hui Li
- Institute of Cardiovascular Sciences, Peking University Health Science Center
| | - Gaigai Zhang
- Department of Geriatrics and Gerontology, Beijing Huaxin Hospital, the First Affiliated Hospital of Tsinghua University and
| | - Qinghua Cui
- Department of Biomedical Informatics, Peking University Health Science Center, Beijing, China
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164
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The proteome of Hypobaric Induced Hypoxic Lung: Insights from Temporal Proteomic Profiling for Biomarker Discovery. Sci Rep 2015; 5:10681. [PMID: 26022216 PMCID: PMC4448130 DOI: 10.1038/srep10681] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/17/2015] [Indexed: 11/08/2022] Open
Abstract
Exposure to high altitude induces physiological responses due to hypoxia. Lungs being at the first level to face the alterations in oxygen levels are critical to counter and balance these changes. Studies have been done analysing pulmonary proteome alterations in response to exposure to hypobaric hypoxia. However, such studies have reported the alterations at specific time points and do not reflect the gradual proteomic changes. These studies also identify the various biochemical pathways and responses induced after immediate exposure and the resolution of these effects in challenge to hypobaric hypoxia. In the present study, using 2-DE/MS approach, we attempt to resolve these shortcomings by analysing the proteome alterations in lungs in response to different durations of exposure to hypobaric hypoxia. Our study thus highlights the gradual and dynamic changes in pulmonary proteome following hypobaric hypoxia. For the first time, we also report the possible consideration of SULT1A1, as a biomarker for the diagnosis of high altitude pulmonary edema (HAPE). Higher SULT1A1 levels were observed in rats as well as in humans exposed to high altitude, when compared to sea-level controls. This study can thus form the basis for identifying biomarkers for diagnostic and prognostic purposes in responses to hypobaric hypoxia.
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165
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Carlile TM, Rojas-Duran MF, Gilbert WV. Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA. Methods Enzymol 2015; 560:219-45. [PMID: 26253973 PMCID: PMC7945874 DOI: 10.1016/bs.mie.2015.03.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA molecules contain a variety of chemically diverse, posttranscriptionally modified bases. The most abundant modified base found in cellular RNAs, pseudouridine (Ψ), has recently been mapped to hundreds of sites in mRNAs, many of which are dynamically regulated. Though the pseudouridine landscape has been determined in only a few cell types and growth conditions, the enzymes responsible for mRNA pseudouridylation are universally conserved, suggesting many novel pseudouridylated sites remain to be discovered. Here, we present Pseudo-seq, a technique that allows the identification of sites of pseudouridylation genome-wide with single-nucleotide resolution. In this chapter, we provide a detailed description of Pseudo-seq. We include protocols for RNA isolation from Saccharomyces cerevisiae, Pseudo-seq library preparation, and data analysis, including descriptions of processing and mapping of sequencing reads, computational identification of sites of pseudouridylation, and assignment of sites to specific pseudouridine synthases. The approach presented here is readily adaptable to any cell or tissue type from which high-quality mRNA can be isolated. Identification of novel pseudouridylation sites is an important first step in elucidating the regulation and functions of these modifications.
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Affiliation(s)
- Thomas M Carlile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Maria F Rojas-Duran
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wendy V Gilbert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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166
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Singh M, Wang Z, Cascio D, Feigon J. Structure and interactions of the CS domain of human H/ACA RNP assembly protein Shq1. J Mol Biol 2015; 427:807-823. [PMID: 25553844 PMCID: PMC4323627 DOI: 10.1016/j.jmb.2014.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 12/27/2022]
Abstract
Shq1 is an essential protein involved in the early steps of biogenesis and assembly of H/ACA ribonucleoprotein particles (RNPs). Shq1 binds to dyskerin (Cbf5 in yeast) at an early step of H/ACA RNP assembly and is subsequently displaced by the H/ACA RNA. Shq1 contains an N-terminal CS and a C-terminal Shq1-specific domain (SSD). Dyskerin harbors many mutations associated with dyskeratosis congenita. Structures of yeast Shq1 SSD bound to Cbf5 revealed that only a subset of these mutations is in the SSD binding site, implicating another subset in the putative CS binding site. Here, we present the crystal structure of human Shq1 CS (hCS) and the nuclear magnetic resonance (NMR) and crystal structures of hCS containing a serine substitution for proline 22 that is associated with some prostate cancers. The structure of hCS is similar to yeast Shq1 CS domain (yCS) and consists of two β-sheets that form an immunoglobulin-like β-sandwich fold. The N-terminal affinity tag sequence AHHHHHH associates with a neighboring protein in the crystal lattice to form an extra β-strand. Deletion of this tag was required to get spectra suitable for NMR structure determination, while the tag was required for crystallization. NMR chemical shift perturbation (CSP) experiments with peptides derived from putative CS binding sites on dyskerin and Cbf5 revealed a conserved surface on CS important for Cbf5/dyskerin binding. A HADDOCK (high-ambiguity-driven protein-protein docking) model of a Shq1-Cbf5 complex that defines the position of CS domain in the pre-H/ACA RNP was calculated using the CSP data.
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Affiliation(s)
- Mahavir Singh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Zhonghua Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- University of California Los Angeles-Department of Energy (UCLA-DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; University of California Los Angeles-Department of Energy (UCLA-DOE) Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
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167
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Affiliation(s)
- Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York, USA
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168
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169
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Abstract
It has long been known that pseudouridine (Ψ) is the most abundant modified nucleotide in stable RNAs, including tRNA, rRNA, and snRNA. Recent studies using massive parallel sequencing have uncovered the presence of hundreds of Ψs in mRNAs as well. In eukaryotes and archaea, RNA pseudouridylation is introduced predominantly by box H/ACA RNPs, RNA-protein complexes each consisting of a single RNA moiety and four core proteins. It has been well established that Ψ plays an essential role in regulating the structure and function of stable RNAs in several model organisms, including yeast, Xenopus laevis, and humans. However, the functional role of Ψ in mRNA remains to be elucidated. One possibility (and true for stop/termination codons) is that Ψ influences decoding during translation. It is imperative, therefore, to establish a system, in which one can site-specifically introduce pseudouridylation into target mRNA and biochemically test the impact of mRNA pseudouridylation on protein translation. Here, we present a method for (1) site-specific conversion of uridine into Ψ in mRNA by designer box H/ACA RNP, (2) detection of Ψ in target mRNA using site-specific labeling followed by nuclease digestion and thin layer chromatography, and (3) analysis of recoding of pseudouridylated premature termination codon in mRNA during translation.
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Affiliation(s)
- Guowei Wu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Chao Huang
- Process Science Downstream, Bristol-Myers Squibb Company, Syracuse, New York, USA
| | - Yi-Tao Yu
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA,Corresponding author:
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170
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Lin X, Zhang CY, Bai XW, Feng B, Xiao DG. Improvement of stress tolerance and leavening ability under multiple baking-associated stress conditions by overexpression of the SNR84 gene in baker's yeast. Int J Food Microbiol 2014; 197:15-21. [PMID: 25555226 DOI: 10.1016/j.ijfoodmicro.2014.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 11/30/2014] [Accepted: 12/13/2014] [Indexed: 10/24/2022]
Abstract
During the bread-making process, industrial baker's yeast cells are exposed to multiple baking-associated stresses, such as elevated high-temperature, high-sucrose and freeze-thaw stresses. There is a high demand for baker's yeast strains that could withstand these stresses with high leavening ability. The SNR84 gene encodes H/ACA snoRNA (small nucleolar RNA), which is known to be involved in pseudouridylation of the large subunit rRNA. However, the function of the SNR84 gene in baker's yeast coping with baking-associated stresses remains unclear. In this study, we explored the effect of SNR84 overexpression on baker's yeast which was exposed to high-temperature, high-sucrose and freeze-thaw stresses. These results suggest that overexpression of the SNR84 gene conferred tolerance of baker's yeast cells to high-temperature, high-sucrose and freeze-thaw stresses and enhanced their leavening ability in high-sucrose and freeze-thaw dough. These findings could provide a valuable insight for breeding of novel stress-resistant baker's yeast strains that are useful for baking.
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Affiliation(s)
- Xue Lin
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Cui-Ying Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Xiao-Wen Bai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Bing Feng
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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171
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Adachi H, Yu YT. Insight into the mechanisms and functions of spliceosomal snRNA pseudouridylation. World J Biol Chem 2014; 5:398-408. [PMID: 25426264 PMCID: PMC4243145 DOI: 10.4331/wjbc.v5.i4.398] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 05/20/2014] [Accepted: 09/10/2014] [Indexed: 02/05/2023] Open
Abstract
Pseudouridines (Ψs) are the most abundant and highly conserved modified nucleotides found in various stable RNAs of all organisms. Most Ψs are clustered in regions that are functionally important for pre-mRNA splicing. Ψ has an extra hydrogen bond donor that endows RNA molecules with distinct properties that contribute significantly to RNA-mediated cellular processes. Experimental data indicate that spliceosomal snRNA pseudouridylation can be catalyzed by both RNA-dependent and RNA-independent mechanisms. Recent work has also demonstrated that pseudouridylation can be induced at novel positions under stress conditions, suggesting a regulatory role for Ψ.
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172
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Abstract
Two articles recently published in Nature and Cell report the first transcriptome-wide maps of pseudouridine (Ψ) at single-base resolution through selective chemical labeling, suggesting new mechanisms and functions of Ψ in mRNA and non-coding RNA molecules.
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173
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Lovejoy AF, Riordan DP, Brown PO. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 2014; 9:e110799. [PMID: 25353621 PMCID: PMC4212993 DOI: 10.1371/journal.pone.0110799] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/17/2014] [Indexed: 12/23/2022] Open
Abstract
We developed a novel technique, called pseudouridine site identification sequencing (PSI-seq), for the transcriptome-wide mapping of pseudouridylation sites with single-base resolution from cellular RNAs based on the induced termination of reverse transcription specifically at pseudouridines following CMCT treatment. PSI-seq analysis of RNA samples from S. cerevisiae correctly detected all of the 43 known pseudouridines in yeast 18S and 25S ribosomal RNA with high specificity. Moreover, application of PSI-seq to the yeast transcriptome revealed the presence of site-specific pseudouridylation within dozens of mRNAs, including RPL11a, TEF1, and other genes implicated in translation. To identify the mechanisms responsible for mRNA pseudouridylation, we genetically deleted candidate pseudouridine synthase (Pus) enzymes and reconstituted their activities in vitro. These experiments demonstrated that the Pus1 enzyme was necessary and sufficient for pseudouridylation of RPL11a mRNA, whereas Pus4 modified TEF1 mRNA, and Pus6 pseudouridylated KAR2 mRNA. Finally, we determined that modification of RPL11a at Ψ -68 was observed in RNA from the related yeast S. mikitae, and Ψ -239 in TEF1 mRNA was maintained in S. mikitae as well as S. pombe, indicating that these pseudouridylations are ancient, evolutionarily conserved RNA modifications. This work establishes that site-specific pseudouridylation of eukaryotic mRNAs is a genetically programmed RNA modification that naturally occurs in multiple yeast transcripts via distinct mechanisms, suggesting that mRNA pseudouridylation may provide an important novel regulatory function. The approach and strategies that we report here should be generally applicable to the discovery of pseudouridylation, or other RNA modifications, in diverse biological contexts.
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Affiliation(s)
- Alexander F. Lovejoy
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (AFL); (DPR)
| | - Daniel P. Riordan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (AFL); (DPR)
| | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
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174
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Turowski TW, Tollervey D. Cotranscriptional events in eukaryotic ribosome synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:129-39. [PMID: 25176256 DOI: 10.1002/wrna.1263] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/16/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
Abstract
Eukaryotic ribosomes are synthesized in a complex, multistep pathway. This begins with transcription of the rDNA genes by a specialized RNA polymerase, accompanied by the cotranscriptional binding of large numbers of ribosome synthesis factors, small nucleolar RNAs and ribosomal proteins. Cleavage of the nascent transcript releases the early pre-40S and pre-60S particles, which acquire export competence in the nucleoplasm prior to translocation through the nuclear pore complexes and final maturation to functional ribosomal subunits in the cytoplasm. This review will focus on the many and complex interactions occurring during pre-rRNA synthesis, particularly in budding yeast in which the pathway is best understood.
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Affiliation(s)
- Tomasz W Turowski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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175
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Basak A, Query CC. A pseudouridine residue in the spliceosome core is part of the filamentous growth program in yeast. Cell Rep 2014; 8:966-73. [PMID: 25127136 DOI: 10.1016/j.celrep.2014.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/30/2014] [Accepted: 07/02/2014] [Indexed: 11/20/2022] Open
Abstract
Although pseudouridine nucleobases are abundant in tRNAs, rRNAs, and small nuclear RNAs (snRNAs), they are not known to have physiologic roles in cell differentiation. We have identified a pseudouridine residue (Ψ28) on spliceosomal U6 snRNA that is induced during filamentous growth of Saccharomyces cerevisiae. Pus1p catalyzes this modification and is upregulated during filamentation. Several U6 snRNA mutants are strongly pseudouridylated at Ψ28. Remarkably, these U6 mutants activate pseudohyphal growth, dependent upon Pus1p, arguing that U6-Ψ28 per se can initiate at least part of the filamentous growth program. We confirmed this by using a designer small nucleolar RNA (snoRNA) targeting U6-U28 pseudouridylation. Conversely, mutants that block U6-U28 pseudouridylation inhibit pseudohyphal growth. U6-U28 pseudouridylation changes the splicing efficiency of suboptimal introns; thus, Pus1p-dependent pseudouridylation of U6 snRNA contributes to the filamentation growth program.
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Affiliation(s)
- Anindita Basak
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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176
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Zhang X, Walker RC, Phizicky EM, Mathews DH. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput 2014; 10:3473-3483. [PMID: 25136272 PMCID: PMC4132867 DOI: 10.1021/ct500107y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Indexed: 12/25/2022]
Abstract
![]()
Modified nucleotides are prevalent
in tRNA. Experimental studies
reveal that these covalent modifications play an important role in
tuning tRNA function. In this study, molecular dynamics (MD) simulations
were used to investigate how modifications alter tRNA dynamics. The
X-ray crystal structures of tRNA(Asp), tRNA(Phe), and tRNA(iMet),
both with and without modifications, were used as initial structures
for 333 ns explicit solvent MD simulations with AMBER. For each tRNA
molecule, three independent trajectory calculations were performed,
giving an aggregate of 6 μs of total MD across six molecules.
The global root-mean-square deviations (RMSD) of atomic positions
show that modifications only introduce significant rigidity to the
global structure of tRNA(Phe). Interestingly, RMSDs of the anticodon
stem-loop (ASL) suggest that modified tRNA has a more rigid structure
compared to the unmodified tRNA in this domain. The anticodon RMSDs
of the modified tRNAs, however, are higher than those of corresponding
unmodified tRNAs. These findings suggest that the rigidity of the
anticodon stem-loop is finely tuned by modifications, where rigidity
in the anticodon arm is essential for tRNA translocation in the ribosome,
and flexibility of the anticodon is important for codon recognition.
Sugar pucker and water residence time of pseudouridines in modified
tRNAs and corresponding uridines in unmodified tRNAs were assessed,
and the results reinforce that pseudouridine favors the 3′-endo
conformation and has a higher tendency to interact with water. Principal
component analysis (PCA) was used to examine correlated motions in
tRNA. Additionally, covariance overlaps of PCAs were compared for
trajectories of the same molecule and between trajectories of modified
and unmodified tRNAs. The comparison suggests that modifications alter
the correlated motions. For the anticodon bases, the extent of stacking
was compared between modified and unmodified molecules, and only unmodified
tRNA(Asp) has significantly higher percentage of stacking time. Overall,
the simulations reveal that the effect of covalent modification on
tRNA dynamics is not simple, with modifications increasing flexibility
in some regions of the structure and increasing rigidity in other
regions.
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Affiliation(s)
- Xiaoju Zhang
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego , La Jolla, California 92093, United States ; Department of Chemistry and Biochemistry, University of California San Diego , La Jolla, California 92093, United States
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center , Rochester, New York 14642, United States
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177
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Fu Y, Dominissini D, Rechavi G, He C. Gene expression regulation mediated through reversible m⁶A RNA methylation. Nat Rev Genet 2014; 15:293-306. [PMID: 24662220 DOI: 10.1038/nrg3724] [Citation(s) in RCA: 1272] [Impact Index Per Article: 127.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cellular RNAs carry diverse chemical modifications that used to be regarded as static and having minor roles in 'fine-tuning' structural and functional properties of RNAs. In this Review, we focus on reversible methylation through the most prevalent mammalian mRNA internal modification, N(6)-methyladenosine (m(6)A). Recent studies have discovered protein 'writers', 'erasers' and 'readers' of this RNA chemical mark, as well as its dynamic deposition on mRNA and other types of nuclear RNA. These findings strongly indicate dynamic regulatory roles that are analogous to the well-known reversible epigenetic modifications of DNA and histone proteins. This reversible RNA methylation adds a new dimension to the developing picture of post-transcriptional regulation of gene expression.
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Affiliation(s)
- Ye Fu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Dan Dominissini
- 1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA. [2] Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel. [3] Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gideon Rechavi
- 1] Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel. [2] Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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178
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Repetto O, Zanussi S, Casarotto M, Canzonieri V, De Paoli P, Cannizzaro R, De Re V. Differential proteomics of Helicobacter pylori associated with autoimmune atrophic gastritis. Mol Med 2014; 20:57-71. [PMID: 24395566 DOI: 10.2119/molmed.2013.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/23/2013] [Indexed: 12/20/2022] Open
Abstract
Atrophic autoimmune gastritis (AAG) is a condition of chronic inflammation and atrophy of stomach mucosa, for which development can be partially triggered by the bacterial pathogen Helicobacter pylori (HP). HP can cause a variety of gastric diseases, such as duodenal ulcer (DU) or gastric cancer (GC). In this study, a comparative proteomic approach was used by two-dimensional fluorescence difference gel electrophoresis (DIGE) to identify differentially expressed proteins of HP strains isolated from patients with AAG, to identify markers of HP strain associated with AAG. Proteome profiles of HP isolated from GC or DU were used as a reference to compare proteomic levels. Proteomics analyses revealed 27 differentially expressed spots in AAG-associated HP in comparison with GC, whereas only 9 differential spots were found in AAG-associated HP profiles compared with DU. Proteins were identified after matrix-assisted laser desorption ionization (MALDI)-TOF and peptide mass fingerprinting. Some AAG-HP differential proteins were common between DU- and GC-HP (peroxiredoxin, heat shock protein 70 [HSP70], adenosine 5'-triphosphate [ATP] synthase subunit α, flagellin A). Our results presented here may suggest that comparative proteomes of HP isolated from AAG and DU share more common protein expression than GC and provide subsets of putative AAG-specific upregulated or downregulated proteins that could be proposed as putative markers of AAG-associated HP. Other comparative studies by two-dimensional maps integrated with functional genomics of candidate proteins will undoubtedly contribute to better decipher the biology of AAG-associated HP strains.
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Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Stefania Zanussi
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Mariateresa Casarotto
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Paolo De Paoli
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Gastroenterology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
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179
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28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures. J Biotechnol 2014; 174:16-21. [PMID: 24480570 DOI: 10.1016/j.jbiotec.2014.01.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 11/21/2022]
Abstract
The mTOR pathway is a conserved master regulator of translational activity that influences the fate of industrially relevant CHO cell cultures, yet its molecular mechanisms remain unclear. Interestingly, rapamycin specific inhibition of the mTOR pathway in CHO cells was found to down-regulate the small nucleolar RNA U19 (snoRNA U19) by 2-fold via translatome profiling. snoRNA U19 guides the two most conserved pseudouridylation modifications on 28S ribosomal RNA (rRNA) that are important for the biogenesis and proper function of ribosomes. In order to further understand the role of snoRNA U19 as a potential player in the mTOR pathway, we measured 28S rRNA pseudouridylation upon rapamycin treatments and/or snoRNA U19 overexpression conditions, thereby characterizing the subsequent effects on ribosome efficiency and global translation by polysome profiling. We showed that 28S rRNA pseudouridylation was increased by rapamycin treatment and/or overexpression of snoRNA U19, but only the latter condition improved ribosome efficiency toward higher global translation, thus implying that the mTOR pathway induces pseudouridylation at different sites along the 28S rRNA possibly with either positive or negative effects on the cellular phenotype. This discovery of snoRNA U19 as a new downstream effector of the mTOR pathway suggests that cell engineering of snoRNAs can be used to regulate translation and improve cellular growth in CHO cell cultures in the future.
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180
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Spenkuch F, Motorin Y, Helm M. Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol 2014; 11:1540-54. [PMID: 25616362 PMCID: PMC4615568 DOI: 10.4161/15476286.2014.992278] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023] Open
Abstract
Pseudouridine (Ψ) is the most abundant of >150 nucleoside modifications in RNA. Although Ψ was discovered as the first modified nucleoside more than half a century ago, neither the enzymatic mechanism of its formation, nor the function of this modification are fully elucidated. We present the consistent picture of Ψ synthases, their substrates and their substrate positions in model organisms of all domains of life as it has emerged to date and point out the challenges that remain concerning higher eukaryotes and the elucidation of the enzymatic mechanism.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Humans
- Intramolecular Transferases/genetics
- Intramolecular Transferases/metabolism
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Nucleic Acid Conformation
- Pseudouridine/metabolism
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Felix Spenkuch
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
| | - Yuri Motorin
- Laboratoire IMoPA; Ingénierie Moléculaire et Physiopathologie Articulaire; BioPôle de l'Université de Lorraine; Campus Biologie-Santé; Faculté de Médecine; Vandoeuvre-les-Nancy Cedex, France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
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181
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Yu YT, Meier UT. RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. RNA Biol 2014; 11:1483-94. [PMID: 25590339 PMCID: PMC4615163 DOI: 10.4161/15476286.2014.972855] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 09/12/2014] [Indexed: 01/13/2023] Open
Abstract
Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs.
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Key Words
- DC, dyskeratosis congenita
- H/ACA
- HH, hoyeraal-hreidarsson syndrome
- PIKK, phosphatidylinositol 3-kinase-related kinase
- PUA, pseudouridylase and archaeosine transglycosylase
- RNA modification
- RNA-guided
- RNP, ribonucleoprotein
- SMN, survival of motor neuron protein
- SSD, SHQ1 specific domain
- U, uridine
- X-DC, X-linked dyskeratosis congenita
- dyskeratosis congenita
- prostate cancer
- pseudouridine
- rRNA
- rRNA, ribosomal RNA
- ribonucleoproteins
- sca, small Cajal body
- snRNA, small nuclear RNA
- sno, small nucleolar
- snoRNA
- snoRNA, small nucleolar RNA
- spliceosomal small nuclear RNA
- tRNA, transfer RNA
- ψ, pseudouridine, 5-ribosyluracil
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MESH Headings
- Dyskeratosis Congenita/genetics
- Dyskeratosis Congenita/metabolism
- Dyskeratosis Congenita/pathology
- Humans
- Isomerism
- Male
- Mutation
- Nucleic Acid Conformation
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Pseudouridine/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Yi-Tao Yu
- University of Rochester Medical Center; Department of Biochemistry and Biophysics; Center for RNA Biology; Rochester, NY USA
| | - U Thomas Meier
- Albert Einstein College of Medicine; Department of Anatomy and Structural Biology; Bronx, NY USA
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182
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Ye F, Zhang L, Jin L, Zheng M, Jiang H, Luo C. Repair of methyl lesions in RNA by oxidative demethylation. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00256c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleic acid methylation is one of the most important epigenetic modifications that have been studied intensively for the past several decades.
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Affiliation(s)
- Fei Ye
- College of Life Sciences
- Zhejiang Sci-Tech University
- Hangzhou
- China
| | - Liyi Zhang
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
| | - Lu Jin
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
| | - Mingyue Zheng
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
| | - Cheng Luo
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
- China
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183
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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184
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Pollard C, De Koker S, Saelens X, Vanham G, Grooten J. Challenges and advances towards the rational design of mRNA vaccines. Trends Mol Med 2013; 19:705-13. [PMID: 24138818 DOI: 10.1016/j.molmed.2013.09.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/12/2013] [Accepted: 09/17/2013] [Indexed: 01/01/2023]
Abstract
In recent years, mRNA vaccines have emerged as a safe and potent approach for the induction of cellular immune responses. Whereas initial studies were limited to the ex vivo loading of dendritic cells (DCs) with antigen-encoding mRNA, recent progress has led to the development of improved mRNA vaccines that enable direct in vivo targeting of DCs. Although preclinical studies demonstrated their potency in inducing antitumor immunity, several bottlenecks hinder the broader application of mRNA vaccines. In this review, we discuss the challenges associated with mRNA-based vaccination strategies, the technological advances that have been made to overcome these limitations, and the hurdles that remain to be tackled for the development of an optimal mRNA vaccine.
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Affiliation(s)
- Charlotte Pollard
- Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, B-2000 Antwerp, Belgium; Laboratory of Molecular Immunology, Department of Biomedical Molecular Biology, Ghent University, B-9052 Ghent, Belgium.
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185
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Joardar A, Jana S, Fitzek E, Gurha P, Majumder M, Chatterjee K, Geisler M, Gupta R. Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10. RNA (NEW YORK, N.Y.) 2013; 19:1279-94. [PMID: 23898217 PMCID: PMC3753934 DOI: 10.1261/rna.039230.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/25/2013] [Indexed: 05/25/2023]
Abstract
Pseudouridines (Ψ) are found in structurally and functionally important regions of RNAs. Six families of Ψ synthases, TruA, TruB, TruD, RsuA, RluA, and Pus10 have been identified. Pus10 is present in Archaea and Eukarya. While most archaeal Pus10 produce both tRNA Ψ54 and Ψ55, some produce only Ψ55. Interestingly, human PUS10 has been implicated in apoptosis and Crohn's and Celiac diseases. Homology models of archaeal Pus10 proteins based on the crystal structure of human PUS10 reveal that there are subtle structural differences in all of these Pus10 proteins. These observations suggest that structural changes in homologous proteins may lead to loss, gain, or change of their functions, warranting the need to study the structure-function relationship of these proteins. Using comparison of structural models and a series of mutations, we identified forefinger loop (reminiscent of that of RluA) and an Arg and a Tyr residue of archaeal Pus10 as critical determinants for its Ψ54, but not for its Ψ55 activity. We also found that a Leu residue, in addition to the catalytic Asp, is essential for both activities. Since forefinger loop is needed for both rRNA and tRNA Ψ synthase activities of RluA, but only for tRNA Ψ54 activity of Pus10, archaeal Pus10 proteins must use a different mechanism of recognition for Ψ55 activity. We propose that archaeal Pus10 uses two distinct mechanisms for substrate uridine recognition and binding. However, since we did not observe any mutation that affected only Ψ55 activity, both mechanisms for archaeal Pus10 activities must share some common features.
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Affiliation(s)
- Archi Joardar
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Sujata Jana
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Elisabeth Fitzek
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901-6509, USA
| | - Priyatansh Gurha
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Kunal Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901-6509, USA
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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