1
|
Chen M, Chen Y, Wang K, Deng X, Chen J. Non‐m 6A RNA modifications in haematological malignancies. Clin Transl Med 2024; 14:e1666. [PMID: 38880983 PMCID: PMC11180698 DOI: 10.1002/ctm2.1666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 06/18/2024] Open
Abstract
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N6-methyladenosine (m6A) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-m6A RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the m6A modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-m6A RNA modifications. In this review, we mainly focus on the roles and implications of non-m6A RNA modifications, including N4-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N1-methyladenosine and N7-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-m6A RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-m6A RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-m6A modifiers in blood cancer.
Collapse
Affiliation(s)
- Meiling Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Yuanzhong Chen
- Department of HematologyFujian Institute of HematologyFujian Provincial Key Laboratory on HematologyFujian Medical University Union HospitalFuzhouChina
| | - Kitty Wang
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Xiaolan Deng
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
| | - Jianjun Chen
- Department of Systems BiologyBeckman Research Institute of City of HopeMonroviaCaliforniaUSA
- Gehr Family Center for Leukemia ResearchCity of Hope Medical Center and Comprehensive Cancer CenterDuarteCaliforniaUSA
| |
Collapse
|
2
|
Xiong Q, Zhang Y. Small RNA modifications: regulatory molecules and potential applications. J Hematol Oncol 2023; 16:64. [PMID: 37349851 PMCID: PMC10286502 DOI: 10.1186/s13045-023-01466-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
Small RNAs (also referred to as small noncoding RNAs, sncRNA) are defined as polymeric ribonucleic acid molecules that are less than 200 nucleotides in length and serve a variety of essential functions within cells. Small RNA species include microRNA (miRNA), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), tRNA-derived small RNA (tsRNA), etc. Current evidence suggest that small RNAs can also have diverse modifications to their nucleotide composition that affect their stability as well as their capacity for nuclear export, and these modifications are relevant to their capacity to drive molecular signaling processes relevant to biogenesis, cell proliferation and differentiation. In this review, we highlight the molecular characteristics and cellular functions of small RNA and their modifications, as well as current techniques for their reliable detection. We also discuss how small RNA modifications may be relevant to the clinical applications for the diagnosis and treatment of human health conditions such as cancer.
Collapse
Affiliation(s)
- Qunli Xiong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
- Abdominal Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| |
Collapse
|
3
|
Li L, Zhu C, Xu S, Xu Q, Xu D, Gan S, Cui X, Tang C. PUS1 is a novel biomarker for evaluating malignancy of human renal cell carcinoma. Aging (Albany NY) 2023; 15:204799. [PMID: 37315299 PMCID: PMC10292901 DOI: 10.18632/aging.204799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Renal cell carcinoma (RCC) is one of the most common malignancies. Despite the rapid development of the oncology research and surgical treatment, the prognosis of RCC has not significantly improved. Thus, exploration of the pathological molecular mechanism and development of new therapeutic targets of RCC are of great importance. Herein, by bioinformatic analysis and in vitro cell experiments, we report that, the expression of pseudouridine synthase 1 (PUS1), belonging to the family of PUS enzymes that participate in RNA modifications, is closely associated with RCC progression. In addition, the upregulated PUS1 expression results in the elevated RCC cancer cell viability, migration, invasion and colony formation ability, whereas the decreased PUS1 expression exerts the opposite effects on RCC cells. Thus, our findings show the potential role of PUS1 in RCC cells, providing with evidence that PUS1 is involved in RCC progression, which may help contribute to RCC diagnosis and intervention in clinic.
Collapse
Affiliation(s)
- Lin Li
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Chongying Zhu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Shouying Xu
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Qiang Xu
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Da Xu
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Sishun Gan
- Department of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai 201805, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, China
| | - Chao Tang
- National Clinical Research Center for Child Health of the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| |
Collapse
|
4
|
Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. THE PLANT CELL 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
Collapse
Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| |
Collapse
|
5
|
Kiss DJ, Oláh J, Tóth G, Varga M, Stirling A, Menyhárd DK, Ferenczy GG. The Structure-Derived Mechanism of Box H/ACA Pseudouridine Synthase Offers a Plausible Paradigm for Programmable RNA Editing. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Dóra Judit Kiss
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Gergely Tóth
- Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány P. stny. 1/a, H-1117 Budapest, Hungary
| | - Máté Varga
- Department of Genetics, ELTE Eötvös Loránd University, Pázmány P. stny. 1/c, H-1117 Budapest, Hungary
| | - András Stirling
- Theoretical Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Dóra K. Menyhárd
- MTA-ELTE Protein Modelling Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány P. stny. 1/a, H-1117 Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest, Hungary
| |
Collapse
|
6
|
Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. NATURE CANCER 2022; 2:932-949. [PMID: 35121864 PMCID: PMC8809511 DOI: 10.1038/s43018-021-00238-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/21/2021] [Indexed: 12/22/2022]
Abstract
Pseudouridine is the most frequent epitranscriptomic modification. However, its cellular functions remain largely unknown. Here we show that the pseudouridine synthase PUS7 is highly expressed in glioblastoma versus normal brain tissues, and high PUS7 expression levels are associated with worse survival in glioblastoma patients. The PUS7 expression and catalytic activity are required for glioblastoma stem cell (GSC) tumorigenesis. Mechanistically, we identified PUS7 targets in GSCs through small RNA pseudouridine sequencing, and showed that pseudouridylation of PUS7-regulated tRNA is critical for codon-specific translational control of key regulators of GSCs. Moreover, we identified chemical inhibitors for PUS7, and showed that these compounds prevented PUS7-mediated pseudouridine modification, suppressed tumorigenesis, and extended lifespan of tumor-bearing mice. Overall, we identified an epitranscriptomic regulatory mechanism in glioblastoma and provided preclinical evidence of a potential therapeutic strategy for glioblastoma.
Collapse
|
7
|
Martinez NM, Su A, Burns MC, Nussbacher JK, Schaening C, Sathe S, Yeo GW, Gilbert WV. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. Mol Cell 2022; 82:645-659.e9. [PMID: 35051350 PMCID: PMC8859966 DOI: 10.1016/j.molcel.2021.12.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/04/2021] [Accepted: 12/17/2021] [Indexed: 02/05/2023]
Abstract
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.
Collapse
Affiliation(s)
- Nicole M Martinez
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA
| | - Amanda Su
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Julia K Nussbacher
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cassandra Schaening
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Wendy V Gilbert
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA.
| |
Collapse
|
8
|
Garus A, Autexier C. Dyskerin: an essential pseudouridine synthase with multifaceted roles in ribosome biogenesis, splicing, and telomere maintenance. RNA (NEW YORK, N.Y.) 2021; 27:1441-1458. [PMID: 34556550 PMCID: PMC8594475 DOI: 10.1261/rna.078953.121] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dyskerin and its homologs are ancient and conserved enzymes that catalyze the most common post-transcriptional modification found in cells, pseudouridylation. The resulting pseudouridines provide stability to RNA molecules and regulate ribosome biogenesis and splicing events. Dyskerin does not act independently-it is the core component of a protein heterotetramer, which associates with RNAs that contain the H/ACA motif. The variety of H/ACA RNAs that guide the function of this ribonucleoprotein (RNP) complex highlights the diversity of cellular processes in which dyskerin participates. When associated with small nucleolar (sno) RNAs, it regulates ribosomal (r) RNAs and ribosome biogenesis. By interacting with small Cajal body (sca) RNAs, it targets small nuclear (sn) RNAs to regulate pre-mRNA splicing. As a component of the telomerase holoenzyme, dyskerin binds to the telomerase RNA to modulate telomere maintenance. In a disease context, dyskerin malfunction can result in multiple detrimental phenotypes. Mutations in DKC1, the gene that encodes dyskerin, cause the premature aging syndrome X-linked dyskeratosis congenita (X-DC), a still incurable disorder that typically leads to bone marrow failure. In this review, we present the classical and most recent findings on this essential protein, discussing the evolutionary, structural, and functional aspects of dyskerin and the H/ACA RNP. The latest research underscores the role that dyskerin plays in the regulation of gene expression, translation efficiency, and telomere maintenance, along with the impacts that defective dyskerin has on aging, cell proliferation, haematopoietic potential, and cancer.
Collapse
Affiliation(s)
- Alexandre Garus
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| |
Collapse
|
9
|
Monajemi H, M. Zain S. How stop codon pseudouridylation induces nonsense suppression. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
iPseU-Layer: Identifying RNA Pseudouridine Sites Using Layered Ensemble Model. Interdiscip Sci 2020; 12:193-203. [PMID: 32170573 DOI: 10.1007/s12539-020-00362-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 01/28/2023]
Abstract
Pseudouridine represents one of the most prevalent post-transcriptional RNA modifications. The identification of pseudouridine sites is an essential step toward understanding RNA functions, RNA structure stabilization, translation process, and RNA stability; however, high-throughput experimental techniques remain expensive and time-consuming in lab explorations and biochemical processes. Thus, how to develop an efficient pseudouridine site identification method based on machine learning is very important both in academic research and drug development. Motived by this, we present an effective layered ensemble model designated as iPseU-Layer for identification of RNA pseudouridine sites. The proposed iPseU-Layer approach is essentially based on three different machine learning layers including: feature selection layer, feature extraction and fusion layer, and prediction layer. The feature selection layer reduces the dimensionality, which can be regarded as a data pre-processing stage. The feature extraction and fusion layer utilizes an ensemble method which is implemented through various machine learning algorithms to generate some outputs. The prediction layer applies classic random forest to identify the final results. Furthermore, we systematically conduct the validation experiments using cross-validation tests and independent test with the current state-of-the-art models. The proposed iPseU-Layer provides a promising predictive performance in terms of sensitivity, specificity, accuracy and Matthews correlation coefficient. Collectively, these findings indicate that the framework of iPseU-Layer is a feasible and effective strategy for the prediction of RNA pseudouridine sites.
Collapse
|
11
|
Abstract
Pseudouridylation is the most abundant of all RNA modifications. Pseudouridylation is dynamic and widespread among many different types of RNAs in living organisms, thus drawing a lot of recent interest from the RNA and epigenetics communities. To successfully carry out an investigation into RNA pseudouridylation, it is desirable to have a convenient and effective method capable of detection and quantification of pseudouridylation. Here, we present two such methods: one relies on pseudouridine (Ψ)-specific CMCT modification followed by reverse transcription/primer-extension (semiquantitative), and the other is based on site-specific cleavage and radiolabeling followed by nuclease digestion and TLC (quantitative). Although only semiquantitative, the CMCT and reverse transcription-based method is capable of detecting multiple Ψs (present in the same RNA molecule) in one reaction. In contrast, the second method, based on site-specific cleavage/labeling, nuclease digestion, and TLC, is quantitative, but can be used to analyze only one site at a time. These two methods can be used independently or in combination.
Collapse
Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Meemanage D DeZoysa
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.
| |
Collapse
|
12
|
Fujikane R, Behm-Ansmant I, Tillault AS, Loegler C, Igel-Bourguignon V, Marguet E, Forterre P, Branlant C, Motorin Y, Charpentier B. Contribution of protein Gar1 to the RNA-guided and RNA-independent rRNA:Ψ-synthase activities of the archaeal Cbf5 protein. Sci Rep 2018; 8:13815. [PMID: 30218085 PMCID: PMC6138745 DOI: 10.1038/s41598-018-32164-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023] Open
Abstract
Archaeal RNA:pseudouridine-synthase (PUS) Cbf5 in complex with proteins L7Ae, Nop10 and Gar1, and guide box H/ACA sRNAs forms ribonucleoprotein (RNP) catalysts that insure the conversion of uridines into pseudouridines (Ψs) in ribosomal RNAs (rRNAs). Nonetheless, in the absence of guide RNA, Cbf5 catalyzes the in vitro formation of Ψ2603 in Pyrococcus abyssi 23S rRNA and of Ψ55 in tRNAs. Using gene-disrupted strains of the hyperthermophilic archaeon Thermococcus kodakarensis, we studied the in vivo contribution of proteins Nop10 and Gar1 to the dual RNA guide-dependent and RNA-independent activities of Cbf5 on 23S rRNA. The single-null mutants of the cbf5, nop10, and gar1 genes are viable, but display a thermosensitive slow growth phenotype. We also generated a single-null mutant of the gene encoding Pus10, which has redundant activity with Cbf5 for in vitro formation of Ψ55 in tRNA. Analysis of the presence of Ψs within the rRNA peptidyl transferase center (PTC) of the mutants demonstrated that Cbf5 but not Pus10 is required for rRNA modification. Our data reveal that, in contrast to Nop10, Gar1 is crucial for in vivo and in vitro RNA guide-independent formation of Ψ2607 (Ψ2603 in P. abyssi) by Cbf5. Furthermore, our data indicate that pseudouridylation at orphan position 2589 (2585 in P. abyssi), for which no PUS or guide sRNA has been identified so far, relies on RNA- and Gar1-dependent activity of Cbf5.
Collapse
Affiliation(s)
- Ryosuke Fujikane
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
- Fukuoka Dental College, Department of Physiological Sciences and Molecular Biology, Section of Cellular and Molecular Regulation, 2-15-1 Tamura, Sawara-ku, Fukuoka, 814-0193, Japan
| | - Isabelle Behm-Ansmant
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Anne-Sophie Tillault
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Christine Loegler
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Valérie Igel-Bourguignon
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Evelyne Marguet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Patrick Forterre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
- Institut Pasteur, Département de Microbiologie, 25 rue du Dr Roux, F-7505, Paris, France
| | - Christiane Branlant
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, F-54500, Nancy, France
| | - Bruno Charpentier
- Université de Lorraine, CNRS, UMR 7365 Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), F-54500, Nancy, France.
| |
Collapse
|
13
|
Martinez NM, Gilbert WV. Pre-mRNA modifications and their role in nuclear processing. QUANTITATIVE BIOLOGY 2018; 6:210-227. [PMID: 30533247 DOI: 10.1007/s40484-018-0147-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Cellular non-coding RNAs are extensively modified post-transcriptionally, with more than 100 chemically distinct nucleotides identified to date. In the past five years, new sequencing based methods have revealed widespread decoration of eukaryotic messenger RNA with diverse RNA modifications whose functions in mRNA metabolism are only beginning to be known. Results Since most of the identified mRNA modifying enzymes are present in the nucleus, these modifications have the potential to function in nuclear pre-mRNA processing including alternative splicing. Here we review recent progress towards illuminating the role of pre-mRNA modifications in splicing and highlight key areas for future investigation in this rapidly growing field. Conclusions Future studies to identify which modifications are added to nascent pre-mRNA and to interrogate the direct effects of individual modifications are likely to reveal new mechanisms by which nuclear pre-mRNA processing is regulated.
Collapse
Affiliation(s)
- Nicole M Martinez
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| |
Collapse
|
14
|
Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
Collapse
Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
| | | | | | | | | | | |
Collapse
|
15
|
|
16
|
Zaringhalam M, Papavasiliou FN. Pseudouridylation meets next-generation sequencing. Methods 2016; 107:63-72. [DOI: 10.1016/j.ymeth.2016.03.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/05/2016] [Accepted: 03/07/2016] [Indexed: 11/15/2022] Open
|
17
|
Hoernes TP, Erlacher MD. Translating the epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27345446 PMCID: PMC5215311 DOI: 10.1002/wrna.1375] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 12/14/2022]
Abstract
RNA modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. Whereas the importance of transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications has been well described and is unquestioned for decades, the significance of internal messenger RNA (mRNA) modifications has only recently been revealed. Novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mRNAs. Thus far, N6‐methyladenosine (m6A), pseudouridine (Ψ), 5‐methylcytosine (m5C) and N1‐methyladenosine (m1A) were identified in eukaryal, and to some extent in prokaryal mRNAs. Several of the functions of these mRNA modifications have previously been reported, but many aspects remain elusive. Modifications can be important factors for the direct regulation of protein synthesis. The potential diversification of genomic information and regulation of RNA expression through editing and modifying mRNAs is versatile and many questions need to be addressed to completely elucidate the role of mRNA modifications. Herein, we summarize and highlight some recent findings on various co‐ and post‐transcriptional modifications, describing the impact of these processes on gene expression, with emphasis on protein synthesis. WIREs RNA 2017, 8:e1375. doi: 10.1002/wrna.1375 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Thomas Philipp Hoernes
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Matthias David Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
18
|
Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M. Cajal bodies are linked to genome conformation. Nat Commun 2016; 7:10966. [PMID: 26997247 PMCID: PMC4802181 DOI: 10.1038/ncomms10966] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/07/2016] [Indexed: 12/12/2022] Open
Abstract
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. Here we examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromosome conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear or nucleolar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. In particular, we observed a number of CB-dependent gene-positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production results in increased splicing noise, even in CB-distal regions. Therefore, we conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity. Nuclear bodies can nucleate at sites of active transcription and are beneficial for efficient gene expression. Here, the authors show that Cajal bodies, a prominent type of nuclear body, contribute to genome organization with global effects on gene expression and RNA splicing fidelity.
Collapse
Affiliation(s)
- Qiuyan Wang
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Iain A Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA.,Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Sergey P Shevtsov
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA.,High-Throughput Imaging Facility (HiTIF), Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, 20892 Maryland, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, 60064 Ilinois, USA
| |
Collapse
|
19
|
Rudchenko MN, Zamyatnin AA. Prospects for using self-assembled nucleic acid structures. BIOCHEMISTRY (MOSCOW) 2016; 80:391-9. [PMID: 25869355 DOI: 10.1134/s000629791504001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
According to the central dogma in molecular biology, nucleic acids are assigned with key functions on storing and executing genetic information in any living cell. However, features of nucleic acids are not limited only with properties providing template-dependent biosynthetic processes. Studies of DNA and RNA unveiled unique features of these polymers able to make various self-assembled three-dimensional structures that, among other things, use the complementarity principle. Here, we review various self-assembled nucleic acid structures as well as application of DNA and RNA to develop nanomaterials, molecular automata, and nanodevices. It can be expected that in the near future results of these developments will allow designing novel next-generation diagnostic systems and medicinal drugs.
Collapse
Affiliation(s)
- M N Rudchenko
- Research Division, Hospital for Special Surgery, New York, NY 10021, USA.
| | | |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
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.
Collapse
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:
| |
Collapse
|
22
|
Spenkuch F, Hinze G, Kellner S, Kreutz C, Micura R, Basché T, Helm M. Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor. Nucleic Acids Res 2014; 42:12735-45. [PMID: 25300485 PMCID: PMC4227767 DOI: 10.1093/nar/gku908] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and 99%. Despite this variegation, formation of SDS-stable complexes occurred instantaneously for all 5FU-substrates. Protein binding was investigated by advanced fluorescence spectroscopy allowing unprecedented simultaneous detection of change in fluorescence lifetime, anisotropy decay, as well as emission and excitation maxima. Determination of Kd values showed that introduction of 5FU into the RNA substrate increased protein affinity by 14× at most. Finally, competition experiments demonstrated reversibility of complex formation for 5FU-RNA. Our results lead us to conclude that the hitherto postulated long-term covalent interaction of TruB with 5FU tRNA is based on the interpretation of artifacts. This is likely true for the entire class of pseudouridine synthases.
Collapse
Affiliation(s)
- Felix Spenkuch
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Gerald Hinze
- Institute of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Stefanie Kellner
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), University of Innsbruck, Innrain 52A, A-60230 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Chemistry and Biomedicine - CCB, University of Innsbruck, Innrain 80/82, A-60230 Innsbruck, Austria
| | - Thomas Basché
- Institute of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| |
Collapse
|
23
|
Guiro J, O'Reilly D. Insights into the U1 small nuclear ribonucleoprotein complex superfamily. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:79-92. [DOI: 10.1002/wrna.1257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/17/2014] [Accepted: 07/14/2014] [Indexed: 12/12/2022]
Affiliation(s)
- J Guiro
- Institute of Biosciences; University of Sao Paulo; Sao Paulo Brazil
| | - D O'Reilly
- Sir William Dunn School of Pathology; Oxford United Kingdom
| |
Collapse
|
24
|
Bratkovič T, Rogelj B. The many faces of small nucleolar RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:438-43. [PMID: 24735946 DOI: 10.1016/j.bbagrm.2014.04.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/07/2014] [Accepted: 04/08/2014] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a class of evolutionally conserved non-coding RNAs traditionally associated with nucleotide modifications in other RNA species. Acting as guides pairing with ribosomal (rRNA) and small nuclear RNAs (snRNAs), snoRNAs direct partner enzymes to specific sites for uridine isomerization or ribose methylation, thereby influencing stability, folding and protein-interacting properties of target RNAs. In recent years, however, numerous non-canonical functions have also been ascribed to certain members of the snoRNA group, ranging from regulation of mRNA editing and/or alternative splicing to posttranscriptional gene silencing by a yet poorly understood pathway that may involve microRNA-like mechanisms. While some of these intriguing snoRNAs (the so-called orphan snoRNAs) have no sequence complementarity to rRNA or snRNA, others apparently display dual functionality, performing both traditional and newly elucidated functions. Here, we review the effects elicited by non-canonical snoRNA activities.
Collapse
Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology, Jamova 39, SI-1000 Ljubljana, Slovenia.
| |
Collapse
|
25
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
26
|
Ge J, Yu YT. RNA pseudouridylation: new insights into an old modification. Trends Biochem Sci 2013; 38:210-8. [PMID: 23391857 PMCID: PMC3608706 DOI: 10.1016/j.tibs.2013.01.002] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/22/2012] [Accepted: 01/07/2013] [Indexed: 12/18/2022]
Abstract
Pseudouridine is the most abundant post-transcriptionally modified nucleotide in various stable RNAs of all organisms. Pseudouridine is derived from uridine via base-specific isomerization, resulting in an extra hydrogen-bond donor that distinguishes it from other nucleotides. In eukaryotes, uridine-to-pseudouridine isomerization is catalyzed primarily by box H/ACA RNPs, ribonucleoproteins that act as pseudouridylases. When introduced into RNA, pseudouridine contributes significantly to RNA-mediated cellular processes. It was recently discovered that pseudouridylation can be induced by stress, suggesting a regulatory role for pseudouridine. It has also been reported that pseudouridine can be artificially introduced into mRNA by box H/ACA RNPs and that such introduction can mediate nonsense-to-sense codon conversion, thus demonstrating a new means of generating coding or protein diversity.
Collapse
Affiliation(s)
- Junhui Ge
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | | |
Collapse
|
27
|
Basturea GN. Research Methods for Detection and Quantitation of RNA Modifications. ACTA ACUST UNITED AC 2013. [DOI: 10.13070/mm.en.3.186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
28
|
Yu AT, Ge J, Yu YT. Pseudouridines in spliceosomal snRNAs. Protein Cell 2011; 2:712-25. [PMID: 21976061 PMCID: PMC4722041 DOI: 10.1007/s13238-011-1087-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/22/2011] [Indexed: 01/14/2023] Open
Abstract
Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.
Collapse
Affiliation(s)
- Andrew T. Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642 USA
| | - Junhui Ge
- Department of Pathology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003 China
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642 USA
| |
Collapse
|