1
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Häfner SJ, Jansson MD, Altinel K, Andersen KL, Abay-Nørgaard Z, Ménard P, Fontenas M, Sørensen DM, Gay DM, Arendrup FS, Tehler D, Krogh N, Nielsen H, Kraushar ML, Kirkeby A, Lund AH. Ribosomal RNA 2'-O-methylation dynamics impact cell fate decisions. Dev Cell 2023; 58:1593-1609.e9. [PMID: 37473757 DOI: 10.1016/j.devcel.2023.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/16/2023] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
Translational regulation impacts both pluripotency maintenance and cell differentiation. To what degree the ribosome exerts control over this process remains unanswered. Accumulating evidence has demonstrated heterogeneity in ribosome composition in various organisms. 2'-O-methylation (2'-O-me) of rRNA represents an important source of heterogeneity, where site-specific alteration of methylation levels can modulate translation. Here, we examine changes in rRNA 2'-O-me during mouse brain development and tri-lineage differentiation of human embryonic stem cells (hESCs). We find distinct alterations between brain regions, as well as clear dynamics during cortex development and germ layer differentiation. We identify a methylation site impacting neuronal differentiation. Modulation of its methylation levels affects ribosome association of the fragile X mental retardation protein (FMRP) and is accompanied by an altered translation of WNT pathway-related mRNAs. Together, these data identify ribosome heterogeneity through rRNA 2'-O-me during early development and differentiation and suggest a direct role for ribosomes in regulating translation during cell fate acquisition.
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Affiliation(s)
- Sophia J Häfner
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kübra Altinel
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kasper L Andersen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Zehra Abay-Nørgaard
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, Faculty of Health and Medical Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Patrice Ménard
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Martin Fontenas
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Daniel M Sørensen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Frederic S Arendrup
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Disa Tehler
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Agnete Kirkeby
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and Department of Neuroscience, Faculty of Health and Medical Science, University of Copenhagen, 2200 Copenhagen, Denmark; Wallenberg Center for Molecular Medicine, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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2
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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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3
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Patel A, Clark KD. Characterizing RNA modifications in the central nervous system and single cells by RNA sequencing and liquid chromatography-tandem mass spectrometry techniques. Anal Bioanal Chem 2023:10.1007/s00216-023-04604-y. [PMID: 36840809 DOI: 10.1007/s00216-023-04604-y] [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: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/26/2023]
Abstract
Post-transcriptional modifications to RNA constitute a newly appreciated layer of translation regulation in the central nervous system (CNS). The identity, stoichiometric quantity, and sequence position of these unusual epitranscriptomic marks are central to their function, making analytical methods that are capable of accurate and reproducible measurements paramount to the characterization of the neuro-epitranscriptome. RNA sequencing-based methods and liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques have been leveraged to provide an early glimpse of the landscape of RNA modifications in bulk CNS tissues. However, recent advances in sample preparation, separations, and detection methods have revealed that individual cells display remarkable heterogeneity in their RNA modification profiles, raising questions about the prevalence and function of cell-specific distributions of post-transcriptionally modified nucleosides in the brain. In this Trends article, we present an overview of RNA sequencing and LC-MS/MS methodologies for the analysis of RNA modifications in the CNS with special emphasis on recent advancements in techniques that facilitate single-cell and subcellular detection.
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Affiliation(s)
- Arya Patel
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Kevin D Clark
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA.
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4
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del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:1289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2'-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications-focusing on those relevant to miRNAs-examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
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Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
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5
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Ren X, Deng R, Zhang K, Sun Y, Li Y, Li J. Single‐Cell Imaging of m
6
A Modified RNA Using m
6
A‐Specific In Situ Hybridization Mediated Proximity Ligation Assay (m
6
AISH‐PLA). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaojun Ren
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
- Department of Chemistry and Biology Faculty of Environment and Life Science Beijing University of Technology Beijing 100124 China
| | - Ruijie Deng
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Kaixiang Zhang
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Yupeng Sun
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Yue Li
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
| | - Jinghong Li
- Department of Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University Beijing 100084 China
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6
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Jaafar M, Paraqindes H, Gabut M, Diaz JJ, Marcel V, Durand S. 2'O-Ribose Methylation of Ribosomal RNAs: Natural Diversity in Living Organisms, Biological Processes, and Diseases. Cells 2021; 10:1948. [PMID: 34440717 PMCID: PMC8393311 DOI: 10.3390/cells10081948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/21/2023] Open
Abstract
Recent findings suggest that ribosomes, the translational machineries, can display a distinct composition depending on physio-pathological contexts. Thanks to outstanding technological breakthroughs, many studies have reported that variations of rRNA modifications, and more particularly the most abundant rRNA chemical modification, the rRNA 2'O-ribose methylation (2'Ome), intrinsically occur in many organisms. In the last 5 years, accumulating reports have illustrated that rRNA 2'Ome varies in human cell lines but also in living organisms (yeast, plant, zebrafish, mouse, human) during development and diseases. These rRNA 2'Ome variations occur either within a single cell line, organ, or patient's sample (i.e., intra-variability) or between at least two biological conditions (i.e., inter-variability). Thus, the ribosomes can tolerate the absence of 2'Ome at some specific positions. These observations question whether variations in rRNA 2'Ome could provide ribosomes with particular translational regulatory activities and functional specializations. Here, we compile recent studies supporting the heterogeneity of ribosome composition at rRNA 2'Ome level and provide an overview of the natural diversity in rRNA 2'Ome that has been reported up to now throughout the kingdom of life. Moreover, we discuss the little evidence that suggests that variations of rRNA 2'Ome can effectively impact the ribosome activity and contribute to the etiology of some human diseases.
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Affiliation(s)
| | | | | | | | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
| | - Sébastien Durand
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
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7
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Ren X, Deng R, Zhang K, Sun Y, Li Y, Li J. Single-Cell Imaging of m 6 A Modified RNA Using m 6 A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m 6 AISH-PLA). Angew Chem Int Ed Engl 2021; 60:22646-22651. [PMID: 34291539 DOI: 10.1002/anie.202109118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 12/31/2022]
Abstract
N6 -methyladenosine (m6 A) modification-the most prevalent mammalian RNA internal modification-plays key regulatory roles in mRNA metabolism. Current approaches for m6 A modified RNA analysis limit at bulk-population level, resulting in a loss of spatiotemporal and cell-to-cell variability information. Here we proposed a m6 A-specific in situ hybridization mediated proximity ligation assay (m6 AISH-PLA) for cellular imaging of m6 A RNA, allowing to identify m6 A modification at specific location in RNAs and image m6 A RNA with single-cell and single-molecule resolution. Using m6 AISH-PLA, we investigated the m6 A level and subcellular location of HSP70 RNA103-m6 A in response to heat shock stress, and found an increased m6 A modified ratio and an increased distribution ratio in cytoplasm under heat shock. m6 AISH-PLA can serve in the study of m6 A RNA in single cells for deciphering epitranscriptomic mechanisms and assisting clinical diagnosis.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing, 100124, China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yupeng Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
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8
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Jiang Y, Zhou W, Zhang X, Wang Y, Yang D, Li S. Protective Effect of Blood Cora Polysaccharides on H9c2 Rat Heart Cells Injury Induced by Oxidative Stress by Activating Nrf2/HO-1 Signal Pathway. Front Nutr 2021; 8:632161. [PMID: 33738296 PMCID: PMC7960668 DOI: 10.3389/fnut.2021.632161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/10/2021] [Indexed: 01/14/2023] Open
Abstract
The protective effect of blood cora polysaccharides (BCP) on H9c2 rat heart cells under oxidative stress was explored with the use of a H9c2 cell oxidative stress model. The ability of BCP to scavenge 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 1,1-diphenyl-2-picrylhydrazyl (DPPH), and hydroxyl radicals and its reducing power were measured in vitro, indicating a more powerful antioxidant effect of BCP compared to a similar concentration of vitamin C. The cellular metabolic activity was tested through the MTT [3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide] assay. Additionally, the relevant oxidation indicator level within the cell supernatant and cells was tested with reagent kits, and mRNA and protein expression levels in the cells were tested through quantitative polymerase chain reaction (qPCR) and western blot. The chemical composition of BCP was determined through high performance liquid chromatography (HPLC). The results show that compared with the normal group, the model group's cell survival rate (28.75 ± 2.56%) decreased, lactate dehydrogenase (LDH) leakage and the malondialdehyde (MDA) content increased, and superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH) levels decreased. The results of qPCR and western blot show that compared with the normal group, the model group's Bcl-2 associated X protein (Bax), caspase-3, nuclear factor erythroid-2 related factor 2 (Nrf2), heme oxygenase-1 (HO-1) expression, NAD(P)H:quinoneoxidoreductase 1 (NQO1), and cytochrome c (Cyt C) decreased, and B-cell lymphoma-2 (Bcl-2) expression was increased, with significant statistical differences. Compared with the model group, the cell survival rate for each BCP-treated group increased, the LDH leakage decreased, the SOD, CAT, and GSH levels in the cells increased, the MDA content decreased, the Bax, caspase-3, Nrf2, HO-1, NQO1, and Cyt C expression was weakened, and the Bcl-2 expression was strengthened. BCP inhibited the reduction of mitochondrial membrane potential caused by H2O2 treatment. According to the component analysis, BCP mainly consist of mannitol, ribose, glucosum anhydricum, galactose, and xylose. It was observed that the Nrf2/HO-1 signaling pathway can be activated, regulated, and controlled by functional BCP to protect H9c2 cells injured by oxidative stress.
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Affiliation(s)
- Yong Jiang
- Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Wei Zhou
- Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Xin Zhang
- Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Ying Wang
- Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Dingyi Yang
- Laboratory for Biorheological Science and Technology of Ministry of Education (Chongqing University), Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
| | - Shujie Li
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, China
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9
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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10
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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11
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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12
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Li X, Liang QX, Lin JR, Peng J, Yang JH, Yi C, Yu Y, Zhang QC, Zhou KR. Epitranscriptomic technologies and analyses. SCIENCE CHINA-LIFE SCIENCES 2020; 63:501-515. [DOI: 10.1007/s11427-019-1658-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/12/2020] [Indexed: 01/28/2023]
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13
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Pichot F, Marchand V, Ayadi L, Bourguignon-Igel V, Helm M, Motorin Y. Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2'-O-Methylations in RNA by RiboMethSeq. Front Genet 2020; 11:38. [PMID: 32117451 PMCID: PMC7031861 DOI: 10.3389/fgene.2020.00038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/13/2020] [Indexed: 01/24/2023] Open
Abstract
A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2′-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successfully applied to detect and quantify Nm residues in various RNA species such as rRNA, tRNA, and snRNA. Such applications require adaptation of the initially published protocol(s), both at the wet bench and in the bioinformatics analysis. In this manuscript, we describe the optimization of RiboMethSeq bioinformatics at the level of initial read treatment, alignment to the reference sequence, counting the 5′- and 3′- ends, and calculation of the RiboMethSeq scores, allowing precise detection and quantification of the Nm-related signal. These improvements introduced in the original pipeline permit a more accurate detection of Nm candidates and a more precise quantification of Nm level variations. Applications of the improved RiboMethSeq treatment pipeline for different cellular RNA types are discussed.
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Affiliation(s)
- Florian Pichot
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France.,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Lilia Ayadi
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France.,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Valérie Bourguignon-Igel
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France.,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France.,Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor (CNRS-UL)/US40 (INSERM), Université de Lorraine, Vandœuvre-lès-Nancy, France
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14
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Bohnsack MT, Sloan KE. Modifications in small nuclear RNAs and their roles in spliceosome assembly and function. Biol Chem 2019; 399:1265-1276. [PMID: 29908124 DOI: 10.1515/hsz-2018-0205] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/28/2018] [Indexed: 01/27/2023]
Abstract
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs). Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNA splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.
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Affiliation(s)
- Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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15
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Burke MF, McLaurin DM, Logan MK, Hebert MD. Alteration of 28S rRNA 2'- O-methylation by etoposide correlates with decreased SMN phosphorylation and reduced Drosha levels. Biol Open 2019; 8:bio041848. [PMID: 30858166 PMCID: PMC6451326 DOI: 10.1242/bio.041848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
The most common types of modification in human rRNA are pseudouridylation and 2'-O ribose methylation. These modifications are performed by small nucleolar ribonucleoproteins (snoRNPs) which contain a guide RNA (snoRNA) that base pairs at specific sites within the rRNA to direct the modification. rRNA modifications can vary, generating ribosome heterogeneity. One possible method that can be used to regulate rRNA modifications is by controlling snoRNP activity. RNA fragments derived from some small Cajal body-specific RNAs (scaRNA 2, 9 and 17) may influence snoRNP activity. Most scaRNAs accumulate in the Cajal body - a subnuclear domain - where they participate in the biogenesis of small nuclear RNPs, but scaRNA 2, 9 and 17 generate nucleolus-enriched fragments of unclear function, and we hypothesize that these fragments form regulatory RNPs that impact snoRNP activity and modulate rRNA modifications. Our previous work has shown that SMN, Drosha and various stresses, including etoposide treatment, may alter regulatory RNP formation. Here we demonstrate that etoposide treatment decreases the phosphorylation of SMN, reduces Drosha levels and increases the 2'-O-methylation of two sites within 28S rRNA. These findings further support a role for SMN and Drosha in regulating rRNA modification, possibly by affecting snoRNP or regulatory RNP activity.
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Affiliation(s)
- Marilyn F Burke
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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16
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Emerging Role of Eukaryote Ribosomes in Translational Control. Int J Mol Sci 2019; 20:ijms20051226. [PMID: 30862090 PMCID: PMC6429320 DOI: 10.3390/ijms20051226] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/06/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of "specialized ribosomes", which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today.
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Motorin Y, Helm M. Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies. Genes (Basel) 2019; 10:genes10010035. [PMID: 30634534 PMCID: PMC6356707 DOI: 10.3390/genes10010035] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 12/17/2022] Open
Abstract
New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell’s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use the term “epitranscriptome”. Due to the high rate of newly published mapping techniques, a significant number of chemically distinct RNA modifications have become amenable to mapping, albeit with variegated accuracy and precision, depending on the nature of the technique. This review gives a brief overview of known techniques, and how they were applied to modification calling.
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Affiliation(s)
- Yuri Motorin
- Laboratoire IMoPA, UMR7365 National Centre for Scientific Research (CNRS)-Lorraine University, Biopôle, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany.
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18
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Motorin Y, Marchand V. Detection and Analysis of RNA Ribose 2'-O-Methylations: Challenges and Solutions. Genes (Basel) 2018; 9:genes9120642. [PMID: 30567409 PMCID: PMC6316082 DOI: 10.3390/genes9120642] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/11/2018] [Accepted: 12/13/2018] [Indexed: 02/07/2023] Open
Abstract
Ribose 2'-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2'-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2'-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2'-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2'-O-methylations.
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Affiliation(s)
- Yuri Motorin
- UMR7365 IMoPA, Biopôle, CNRS-Lorraine University, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.
| | - Virginie Marchand
- UMS2008 IBSLor, Biopôle, CNRS-Lorraine University-INSERM, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-les-Nancy, France.
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Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
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20
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Marchand V, Ayadi L, Ernst FGM, Hertler J, Bourguignon‐Igel V, Galvanin A, Kotter A, Helm M, Lafontaine DLJ, Motorin Y. AlkAniline‐Seq: Profiling of m
7
G and m
3
C RNA Modifications at Single Nucleotide Resolution. Angew Chem Int Ed Engl 2018; 57:16785-16790. [DOI: 10.1002/anie.201810946] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Virginie Marchand
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Lilia Ayadi
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Felix G. M. Ernst
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Jasmin Hertler
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Valérie Bourguignon‐Igel
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Adeline Galvanin
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Denis L. J. Lafontaine
- RNA Molecular BiologyULB-Cancer Research Center (U-CRC)Center for Microscopy and Molecular Imaging (CMMI)Fonds de la Recherche Scientifique (FRS)Université Libre de Bruxelles (ULB) BioPark campus Gosselies Belgium
| | - Yuri Motorin
- Lorraine UniversityUMS2008 IBSLor CNRS-UL-INSERM, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
- Lorraine UniversityUMR7365 IMoPA CNRS-UL, Biopôle UL 9, Avenue de la Forêt de Haye 54505 Vandoeuvre-les-Nancy France
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21
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Andersen KL, Nielsen H. Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. Biomolecules 2018; 8:E128. [PMID: 30380771 PMCID: PMC6315972 DOI: 10.3390/biom8040128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022] Open
Abstract
In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.
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MESH Headings
- Base Sequence
- Cell Survival
- Conserved Sequence
- Gene Expression Regulation
- Gene Knockdown Techniques
- Genome
- Methylation
- Nucleic Acid Conformation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Tetrahymena/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Kasper L Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200N Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
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Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure. Biomolecules 2018; 8:biom8040125. [PMID: 30366442 PMCID: PMC6316459 DOI: 10.3390/biom8040125] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/10/2018] [Accepted: 10/18/2018] [Indexed: 01/17/2023] Open
Abstract
Chemical modifications of RNA have recently gained new attention in biological sciences. They occur notably on messenger RNA (mRNA) and ribosomal RNA (rRNA) and are important for various cellular functions, but their molecular mechanism of action is yet to be understood in detail. Ribosomes are large ribonucleoprotein assemblies, which synthesize proteins in all organisms. Human ribosomes, for example, carry more than 200 modified nucleotides, which are introduced during biogenesis. Chemically modified nucleotides may appear to be only scarcely different from canonical nucleotides, but modifications such as methylations can in fact modulate their chemical and topological properties in the RNA and alter or modulate the overall translation efficiency of the ribosomes resulting in dysfunction of the translation machinery. Recent functional analysis and high-resolution ribosome structures have revealed a large repertoire of modification sites comprising different modification types. In this review, we focus on 2′-O-methylations (2′-O-Me) and discuss the structural insights gained through our recent cryo electron microscopy (cryo-EM) high-resolution structural analysis of the human ribosome, such as their locations and their influence on the secondary and tertiary structures of human rRNAs. The detailed analysis presented here reveals that ribose conformations of the rRNA backbone differ when the 2′-OH hydroxyl position is methylated, with 3′-endo conformations being the default and the 2′-endo conformations being characteristic in that the associated base is flipped-out. We compare currently known 2′-O-Me sites in human rRNAs evaluated using RiboMethSeq and cryo-EM structural analysis and discuss their involvement in several human diseases.
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23
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Marcel V, Nguyen Van Long F, Diaz JJ. 40 Years of Research Put p53 in Translation. Cancers (Basel) 2018; 10:E152. [PMID: 29883412 PMCID: PMC5977125 DOI: 10.3390/cancers10050152] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/15/2018] [Accepted: 05/18/2018] [Indexed: 12/18/2022] Open
Abstract
Since its discovery in 1979, p53 has shown multiple facets. Initially the tumor suppressor p53 protein was considered as a stress sensor able to maintain the genome integrity by regulating transcription of genes involved in cell cycle arrest, apoptosis and DNA repair. However, it rapidly came into light that p53 regulates gene expression to control a wider range of biological processes allowing rapid cell adaptation to environmental context. Among them, those related to cancer have been extensively documented. In addition to its role as transcription factor, scattered studies reported that p53 regulates miRNA processing, modulates protein activity by direct interaction or exhibits RNA-binding activity, thus suggesting a role of p53 in regulating several layers of gene expression not restricted to transcription. After 40 years of research, it appears more and more clearly that p53 is strongly implicated in translational regulation as well as in the control of the production and activity of the translational machinery. Translation control of specific mRNAs could provide yet unsuspected capabilities to this well-known guardian of the genome.
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Affiliation(s)
- Virginie Marcel
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
| | - Flora Nguyen Van Long
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
| | - Jean-Jacques Diaz
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France.
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24
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Glabonjat RA, Raber G, Jensen KB, Guttenberger N, Zangger K, Francesconi KA. A 2- O
-Methylriboside Unknown Outside the RNA World Contains Arsenic. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ronald A. Glabonjat
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Georg Raber
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kenneth B. Jensen
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Nikolaus Guttenberger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Klaus Zangger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kevin A. Francesconi
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
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25
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Glabonjat RA, Raber G, Jensen KB, Guttenberger N, Zangger K, Francesconi KA. A 2-O
-Methylriboside Unknown Outside the RNA World Contains Arsenic. Angew Chem Int Ed Engl 2017; 56:11963-11965. [DOI: 10.1002/anie.201706310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Ronald A. Glabonjat
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Georg Raber
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kenneth B. Jensen
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Nikolaus Guttenberger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Klaus Zangger
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
| | - Kevin A. Francesconi
- Institute of Chemistry; NAWI Graz; University of Graz; Universitaetsplatz 1/I 8010 Graz Austria
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Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, Dominissini D, He C. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nat Methods 2017; 14:695-698. [PMID: 28504680 DOI: 10.1038/nmeth.4294] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/18/2017] [Indexed: 12/30/2022]
Abstract
The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.
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Affiliation(s)
- Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA
| | - Sharon Moshitch-Moshkovitz
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Dali Han
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA
| | - Nitzan Kol
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Ninette Amariglio
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Gideon Rechavi
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dan Dominissini
- Cancer Research Center, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Wohl Centre for Translational Medicine, Chaim Sheba Medical Center, Tel-Hashomer, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
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27
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Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M. High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Res 2017; 45:2341-2353. [PMID: 28031372 PMCID: PMC5389715 DOI: 10.1093/nar/gkw1321] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/08/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
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MESH Headings
- Algorithms
- Base Sequence
- Cross-Linking Reagents/chemistry
- Databases, Genetic
- High-Throughput Nucleotide Sequencing/methods
- Immunoprecipitation
- Methylation
- Protein Binding
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Ribose/metabolism
- Software
- Transcriptome
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Rafal Gumienny
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Switzerland
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
| | - Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Arnau Vina-Vilaseca
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Switzerland
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland
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28
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Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation. Biomolecules 2017; 7:biom7010013. [PMID: 28208788 PMCID: PMC5372725 DOI: 10.3390/biom7010013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 02/02/2017] [Indexed: 12/16/2022] Open
Abstract
Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.
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29
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30
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Häfner S. Imagine. Microbes Infect 2016; 19:75-78. [PMID: 27876527 DOI: 10.1016/j.micinf.2016.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Sophia Häfner
- University of Copenhagen, BRIC Biotech Research & Innovation Centre, Lund Group, 2200 Copenhagen, Denmark.
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