1
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Zhou KI, Pecot CV, Holley CL. 2'- O-methylation (Nm) in RNA: progress, challenges, and future directions. RNA (NEW YORK, N.Y.) 2024; 30:570-582. [PMID: 38531653 PMCID: PMC11019748 DOI: 10.1261/rna.079970.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
RNA 2'-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5' cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However, these methods have mostly been applied to abundant RNAs such as rRNA, and the validity of the internal mRNA Nm sites detected with these approaches remains controversial. Nonetheless, Nm in both coding and noncoding RNAs has been demonstrated to impact cellular processes, including translation and splicing. In addition, Nm modifications at the 5' cap and possibly at internal sites in mRNA serve to prevent the binding of nucleic acid sensors, thus preventing the activation of the innate immune response by self-mRNAs. Finally, Nm has been implicated in a variety of diseases including cancer, cardiovascular diseases, and neurologic syndromes. In this review, we discuss current challenges in determining the distribution, regulation, function, and disease relevance of Nm, as well as potential future directions for the field.
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Affiliation(s)
- Katherine I Zhou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- University of North Carolina RNA Discovery Center, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christopher L Holley
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
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2
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Gilbert WV. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA (NEW YORK, N.Y.) 2024; 30:530-536. [PMID: 38531650 PMCID: PMC11019745 DOI: 10.1261/rna.079975.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Pseudouridine is an abundant mRNA modification found in diverse organisms ranging from bacteria and viruses to multicellular plants and humans. New developments in pseudouridine profiling provide quantitative tools to map mRNA pseudouridylation sites. Sparse biochemical studies establish the potential for mRNA pseudouridylation to affect most stages of the mRNA life cycle from birth to death. This recent progress sets the stage for deeper investigations into the molecular and cellular functions of specific mRNA pseudouridines, including in disease.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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3
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Esteva-Socias M, Aguilo F. METTL3 as a master regulator of translation in cancer: mechanisms and implications. NAR Cancer 2024; 6:zcae009. [PMID: 38444581 PMCID: PMC10914372 DOI: 10.1093/narcan/zcae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
Translational regulation is an important step in the control of gene expression. In cancer cells, the orchestration of both global control of protein synthesis and selective translation of specific mRNAs promote tumor cell survival, angiogenesis, transformation, invasion and metastasis. N6-methyladenosine (m6A), the most prevalent mRNA modification in higher eukaryotes, impacts protein translation. Over the past decade, the development of m6A mapping tools has facilitated comprehensive functional investigations, revealing the involvement of this chemical mark, together with its writer METTL3, in promoting the translation of both oncogenes and tumor suppressor transcripts, with the impact being context-dependent. This review aims to consolidate our current understanding of how m6A and METTL3 shape translation regulation in the realm of cancer biology. In addition, it delves into the role of cytoplasmic METTL3 in protein synthesis, operating independently of its catalytic activity. Ultimately, our goal is to provide critical insights into the interplay between m6A, METTL3 and translational regulation in cancer, offering a deeper comprehension of the mechanisms sustaining tumorigenesis.
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Affiliation(s)
- Margalida Esteva-Socias
- Department of Molecular Biology, Umeå University, SE-901 85Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 85Umeå, Sweden
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 85Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 85Umeå, Sweden
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4
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Jörg M, Plehn JE, Kristen M, Lander M, Walz L, Lietz C, Wijns J, Pichot F, Rojas-Charry L, Wirtz Martin KM, Ruffini N, Kreim N, Gerber S, Motorin Y, Endres K, Rossmanith W, Methner A, Helm M, Friedland K. N1-methylation of adenosine (m 1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer's disease. Mol Psychiatry 2024:10.1038/s41380-024-02421-y. [PMID: 38287100 DOI: 10.1038/s41380-024-02421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024]
Abstract
One mechanism of particular interest to regulate mRNA fate post-transcriptionally is mRNA modification. Especially the extent of m1A mRNA methylation is highly discussed due to methodological differences. However, one single m1A site in mitochondrial ND5 mRNA was unanimously reported by different groups. ND5 is a subunit of complex I of the respiratory chain. It is considered essential for the coupling of oxidation and proton transport. Here we demonstrate that this m1A site might be involved in the pathophysiology of Alzheimer's disease (AD). One of the pathological hallmarks of this neurodegenerative disease is mitochondrial dysfunction, mainly induced by Amyloid β (Aβ). Aβ mainly disturbs functions of complex I and IV of the respiratory chain. However, the molecular mechanism of complex I dysfunction is still not fully understood. We found enhanced m1A methylation of ND5 mRNA in an AD cell model as well as in AD patients. Formation of this m1A methylation is catalyzed by increased TRMT10C protein levels, leading to translation repression of ND5. As a consequence, here demonstrated for the first time, TRMT10C induced m1A methylation of ND5 mRNA leads to mitochondrial dysfunction. Our findings suggest that this newly identified mechanism might be involved in Aβ-induced mitochondrial dysfunction.
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Affiliation(s)
- Marko Jörg
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Johanna E Plehn
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marco Kristen
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lukas Walz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christine Lietz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Julie Wijns
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Liliana Rojas-Charry
- Institute of Molecular Medicine, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Katja M Wirtz Martin
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Nicolas Ruffini
- Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany
| | - Nastasja Kreim
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, UMS2008 IBSLor CNRS, Université de Lorraine-INSERM, Biopôle, 9 Avenue de la Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France
- IMoPA, UMR7365 CNRS, Université de Lorraine, Biopôle, 9 Avenue de la Forêt de Haye, 54505, Vandœuvre-lès-Nancy, France
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131, Mainz, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straβe 13, 1090, Vienna, Austria
| | - Axel Methner
- Institute of Molecular Medicine, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany.
| | - Kristina Friedland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany.
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5
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Rodell R, Robalin N, Martinez NM. Why U matters: detection and functions of pseudouridine modifications in mRNAs. Trends Biochem Sci 2024; 49:12-27. [PMID: 38097411 DOI: 10.1016/j.tibs.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 01/07/2024]
Abstract
The uridine modifications pseudouridine (Ψ), dihydrouridine, and 5-methyluridine are present in eukaryotic mRNAs. Many uridine-modifying enzymes are associated with human disease, underscoring the importance of uncovering the functions of uridine modifications in mRNAs. These modified uridines have chemical properties distinct from those of canonical uridines, which impact RNA structure and RNA-protein interactions. Ψ, the most abundant of these uridine modifications, is present across (pre-)mRNAs. Recent work has shown that many Ψs are present at intermediate to high stoichiometries that are likely conducive to function and at locations that are poised to influence pre-/mRNA processing. Technological innovations and mechanistic investigations are unveiling the functions of uridine modifications in pre-mRNA splicing, translation, and mRNA stability, which are discussed in this review.
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Affiliation(s)
- Rebecca Rodell
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Nicolas Robalin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Nicole M Martinez
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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6
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Monziani A, Ulitsky I. Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends Genet 2023; 39:908-923. [PMID: 37783604 DOI: 10.1016/j.tig.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs) display features different from those of 'regular' long ncRNAs (lncRNAs) and, more importantly, they can exert independent and unrelated functions to those of the encoded snoRNAs. Here, we review and summarize past and recent evidence that ncSNHGs form a defined subclass among the plethora of lncRNAs, and discuss future research that can further elucidate their biological relevance.
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Affiliation(s)
- Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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7
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Arzumanian VA, Kurbatov IY, Ptitsyn KG, Khmeleva SA, Kurbatov LK, Radko SP, Poverennaya EV. Identifying N6-Methyladenosine Sites in HepG2 Cell Lines Using Oxford Nanopore Technology. Int J Mol Sci 2023; 24:16477. [PMID: 38003667 PMCID: PMC10671286 DOI: 10.3390/ijms242216477] [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: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
RNA modifications, particularly N6-methyladenosine (m6A), are pivotal regulators of RNA functionality and cellular processes. We analyzed m6A modifications by employing Oxford Nanopore technology and the m6Anet algorithm, focusing on the HepG2 cell line. We identified 3968 potential m6A modification sites in 2851 transcripts, corresponding to 1396 genes. A gene functional analysis revealed the active involvement of m6A-modified genes in ubiquitination, transcription regulation, and protein folding processes, aligning with the known role of m6A modifications in histone ubiquitination in cancer. To ensure data robustness, we assessed reproducibility across technical replicates. This study underscores the importance of evaluating algorithmic reproducibility, especially in supervised learning. Furthermore, we examined correlations between transcriptomic, translatomic, and proteomic levels. A strong transcriptomic-translatomic correlation was observed. In conclusion, our study deepens our understanding of m6A modifications' multifaceted impacts on cellular processes and underscores the importance of addressing reproducibility concerns in analytical approaches.
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Affiliation(s)
| | | | | | | | | | | | - Ekaterina V. Poverennaya
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 119121 Moscow, Russia; (V.A.A.); (I.Y.K.); (K.G.P.); (S.A.K.); (L.K.K.); (S.P.R.)
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8
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Benčić P, Keppler M, Kuge M, Qiu D, Schütte LM, Häner M, Strack K, Jessen HJ, Andexer JN, Loenarz C. Non-canonical nucleosides: Biomimetic triphosphorylation, incorporation into mRNA and effects on translation and structure. FEBS J 2023; 290:4899-4920. [PMID: 37329249 DOI: 10.1111/febs.16889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/24/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
Recent advances in mRNA therapeutics demand efficient toolkits for the incorporation of nucleoside analogues into mRNA suitable for downstream applications. Herein, we report the application of a versatile enzyme cascade for the triphosphorylation of a broad range of nucleoside analogues, including unprotected nucleobases containing chemically labile moieties. Our biomimetic system was suitable for the preparation of nucleoside triphosphates containing adenosine, cytidine, guanosine, uridine and non-canonical core structures, as determined by capillary electrophoresis coupled to mass spectrometry. This enabled us to establish an efficient workflow for transcribing and purifying functional mRNA containing these nucleoside analogues, combined with mass spectrometric verification of analogue incorporation. Our combined methodology allows for analyses of how incorporation of nucleoside analogues that are commercially unavailable as triphosphates affect mRNA properties: The translational fidelity of the produced mRNA was demonstrated in analyses of how incorporated adenosine analogues impact translational recoding. For the SARS-CoV-2 frameshifting site, analyses of the mRNA pseudoknot structure using circular dichroism spectroscopy allowed insight into how the pharmacologically active 7-deazaadenosine destabilises RNA secondary structure, consistent with observed changes in recoding efficiency.
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Affiliation(s)
- Patricia Benčić
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Michael Keppler
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Marco Kuge
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Danye Qiu
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Lena M Schütte
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | - Markus Häner
- Institute of Organic Chemistry, University of Freiburg, Germany
| | - Katharina Strack
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
| | | | | | - Christoph Loenarz
- Institute of Pharmaceutical Sciences, University of Freiburg, Germany
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9
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Chehelgerdi M, Chehelgerdi M. The use of RNA-based treatments in the field of cancer immunotherapy. Mol Cancer 2023; 22:106. [PMID: 37420174 PMCID: PMC10401791 DOI: 10.1186/s12943-023-01807-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/09/2023] Open
Abstract
Over the past several decades, mRNA vaccines have evolved from a theoretical concept to a clinical reality. These vaccines offer several advantages over traditional vaccine techniques, including their high potency, rapid development, low-cost manufacturing, and safe administration. However, until recently, concerns over the instability and inefficient distribution of mRNA in vivo have limited their utility. Fortunately, recent technological advancements have mostly resolved these concerns, resulting in the development of numerous mRNA vaccination platforms for infectious diseases and various types of cancer. These platforms have shown promising outcomes in both animal models and humans. This study highlights the potential of mRNA vaccines as a promising alternative approach to conventional vaccine techniques and cancer treatment. This review article aims to provide a thorough and detailed examination of mRNA vaccines, including their mechanisms of action and potential applications in cancer immunotherapy. Additionally, the article will analyze the current state of mRNA vaccine technology and highlight future directions for the development and implementation of this promising vaccine platform as a mainstream therapeutic option. The review will also discuss potential challenges and limitations of mRNA vaccines, such as their stability and in vivo distribution, and suggest ways to overcome these issues. By providing a comprehensive overview and critical analysis of mRNA vaccines, this review aims to contribute to the advancement of this innovative approach to cancer treatment.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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10
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Jones JD, Franco MK, Smith TJ, Snyder LR, Anders AG, Ruotolo BT, Kennedy RT, Koutmou KS. Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation. RSC Chem Biol 2023; 4:363-378. [PMID: 37181630 PMCID: PMC10170649 DOI: 10.1039/d2cb00229a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/15/2023] [Indexed: 02/22/2023] Open
Abstract
Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Laura R Snyder
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Anna G Anders
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
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11
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Petri BJ, Klinge CM. m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer. J Mol Endocrinol 2023; 70:JME-22-0110. [PMID: 36367225 PMCID: PMC9790079 DOI: 10.1530/jme-22-0110] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
Abstract
Epitranscriptomic modification of RNA regulates human development, health, and disease. The true diversity of the transcriptome in breast cancer including chemical modification of transcribed RNA (epitranscriptomics) is not well understood due to limitations of technology and bioinformatic analysis. N-6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of mRNA and regulates splicing, stability, translation, and intracellular localization of transcripts depending on m6A association with reader RNA-binding proteins. m6A methylation is catalyzed by the METTL3 complex and removed by specific m6A demethylase ALKBH5, with the role of FTO as an 'eraser' uncertain. In this review, we provide an overview of epitranscriptomics related to mRNA and focus on m6A in mRNA and its detection. We summarize current knowledge on altered levels of writers, readers, and erasers of m6A and their roles in breast cancer and their association with prognosis. We summarize studies identifying m6A peaks and sites in genes in breast cancer cells.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
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12
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L’ARNm et ses modifications chez les eucaryotes*. BULLETIN DE L'ACADÉMIE NATIONALE DE MÉDECINE 2022. [DOI: 10.1016/j.banm.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Hertler J, Slama K, Schober B, Özrendeci Z, Marchand V, Motorin Y, Helm M. Synthesis of point-modified mRNA. Nucleic Acids Res 2022; 50:e115. [PMID: 36062567 PMCID: PMC9723659 DOI: 10.1093/nar/gkac719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/20/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Synthetic mRNA has recently moved into the focus of therapeutic and vaccination efforts. Incorporation of modified nucleotides during in vitro transcription can improve translation and attenuate immunogenicity, but is limited to triphosphate nucleotides which are accepted by RNA polymerases, and their incorporation is either random or complete. In contrast, site-specific modification, herein termed 'point modification' in analogy to point mutations, holds significant technical challenge. We developed fundamental techniques for isolation of long, translatable and internally point-modified mRNAs. Enabling concepts include three-way-one-pot splint ligations, and isolation of mRNA by real-time elution from agarose gels. The use of blue light permitted visualization of mRNA in pre-stained gels without the photochemical damage associated with the use of hard UV-radiation. This allowed visualization of the mRNA through its migration in the agarose gel, which in turn, was a prerequisite for its recovery by electroelution into precast troughs. Co-eluting agarose particles were quantified and found to not be detrimental to mRNA translation in vitro. Translation of EGFP-coding mRNA into functional protein was quantified by incorporation of 35S-labelled methionine and by in-gel EGFP fluorescence. This enabled the functional analysis of point modifications, specifically of ribose methylations in the middle of a 1371 nt long mRNA.
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Affiliation(s)
| | | | - Benedikt Schober
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Zeynep Özrendeci
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Virginie Marchand
- IMoPA UMR7365 CNRS-UL, BioPole Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - 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
| | - Mark Helm
- To whom correspondence should be addressed. Tel: +49 6131 392 5731; Fax: +49 6131 392 0373;
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14
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Kim KQ, Burgute BD, Tzeng SC, Jing C, Jungers C, Zhang J, Yan LL, Vierstra RD, Djuranovic S, Evans BS, Zaher HS. N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products. Cell Rep 2022; 40:111300. [PMID: 35988540 PMCID: PMC9376333 DOI: 10.1016/j.celrep.2022.111300] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 06/07/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Synthetic mRNA technology is a promising avenue for treating and preventing disease. Key to the technology is the incorporation of modified nucleotides such as N1-methylpseudouridine (m1Ψ) to decrease immunogenicity of the RNA. However, relatively few studies have addressed the effects of modified nucleotides on the decoding process. Here, we investigate the effect of m1Ψ and the related modification pseudouridine (Ψ) on translation. In a reconstituted system, we find that m1Ψ does not significantly alter decoding accuracy. More importantly, we do not detect an increase in miscoded peptides when mRNA containing m1Ψ is translated in cell culture, compared with unmodified mRNA. We also find that m1Ψ does not stabilize mismatched RNA-duplex formation and only marginally promotes errors during reverse transcription. Overall, our results suggest that m1Ψ does not significantly impact translational fidelity, a welcome sign for future RNA therapeutics.
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Affiliation(s)
- Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Crystal Jing
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Courtney Jungers
- Department of Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Junya Zhang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D. Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | | | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA,Corresponding author
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15
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Multiple Roles of m6A RNA Modification in Translational Regulation in Cancer. Int J Mol Sci 2022; 23:ijms23168971. [PMID: 36012237 PMCID: PMC9408962 DOI: 10.3390/ijms23168971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Despite its discovery in the early 1970s, m6A modification within mRNA molecules has only powerfully entered the oncology field in recent years. This chemical modification can control all aspects of the maturation of mRNAs, both in the nucleus and in the cytoplasm. Thus, the alteration in expression levels of writers, erasers, and readers may significantly contribute to the alteration of gene expression observed in cancer. In particular, the activation of oncogenic pathways can lead to an alteration of the global rate of mRNA translation or the selective translation of specific mRNAs. In both cases, m6A can play an important role. In this review, we highlight the role of m6A in the regulation of translation by focusing on regulatory mechanisms and cancer-related functions of this novel but still controversial field.
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16
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mRNA and tRNA modification states influence ribosome speed and frame maintenance during poly(lysine) peptide synthesis. J Biol Chem 2022; 298:102039. [PMID: 35595100 PMCID: PMC9207662 DOI: 10.1016/j.jbc.2022.102039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/16/2022] Open
Abstract
Ribosome speed is dictated by multiple factors including substrate availability, cellular conditions, and product (peptide) formation. Translation slows during the synthesis of cationic peptide sequences, potentially influencing the expression of thousands of proteins. Available evidence suggests that ionic interactions between positively charged nascent peptides and the negatively charged ribosome exit tunnel impede translation. However, this hypothesis was difficult to test directly because of inability to decouple the contributions of amino acid charge from mRNA sequence and tRNA identity/abundance in cells. Furthermore, it is unclear if other components of the translation system central to ribosome function (e.g., RNA modification) influence the speed and accuracy of positively charged peptide synthesis. In this study, we used a fully reconstituted Escherichia coli translation system to evaluate the effects of peptide charge, mRNA sequence, and RNA modification status on the translation of lysine-rich peptides. Comparison of translation reactions on poly(lysine)-encoding mRNAs conducted with either Lys-tRNALys or Val-tRNALys reveals that that amino acid charge, while important, only partially accounts for slowed translation on these transcripts. We further find that in addition to peptide charge, mRNA sequence and both tRNA and mRNA modification status influence the rates of amino acid addition and the ribosome’s ability to maintain frame (instead of entering the −2, −1, and +1 frames) during poly(lysine) peptide synthesis. Our observations lead us to expand the model for explaining how the ribosome slows during poly(lysine) peptide synthesis and suggest that posttranscriptional RNA modifications can provide cells a mechanism to precisely control ribosome movements along an mRNA.
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17
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Abe N, Imaeda A, Inagaki M, Li Z, Kawaguchi D, Onda K, Nakashima Y, Uchida S, Hashiya F, Kimura Y, Abe H. Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. ACS Chem Biol 2022; 17:1308-1314. [PMID: 35608277 DOI: 10.1021/acschembio.1c00996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5'-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2'-O-methylated nucleotides at the 5' end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.
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Affiliation(s)
- Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Akihiro Imaeda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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18
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Chemical modifications to mRNA nucleobases impact translation elongation and termination. Biophys Chem 2022; 285:106780. [DOI: 10.1016/j.bpc.2022.106780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022]
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19
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Ouranidis A, Vavilis T, Mandala E, Davidopoulou C, Stamoula E, Markopoulou CK, Karagianni A, Kachrimanis K. mRNA Therapeutic Modalities Design, Formulation and Manufacturing under Pharma 4.0 Principles. Biomedicines 2021; 10:50. [PMID: 35052730 PMCID: PMC8773365 DOI: 10.3390/biomedicines10010050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022] Open
Abstract
In the quest for a formidable weapon against the SARS-CoV-2 pandemic, mRNA therapeutics have stolen the spotlight. mRNA vaccines are a prime example of the benefits of mRNA approaches towards a broad array of clinical entities and druggable targets. Amongst these benefits is the rapid cycle "from design to production" of an mRNA product compared to their peptide counterparts, the mutability of the production line should another target be chosen, the side-stepping of safety issues posed by DNA therapeutics being permanently integrated into the transfected cell's genome and the controlled precision over the translated peptides. Furthermore, mRNA applications are versatile: apart from vaccines it can be used as a replacement therapy, even to create chimeric antigen receptor T-cells or reprogram somatic cells. Still, the sudden global demand for mRNA has highlighted the shortcomings in its industrial production as well as its formulation, efficacy and applicability. Continuous, smart mRNA manufacturing 4.0 technologies have been recently proposed to address such challenges. In this work, we examine the lab and upscaled production of mRNA therapeutics, the mRNA modifications proposed that increase its efficacy and lower its immunogenicity, the vectors available for delivery and the stability considerations concerning long-term storage.
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Affiliation(s)
- Andreas Ouranidis
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Department of Chemical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Theofanis Vavilis
- Laboratory of Biology and Genetics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Evdokia Mandala
- Fourth Department of Internal Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Christina Davidopoulou
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Eleni Stamoula
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Catherine K Markopoulou
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anna Karagianni
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Kyriakos Kachrimanis
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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20
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Svitkin YV, Gingras AC, Sonenberg N. Membrane-dependent relief of translation elongation arrest on pseudouridine- and N1-methyl-pseudouridine-modified mRNAs. Nucleic Acids Res 2021; 50:7202-7215. [PMID: 34933339 PMCID: PMC9303281 DOI: 10.1093/nar/gkab1241] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of therapeutically important proteins has benefited dramatically from the advent of chemically modified mRNAs that feature decreased lability and immunogenicity. This had a momentous effect on the rapid development of COVID-19 mRNA vaccines. Incorporation of the naturally occurring pseudouridine (Ψ) or N1-methyl-pseudouridine (N1mΨ) into in vitro transcribed mRNAs prevents the activation of unwanted immune responses by blocking eIF2α phosphorylation, which inhibits translation. Here, we report that Ψs in luciferase (Luc) mRNA exacerbate translation pausing in nuclease-untreated rabbit reticulocyte lysate (uRRL) and promote the formation of high-order-ribosome structures. The major deceleration of elongation occurs at the Ψ-rich nucleotides 1294-1326 of Ψ-Luc mRNA and results in premature termination of translation. The impairment of translation is mainly due to the shortage of membranous components. Supplementing uRRL with canine microsomal membranes (CMMs) relaxes the impediments to ribosome movement, resolves collided ribosomes, and greatly enhances full-size luciferase production. CMMs also strongly stimulated an extremely inefficient translation of N1mΨ-Luc mRNA in uRRL. Evidence is presented that translational pausing can promote membrane recruitment of polysomes with nascent polypeptides that lack a signal sequence. Our results highlight an underappreciated role of membrane binding to polysomes in the prevention of ribosome collision and premature release of nascent polypeptides.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1×5, Canada
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Institute, Montréal, Québec H3A 1A3, Canada
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21
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Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
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22
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Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs: switching atoms means shifting paradigms. FEBS Lett 2021; 595:2310-2322. [PMID: 34468991 PMCID: PMC9290505 DOI: 10.1002/1873-3468.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023]
Abstract
The structure, stability, and function of various coding and noncoding RNAs are influenced by chemical modifications. Pseudouridine (Ψ) is one of the most abundant post‐transcriptional RNA base modifications and has been detected at individual positions in tRNAs, rRNAs, mRNAs, and snRNAs, which are referred to as Ψ‐sites. By allowing formation of additional bonds with neighboring atoms, Ψ strengthens RNA–RNA and RNA–protein interactions. Although many aspects of the underlying modification reactions remain unclear, the advent of new transcriptome‐wide methods to quantitatively detect Ψ‐sites has recently changed our perception of the functional roles and importance of Ψ. For instance, it is now clear that the occurrence of Ψs appears to be directly linked to the lifetime and the translation efficiency of a given mRNA molecule. Furthermore, the administration of Ψ‐containing RNAs reduces innate immune responses, which appears strikingly advantageous for the development of generations of mRNA‐based vaccines. In this review, we aim to comprehensively summarize recent discoveries that highlight the impact of Ψ on various types of RNAs and outline possible novel biomedical applications of Ψ.
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Affiliation(s)
- Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rahul Mehta
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
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23
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Gao M, Zhang Q, Feng XH, Liu J. Synthetic modified messenger RNA for therapeutic applications. Acta Biomater 2021; 131:1-15. [PMID: 34133982 PMCID: PMC8198544 DOI: 10.1016/j.actbio.2021.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/16/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Synthetic modified messenger RNA (mRNA) has manifested great potentials for therapeutic applications such as vaccines and gene therapies, with the recent mRNA vaccines for global pandemic COVID-19 (corona virus disease 2019) attracting the tremendous attention. The chemical modifications and delivery vehicles of synthetic mRNAs are the two key factors for their in vivo therapeutic applications. Chemical modifications like nucleoside methylation endow the synthetic mRNAs with high stability and reduced stimulation of innate immunity. The development of scalable production of synthetic mRNA and efficient mRNA formulation and delivery strategies in recent years have remarkably advanced the field. It is worth noticing that we had limited knowledge on the roles of mRNA modifications in the past. However, the last decade has witnessed not only new discoveries of several naturally occurring mRNA modifications but also substantial advances in understanding their roles on regulating gene expression. It is highly necessary to reconsider the therapeutic system made by synthetic modified mRNAs and delivery vectors. In this review, we will mainly discuss the roles of various chemical modifications on synthetic mRNAs, briefly summarize the progresses of mRNA delivery strategies, and highlight some latest mRNA therapeutics applications including infectious disease vaccines, cancer immunotherapy, mRNA-based genetic reprogramming and protein replacement, mRNA-based gene editing. Statement of significance The development of synthetic mRNA drug holds great promise but lies behind small molecule and protein drugs largely due to the challenging issues regarding its stability, immunogenicity and potency. In the last 15 years, these issues have beensubstantially addressed by synthesizing chemically modified mRNA and developing powerful delivery systems; the mRNA therapeutics has entered an exciting new era begun with the approved mRNA vaccines for the COVID-19 infection disease. Here, we provide recent progresses in understanding the biological roles of various RNA chemical modifications, in developing mRNA delivery systems, and in advancing the emerging mRNA-based therapeutic applications, with the purpose to inspire the community to spawn new ideas for curing diseases.
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24
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Valadon C, Namy O. The Importance of the Epi-Transcriptome in Translation Fidelity. Noncoding RNA 2021; 7:51. [PMID: 34564313 PMCID: PMC8482273 DOI: 10.3390/ncrna7030051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases.
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Affiliation(s)
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France;
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25
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Schauerte M, Pozhydaieva N, Höfer K. Shaping the Bacterial Epitranscriptome-5'-Terminal and Internal RNA Modifications. Adv Biol (Weinh) 2021; 5:e2100834. [PMID: 34121369 DOI: 10.1002/adbi.202100834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/07/2021] [Indexed: 11/11/2022]
Abstract
All domains of life utilize a diverse set of modified ribonucleotides that can impact the sequence, structure, function, stability, and the fate of RNAs, as well as their interactions with other molecules. Today, more than 160 different RNA modifications are known that decorate the RNA at the 5'-terminus or internal RNA positions. The boost of next-generation sequencing technologies sets the foundation to identify and study the functional role of RNA modifications. The recent advances in the field of RNA modifications reveal a novel regulatory layer between RNA modifications and proteins, which is central to developing a novel concept called "epitranscriptomics." The majority of RNA modifications studies focus on the eukaryotic epitranscriptome. In contrast, RNA modifications in prokaryotes are poorly characterized. This review outlines the current knowledge of the prokaryotic epitranscriptome focusing on mRNA modifications. Here, it is described that several internal and 5'-terminal RNA modifications either present or likely present in prokaryotic mRNA. Thereby, the individual techniques to identify these epitranscriptomic modifications, their writers, readers and erasers, and their proposed functions are explored. Besides that, still unanswered questions in the field of prokaryotic epitranscriptomics are pointed out, and its future perspectives in the dawn of next-generation sequencing technologies are outlined.
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Affiliation(s)
- Maik Schauerte
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Nadiia Pozhydaieva
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
| | - Katharina Höfer
- Max-Planck-Institute for terrestrial Microbiology, Marburg, Hessen, 35043, Germany
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26
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Abstract
The mRNA epitranscriptome imparts diversity to gene expression by installing chemical modifications. Advances in detection methods have identified chemical modifications in eukaryotic, bacterial, and viral messenger RNAs (mRNAs). The biological functions of modifications in mRNAs still remain to be understood. Chemical modifications are introduced in synthetic mRNAs meant for therapeutic applications to maximize expression from the synthetic mRNAs and to evade the host immune response. This overview provides a background of chemical modifications found in mRNAs, with an emphasis on pseudouridine and its known effects on the mRNA life cycle, its potential applications in synthetic mRNA, and the methods used to assess its effects on mRNA translation.
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Affiliation(s)
- Bijoyita Roy
- RNA and Genome Editing, New England Biolabs Inc, Ipswich, MA, USA.
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27
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Abstract
Following its transcription, RNA can be modified by >170 chemically distinct types of modifications - the epitranscriptome. In recent years, there have been substantial efforts to uncover and characterize the modifications present on mRNA, motivated by the potential of such modifications to regulate mRNA fate and by discoveries and advances in our understanding of N 6-methyladenosine (m6A). Here, we review our knowledge regarding the detection, distribution, abundance, biogenesis, functions and possible mechanisms of action of six of these modifications - pseudouridine (Ψ), 5-methylcytidine (m5C), N 1-methyladenosine (m1A), N 4-acetylcytidine (ac4C), ribose methylations (Nm) and N 7-methylguanosine (m7G). We discuss the technical and analytical aspects that have led to inconsistent conclusions and controversies regarding the abundance and distribution of some of these modifications. We further highlight shared commonalities and important ways in which these modifications differ with respect to m6A, based on which we speculate on their origin and their ability to acquire functions over evolutionary timescales.
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28
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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29
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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30
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Jones JD, Monroe J, Koutmou KS. A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1586. [PMID: 31960607 PMCID: PMC8243748 DOI: 10.1002/wrna.1586] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/21/2019] [Accepted: 01/04/2020] [Indexed: 01/16/2023]
Abstract
Cells use chemical modifications to alter the sterics, charge, and conformations of large biomolecules, modulating their biogenesis, function, and stability. Until recently post-transcriptional RNA modifications were thought to be largely limited to nonprotein coding RNA species. However, this dogma has rapidly transformed with the discovery of a host of modifications in protein coding messenger RNAs (mRNAs). Recent advancements in genome-wide sequencing technologies have enabled the identification of mRNA modifications as a potential new frontier in gene regulation-leading to the development of the epitranscriptome field. As a result, there has been a flurry of multiple groundbreaking discoveries, including new modifications, nucleoside modifying enzymes ("writers" and "erasers"), and RNA binding proteins that recognize chemical modifications ("readers"). These discoveries opened the door to understanding how post-transcriptional mRNA modifications can modulate the mRNA lifecycle, and established a link between the epitranscriptome and human health and disease. Despite a rapidly growing recognition of their importance, fundamental questions regarding the identity, prevalence, and functional consequences of mRNA modifications remain to be answered. Here, we highlight quantitative studies that characterize mRNA modification abundance, frequency, and interactions with cellular machinery. As the field progresses, we see a need for the further integration of quantitative and reductionist approaches to complement transcriptome wide studies in order to establish a molecular-level framework for understanding the consequences of mRNA chemical modifications on biological processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Joshua D. Jones
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
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31
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Yang S, Wu F, Peng S, Wang F, Chen Y, Yuan Y, Weng X, Zhou X. A m 6 A Sensing Method by Its Impact on the Stability of RNA Double Helix. Chem Biodivers 2020; 17:e2000050. [PMID: 32372485 DOI: 10.1002/cbdv.202000050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023]
Abstract
N6 -Methyladenosine (m6 A) is one of the most important RNA modifications in epigenetics. The development of detection method for m6 A is limited by its abundance and structure. Although it has been previously reported that its presence has an impact on the complementary pairing of RNA, few assays have been developed using this finding. We used this discovery and designed a detection method based on Cas13a system, which has different fluorescence signals for target RNAs containing m6 A modification and target RNAs without m6 A modification. We verified the fact that the presence of m6 A could cause the instability of dsRNA using the Cas13a system and provided a new direction and strategy for the development of m6 A detection methods in the future.
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Affiliation(s)
- Shixi Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, P. R. China
| | - Yi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Yushu Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
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32
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Abstract
Chemical modifications of RNAs have long been established as key modulators of nonprotein-coding RNA structure and function in cells. There is a growing appreciation that messenger RNA (mRNA) sequences responsible for directing protein synthesis can also be posttranscriptionally modified. The enzymatic incorporation of mRNA modifications has many potential outcomes, including changing mRNA stability, protein recruitment, and translation. We tested how one of the most common modifications present in mRNA coding regions, pseudouridine (Ψ), impacts protein synthesis using a fully reconstituted bacterial translation system and human cells. Our work reveals that replacing a single uridine nucleotide with Ψ in an mRNA codon impedes amino acid addition and EF-Tu GTPase activation. A crystal structure of the Thermus thermophilus 70S ribosome with a tRNAPhe bound to a ΨUU codon in the A site supports these findings. We also find that the presence of Ψ can promote the low-level synthesis of multiple peptide products from a single mRNA sequence in the reconstituted translation system as well as human cells, and increases the rate of near-cognate Val-tRNAVal reacting on a ΨUU codon. The vast majority of Ψ moieties in mRNAs are found in coding regions, and our study suggests that one consequence of the ribosome encountering Ψ can be to modestly alter both translation speed and mRNA decoding.
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33
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Elliott BA, Ho HT, Ranganathan SV, Vangaveti S, Ilkayeva O, Abou Assi H, Choi AK, Agris PF, Holley CL. Modification of messenger RNA by 2'-O-methylation regulates gene expression in vivo. Nat Commun 2019; 10:3401. [PMID: 31363086 PMCID: PMC6667457 DOI: 10.1038/s41467-019-11375-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Epitranscriptomic modifications of mRNA are important regulators of gene expression. While internal 2'-O-methylation (Nm) has been discovered on mRNA, questions remain about its origin and function in cells and organisms. Here, we show that internal Nm modification can be guided by small nucleolar RNAs (snoRNAs), and that these Nm sites can regulate mRNA and protein expression. Specifically, two box C/D snoRNAs (SNORDs) and the 2'-O-methyltransferase fibrillarin lead to Nm modification in the protein-coding region of peroxidasin (Pxdn). The presence of Nm modification increases Pxdn mRNA expression but inhibits its translation, regulating PXDN protein expression and enzyme activity both in vitro and in vivo. Our findings support a model in which snoRNA-guided Nm modifications of mRNA can regulate physiologic gene expression by altering mRNA levels and tuning protein translation.
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Affiliation(s)
- Brittany A Elliott
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Hsiang-Ting Ho
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | | | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, 12222, USA
| | - Olga Ilkayeva
- Duke Molecular Physiology Institute, Duke University, Durham, NC, 27701, USA
| | - Hala Abou Assi
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Alex K Choi
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
| | - Paul F Agris
- Department of Medicine, Duke University Medical Center, Durham, NC, 27705, USA
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