1
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Gao N, Yu A, Yang W, Zhang X, Shen Y, Fu X. Enzymatic de novo oligonucleotide synthesis: Emerging techniques and advancements. Biotechnol Adv 2025; 82:108604. [PMID: 40368114 DOI: 10.1016/j.biotechadv.2025.108604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Revised: 04/23/2025] [Accepted: 05/10/2025] [Indexed: 05/16/2025]
Abstract
Oligonucleotide synthesis serves as a cornerstone of modern life sciences, enabling groundbreaking advancements across molecular diagnostics, therapeutic development, and transformative technologies including DNA data storage and programmable biological systems. While phosphoramidite-based chemical synthesis remains the industrial standard, its limitations in producing long-sequence constructs, cumulative error rates, and reliance on toxic solvents pose significant challenges for next-generation applications. Emerging enzymatic synthesis approaches offer a paradigm shift by harnessing the inherent precision and environmental sustainability of biological systems. This comprehensive review systematically examines the evolving landscape of oligonucleotide synthesis technologies. We first analyze the mechanistic foundations and persistent limitations of conventional chemical methods, followed by a critical evaluation of enzymatic strategies with particular emphasis on terminal deoxynucleotidyl transferase (TdT)-mediated template-independent polymerization. The work provides detailed insights into enzymatic reaction engineering, including substrate specificity profiling of nucleotide analogs and innovative solid-phase synthesis platforms enabling iterative nucleotide addition. Furthermore, we discuss emerging high-throughput synthesis architectures and commercial translation efforts. In summary, this review comprehensively encapsulates the advancements and commercialization status of enzymatic synthesis technologies, offering valuable guidance that can expedite the innovative development of enzymatic oligonucleotide manufacturing platforms.
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Affiliation(s)
- Nanfeng Gao
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China
| | - Aimiao Yu
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China
| | - Weikang Yang
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China
| | - Xiandi Zhang
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China
| | - Yue Shen
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Fu
- BGI Research, Changzhou 213299, China; BGI Research, Shenzhen 518083, China.
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2
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Wiegand DJ, Rittichier J, Meyer E, Lee H, Conway NJ, Ahlstedt D, Yurtsever Z, Rainone D, Kuru E, Church GM. Template-independent enzymatic synthesis of RNA oligonucleotides. Nat Biotechnol 2025; 43:762-772. [PMID: 38997579 DOI: 10.1038/s41587-024-02244-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 04/11/2024] [Indexed: 07/14/2024]
Abstract
RNA oligonucleotides have emerged as a powerful therapeutic modality to treat disease, yet current manufacturing methods may not be able to deliver on anticipated future demand. Here, we report the development and optimization of an aqueous-based, template-independent enzymatic RNA oligonucleotide synthesis platform as an alternative to traditional chemical methods. The enzymatic synthesis of RNA oligonucleotides is made possible by controlled incorporation of reversible terminator nucleotides with a common 3'-O-allyl ether blocking group using new CID1 poly(U) polymerase mutant variants. We achieved an average coupling efficiency of 95% and demonstrated ten full cycles of liquid phase synthesis to produce natural and therapeutically relevant modified sequences. We then qualitatively assessed the platform on a solid phase, performing enzymatic synthesis of several N + 5 oligonucleotides on a controlled-pore glass support. Adoption of an aqueous-based process will offer key advantages including the reduction of solvent use and sustainable therapeutic oligonucleotide manufacturing.
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Affiliation(s)
- Daniel J Wiegand
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
- EnPlusOne Biosciences Inc., Watertown, MA, USA
| | - Jonathan Rittichier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
- EnPlusOne Biosciences Inc., Watertown, MA, USA
| | - Ella Meyer
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
- EnPlusOne Biosciences Inc., Watertown, MA, USA
| | - Howon Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | - Nicholas J Conway
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA
| | | | | | | | - Erkin Kuru
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA.
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Boston, MA, USA.
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3
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Yang Y, Sakurai M. Advances in Detection Methods for A-to-I RNA Editing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2025; 16:e70014. [PMID: 40223708 PMCID: PMC11995373 DOI: 10.1002/wrna.70014] [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: 12/06/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/15/2025]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a key post-transcriptional modification that influences gene expression and various cellular processes. Advances in sequencing technologies have greatly contributed to the identification of A-to-I editing sites, providing insights into their distribution across coding and non-coding regions. These developments have facilitated the discovery of functionally relevant editing events and have advanced the understanding of their biological roles. This review presents the evolution of methodologies for RNA editing detection and examines recent advances, including chemically-assisted, enzyme-assisted, and quantitative approaches. By evaluating these techniques, we aim to help researchers select the most effective tools for investigating RNA editing and its broader implications in health and disease.
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Affiliation(s)
- Yuxi Yang
- Research Institute for Biomedical SciencesTokyo University of ScienceChibaJapan
| | - Masayuki Sakurai
- Research Institute for Biomedical SciencesTokyo University of ScienceChibaJapan
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4
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Nikkel DJ, Kaur R, Wetmore SD. How Can One Metal Power Nucleic Acid Phosphodiester Bond Cleavage by a Nuclease? Multiscale Computational Studies Highlight a Diverse Mechanistic Landscape. J Phys Chem B 2025; 129:3-18. [PMID: 39720842 DOI: 10.1021/acs.jpcb.4c05875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2024]
Abstract
Despite the remarkable resistance of the nucleic acid phosphodiester backbone to degradation affording genetic stability, the P-O bond must be broken during DNA repair and RNA metabolism, among many other critical cellular processes. Nucleases are powerful enzymes that can enhance the uncatalyzed rate of phosphodiester bond cleavage by up to ∼1017-fold. Despite the most well accepted hydrolysis mechanism involving two metals (MA2+ to activate a water nucleophile and MB2+ to stabilize the leaving group), experimental evidence suggests that some nucleases can use a single metal to facilitate the chemical step, a controversial concept in the literature. The present perspective uses the case studies of four nucleases (I-PpoI, APE1, and bacterial and human EndoV) to highlight how computational approaches ranging from quantum mechanical (QM) cluster models to molecular dynamics (MD) simulations and combined quantum mechanics-molecular mechanics (QM/MM) calculations can reveal the atomic level details necessary to understand how a nuclease can use a single metal to facilitate this difficult chemistry. The representative nucleases showcase how different amino acid residues (e.g., histidine, aspartate) can fulfill the role of the first metal (MA2+) in the two-metal-mediated mechanisms. Nevertheless, differences in active site architectures afford diversity in the single-metal-mediated mechanism in terms of the metal-substrate coordination, the role of the metal, and the identities of the general acid and base. The greater understanding of the catalytic mechanisms of nucleases obtained from the body of work reviewed can be used to further explore the progression of diseases associated with nuclease (mis)activity and the development of novel nuclease applications such as disease diagnostics, gene engineering, and therapeutics.
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Affiliation(s)
- Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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5
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Kaur R, Nikkel DJ, Wetmore SD. Mechanism of Nucleic Acid Phosphodiester Bond Cleavage by Human Endonuclease V: MD and QM/MM Calculations Reveal a Versatile Metal Dependence. J Phys Chem B 2024; 128:9455-9469. [PMID: 39359137 DOI: 10.1021/acs.jpcb.4c05846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Human endonuclease V (EndoV) catalytically removes deaminated nucleobases by cleaving the phosphodiester bond as part of RNA metabolism. Despite being implicated in several diseases (cancers, cardiovascular diseases, and neurological disorders) and potentially being a useful tool in biotechnology, details of the human EndoV catalytic pathway remain unclear due to limited experimental information beyond a crystal structure of the apoenzyme and select mutational data. Since a mechanistic understanding is critical for further deciphering the central roles and expanding applications of human EndoV in medicine and biotechnology, molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations were used to unveil the atomistic details of the catalytic pathway. Due to controversies surrounding the number of metals required for nuclease activity, enzyme-substrate models with different numbers of active site metals and various metal-substrate binding configurations were built based on structural data for other nucleases. Subsequent MD simulations revealed the structure and stability of the human EndoV-substrate complex for a range of active site metal binding architectures. Four unique pathways were then characterized using QM/MM that vary in metal number (one versus two) and modes of substrate coordination [direct versus indirect (water-mediated)], with several mechanisms being fully consistent with experimental structural, kinetic, and mutational data for related nucleases, including members of the EndoV family. Beyond uncovering key roles for several active site amino acids (D240 and K155), our calculations highlight that while one metal is essential for human EndoV activity, the enzyme can benefit from using two metals due to the presence of two suitable metal binding sites. By directly comparing one- versus two-metal-mediated P-O bond cleavage reactions within the confines of the same active site, our work brings a fresh perspective to the "number of metals" controversy.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge T1K 3M4, Alberta, Canada
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6
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Cheng H, Yu J, Wong CC. Adenosine-to-Inosine RNA editing in cancer: molecular mechanisms and downstream targets. Protein Cell 2024:pwae039. [PMID: 39126156 DOI: 10.1093/procel/pwae039] [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: 03/27/2024] [Indexed: 08/12/2024] Open
Abstract
Adenosine-to-Inosine (A-to-I), one of the most prevalent RNA modifications, has recently garnered significant attention. The A-to-I modification actively contributes to biological and pathological processes by affecting the structure and function of various RNA molecules, including double stranded RNA, transfer RNA, microRNA, and viral RNA. Increasing evidence suggests that A-to-I plays a crucial role in the development of human disease, particularly in cancer, and aberrant A-to-I levels are closely associated with tumorigenesis and progression through regulation of the expression of multiple oncogenes and tumor suppressor genes. Currently, the underlying molecular mechanisms of A-to-I modification in cancer are not comprehensively understood. Here, we review the latest advances regarding the A-to-I editing pathways implicated in cancer, describing their biological functions and their connections to the disease.
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Affiliation(s)
- Hao Cheng
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 518172, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 518172, China
| | - Chi Chun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR 518172, China
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7
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Tao WB, Xiong J, Yuan BF. Site-specific quantification of Adenosine-to-Inosine RNA editing by Endonuclease-Mediated qPCR. Bioorg Med Chem 2024; 110:117837. [PMID: 39013280 DOI: 10.1016/j.bmc.2024.117837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
RNA molecules contain diverse modified nucleobases that play pivotal roles in numerous biological processes. Adenosine-to-inosine (A-to-I) RNA editing, one of the most prevalent RNA modifications in mammalian cells, is linked to a multitude of human diseases. To unveil the functions of A-to-I RNA editing, accurate quantification of inosine at specific sites is essential. In this study, we developed an endonuclease-mediated cleavage and real-time fluorescence quantitative PCR method for A-to-I RNA editing (EM-qPCR) to quantitatively analyze A-to-I RNA editing at a single site. By employing this method, we successfully quantified the levels of A-to-I RNA editing on various transfer RNA (tRNA) molecules at position 34 (I34) in mammalian cells with precision. Subsequently, this method was applied to tissues from sleep-deprived mice, revealing a notable alteration in the levels of I34 between sleep-deprived and control mice. The proposed method sets a precedent for the quantitative analysis of A-to-I RNA editing at specific sites, facilitating a deeper understanding of the biological implications of A-to-I RNA editing.
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Affiliation(s)
- Wan-Bing Tao
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China
| | - Jun Xiong
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China; Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, PR China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China; Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, PR China; Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, PR China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, PR China.
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8
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Quillin A, Arnould B, Knutson SD, Heemstra JM. Spatial Visualization of A-to-I Editing in Cells Using Endonuclease V Immunostaining Assay (EndoVIA). ACS CENTRAL SCIENCE 2024; 10:1396-1405. [PMID: 39071059 PMCID: PMC11273454 DOI: 10.1021/acscentsci.4c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/30/2024]
Abstract
Adenosine-to-inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions, and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily on in vitro characterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed endonuclease V (EndoV), a magnesium-dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces an endonuclease V immunostaining assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.
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Affiliation(s)
- Alexandria
L. Quillin
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Benoît Arnould
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
| | - Steve D. Knutson
- Merck
Center for Catalysis, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
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9
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XIONG J, FENG T, YUAN BF. [Advances in mapping analysis of ribonucleic acid modifications through sequencing]. Se Pu 2024; 42:632-645. [PMID: 38966972 PMCID: PMC11224946 DOI: 10.3724/sp.j.1123.2023.12025] [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: 12/20/2023] [Indexed: 07/06/2024] Open
Abstract
Over 170 chemical modifications have been discovered in various types of ribonucleic acids (RNAs), including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). These RNA modifications play crucial roles in a wide range of biological processes such as gene expression regulation, RNA stability maintenance, and protein translation. RNA modifications represent a new dimension of gene expression regulation known as the "epitranscriptome". The discovery of RNA modifications and the relevant writers, erasers, and readers provides an important basis for studies on the dynamic regulation and physiological functions of RNA modifications. Owing to the development of detection technologies for RNA modifications, studies on RNA epitranscriptomes have progressed to the single-base resolution, multilayer, and full-coverage stage. Transcriptome-wide methods help discover new RNA modification sites and are of great importance for elucidating the molecular regulatory mechanisms of epitranscriptomics, exploring the disease associations of RNA modifications, and understanding their clinical applications. The existing RNA modification sequencing technologies can be categorized according to the pretreatment approach and sequencing principle as direct high-throughput sequencing, antibody-enrichment sequencing, enzyme-assisted sequencing, chemical labeling-assisted sequencing, metabolic labeling sequencing, and nanopore sequencing technologies. These methods, as well as studies on the functions of RNA modifications, have greatly expanded our understanding of epitranscriptomics. In this review, we summarize the recent progress in RNA modification detection technologies, focusing on the basic principles, advantages, and limitations of different methods. Direct high-throughput sequencing methods do not require complex RNA pretreatment and allow for the mapping of RNA modifications using conventional RNA sequencing methods. However, only a few RNA modifications can be analyzed by high-throughput sequencing. Antibody enrichment followed by high-throughput sequencing has emerged as a crucial approach for mapping RNA modifications, significantly advancing the understanding of RNA modifications and their regulatory functions in different species. However, the resolution of antibody-enrichment sequencing is limited to approximately 100-200 bp. Although chemical crosslinking techniques can achieve single-base resolution, these methods are often complex, and the specificity of the antibodies used in these methods has raised concerns. In particular, the issue of off-target binding by the antibodies requires urgent attention. Enzyme-assisted sequencing has improved the accuracy of the localization analysis of RNA modifications and enables stoichiometric detection with single-base resolution. However, the enzymes used in this technique show poor reactivity, specificity, and sequence preference. Chemical labeling sequencing has become a widely used approach for profiling RNA modifications, particularly by altering reverse transcription (RT) signatures such as RT stops, misincorporations, and deletions. Chemical-assisted sequencing provides a sequence-independent RNA modification detection strategy that enables the localization of multiple RNA modifications. Additionally, when combined with the biotin-streptavidin affinity method, low-abundance RNA modifications can be enriched and detected. Nevertheless, the specificity of many chemical reactions remains problematic, and the development of specific reaction probes for particular modifications should continue in the future to achieve the precise localization of RNA modifications. As an indirect localization method, metabolic labeling sequencing specifically localizes the sites at which modifying enzymes act, which is of great significance in the study of RNA modification functions. However, this method is limited by the intracellular labeling of RNA and cannot be applied to biological samples such as clinical tissues and blood samples. Nanopore sequencing is a direct RNA-sequencing method that does not require RT or the polymerase chain reaction (PCR). However, challenges in analyzing the data obtained from nanopore sequencing, such as the high rate of false positives, must be resolved. Discussing sequencing analysis methods for various types of RNA modifications is instructive for the future development of novel RNA modification mapping technologies, and will aid studies on the functions of RNA modifications across the entire transcriptome.
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10
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Mitsuoka K, Kim JI, Yoshida A, Matsumoto A, Aoki-Shioi N, Iwai S, Kuraoka I. Base preference for inosine 3'-riboendonuclease activity of human endonuclease V: implications for cleavage of poly-A tails containing inosine. Sci Rep 2024; 14:14973. [PMID: 38951658 PMCID: PMC11217400 DOI: 10.1038/s41598-024-65814-7] [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: 12/22/2023] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
Deamination of bases is a form of DNA damage that occurs spontaneously via the hydrolysis and nitrosation of living cells, generating hypoxanthine from adenine. E. coli endonuclease V (eEndoV) cleaves hypoxanthine-containing double-stranded DNA, whereas human endonuclease V (hEndoV) cleaves hypoxanthine-containing RNA; however, hEndoV in vivo function remains unclear. To date, hEndoV has only been examined using hypoxanthine, because it binds closely to the base located at the cleavage site. Here, we examined whether hEndoV cleaves other lesions (e.g., AP site, 6-methyladenine, xanthine) to reveal its function and whether 2'-nucleoside modification affects its cleavage activity. We observed that hEndoV is hypoxanthine-specific; its activity was the highest with 2'-OH modification in ribose. The cleavage activity of hEndoV was compared based on its base sequence. We observed that it has specificity for adenine located on the 3'-end of hypoxanthine at the cleavage site, both before and after cleavage. These data suggest that hEndoV recognizes and cleaves the inosine generated on the poly A tail to maintain RNA quality. Our results provide mechanistic insight into the role of hEndoV in vivo.
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Affiliation(s)
- Kazuma Mitsuoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Jung In Kim
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Aya Yoshida
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Akane Matsumoto
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Narumi Aoki-Shioi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180, Japan.
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11
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Schmitt MA, Tittle JM, Fisk JD. Codon decoding by orthogonal tRNAs interrogates the in vivo preferences of unmodified adenosine in the wobble position. Front Genet 2024; 15:1386299. [PMID: 38706795 PMCID: PMC11066159 DOI: 10.3389/fgene.2024.1386299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024] Open
Abstract
The in vivo codon decoding preferences of tRNAs with an authentic adenosine residue at position 34 of the anticodon, the wobble position, are largely unexplored because very few unmodified A34 tRNA genes exist across the three domains of life. The expanded wobble rules suggest that unmodified adenosine pairs most strongly with uracil, modestly with cytosine, and weakly with guanosine and adenosine. Inosine, a modified adenosine, on the other hand, pairs strongly with both uracil and cytosine and to a lesser extent adenosine. Orthogonal pair directed sense codon reassignment experiments offer a tool with which to interrogate the translational activity of A34 tRNAs because the introduced tRNA can be engineered with any anticodon. Our fluorescence-based screen utilizes the absolute requirement of tyrosine at position 66 of superfolder GFP for autocatalytic fluorophore formation. The introduced orthogonal tRNA competes with the endogenous translation machinery to incorporate tyrosine in response to a codon typically assigned another meaning in the genetic code. We evaluated the codon reassignment efficiencies of 15 of the 16 possible orthogonal tRNAs with A34 anticodons. We examined the Sanger sequencing chromatograms for cDNAs from each of the reverse transcribed tRNAs for evidence of inosine modification. Despite several A34 tRNAs decoding closely-related C-ending codons, partial inosine modification was detected for only three species. These experiments employ a single tRNA body with a single attached amino acid to interrogate the behavior of different anticodons in the background of in vivo E. coli translation and greatly expand the set of experimental measurements of the in vivo function of A34 tRNAs in translation. For the most part, unmodified A34 tRNAs largely pair with only U3 codons as the original wobble rules suggest. In instances with GC pairs in the first two codon positions, unmodified A34 tRNAs decode the C- and G-ending codons as well as the expected U-ending codon. These observations support the "two-out-of-three" and "strong and weak" codon hypotheses.
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Affiliation(s)
| | | | - John D. Fisk
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
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12
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Quillin AL, Arnould B, Knutson SD, Heemstra JM. Spatial visualization of A-to-I Editing in cells using Endonuclease V Immunostaining Assay (EndoVIA). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583344. [PMID: 38496620 PMCID: PMC10942280 DOI: 10.1101/2024.03.04.583344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Adenosine-to-Inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited. Current methods rely primarily on in vitro characterization of extracted RNA that ultimately erases subcellular localization and cell-to-cell heterogeneity. To address these challenges, we have repurposed Endonuclease V (EndoV), a magnesium dependent ribonuclease that cleaves inosine bases in edited RNA, to selectively bind and detect A-to-I edited RNA in cells. The work herein introduces Endonuclease V Immunostaining Assay (EndoVIA), a workflow that provides spatial visualization of edited transcripts, enables rapid quantification of overall inosine abundance, and maps the landscape of A-to-I editing within the transcriptome at the nanoscopic level.
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13
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Tan MH. Identification of Bona Fide RNA Editing Sites: History, Challenges, and Opportunities. Acc Chem Res 2023; 56:3033-3044. [PMID: 37827987 DOI: 10.1021/acs.accounts.3c00462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by the adenosine deaminase acting on the RNA (ADAR) family of enzymes of which there are three members (ADAR1, ADAR2, and ADAR3), is a major gene regulatory mechanism that diversifies the transcriptome. It is widespread in many metazoans, including humans. As inosine is interpreted by cellular machineries mainly as guanosine, A-to-I editing effectively gives A-to-G nucleotide changes. Depending on its location, an editing event can generate new protein isoforms or influence other RNA processing pathways. Researchers have found that ADAR-mediated editing performs diverse functions. For example, it enables living organisms such as cephalopods to adapt rapidly to fluctuating environmental conditions such as water temperature. In development, the loss of ADAR1 is embryonically lethal partly because endogenous double-stranded RNAs (dsRNAs) are no longer marked by inosines, which signal "self", and thus cause the melanoma differentiation-associated protein 5 (MDA5) sensor to trigger a deleterious interferon response. Hence, ADAR1 plays a key role in preventing aberrant activation of the innate immune system. Furthermore, ADAR enzymes have been implicated in myriad human diseases. Intriguingly, some cancer cells are known to exploit ADAR1 activity to dodge immune responses. However, the exact identities of immunogenic RNAs in different biological contexts have remained elusive. Consequently, there is tremendous interest in identifying inosine-containing RNAs in the cell.The identification of A-to-I RNA editing sites is dependent on the sequencing of nucleic acids. Technological and algorithmic advancements over the past decades have revolutionized the way editing events are detected. At the beginning, the discovery of editing sites relies on Sanger sequencing, a first-generation technology. Both RNA, which is reverse transcribed into complementary DNA (cDNA), and genomic DNA (gDNA) from the same source are analyzed. After sequence alignment, one would require an adenosine to be present in the genome but a guanosine to be detected in the RNA sample for a position to be declared as an editing site. However, an issue with Sanger sequencing is its low throughput. Subsequently, Illumina sequencing, a second-generation technology, was invented. By permitting the simultaneous interrogation of millions of molecules, it enables many editing sites to be identified rapidly. However, a key challenge is that the Illumina platform produces short sequencing reads that can be difficult to map accurately. To tackle the challenge, we and others developed computational workflows with a series of filters to discard sites that are likely to be false positives. When Illumina sequencing data sets are properly analyzed, A-to-G variants should emerge as the most dominant mismatch type. Moreover, the quantitative nature of the data allows us to build a comprehensive atlas of editing-level measurements across different biological contexts, providing deep insights into the spatiotemporal dynamics of RNA editing. However, difficulties remain in identifying true A-to-I editing sites in short protein-coding exons or in organisms and diseases where DNA mutations and genomic polymorphisms are prevalent and mostly unknown. Nanopore sequencing, a third-generation technology, promises to address the difficulties, as it allows native RNAs to be sequenced without conversion to cDNA, preserving base modifications that can be directly detected through machine learning. We recently demonstrated that nanopore sequencing could be used to identify A-to-I editing sites in native RNA directly. Although further work is needed to enhance the detection accuracy in single molecules from fewer cells, the nanopore technology holds the potential to revolutionize epitranscriptomic studies.
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Affiliation(s)
- Meng How Tan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Singapore
- HP-NTU Digital Manufacturing Corporate Laboratory, Nanyang Technological University, Singapore 637460, Singapore
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14
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Wei Q, Han S, Yuan K, He Z, Chen Y, Xi X, Han J, Yan S, Chen Y, Yuan B, Weng X, Zhou X. Transcriptome-wide profiling of A-to-I RNA editing by Slic-seq. Nucleic Acids Res 2023; 51:e87. [PMID: 37470992 PMCID: PMC10484733 DOI: 10.1093/nar/gkad604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/23/2023] [Accepted: 07/13/2023] [Indexed: 07/21/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional processing event involved in diversifying the transcriptome and is responsible for various biological processes. In this context, we developed a new method based on the highly selective cleavage activity of Endonuclease V against Inosine and the universal activity of sodium periodate against all RNAs to enrich the inosine-containing RNA and accurately identify the editing sites. We validated the reliability of our method in human brain in both Alu and non-Alu elements. The conserved sites of A-to-I editing in human cells (HEK293T, HeLa, HepG2, K562 and MCF-7) primarily occurs in the 3'UTR of the RNA, which are highly correlated with RNA binding and protein binding. Analysis of the editing sites between the human brain and mouse brain revealed that the editing of exons is more conserved than that in other regions. This method was applied to three neurological diseases (Alzheimer's, epilepsy and ageing) of mouse brain, reflecting that A-to-I editing sites significantly decreased in neuronal activity genes.
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Affiliation(s)
- Qi Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Shaoqing Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Kexin Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Xin Xi
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Jingyu Han
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Shen Yan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Bifeng Yuan
- School of Public Health, Wuhan University, Wuhan, HuBei 430071, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, PR China
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, PR China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
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15
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Zhang Z, Bae B, Cuddleston WH, Miura P. Coordination of alternative splicing and alternative polyadenylation revealed by targeted long read sequencing. Nat Commun 2023; 14:5506. [PMID: 37679364 PMCID: PMC10484994 DOI: 10.1038/s41467-023-41207-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Nervous system development is associated with extensive regulation of alternative splicing (AS) and alternative polyadenylation (APA). AS and APA have been extensively studied in isolation, but little is known about how these processes are coordinated. Here, the coordination of cassette exon (CE) splicing and APA in Drosophila was investigated using a targeted long-read sequencing approach we call Pull-a-Long-Seq (PL-Seq). This cost-effective method uses cDNA pulldown and Nanopore sequencing combined with an analysis pipeline to quantify inclusion of alternative exons in connection with alternative 3' ends. Using PL-Seq, we identified genes that exhibit significant differences in CE splicing depending on connectivity to short versus long 3'UTRs. Genomic long 3'UTR deletion was found to alter upstream CE splicing in short 3'UTR isoforms and ELAV loss differentially affected CE splicing depending on connectivity to alternative 3'UTRs. This work highlights the importance of considering connectivity to alternative 3'UTRs when monitoring AS events.
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Affiliation(s)
- Zhiping Zhang
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | - Bongmin Bae
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Pedro Miura
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Department of Biology, University of Nevada, Reno, Reno, NV, USA.
- Institute for System Genomics, University of Connecticut, Storrs, CT, USA.
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Abstract
Cardiovascular disease still remains the leading cause of morbidity and mortality worldwide. Current pharmacological or interventional treatments help to tackle symptoms and even reduce mortality, but cardiovascular disease cases continue to rise. The emergence of novel therapeutic strategies that precisely and efficiently combat cardiovascular disease is therefore deemed more essential than ever. RNA editing, the cell-intrinsic deamination of adenosine or cytidine RNA residues, changes the molecular identity of edited nucleotides, severely altering the fate of RNA molecules involved in key biological processes. The most common type of RNA editing is the deamination of adenosine residue to inosine (A-to-I), which is catalysed by adenosine deaminases acting on RNA (ADARs). Recent efforts have convincingly liaised RNA editing-based mechanisms to the pathophysiology of the cardiovascular system. In this review, we will briefly introduce the basic concepts of the RNA editing field of research. We will particularly focus our discussion on the therapeutic exploitation of RNA editing as a novel therapeutic tool as well as the future perspectives for its use in cardiovascular disease treatment.
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Biochemical and mutational studies of an endonuclease V from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A. World J Microbiol Biotechnol 2023; 39:90. [PMID: 36752840 DOI: 10.1007/s11274-023-03526-2] [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: 12/03/2022] [Accepted: 01/16/2023] [Indexed: 02/09/2023]
Abstract
Endonuclease V (EndoV), which is widespread in bacteria, eukarya and Archaea, can cleave hypoxanthine (Hx)-containing DNA or RNA strand, and play an essential role in Hx repair. However, our understanding on archaeal EndoV's function remains incomplete. The model archaeon Sulfolobus islandicus REY15A encodes a putative EndoV protein (Sis-EndoV). Herein, we probed the biochemical characteristics of Sis-EndoV and dissected the roles of its seven conserved residues. Our biochemical data demonstrate that Sis-EndoV displays maximum cleavage efficiency at above 60 °C and at pH 7.0-9.0, and the enzyme activity is dependent on a divalent metal ion, among which Mg2+ is optimal. Importantly, we first measured the activation energy for cleaving Hx-containing ssDNA by Sis-EndoV to be 9.6 ± 0.8 kcal/mol by kinetic analyses, suggesting that chemical catalysis might be a rate-limiting step for catalysis. Mutational analyses show that residue D38 in Sis-EndoV is essential for catalysis, but has no role in DNA binding. Furthermore, we first revealed that residues Y41 and D189 in Sis-EndoV are involved in both DNA cleavage and DNA binding, but residues F77, H103, K156 and F161 are only responsible for DNA binding.
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18
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Pichot F, Hogg MC, Marchand V, Bourguignon V, Jirström E, Farrell C, Gibriel HA, Prehn JH, Motorin Y, Helm M. Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines. Comput Struct Biotechnol J 2022; 21:401-417. [PMID: 36618980 PMCID: PMC9798144 DOI: 10.1016/j.csbj.2022.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always fully modified. Combinations and permutations of partially modified sites in tRNAs can generate a plethora of tRNA isoforms, termed modivariants. Here, we investigate the stoichiometry of incompletely modified sites in tRNAs from human cell lines for their information content. Using a panel of RNA modification mapping methods, we assess the stoichiometry of sites that contain the modifications 5-methylcytidine (m5C), 2'-O-ribose methylation (Nm), 3-methylcytidine (m3C), 7-methylguanosine (m7G), and Dihydrouridine (D). We discovered that up to 75% of sites can be incompletely modified and that the differential modification status of a cellular tRNA population holds information that allows to discriminate e.g. different cell lines. As a further aspect, we investigated potential causal connectivity between tRNA modification and its processing into tRNA fragments (tiRNAs and tRFs). Upon exposure of cultured living cells to cell-penetrating angiogenin, the modification patterns of the corresponding RNA populations was changed. Importantly, we also found that tsRNAs were significantly less modified than their parent tRNAs at numerous sites, suggesting that tsRNAs might derive chiefly from hypomodified tRNAs.
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Affiliation(s)
- Florian Pichot
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Marion C. Hogg
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Elisabeth Jirström
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Cliona Farrell
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Hesham A. Gibriel
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Jochen H.M. Prehn
- Department of Physiology and Medical Physics and SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, IBSLor (UAR2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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Sikorski V, Vento A, Kankuri E, IHD-EPITRAN Consortium. Emerging roles of the RNA modifications N6-methyladenosine and adenosine-to-inosine in cardiovascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:426-461. [PMID: 35991314 PMCID: PMC9366019 DOI: 10.1016/j.omtn.2022.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cardiovascular diseases lead the mortality and morbidity disease metrics worldwide. A multitude of chemical base modifications in ribonucleic acids (RNAs) have been linked with key events of cardiovascular diseases and metabolic disorders. Named either RNA epigenetics or epitranscriptomics, the post-transcriptional RNA modifications, their regulatory pathways, components, and downstream effects substantially contribute to the ways our genetic code is interpreted. Here we review the accumulated discoveries to date regarding the roles of the two most common epitranscriptomic modifications, N6-methyl-adenosine (m6A) and adenosine-to-inosine (A-to-I) editing, in cardiovascular disease.
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Affiliation(s)
- Vilbert Sikorski
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Antti Vento
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - IHD-EPITRAN Consortium
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland
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Felix AS, Quillin AL, Mousavi S, Heemstra JM. Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications. Acc Chem Res 2022; 55:2271-2279. [PMID: 35900335 PMCID: PMC9388579 DOI: 10.1021/acs.accounts.2c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.
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Affiliation(s)
- Ansley S. Felix
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Alexandria L. Quillin
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Shikufa Mousavi
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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21
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Chen JJ, You XJ, Li L, Xie NB, Ding JH, Yuan BF, Feng YQ. Single-Base Resolution Detection of Adenosine-to-Inosine RNA Editing by Endonuclease-Mediated Sequencing. Anal Chem 2022; 94:8740-8747. [PMID: 35678728 DOI: 10.1021/acs.analchem.2c01226] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA molecules contain diverse modifications that play crucial roles in a wide variety of biological processes. Adenosine-to-inosine (A-to-Ino) RNA editing is one of the most prevalent modifications among all types of RNA. Abnormal A-to-InoRNA editing has been demonstrated to be associated with many human diseases. Identification of A-to-Ino editing sites is indispensable to deciphering their biological roles. Herein, by employing the unique property of human endonuclease V (hEndoV), we proposed a hEndoV-mediated sequencing (hEndoV-seq) method for the single-base resolution detection of A-to-InoRNA editing sites. In this approach, the terminal 3'OH of RNA is first blocked by 3'-deoxyadenosine (3'-deoxy-A). Specific cleavage of Ino sites by hEndoV protein produces new terminal 3'OH, which can be identified by sequencing analysis, and therefore offers the site-specific detection of Ino in RNA. The principle of hEndoV-seq is straightforward and the analytical procedure is simple. No chemical reaction is involved in the sequencing library preparation. The whole procedure in hEndoV-seq is carried out under mild conditions and RNA is not prone to degradation. Taken together, the proposed hEndoV-seq method is capable of site-specific identification of A-to-Ino editing in RNA, which provides a valuable tool for elucidating the functions of A-to-Ino editing in RNA.
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Affiliation(s)
- Juan-Juan Chen
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xue-Jiao You
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China
| | - Lin Li
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Neng-Bin Xie
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Public Health, Wuhan University, Wuhan 430071, China.,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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22
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Klumpers MJ, Witte WD, Gattuso G, Schiavello E, Terenziani M, Massimino M, Gidding CEM, Vermeulen SH, Driessen CM, van Herpen CM, van Meerten E, Guchelaar HJ, Coenen MJH, te Loo DMWM. Genome-Wide Analyses of Nephrotoxicity in Platinum-Treated Cancer Patients Identify Association with Genetic Variant in RBMS3 and Acute Kidney Injury. J Pers Med 2022; 12:jpm12060892. [PMID: 35743677 PMCID: PMC9224783 DOI: 10.3390/jpm12060892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 02/06/2023] Open
Abstract
Nephrotoxicity is a common and dose-limiting side effect of platinum compounds, which often manifests as acute kidney injury or hypomagnesemia. This study aimed to investigate the genetic risk loci for platinum-induced nephrotoxicity. Platinum-treated brain tumor and head–neck tumor patients were genotyped with genome-wide coverage. The data regarding the patient and treatment characteristics and the laboratory results reflecting the nephrotoxicity during and after the platinum treatment were collected from the medical records. Linear and logistic regression analyses were performed to investigate the associations between the genetic variants and the acute kidney injury and hypomagnesemia phenotypes. A cohort of 195 platinum-treated patients was included, and 9,799,032 DNA variants passed the quality control. An association was identified between RBMS3 rs10663797 and acute kidney injury (coefficient −0.10 (95% confidence interval −0.13–−0.06), p-value 2.72 × 10−8). The patients who carried an AC deletion at this locus had statistically significantly lower glomerular filtration rates after platinum treatment. Previously reported associations, such as BACH2 rs4388268, could not be replicated in this study’s cohort. No statistically significant associations were identified for platinum-induced hypomagnesemia. The genetic variant in RBMS3 was not previously linked to nephrotoxicity or related traits. The validation of this study’s results in independent cohorts is needed to confirm this novel association.
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Affiliation(s)
- Marije J. Klumpers
- Department of Pediatrics, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands;
| | - Ward De Witte
- Department of Human Genetics, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands; (W.D.W.); (M.J.H.C.)
| | - Giovanna Gattuso
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy; (G.G.); (E.S.); (M.T.); (M.M.)
| | - Elisabetta Schiavello
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy; (G.G.); (E.S.); (M.T.); (M.M.)
| | - Monica Terenziani
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy; (G.G.); (E.S.); (M.T.); (M.M.)
| | - Maura Massimino
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Giacomo Venezian, 1, 20133 Milan, Italy; (G.G.); (E.S.); (M.T.); (M.M.)
| | - Corrie E. M. Gidding
- Princess Maxima Center for Pediatric Oncology, Postbox 113, 3720 AC Bilthoven, The Netherlands;
| | - Sita H. Vermeulen
- Department for Health Evidence, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands;
| | - Chantal M. Driessen
- Department of Medical Oncology, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands; (C.M.D.); (C.M.v.H.)
| | - Carla M. van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands; (C.M.D.); (C.M.v.H.)
| | - Esther van Meerten
- Department of Medical Oncology, Erasmus MC Cancer Institute, Postbox 2040, 3000 CA Rotterdam, The Netherlands;
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, Postbox 9600, 2300 RC Leiden, The Netherlands;
| | - Marieke J. H. Coenen
- Department of Human Genetics, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands; (W.D.W.); (M.J.H.C.)
| | - D. Maroeska W. M. te Loo
- Department of Pediatrics, Radboud University Medical Center, Postbox 9101, 6500 HB Nijmegen, The Netherlands;
- Correspondence: ; Tel.: +31-24-361-44-15
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Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. NATURE REVIEWS. METHODS PRIMERS 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
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24
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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25
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“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. Life (Basel) 2022; 12:life12020252. [PMID: 35207539 PMCID: PMC8879553 DOI: 10.3390/life12020252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 01/25/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022] Open
Abstract
The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.
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26
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Endo M, Kim JI, Shioi NA, Iwai S, Kuraoka I. Arabidopsis thaliana endonuclease V is a ribonuclease specific for inosine-containing single-stranded RNA. Open Biol 2021; 11:210148. [PMID: 34665969 PMCID: PMC8526164 DOI: 10.1098/rsob.210148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Endonuclease V is highly conserved, both structurally and functionally, from bacteria to humans, and it cleaves the deoxyinosine-containing double-stranded DNA in Escherichia coli, whereas in Homo sapiens it catalyses the inosine-containing single-stranded RNA. Thus, deoxyinosine and inosine are unexpectedly produced by the deamination reactions of adenine in DNA and RNA, respectively. Moreover, adenosine-to-inosine (A-to-I) RNA editing is carried out by adenosine deaminase acting on dsRNA (ADARs). We focused on Arabidopsis thaliana endonuclease V (AtEndoV) activity exhibiting variations in DNA or RNA substrate specificities. Since no ADAR was observed for A-to-I editing in A. thaliana, the possibility of inosine generation by A-to-I editing can be ruled out. Purified AtEndoV protein cleaved the second and third phosphodiester bonds, 3' to inosine in single-strand RNA, at a low reaction temperature of 20-25°C, whereas the AtEndoV (Y100A) protein bearing a mutation in substrate recognition sites did not cleave these bonds. Furthermore, AtEndoV, similar to human EndoV, prefers RNA substrates over DNA substrates, and it could not cleave the inosine-containing double-stranded RNA. Thus, we propose the possibility that AtEndoV functions as an RNA substrate containing inosine induced by RNA damage, and not by A-to-I RNA editing in vivo.
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Affiliation(s)
- Megumi Endo
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Jung In Kim
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Narumi Aoki Shioi
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
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27
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Off-target effects of base editors: what we know and how we can reduce it. Curr Genet 2021; 68:39-48. [PMID: 34515826 DOI: 10.1007/s00294-021-01211-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
The recently discovered CRISPR-Cas9 modification, base editors (BEs), is considered as one of the most promising tools for correcting disease-causing mutations in humans, since it allows point substitutions to be edited without generating double-stranded DNA breaks, and, therefore, with a significant decrease in non-specific activity. Until recently, this method was considered the safest, but at the same time, it is quite effective. However, recent studies of non-specific activity of BEs revealed that some of them lead to the formation of a huge number of off-targets in both DNA and RNA, occurring due to the nature of the Cas9-fused proteins used. In this review article, we have considered and combined data from numerous studies about the most commonly used and more described in detail APOBEC-based BEs and Target-AID version of CBE, as well as ABE7 and ABE8 with their basic modifications into TadA to improve BEs' specificity. In our opinion, modern advances in molecular genetics make it possible to dramatically reduce the off-target activity of base editors due to introducing mutations into the domains of deaminases or inhibition of Cas9 by anti-CRISPR proteins, which returns BEs to the leading position in genome editing technologies.
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28
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Knutson SD, Heemstra JM. Protein-based molecular recognition tools for detecting and profiling RNA modifications. Curr Opin Struct Biol 2021; 69:1-10. [PMID: 33445115 PMCID: PMC8272725 DOI: 10.1016/j.sbi.2020.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/18/2022]
Abstract
RNA undergoes extensive biochemical modification following transcription. In addition to RNA splicing, transcripts are processed by a suite of enzymes that alter the chemical structure of different nucleobases. Broadly termed as 'RNA editing,' these modifications impart significant functional changes to translation, localization, and stability of individual transcripts within the cell. These changes are dynamic and required for a number of critical cellular processes, and dysregulation of these pathways is responsible for several disease states. Accurately detecting, measuring, and mapping different RNA modifications across the transcriptome is vital to understanding their broader functions as well as leveraging these events as diagnostic biomarkers. Here, we review recent advances in profiling several types of RNA modifications, with particular emphasis on adenosine-to-inosine (A-to-I) and N6-methyladenosine (m6A) RNA editing. We especially highlight approaches that utilize proteins to detect or enrich modified RNA transcripts before sequencing, and we summarize recent insights yielded from these techniques.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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29
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Knutson SD, Arthur RA, Johnston HR, Heemstra JM. Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021; 60:17009-17017. [PMID: 33979483 PMCID: PMC8562906 DOI: 10.1002/anie.202102762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing is a conserved eukaryotic RNA modification that contributes to development, immune response, and overall cellular function. Here, we utilize Endonuclease V (EndoV), which binds specifically to inosine in RNA, to develop an EndoV-linked immunosorbency assay (EndoVLISA) as a rapid, plate-based chemiluminescent method for measuring global A-to-I editing signatures in cellular RNA. We first optimize and validate our assay with chemically synthesized oligonucleotides. We then demonstrate rapid detection of inosine content in treated cell lines, demonstrating equivalent performance against current standard RNA-seq approaches. Lastly, we deploy our EndoVLISA for profiling differential A-to-I RNA editing signatures in normal and diseased human tissue, illustrating the utility of our platform as a diagnostic bioassay. Together, the EndoVLISA method is cost-effective, straightforward, and utilizes common laboratory equipment, offering a highly accessible new approach for studying A-to-I editing. Moreover, the multi-well plate format makes this the first assay amenable for direct high-throughput quantification of A-to-I editing for applications in disease detection and drug development.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
| | - Robert A Arthur
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
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30
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Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102762] [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]
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31
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Bartee D, Thalalla Gamage S, Link CN, Meier JL. Arrow pushing in RNA modification sequencing. Chem Soc Rev 2021; 50:9482-9502. [PMID: 34259263 DOI: 10.1039/d1cs00214g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methods to accurately determine the location and abundance of RNA modifications are critical to understanding their functional role. In this review, we describe recent efforts in which chemical reactivity and next-generation sequencing have been integrated to detect modified nucleotides in RNA. For eleven exemplary modifications, we detail chemical, enzymatic, and metabolic labeling protocols that can be used to differentiate them from canonical nucleobases. By emphasizing the molecular rationale underlying these detection methods, our survey highlights new opportunities for chemistry to define the role of RNA modifications in disease.
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Affiliation(s)
- David Bartee
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Courtney N Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 538 Chandler St, Frederick, MD 21702, USA.
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32
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Kong XY, Huse C, Yang K, Øgaard J, Berges N, Vik ES, Nawaz MS, Quiles-Jiménez A, Abbas A, Gregersen I, Holm S, Bjerkli V, Rashidi A, Fladeby C, Suganthan R, Sagen EL, Skjelland M, Lång A, Bøe SO, Bjørås M, Aukrust P, Alseth I, Halvorsen B, Dahl TB. Endonuclease V Regulates Atherosclerosis Through C-C Motif Chemokine Ligand 2-Mediated Monocyte Infiltration. J Am Heart Assoc 2021; 10:e020656. [PMID: 34259011 PMCID: PMC8483470 DOI: 10.1161/jaha.120.020656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background In cardiovascular diseases, atherosclerotic disorder are the most frequent and important with respect to morbidity and mortality. Inflammation mediated by immune cells is central in all parts of the atherosclerotic progress, and further understanding of the underlying mechanisms is needed. Growing evidence suggests that deamination of adenosine‐to‐inosine in RNA is crucial for a correct immune response; nevertheless, the role of adenosine‐to‐inosine RNA editing in atherogenesis has barely been studied. Several proteins have affinity for inosines in RNA, one being ENDOV (endonuclease V), which binds and cleaves RNA at inosines. Data on ENDOV in atherosclerosis are lacking. Methods and Results Quantitative polymerase chain reaction on ENDOV mRNA showed an increased level in human carotid atherosclerotic plaques compared with control veins. Inosine‐ribonuclease activity as measured by an enzyme activity assay is detected in immune cells relevant for the atherosclerotic process. Abolishing EndoV in atherogenic apolipoprotein E‐deficient (ApoE−/−) mice reduces the atherosclerotic plaque burden, both in size and lipid content. In addition, in a brain stroke model, mice without ENDOV suffer less damage than control mice. Finally, lack of EndoV reduces the recruitment of monocytes to atherosclerotic lesions in atherogenic ApoE−/− mice. Conclusions ENDOV is upregulated in human atherosclerotic lesions, and data from mice suggest that ENDOV promotes atherogenesis by enhancing the monocyte recruitment into the atherosclerotic lesion, potentially by increasing the effect of CCL2 activation on these cells.
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Affiliation(s)
- Xiang Yi Kong
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Camilla Huse
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway
| | - Kuan Yang
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Jonas Øgaard
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Natalia Berges
- Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway.,Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Erik Sebastian Vik
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Meh Sameen Nawaz
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Ana Quiles-Jiménez
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway
| | | | - Ida Gregersen
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway
| | - Sverre Holm
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Vigdis Bjerkli
- Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway
| | - Azita Rashidi
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Cathrine Fladeby
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Rajikala Suganthan
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Ellen Lund Sagen
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Mona Skjelland
- Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway.,Department of Neurology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Anna Lång
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Stig Ove Bøe
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Magnar Bjørås
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway.,Department of Clinical and Molecular Medicine Norwegian University of Science and Technology Trondheim Norway
| | - Pål Aukrust
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway.,Section of Clinical Immunology and Infectious Diseases Oslo University Hospital, Rikshospitalet Oslo Norway.,K.G. Jebsen, The Faculty of Health Sciences The Arctic University of Tromsø Tromsø Norway
| | - Ingrun Alseth
- Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
| | - Bente Halvorsen
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Institute of Clinical Medicine Faculty of Medicine University of Oslo Norway
| | - Tuva Børresdatter Dahl
- Research Institute for Internal Medicine Oslo University Hospital, Rikshospitalet Oslo Norway.,Department of Microbiology Oslo University Hospital, Rikshospitalet Oslo Norway
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33
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Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
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34
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Sikorski V, Karjalainen P, Blokhina D, Oksaharju K, Khan J, Katayama S, Rajala H, Suihko S, Tuohinen S, Teittinen K, Nummi A, Nykänen A, Eskin A, Stark C, Biancari F, Kiss J, Simpanen J, Ropponen J, Lemström K, Savinainen K, Lalowski M, Kaarne M, Jormalainen M, Elomaa O, Koivisto P, Raivio P, Bäckström P, Dahlbacka S, Syrjälä S, Vainikka T, Vähäsilta T, Tuncbag N, Karelson M, Mervaala E, Juvonen T, Laine M, Laurikka J, Vento A, Kankuri E. Epitranscriptomics of Ischemic Heart Disease-The IHD-EPITRAN Study Design and Objectives. Int J Mol Sci 2021; 22:6630. [PMID: 34205699 PMCID: PMC8235045 DOI: 10.3390/ijms22126630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022] Open
Abstract
Epitranscriptomic modifications in RNA can dramatically alter the way our genetic code is deciphered. Cells utilize these modifications not only to maintain physiological processes, but also to respond to extracellular cues and various stressors. Most often, adenosine residues in RNA are targeted, and result in modifications including methylation and deamination. Such modified residues as N-6-methyl-adenosine (m6A) and inosine, respectively, have been associated with cardiovascular diseases, and contribute to disease pathologies. The Ischemic Heart Disease Epitranscriptomics and Biomarkers (IHD-EPITRAN) study aims to provide a more comprehensive understanding to their nature and role in cardiovascular pathology. The study hypothesis is that pathological features of IHD are mirrored in the blood epitranscriptome. The IHD-EPITRAN study focuses on m6A and A-to-I modifications of RNA. Patients are recruited from four cohorts: (I) patients with IHD and myocardial infarction undergoing urgent revascularization; (II) patients with stable IHD undergoing coronary artery bypass grafting; (III) controls without coronary obstructions undergoing valve replacement due to aortic stenosis and (IV) controls with healthy coronaries verified by computed tomography. The abundance and distribution of m6A and A-to-I modifications in blood RNA are charted by quantitative and qualitative methods. Selected other modified nucleosides as well as IHD candidate protein and metabolic biomarkers are measured for reference. The results of the IHD-EPITRAN study can be expected to enable identification of epitranscriptomic IHD biomarker candidates and potential drug targets.
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Affiliation(s)
- Vilbert Sikorski
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (V.S.); (D.B.); (E.M.)
| | - Pasi Karjalainen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Daria Blokhina
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (V.S.); (D.B.); (E.M.)
| | - Kati Oksaharju
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Jahangir Khan
- Tampere Heart Hospital, Tampere University Hospital, 33520 Tampere, Finland; (J.K.); (J.L.)
| | | | - Helena Rajala
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Satu Suihko
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Suvi Tuohinen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Kari Teittinen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Annu Nummi
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Antti Nykänen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Arda Eskin
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey;
| | - Christoffer Stark
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Fausto Biancari
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
- Heart Center, Turku University Hospital and Department of Surgery, University of Turku, 20521 Turku, Finland
- Research Unit of Surgery, Anesthesiology and Critical Care, University of Oulu, 90014 Oulu, Finland
| | - Jan Kiss
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Jarmo Simpanen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Jussi Ropponen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Karl Lemström
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Kimmo Savinainen
- Clinical Biobank Tampere, Tampere University Hospital, 33520 Tampere, Finland;
| | - Maciej Lalowski
- Helsinki Institute of Life Science (HiLIFE), Meilahti Clinical Proteomics Core Facility, Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland;
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Department of Biomedical Proteomics, 61-704 Poznan, Poland
| | - Markku Kaarne
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Mikko Jormalainen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Outi Elomaa
- Folkhälsan Research Center, 00250 Helsinki, Finland; (S.K.); (O.E.)
| | - Pertti Koivisto
- Chemistry Unit, Finnish Food Authority, 00790 Helsinki, Finland;
| | - Peter Raivio
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Pia Bäckström
- Helsinki Biobank, Hospital District of Helsinki and Uusimaa, 00029 Helsinki, Finland;
| | - Sebastian Dahlbacka
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Simo Syrjälä
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Tiina Vainikka
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Tommi Vähäsilta
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Nurcan Tuncbag
- Department of Chemical and Biological Engineering, College of Engineering, Koç University, 34450 Istanbul, Turkey;
- School of Medicine, Koç University, 34450 Istanbul, Turkey
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia;
| | - Eero Mervaala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (V.S.); (D.B.); (E.M.)
| | - Tatu Juvonen
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
- Research Unit of Surgery, Anesthesiology and Critical Care, University of Oulu, 90014 Oulu, Finland
| | - Mika Laine
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Jari Laurikka
- Tampere Heart Hospital, Tampere University Hospital, 33520 Tampere, Finland; (J.K.); (J.L.)
| | - Antti Vento
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland; (P.K.); (K.O.); (H.R.); (S.S.); (S.T.); (K.T.); (A.N.); (A.N.); (C.S.); (F.B.); (J.K.); (J.S.); (J.R.); (K.L.); (M.K.); (M.J.); (P.R.); (S.D.); (S.S.); (T.V.); (T.V.); (T.J.); (M.L.); (A.V.)
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland; (V.S.); (D.B.); (E.M.)
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Knutson SD, Heemstra JM. EndoVIPER-seq for Improved Detection of A-to-I Editing Sites in Cellular RNA. ACTA ACUST UNITED AC 2021; 12:e82. [PMID: 32469473 DOI: 10.1002/cpch.82] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Adenosine to-inosine (A-to-I) RNA editing is a conserved post-transcriptional modification that is critical for a variety of cellular processes. A-to-I editing is widespread in nearly all types of RNA, directly imparting significant global changes in cellular function and behavior. Dysfunctional RNA editing is also implicated in a number of diseases, and A-to-I editing activity is rapidly becoming an important biomarker for early detection of cancer, immune disorders, and neurodegeneration. While millions of sites have been identified, the biological function of the majority of these sites is unknown, and the regulatory mechanisms for controlling editing activity at individual sites is not well understood. Robust detection and mapping of A-to-I editing activity throughout the transcriptome is vital for understanding these properties and how editing affects cellular behavior. However, accurately identifying A-to-I editing sites is challenging because of inherent sampling errors present in RNA-seq. We recently developed Endonuclease V immunoprecipitation enrichment sequencing (EndoVIPER-seq) to directly address this challenge by enrichment of A-to-I edited RNAs prior to sequencing. This protocol outlines how to process cellular RNA, enrich for A-to-I edited transcripts with EndoVIPER pulldown, and prepare libraries suitable for generating RNA-seq data. © 2020 Wiley Periodicals LLC. Basic Protocol 1: mRNA fragmentation and glyoxalation Basic Protocol 2: EndoVIPER pulldown Basic Protocol 3: RNA-seq library preparation and data analysis.
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Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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Torres AG, Martí E. Toward an Understanding of Extracellular tRNA Biology. Front Mol Biosci 2021; 8:662620. [PMID: 33937338 PMCID: PMC8082309 DOI: 10.3389/fmolb.2021.662620] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Extracellular RNAs (exRNAs) including abundant full length tRNAs and tRNA fragments (tRFs) have recently garnered attention as a promising source of biomarkers and a novel mediator in cell-to-cell communication in eukaryotes. Depending on the physiological state of cells, tRNAs/tRFs are released to the extracellular space either contained in extracellular vesicles (EVs) or free, through a mechanism that is largely unknown. In this perspective article, we propose that extracellular tRNAs (ex-tRNAs) and/or extracellular tRFs (ex-tRFs) are relevant paracrine signaling molecules whose activity depends on the mechanisms of release by source cells and capture by recipient cells. We speculate on how ex-tRNA/ex-tRFs orchestrate the effects in target cells, depending on the type of sequence and the mechanisms of uptake. We further propose that tRNA modifications may be playing important roles in ex-tRNA biology.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Martí
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Epidemiología y Salud Pública, Madrid, Spain
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Marceca GP, Tomasello L, Distefano R, Acunzo M, Croce CM, Nigita G. Detecting and Characterizing A-To-I microRNA Editing in Cancer. Cancers (Basel) 2021; 13:1699. [PMID: 33916692 PMCID: PMC8038323 DOI: 10.3390/cancers13071699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 12/25/2022] Open
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer.
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Affiliation(s)
- Gioacchino P. Marceca
- Department of Clinical and Experimental Medicine, University of Catania, 95125 Catania, Italy
| | - Luisa Tomasello
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Rosario Distefano
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA; (L.T.); (R.D.); (C.M.C.)
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Erdmann EA, Mahapatra A, Mukherjee P, Yang B, Hundley HA. To protect and modify double-stranded RNA - the critical roles of ADARs in development, immunity and oncogenesis. Crit Rev Biochem Mol Biol 2020; 56:54-87. [PMID: 33356612 DOI: 10.1080/10409238.2020.1856768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenosine deaminases that act on RNA (ADARs) are present in all animals and function to both bind double-stranded RNA (dsRNA) and catalyze the deamination of adenosine (A) to inosine (I). As inosine is a biological mimic of guanosine, deamination by ADARs changes the genetic information in the RNA sequence and is commonly referred to as RNA editing. Millions of A-to-I editing events have been reported for metazoan transcriptomes, indicating that RNA editing is a widespread mechanism used to generate molecular and phenotypic diversity. Loss of ADARs results in lethality in mice and behavioral phenotypes in worm and fly model systems. Furthermore, alterations in RNA editing occur in over 35 human pathologies, including several neurological disorders, metabolic diseases, and cancers. In this review, a basic introduction to ADAR structure and target recognition will be provided before summarizing how ADARs affect the fate of cellular RNAs and how researchers are using this knowledge to engineer ADARs for personalized medicine. In addition, we will highlight the important roles of ADARs and RNA editing in innate immunity and cancer biology.
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Affiliation(s)
- Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
| | - Boyoon Yang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, IN, USA
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Álvarez B, Mencía M, de Lorenzo V, Fernández LÁ. In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9. Nat Commun 2020; 11:6436. [PMID: 33353963 PMCID: PMC7755918 DOI: 10.1038/s41467-020-20230-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
In vivo mutagenesis systems accelerate directed protein evolution but often show restricted capabilities and deleterious off-site mutations on cells. To overcome these limitations, here we report an in vivo platform to diversify specific DNA segments based on protein fusions between various base deaminases (BD) and the T7 RNA polymerase (T7RNAP) that recognizes a cognate promoter oriented towards the target sequence. Transcriptional elongation of these fusions generates transitions C to T or A to G on both DNA strands and in long DNA segments. To delimit the boundaries of the diversified DNA, the catalytically dead Cas9 (dCas9) is tethered with custom-designed crRNAs as a "roadblock" for BD-T7RNAP elongation. Using this T7-targeted dCas9-limited in vivo mutagenesis (T7-DIVA) system, rapid molecular evolution of the antibiotic resistance gene TEM-1 is achieved. While the efficiency is demonstrated in E. coli, the system can be adapted to a variety of bacterial and eukaryotic hosts.
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Affiliation(s)
- Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain
| | - Mario Mencía
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), Nicolas Cabrera 1, Campus UAM Cantoblanco, 28049, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049, Madrid, Spain.
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Liu X, Chen R, Sun Y, Chen R, Zhou J, Tian Q, Tao X, Zhang Z, Luo GZ, Xie W. Crystal structure of the yeast heterodimeric ADAT2/3 deaminase. BMC Biol 2020; 18:189. [PMID: 33272269 PMCID: PMC7713142 DOI: 10.1186/s12915-020-00920-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear. RESULTS Here, we report a 2.8-Å crystal structure of Saccharomyces cerevisiae ADAT2/3 (ScADAT2/3), revealing its heterodimeric assembly and substrate recognition mechanism. While each subunit clearly contains a domain resembling their prokaryotic homolog TadA, suggesting an evolutionary gene duplication event, they also display accessory domains for additional structural or functional purposes. The N-lobe of ScADAT3 exhibits a positively charged region with a potential role in the recognition and binding of tRNA, supported by our biochemical analysis. Interestingly, ScADAT3 employs its C-terminus to block tRNA's entry into its pseudo-active site and thus inactivates itself for deamination despite the preservation of a zinc-binding site, a mechanism possibly shared only among yeasts. CONCLUSIONS Combining the structural with biochemical, bioinformatic, and in vivo functional studies, we propose a stepwise model for the pathway of deamination by ADAT2/3. Our work provides insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis.
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Affiliation(s)
- Xiwen Liu
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China ,grid.12981.330000 0001 2360 039XDepartment of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Erheng Rd., Guangzhou, 510655 Guangdong People’s Republic of China
| | - Ruoyu Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Yujie Sun
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Ran Chen
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Jie Zhou
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Qingnan Tian
- grid.207374.50000 0001 2189 3846School of Life Sciences, Zhengzhou University, 100 Kexue Rd., Zhengzhou, 450001 Henan People’s Republic of China
| | - Xuan Tao
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong China
| | - Zhang Zhang
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Guan-zheng Luo
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
| | - Wei Xie
- grid.12981.330000 0001 2360 039XMOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 W. Xingang Rd., Guangzhou, 510275 Guangdong People’s Republic of China
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42
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Majumdar C, McKibbin PL, Krajewski AE, Manlove AH, Lee JK, David SS. Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY. J Am Chem Soc 2020; 142:20340-20350. [PMID: 33202125 DOI: 10.1021/jacs.0c06767] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediatedadenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogues of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analogue substrates with their experimental and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogues that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogues paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analogue duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogues to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analogue SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.
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Affiliation(s)
- Chandrima Majumdar
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Paige L McKibbin
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Allison E Krajewski
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Amelia H Manlove
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Jeehiun K Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08854, United States
| | - Sheila S David
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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43
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Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA. DNA capture by a CRISPR-Cas9-guided adenine base editor. Science 2020; 369:566-571. [PMID: 32732424 DOI: 10.1126/science.abb1390] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/27/2020] [Indexed: 12/22/2022]
Abstract
CRISPR-Cas-guided base editors convert A•T to G•C, or C•G to T•A, in cellular DNA for precision genome editing. To understand the molecular basis for DNA adenosine deamination by adenine base editors (ABEs), we determined a 3.2-angstrom resolution cryo-electron microscopy structure of ABE8e in a substrate-bound state in which the deaminase domain engages DNA exposed within the CRISPR-Cas9 R-loop complex. Kinetic and structural data suggest that ABE8e catalyzes DNA deamination up to ~1100-fold faster than earlier ABEs because of mutations that stabilize DNA substrates in a constrained, transfer RNA-like conformation. Furthermore, ABE8e's accelerated DNA deamination suggests a previously unobserved transient DNA melting that may occur during double-stranded DNA surveillance by CRISPR-Cas9. These results explain ABE8e-mediated base-editing outcomes and inform the future design of base editors.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Cody M Palumbo
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kevin T Zhao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, CA 95616, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.,Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
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44
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Kong XY, Vik ES, Nawaz MS, Berges N, Dahl TB, Vågbø C, Suganthan R, Segers F, Holm S, Quiles-Jiménez A, Gregersen I, Fladeby C, Aukrust P, Bjørås M, Klungland A, Halvorsen B, Alseth I. Deletion of Endonuclease V suppresses chemically induced hepatocellular carcinoma. Nucleic Acids Res 2020; 48:4463-4479. [PMID: 32083667 PMCID: PMC7192598 DOI: 10.1093/nar/gkaa115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/08/2020] [Accepted: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Endonuclease V (EndoV) is a conserved inosine-specific ribonuclease with unknown biological function. Here, we present the first mouse model lacking EndoV, which is viable without visible abnormalities. We show that endogenous murine EndoV cleaves inosine-containing RNA in vitro, nevertheless a series of experiments fails to link an in vivo function to processing of such transcripts. As inosine levels and adenosine-to-inosine editing often are dysregulated in hepatocellular carcinoma (HCC), we chemically induced HCC in mice. All mice developed liver cancer, however, EndoV−/− tumors were significantly fewer and smaller than wild type tumors. Opposed to human HCC, adenosine deaminase mRNA expression and site-specific editing were unaltered in our model. Loss of EndoV did not affect editing levels in liver tumors, however mRNA expression of a selection of cancer related genes were reduced. Inosines are also found in certain tRNAs and tRNAs are cleaved during stress to produce signaling entities. tRNA fragmentation was dysregulated in EndoV−/− livers and apparently, inosine-independent. We speculate that the inosine-ribonuclease activity of EndoV is disabled in vivo, but RNA binding allowed to promote stabilization of transcripts or recruitment of proteins to fine-tune gene expression. The EndoV−/− tumor suppressive phenotype calls for related studies in human HCC.
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Affiliation(s)
- Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Erik Sebastian Vik
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Meh Sameen Nawaz
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Natalia Berges
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Tuva Børresdatter Dahl
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Cathrine Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Filip Segers
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway
| | - Cathrine Fladeby
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, NO-0424 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University ofOslo, NO-0317 Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital HF, Rikshospitalet, NO-0424 Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, NO-0317 Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, NO-0424 Oslo, Norway
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45
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Knutson SD, Arthur RA, Johnston HR, Heemstra JM. Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V. J Am Chem Soc 2020; 142:5241-5251. [PMID: 32109061 DOI: 10.1021/jacs.9b13406] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Creating accurate maps of A-to-I RNA editing activity is vital to improving our understanding of the biological role of this process and harnessing it as a signal for disease diagnosis. Current RNA sequencing techniques are susceptible to random sampling limitations due to the complexity of the transcriptome and require large amounts of RNA material, specialized instrumentation, and high read counts to accurately interrogate A-to-I editing sites. To address these challenges, we show that Escherichia coli Endonuclease V (eEndoV), an inosine-cleaving enzyme, can be repurposed to bind and isolate A-to-I edited transcripts from cellular RNA. While Mg2+ enables eEndoV to catalyze RNA cleavage, we show that similar levels of Ca2+ instead promote binding of inosine without cleavage and thus enable high affinity capture of inosine in RNA. We leverage this capability to demonstrate EndoVIPER-seq (Endonuclease V inosine precipitation enrichment sequencing) as a facile and effective method to enrich A-to-I edited transcripts prior to RNA-seq, producing significant increases in the coverage and detection of identified editing sites. We envision the use of this approach as a straightforward and cost-effective strategy to improve the epitranscriptomic informational density of RNA samples, facilitating a deeper understanding of the functional roles of A-to-I editing.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Robert A Arthur
- Emory Integrated Computational Core, Emory Integrated Core Facilities, Emory University, Atlanta, Georgia 30322, United States
| | - H Richard Johnston
- Department of Human Genetics, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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46
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Berges N, Nawaz MS, Børresdatter Dahl T, Hagen L, Bjørås M, Laerdahl JK, Alseth I. Complex alternative splicing of human Endonuclease V mRNA, but evidence for only a single protein isoform. PLoS One 2019; 14:e0225081. [PMID: 31703097 PMCID: PMC6839837 DOI: 10.1371/journal.pone.0225081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/27/2019] [Indexed: 12/22/2022] Open
Abstract
Endonuclease V (ENDOV) is a ribonuclease with affinity for inosine which is the deamination product of adenosine. The genomes of most organisms, including human, encode ENDOV homologs, yet knowledge about in vivo functions and gene regulation is sparse. To contribute in this field, we analyzed mRNA and protein expression of human ENDOV (hENDOV). Analyses of public sequence databases revealed numerous hENDOV transcript variants suggesting extensive alternative splicing. Many of the transcripts lacked one or more exons corresponding to conserved regions of the ENDOV core domain, suggesting that these transcripts do not encode for active proteins. Three complete transcripts were found with open reading frames encoding 282, 308 and 309 amino acids, respectively. Recombinant hENDOV 308 and hENDOV 309 share the same cleavage activity as hENDOV 282 which is the variant that has been used in previous studies of hENDOV. However, hENDOV 309 binds inosine-containing RNA with stronger affinity than the other isoforms. Overexpressed GFP-fused isoforms were found in cytoplasm, nucleoli and arsenite induced stress granules in human cells as previously reported for hENDOV 282. RT-qPCR analysis of the 3’-termini showed that hENDOV 308 and hENDOV 309 transcripts are more abundant than hENDOV 282 transcripts in immortalized cell lines, but not in primary cells, suggesting that cells regulate hENDOV mRNA expression. In spite of the presence of all three full-length transcripts, mass spectrometry analyses identified peptides corresponding to the hENDOV 309 isoform only. This result suggests that further studies of human ENDOV should rather encompass the hENDOV 309 isoform.
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Affiliation(s)
- Natalia Berges
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Meh Sameen Nawaz
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Tuva Børresdatter Dahl
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology and Central Norway Regional Health Authority, Trondheim, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jon K. Laerdahl
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- * E-mail:
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47
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Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase. Mol Cell 2019; 76:44-56.e3. [PMID: 31444105 DOI: 10.1016/j.molcel.2019.06.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/16/2019] [Accepted: 06/27/2019] [Indexed: 02/01/2023]
Abstract
Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.
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48
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Handley MT, Reddy K, Wills J, Rosser E, Kamath A, Halachev M, Falkous G, Williams D, Cox P, Meynert A, Raymond ES, Morrison H, Brown S, Allan E, Aligianis I, Jackson AP, Ramsahoye BH, von Kriegsheim A, Taylor RW, Finch AJ, FitzPatrick DR. ITPase deficiency causes a Martsolf-like syndrome with a lethal infantile dilated cardiomyopathy. PLoS Genet 2019; 15:e1007605. [PMID: 30856165 PMCID: PMC6428344 DOI: 10.1371/journal.pgen.1007605] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 03/21/2019] [Accepted: 12/27/2018] [Indexed: 12/30/2022] Open
Abstract
Typical Martsolf syndrome is characterized by congenital cataracts, postnatal microcephaly, developmental delay, hypotonia, short stature and biallelic hypomorphic mutations in either RAB3GAP1 or RAB3GAP2. Genetic analysis of 85 unrelated "mutation negative" probands with Martsolf or Martsolf-like syndromes identified two individuals with different homozygous null mutations in ITPA, the gene encoding inosine triphosphate pyrophosphatase (ITPase). Both probands were from multiplex families with a consistent, lethal and highly distinctive disorder; a Martsolf-like syndrome with infantile-onset dilated cardiomyopathy. Severe ITPase-deficiency has been previously reported with infantile epileptic encephalopathy (MIM 616647). ITPase acts to prevent incorporation of inosine bases (rI/dI) into RNA and DNA. In Itpa-null cells dI was undetectable in genomic DNA. dI could be identified at a low level in mtDNA without detectable mitochondrial genome instability, mtDNA depletion or biochemical dysfunction of the mitochondria. rI accumulation was detectable in proband-derived lymphoblastoid RNA. In Itpa-null mouse embryos rI was detectable in the brain and kidney with the highest level seen in the embryonic heart (rI at 1 in 385 bases). Transcriptome and proteome analysis in mutant cells revealed no major differences with controls. The rate of transcription and the total amount of cellular RNA also appeared normal. rI accumulation in RNA-and by implication rI production-correlates with the severity of organ dysfunction in ITPase deficiency but the basis of the cellulopathy remains cryptic. While we cannot exclude cumulative minor effects, there are no major anomalies in the production, processing, stability and/or translation of mRNA.
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Affiliation(s)
- Mark T. Handley
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Section of Genetics, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kigndom
| | - Kaalak Reddy
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- University of Florida College of Medicine, Center for NeuroGenetics, Gainesville, United States of America
| | - Jimi Wills
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond St Hospital, London, United Kingdom
| | - Archith Kamath
- Medical School, University of Oxford, John Radcliffe Hospital Oxford United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Denise Williams
- Department of Clinical Genetics, Birmingham Women's and Children's NHSFT, Birmingham, United Kingdom
| | - Phillip Cox
- Department of Histopathology, Birmingham Women's and Children's NHSFT, Birmingham United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor S. Raymond
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Harris Morrison
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Brown
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Emma Allan
- CBS-IGMM Transgenic Unit, University of Edinburgh, Edinburgh, United Kingdom
| | - Irene Aligianis
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P. Jackson
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernard H. Ramsahoye
- Centre for Genetic and Experimental Medicine, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex von Kriegsheim
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew J. Finch
- Edinburgh Cancer Research Centre, MRC Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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49
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Kung CP, Maggi LB, Weber JD. The Role of RNA Editing in Cancer Development and Metabolic Disorders. Front Endocrinol (Lausanne) 2018; 9:762. [PMID: 30619092 PMCID: PMC6305585 DOI: 10.3389/fendo.2018.00762] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.
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Affiliation(s)
- Che-Pei Kung
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Leonard B. Maggi
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jason D. Weber
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
- Siteman Cancer Center, Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, United States
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50
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Torres AG, Wulff TF, Rodríguez-Escribà M, Camacho N, Ribas de Pouplana L. Detection of Inosine on Transfer RNAs without a Reverse Transcription Reaction. Biochemistry 2018; 57:5641-5647. [PMID: 30199619 DOI: 10.1021/acs.biochem.8b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Inosine at the "wobble" position (I34) is one of the few essential posttranscriptional modifications in tRNAs (tRNAs). It results from the deamination of adenosine and occurs in bacteria on tRNAArgACG and in eukarya on six or seven additional tRNA substrates. Because inosine is structurally a guanosine analogue, reverse transcriptases recognize it as a guanosine. Most methods used to examine the presence of inosine rely on this phenomenon and detect the modified base as a change in the DNA sequence that results from the reverse transcription reaction. These methods, however, cannot always be applied to tRNAs because reverse transcription can be compromised by the presence of other posttranscriptional modifications. Here we present SL-ID (splinted ligation-based inosine detection), a reverse transcription-free method for detecting inosine based on an I34-dependent specific cleavage of tRNAs by endonuclease V, followed by a splinted ligation and polyacrylamide gel electrophoresis analysis. We show that the method can detect I34 on different tRNA substrates and can be applied to total RNA derived from different species, cell types, and tissues. Here we apply the method to solve previous controversies regarding the modification status of mammalian tRNAArgACG.
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Affiliation(s)
- Adrian G Torres
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Thomas F Wulff
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , Parc Científic de Barcelona, C/Baldiri Reixac 10 , 08028 Barcelona , Catalonia , Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , P/Lluis Companys 23 , 08010 Barcelona , Catalonia , Spain
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