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Kurata H, Harun-Or-Roshid M, Mehedi Hasan M, Tsukiyama S, Maeda K, Manavalan B. MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models. Methods 2024; 227:37-47. [PMID: 38729455 DOI: 10.1016/j.ymeth.2024.05.004] [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: 09/22/2023] [Revised: 04/22/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
RNA modification serves as a pivotal component in numerous biological processes. Among the prevalent modifications, 5-methylcytosine (m5C) significantly influences mRNA export, translation efficiency and cell differentiation and are also associated with human diseases, including Alzheimer's disease, autoimmune disease, cancer, and cardiovascular diseases. Identification of m5C is critically responsible for understanding the RNA modification mechanisms and the epigenetic regulation of associated diseases. However, the large-scale experimental identification of m5C present significant challenges due to labor intensity and time requirements. Several computational tools, using machine learning, have been developed to supplement experimental methods, but identifying these sites lack accuracy and efficiency. In this study, we introduce a new predictor, MLm5C, for precise prediction of m5C sites using sequence data. Briefly, we evaluated eleven RNA sequence-derived features with four basic machine learning algorithms to generate baseline models. From these 44 models, we ranked them based on their performance and subsequently stacked the Top 20 baseline models as the best model, named MLm5C. The MLm5C outperformed the-state-of-the-art predictors. Notably, the optimization of the sequence length surrounding the modification sites significantly improved the prediction performance. MLm5C is an invaluable tool in accelerating the detection of m5C sites within the human genome, thereby facilitating in the characterization of their roles in post-transcriptional regulation.
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Affiliation(s)
- Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan.
| | - Md Harun-Or-Roshid
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Md Mehedi Hasan
- Division of Biotetecnology and Molecular Medicine, Department of Pathobiological Science, School of Veterinary Medicine, Lousiana State University, Baton Rouge, LA 70803, USA
| | - Sho Tsukiyama
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Kazuhiro Maeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Balachandran Manavalan
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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2
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Jiang X, Zhan L, Tang X. RNA modifications in physiology and pathology: Progressing towards application in clinical settings. Cell Signal 2024; 121:111242. [PMID: 38851412 DOI: 10.1016/j.cellsig.2024.111242] [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: 02/16/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.
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Affiliation(s)
- Xue Jiang
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu 223005, China
| | - Lijuan Zhan
- College of Pharmacy and Traditional Chinese Medicine, Jiangsu College of Nursing, Huaian, Jiangsu 223005, China.
| | - Xiaozhu Tang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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3
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He B, Chen Y, Yi C. Quantitative mapping of the mammalian epitranscriptome. Curr Opin Genet Dev 2024; 87:102212. [PMID: 38823337 DOI: 10.1016/j.gde.2024.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 06/03/2024]
Abstract
The epitranscriptome encompasses a diverse array of dynamic and reversible RNA modifications, affecting both coding and noncoding RNAs. Over 170 types of RNA chemical modifications have been identified, underscoring the need for innovative detection methods to deepen our understanding of RNA modification roles and mechanisms. In particular, the base resolution and quantitative information on RNA modifications are critical for understanding the regulation and functions of RNA modifications. Based on detection throughput and principles, existing quantitative RNA modification detection methods can be categorized into two groups, including next-generation sequencing and nanopore direct RNA sequencing. In this review, we focus on methodologies for elucidating the base resolution and stoichiometric information of RNA modifications. In addition, we further discuss the challenges and the potential prospects of the quantitative RNA modification detection methods.
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Affiliation(s)
- Bo He
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yuting Chen
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China
| | - Chengqi Yi
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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4
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Guarnacci M, Preiss T. The je ne sais quoi of 5-methylcytosine in messenger RNA. RNA (NEW YORK, N.Y.) 2024; 30:560-569. [PMID: 38531644 PMCID: PMC11019750 DOI: 10.1261/rna.079982.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
The potential presence of 5-methylcytosine as a sparse internal modification of mRNA was first raised in 1975, and a first map of the modification was also part of the epitranscriptomics "big bang" in 2012. Since then, the evidence for its presence in mRNA has firmed up, and initial insights have been gained into the molecular function and broader biological relevance of 5-methylcytosine when present in mRNA. Here, we summarize the status quo of the field, outline some of its current challenges, and suggest how to address them in future work.
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Affiliation(s)
- Marco Guarnacci
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, Division of Genome Science and Cancer, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
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5
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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6
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Dai Q, Ye C, Irkliyenko I, Wang Y, Sun HL, Gao Y, Liu Y, Beadell A, Perea J, Goel A, He C. Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA. Nat Biotechnol 2024:10.1038/s41587-023-02034-w. [PMID: 38168991 DOI: 10.1038/s41587-023-02034-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024]
Abstract
Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level and incomplete C-to-U conversion of certain DNA sequences. We present ultrafast BS-seq (UBS-seq), which uses highly concentrated bisulfite reagents and high reaction temperatures to accelerate the bisulfite reaction by ~13-fold, resulting in reduced DNA damage and lower background noise. UBS-seq allows library construction from small amounts of purified genomic DNA, such as from cell-free DNA or directly from 1 to 100 mouse embryonic stem cells, with less overestimation of 5mC level and higher genome coverage than conventional BS-seq. Additionally, UBS-seq quantitatively maps RNA 5-methylcytosine (m5C) from low inputs of mRNA and allows the detection of m5C stoichiometry in highly structured RNA sequences. Our UBS-seq results identify NSUN2 as the major 'writer' protein responsible for the deposition of ~90% of m5C sites in HeLa mRNA and reveal enriched m5C sites in 5'-regions of mammalian mRNA, which may have functional roles in mRNA translation regulation.
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Affiliation(s)
- Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Iryna Irkliyenko
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Yiding Wang
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics & System Biology, The University of Chicago, Chicago, IL, USA
| | - Hui-Lung Sun
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yun Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yushuai Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Alana Beadell
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - José Perea
- Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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7
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Zhang LS, Dai Q, He C. Base-Resolution Sequencing Methods for Whole-Transcriptome Quantification of mRNA Modifications. Acc Chem Res 2024; 57:47-58. [PMID: 38079380 PMCID: PMC10765377 DOI: 10.1021/acs.accounts.3c00532] [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] [Received: 08/30/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
RNA molecules are not merely a combination of four bases of A, C, G, and U. Chemical modifications occur in almost all RNA species and play diverse roles in gene expression regulation. The abundant cellular RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), are known to have the highest density of RNA modifications, which exert critical functions in rRNA and tRNA biogenesis, stability, and subsequent translation. In recent years, modifications on low-abundance RNA species in mammalian cells, such as messenger RNA (mRNA), regulatory noncoding RNA (ncRNA), and chromatin-associated RNA (caRNA), have been shown to contain multiple different chemical modifications with functional significance. As the most abundant mRNA modification in mammals, N6-methyladenosine (m6A) affects nearly every stage of mRNA processing and metabolism, with the antibody-based m6A-MeRIP-seq (methylated RNA immunoprecipitation sequencing) followed by high-throughput sequencing widely employed in mapping m6A distribution transcriptome-wide in diverse biological systems. In addition to m6A, other chemical modifications such as pseudouridine (Ψ), 2'-O-methylation (Nm), 5-methylcytidine (m5C), internal N7-methylguanosine (m7G), N1-methyladenosine (m1A), N4-acetylcytidine (ac4C), etc. also exist in polyA-tailed RNA in mammalian cells, requiring effective mapping approaches for whole-transcriptome profiling of these non-m6A mRNA modifications. Like m6A, the antibody-based enrichment followed by sequencing has been the primary method to study distributions of these modifications. Methods to more quantitatively map these modifications would dramatically improve our understanding of distributions and modification density of these chemical marks on RNA, thereby bettering informing functional implications. In this Account, aimed at both single-base resolution and modification fraction quantification, we summarize our recent advances in developing a series of chemistry- or biochemistry-based methods to quantitatively map RNA modifications, including m6A, Ψ, m5C, m1A, 2'-O-methylation (Nm), and internal m7G, in mammalian mRNA at base resolution. These new methods, including m6A-SAC-seq, eTAM-seq, BID-seq, UBS-seq, DAMM-seq, m1A-quant-seq, Nm-Mut-seq, and m7G-quant-seq, promise to conduct base-resolution mapping of most major mRNA modifications with low RNA input and uncover dynamic changes in modification stoichiometry during biological and physiological processes, facilitating future investigations on these RNA modifications in regulating cellular gene expression and as potential biomarkers for clinical diagnosis and prognosis. These quantitative sequencing methods allow the mapping of most mRNA modifications with limited input sample requirements. The same modifications on diverse RNA species, such as caRNA, ncRNA, nuclear nascent RNA, mitochondrial RNA, cell-free RNA (cfRNA), etc., could be sequenced using the same methods.
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Affiliation(s)
- Li-Sheng Zhang
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, The Hong Kong University of
Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
- Division
of Life Science, The Hong Kong University
of Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
| | - Qing Dai
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
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8
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [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: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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Liu HT, Rau CS, Liu YW, Hsieh TM, Huang CY, Chien PC, Lin HP, Wu CJ, Chuang PC, Hsieh CH. Deciphering the Divergent Gene Expression Landscapes of m6A/m5C/m1A Methylation Regulators in Hepatocellular Carcinoma Through Single-Cell and Bulk RNA Transcriptomic Analysis. J Hepatocell Carcinoma 2023; 10:2383-2395. [PMID: 38164510 PMCID: PMC10758181 DOI: 10.2147/jhc.s448047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction RNA modifications mediated by the m6A, m1A, and m5C regulatory genes are crucial for the progression of malignancy. This study aimed to explore the expression of regulator genes for m6A/m5C/m1A methylation at the single-cell level and to validate their expression in cancerous and adjacent para-cancerous liver tissues of adult patients with HCC who underwent tumor resection. Methods The bulk sequencing from The Cancer Genome Atlas (TCGA) database and the single-cell RNA sequencing (scRNA-seq) data obtained from the Gene Expression Omnibus (GEO) database were used to identify the dysregulated m6A/m5C/m1A genes for hepatocellular carcinoma (HCC). A real-time polymerase chain reaction (real-time PCR) was used to measure the expression of dysregulated m6A/m5C/m1A genes in collected human HCC tissues and compared with adjacent para-cancerous liver tissues. Immune cell infiltration with these significantly expressed methylation-related genes was evaluated using Timer2.0. Results A discrepancy in m6A/m5C/m1A gene expression was observed between bulk sequencing and scRNA-seq. The clustered heatmap of the scRNA-seq-identified dysregulated m6A/m5C/m1A genes in TCGA cohort revealed heterogeneous expression of these methylation regulators within the cancer, whereas their expression in the adjacent liver tissues was more homogeneous. The real-time PCR validated the significant overexpression of DNMT1, NSUN5, TRMT6, IGF2BP1, and IGFBP3, which were identified using scRNA-seq, and IGFBP2, which was identified using bulk sequencing. These dysregulated methylation genes are mainly correlated with the infiltration of natural killer cells. Discussion This study suggests that cellular diversity inside tumors contributes to the discrepancy in the expression of methylation regulator genes between traditional bulk sequencing and scRNA-seq. This study identified five regulatory genes that will be the focus of further studies regarding the function of m6A/m5C/m1A in HCC.
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Affiliation(s)
- Hang-Tsung Liu
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Cheng-Shyuan Rau
- Department of Neurosurgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Yueh-Wei Liu
- Department of General Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Ting-Min Hsieh
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chun-Ying Huang
- Department of Trauma Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Peng-Chen Chien
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Hui-Ping Lin
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Chia-Jung Wu
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
| | - Pei-Chin Chuang
- Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, 83301, Taiwan
| | - Ching-Hua Hsieh
- Department of Plastic Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, 83301, Taiwan
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [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: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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11
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Djihinto OY, Meacci D, Medjigodo AA, Bernardini F, Djogbénou LS. Relative expression of key genes involved in nucleic acids methylation in Anopheles gambiae sensu stricto. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:754-766. [PMID: 37417368 DOI: 10.1111/mve.12681] [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: 04/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
In vertebrates, enzymes responsible for DNA methylation, one of the epigenetic mechanisms, are encoded by genes falling into the cytosine methyltransferases genes family (Dnmt1, Dnmt3a,b and Dnmt3L). However, in Diptera, only the methyltransferase Dnmt2 was found, suggesting that DNA methylation might act differently for species in this order. Moreover, genes involved in epigenetic dynamics, such as Ten-eleven Translocation dioxygenases (TET) and Methyl-CpG-binding domain (MBDs), present in vertebrates, might play a role in insects. This work aimed at investigating nucleic acids methylation in the malaria vector Anopheles gambiae (Diptera: Culicidae) by analysing the expression of Dnmt2, TET2 and MBDs genes using quantitative real-time polymerase chain reaction (qRT-PCR) at pre-immature stages and in reproductive tissues of adult mosquitoes. In addition, the effect of two DNA methylation inhibitors on larval survival was evaluated. The qPCR results showed an overall low expression of Dnmt2 at all developmental stages and in adult reproductive tissues. In contrast, MBD and TET2 showed an overall higher expression. In adult mosquito reproductive tissues, the expression level of the three genes in males' testes was significantly higher than that in females' ovaries. The chemical treatments did not affect larval survival. The findings suggest that mechanisms other than DNA methylation underlie epigenetic regulation in An. gambiae.
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Affiliation(s)
- Oswald Y Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Adandé A Medjigodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Institut Régional de Santé Publique (IRSP), University of Abomey-Calavi, Ouidah, Benin
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12
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [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: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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13
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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14
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Yu Y, Lu S, Liu X, Li Y, Xu J. Identification and analysis of RNA-5-methylcytosine-related key genes in osteoarthritis. BMC Genomics 2023; 24:539. [PMID: 37700248 PMCID: PMC10496305 DOI: 10.1186/s12864-023-09651-4] [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: 05/03/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND 5-methylcytosine (m5C) modification is widely associated with many biological and pathological processes. However, knowledge of m5C modification in osteoarthritis (OA) remains lacking. Thus, our study aimed to identify common m5C features in OA. RESULTS In the present study, we identified 1395 differentially methylated genes (DMGs) and 1673 differentially expressed genes (DEGs) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq) and RNA-sequencing. A co-expression analysis of DMGs and DEGs showed that the expression of 133 genes was significantly affected by m5C methylation. A protein-protein interaction network of the 133 genes was constructed using the STRING database, and the cytoHubba plug-in of Cytoscape was used to hub genes were screen out 11 hub genes, including MMP14, VTN, COL15A1, COL6A2, SPARC, COL5A1, COL6A3, COL6A1, COL8A2, ADAMTS2 and COL7A1. The Pathway enrichment analysis by the ClueGO and CluePedia plugins in Cytoscape showed that the hub genes were significantly enriched in collagen degradation and extracellular matrix degradation. CONCLUSIONS Our study indicated that m5C modification might play an important role in OA pathogenesis, and the present study provides worthwhile insight into identifying m5C-related therapeutic targets in OA.
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Affiliation(s)
- Yang Yu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shitao Lu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoming Liu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yu Li
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianzhong Xu
- Department of Orthopedics, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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15
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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16
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Li Y, Xue M, Deng X, Dong L, Nguyen LXT, Ren L, Han L, Li C, Xue J, Zhao Z, Li W, Qing Y, Shen C, Tan B, Chen Z, Leung K, Wang K, Swaminathan S, Li L, Wunderlich M, Mulloy JC, Li X, Chen H, Zhang B, Horne D, Rosen ST, Marcucci G, Xu M, Li Z, Wei M, Tian J, Shen B, Su R, Chen J. TET2-mediated mRNA demethylation regulates leukemia stem cell homing and self-renewal. Cell Stem Cell 2023; 30:1072-1090.e10. [PMID: 37541212 PMCID: PMC11166201 DOI: 10.1016/j.stem.2023.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 05/10/2023] [Accepted: 07/03/2023] [Indexed: 08/06/2023]
Abstract
TET2 is recurrently mutated in acute myeloid leukemia (AML) and its deficiency promotes leukemogenesis (driven by aggressive oncogenic mutations) and enhances leukemia stem cell (LSC) self-renewal. However, the underlying cellular/molecular mechanisms have yet to be fully understood. Here, we show that Tet2 deficiency significantly facilitates leukemogenesis in various AML models (mediated by aggressive or less aggressive mutations) through promoting homing of LSCs into bone marrow (BM) niche to increase their self-renewal/proliferation. TET2 deficiency in AML blast cells increases expression of Tetraspanin 13 (TSPAN13) and thereby activates the CXCR4/CXCL12 signaling, leading to increased homing/migration of LSCs into BM niche. Mechanistically, TET2 deficiency results in the accumulation of methyl-5-cytosine (m5C) modification in TSPAN13 mRNA; YBX1 specifically recognizes the m5C modification and increases the stability and expression of TSPAN13 transcripts. Collectively, our studies reveal the functional importance of TET2 in leukemogenesis, leukemic blast cell migration/homing, and LSC self-renewal as an mRNA m5C demethylase.
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Affiliation(s)
- Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Radiation Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Meilin Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Le Xuan Truong Nguyen
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Lili Ren
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Pathology, Harbin Medical University, Harbin 150081, China
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110001, Liaoning, China
| | - Chenying Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Hematology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 31003, Zhejiang, China
| | - Jianhuang Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Brandon Tan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Srividya Swaminathan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Department of Pediatrics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Ling Li
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin 150081, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Bin Zhang
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Steven T Rosen
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Department of Hematology/Hematopoietic Cell Transplantation, City of Hope, Duarte, CA 91010, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Mingjiang Xu
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110001, Liaoning, China
| | - Jingyan Tian
- State Key Laboratory of Medical Genomics, Clinical Trial Center, Shanghai Institute of Endocrine and Metabolic Diseases, Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA.
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17
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Han G, Noh D, Lee H, Lee S, Kim S, Yoon HY, Lee SH. Advances in mRNA therapeutics for cancer immunotherapy: From modification to delivery. Adv Drug Deliv Rev 2023; 199:114973. [PMID: 37369262 PMCID: PMC10290897 DOI: 10.1016/j.addr.2023.114973] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 06/29/2023]
Abstract
RNA vaccines have demonstrated their ability to solve the issues posed by the COVID-19 pandemic. This success has led to the renaissance of research into mRNA and their nanoformulations as potential therapeutic modalities for various diseases. The potential of mRNA as a template for synthesizing proteins and protein fragments for cancer immunotherapy is now being explored. Despite the promise, the use of mRNA in cancer immunotherapy is limited by challenges, such as low stability against extracellular RNases, poor delivery efficiency to the target organs and cells, short circulatory half-life, variable expression levels and duration. This review highlights recent advances in chemical modification and advanced delivery systems that are helping to address these challenges and unlock the biological and pharmacological potential of mRNA therapeutics in cancer immunotherapy. The review concludes by discussing future perspectives for mRNA-based cancer immunotherapy, which holds great promise as a next-generation therapeutic modality.
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Affiliation(s)
- Geonhee Han
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Dahye Noh
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Hwarang-ro14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792; Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Hokyung Lee
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Fundamental Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Sangmin Lee
- Department of Fundamental Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Sehoon Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Fundamental Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, 1 Hoegi-dong, Dongdaemun-gu, Seoul 02447, Republic of Korea
| | - Hong Yeol Yoon
- Medicinal Materials Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea; Division of Bio-Medical Science &Technology, KIST School, University of Science and Technology, Hwarang-ro14-gil 5, Seongbuk-gu, Seoul, Republic of Korea 02792.
| | - Soo Hyeon Lee
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, Palo Alto, CA 94304, USA.
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18
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Xiong Q, Zhang Y. Small RNA modifications: regulatory molecules and potential applications. J Hematol Oncol 2023; 16:64. [PMID: 37349851 PMCID: PMC10286502 DOI: 10.1186/s13045-023-01466-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 06/24/2023] Open
Abstract
Small RNAs (also referred to as small noncoding RNAs, sncRNA) are defined as polymeric ribonucleic acid molecules that are less than 200 nucleotides in length and serve a variety of essential functions within cells. Small RNA species include microRNA (miRNA), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), tRNA-derived small RNA (tsRNA), etc. Current evidence suggest that small RNAs can also have diverse modifications to their nucleotide composition that affect their stability as well as their capacity for nuclear export, and these modifications are relevant to their capacity to drive molecular signaling processes relevant to biogenesis, cell proliferation and differentiation. In this review, we highlight the molecular characteristics and cellular functions of small RNA and their modifications, as well as current techniques for their reliable detection. We also discuss how small RNA modifications may be relevant to the clinical applications for the diagnosis and treatment of human health conditions such as cancer.
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Affiliation(s)
- Qunli Xiong
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China
- Abdominal Oncology Ward, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yaguang Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics and Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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19
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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20
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Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [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: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
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Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
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21
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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22
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Prall W, Ganguly DR, Gregory BD. The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future. THE PLANT CELL 2023; 35:1801-1816. [PMID: 36794718 PMCID: PMC10226571 DOI: 10.1093/plcell/koad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 01/09/2023] [Indexed: 05/30/2023]
Abstract
Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g. splicing, polyadenylation, etc.) and functionality (e.g. translation, transport, etc.) of these protein-encoding molecules. Here, we focus our attention on the current understanding of the collection of covalent nucleotide modifications known to occur on mRNAs in plants, how they are detected and studied, and the most outstanding future questions of each of these important epitranscriptomic regulatory signals.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Diep R Ganguly
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, 433 S. University Ave., Philadelphia, PA 19104, USA
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23
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Jones JD, Franco MK, Smith TJ, Snyder LR, Anders AG, Ruotolo BT, Kennedy RT, Koutmou KS. Methylated guanosine and uridine modifications in S. cerevisiae mRNAs modulate translation elongation. RSC Chem Biol 2023; 4:363-378. [PMID: 37181630 PMCID: PMC10170649 DOI: 10.1039/d2cb00229a] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/15/2023] [Indexed: 02/22/2023] Open
Abstract
Chemical modifications to protein encoding messenger RNAs (mRNAs) influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. While LC-MS/MS is arguably the most essential tool available for studying analogous protein post-translational modifications, the high-throughput discovery and quantitative characterization of mRNA modifications by LC-MS/MS has been hampered by the difficulty of obtaining sufficient quantities of pure mRNA and limited sensitivities for modified nucleosides. We have overcome these challenges by improving the mRNA purification and LC-MS/MS pipelines. The methodologies we developed result in no detectable non-coding RNA modifications signals in our purified mRNA samples, quantify 50 ribonucleosides in a single analysis, and provide the lowest limit of detection reported for ribonucleoside modification LC-MS/MS analyses. These advancements enabled the detection and quantification of 13 S. cerevisiae mRNA ribonucleoside modifications and reveal the presence of four new S. cerevisiae mRNA modifications at low to moderate levels (1-methyguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, and 5-methyluridine). We identified four enzymes that incorporate these modifications into S. cerevisiae mRNAs (Trm10, Trm11, Trm1, and Trm2, respectively), though our results suggest that guanosine and uridine nucleobases are also non-enzymatically methylated at low levels. Regardless of whether they are incorporated in a programmed manner or as the result of RNA damage, we reasoned that the ribosome will encounter the modifications that we detect in cells. To evaluate this possibility, we used a reconstituted translation system to investigate the consequences of modifications on translation elongation. Our findings demonstrate that the introduction of 1-methyguanosine, N2-methylguanosine and 5-methyluridine into mRNA codons impedes amino acid addition in a position dependent manner. This work expands the repertoire of nucleoside modifications that the ribosome must decode in S. cerevisiae. Additionally, it highlights the challenge of predicting the effect of discrete modified mRNA sites on translation de novo because individual modifications influence translation differently depending on mRNA sequence context.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Monika K Franco
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Tyler J Smith
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Laura R Snyder
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Anna G Anders
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, 930 N University Ann Arbor MI 48109 USA +1-734-764-5650
- Program in Chemical Biology, University of Michigan, 930 N University Ann Arbor MI 48109 USA
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24
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Danan CH, Naughton KE, Hayer KE, Vellappan S, McMillan EA, Zhou Y, Matsuda R, Nettleford SK, Katada K, Parham LR, Ma X, Chowdhury A, Wilkins BJ, Shah P, Weitzman MD, Hamilton KE. Intestinal transit amplifying cells require METTL3 for growth factor signaling, KRAS expression, and cell survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535853. [PMID: 37066277 PMCID: PMC10104132 DOI: 10.1101/2023.04.06.535853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intestinal epithelial transit amplifying cells are essential stem progenitors required for intestinal homeostasis, but their rapid proliferation renders them vulnerable to DNA damage from radiation and chemotherapy. Despite their critical roles in intestinal homeostasis and disease, few studies have described genes that are essential to transit amplifying cell function. We report that the RNA methyltransferase, METTL3, is required for survival of transit amplifying cells in the murine small intestine. Transit amplifying cell death after METTL3 deletion was associated with crypt and villus atrophy, loss of absorptive enterocytes, and uniform wasting and death in METTL3-depleted mice. Ribosome profiling and sequencing of methylated RNAs in enteroids and in vivo demonstrated decreased translation of hundreds of unique methylated transcripts after METTL3 deletion, particularly transcripts involved in growth factor signal transduction such as Kras. Further investigation confirmed a novel relationship between METTL3 and Kras methylation and protein levels in vivo. Our study identifies METTL3 as an essential factor supporting the homeostasis of small intestinal tissue via direct maintenance of transit amplifying cell survival. We highlight the crucial role of RNA modifications in regulating growth factor signaling in the intestine, with important implications for both homeostatic tissue renewal and epithelial regeneration.
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Affiliation(s)
- Charles H. Danan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kaitlyn E. Naughton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sangeevan Vellappan
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Emily A. McMillan
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yusen Zhou
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Rina Matsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shaneice K. Nettleford
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R. Parham
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xianghui Ma
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Afrah Chowdhury
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Premal Shah
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
- Human Genetics Institute of New Jersey, Piscataway, NJ, 08854, USA
| | - Matthew D. Weitzman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine; University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn E. Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition; Department of Pediatrics; Children’s Hospital of Philadelphia; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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25
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Zhang S, Shen T, Zeng Y. Epigenetic Modifications in Prostate Cancer Metastasis and Microenvironment. Cancers (Basel) 2023; 15:cancers15082243. [PMID: 37190171 DOI: 10.3390/cancers15082243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The gradual evolution of prostate tissue from benign tumor to malignant lesion or distant metastasis is driven by intracellular epigenetic changes and the tumor microenvironment remodeling. With the continuous study of epigenetic modifications, these tumor-driving forces are being discovered and are providing new treatments for cancer. Here we introduce the classification of epigenetic modification and highlight the role of epigenetic modification in tumor remodeling and communication of the tumor microenvironment.
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Affiliation(s)
- Shouyi Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang 110042, China
| | - Tao Shen
- Department of Urology, Second Affiliated Hospital of Shenyang Medical College, No. 20 Beijiu Road, Heping District, Shenyang 110001, China
| | - Yu Zeng
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang 110042, China
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26
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Shen L, Ma J, Li P, Wu Y, Yu H. Recent advances in the plant epitranscriptome. Genome Biol 2023; 24:43. [PMID: 36882788 PMCID: PMC9990323 DOI: 10.1186/s13059-023-02872-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/12/2023] [Indexed: 03/09/2023] Open
Abstract
Chemical modifications of RNAs, known as the epitranscriptome, are emerging as widespread regulatory mechanisms underlying gene regulation. The field of epitranscriptomics advances recently due to improved transcriptome-wide sequencing strategies for mapping RNA modifications and intensive characterization of writers, erasers, and readers that deposit, remove, and recognize RNA modifications, respectively. Herein, we review recent advances in characterizing plant epitranscriptome and its regulatory mechanisms in post-transcriptional gene regulation and diverse physiological processes, with main emphasis on N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We also discuss the potential and challenges for utilization of epitranscriptome editing in crop improvement.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
| | - Jinqi Ma
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Ping Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yujin Wu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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27
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Dynamics of RNA m 5C modification during brain development. Genomics 2023; 115:110604. [PMID: 36889368 DOI: 10.1016/j.ygeno.2023.110604] [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: 10/19/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Post-transcriptional RNA modifications have been recognized as key regulators of neuronal differentiation and synapse development in the mammalian brain. While distinct sets of 5-methylcytosine (m5C) modified mRNAs have been detected in neuronal cells and brain tissues, no study has been performed to characterize methylated mRNA profiles in the developing brain. Here, together with regular RNA-seq, we performed transcriptome-wide bisulfite sequencing to compare RNA cytosine methylation patterns in neural stem cells (NSCs), cortical neuronal cultures, and brain tissues at three postnatal stages. Among 501 m5C sites identified, approximately 6% are consistently methylated across all five conditions. Compared to m5C sites identified in NSCs, 96% of them were hypermethylated in neurons and enriched for genes involved in positive transcriptional regulation and axon extension. In addition, brains at the early postnatal stage demonstrated substantial changes in both RNA cytosine methylation and gene expression of RNA cytosine methylation readers, writers, and erasers. Furthermore, differentially methylated transcripts were significantly enriched for genes regulating synaptic plasticity. Altogether, this study provides a brain epitranscriptomic dataset as a new resource and lays the foundation for further investigations into the role of RNA cytosine methylation during brain development.
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28
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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: 6] [Impact Index Per Article: 3.0] [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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29
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Yan Y, Wei W, Long S, Ye S, Yang B, Jiang J, Li X, Chen J. The role of RNA modification in the generation of acquired drug resistance in glioma. Front Genet 2022; 13:1032286. [DOI: 10.3389/fgene.2022.1032286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Glioma is the most common malignant tumor in the central nervous system. The clinical treatment strategy is mainly surgery combined with concurrent temozolomide chemotherapy, but patients can develop drug resistance during treatment, which severely limits its therapeutic efficacy. Epigenetic regulation at the RNA level is plastic and adaptable, and it can induce a variety of tumor responses to drugs. The regulators of RNA modification include methyltransferases, demethylases, and methylation binding proteins; these are also considered to play an important role in the development, prognosis, and therapeutic response of gliomas, which provides a basis for finding new targets of epigenetic drugs and resetting the sensitivity of tumor cells to temozolomide. This review discusses the relationship between the development of adaptive drug resistance and RNA modification in glioma and summarizes the progress of several major RNA modification strategies in this field, especially RNA m6A modification, m5C modification, and adenosine-to-inosine editing.
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30
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:ijms232213851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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31
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Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
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32
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RNA modifications in aging-associated cardiovascular diseases. Aging (Albany NY) 2022; 14:8110-8136. [PMID: 36178367 PMCID: PMC9596201 DOI: 10.18632/aging.204311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022]
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide that bears an enormous healthcare burden and aging is a major contributing factor to CVDs. Functional gene expression network during aging is regulated by mRNAs transcriptionally and by non-coding RNAs epi-transcriptionally. RNA modifications alter the stability and function of both mRNAs and non-coding RNAs and are involved in differentiation, development, and diseases. Here we review major chemical RNA modifications on mRNAs and non-coding RNAs, including N6-adenosine methylation, N1-adenosine methylation, 5-methylcytidine, pseudouridylation, 2′ -O-ribose-methylation, and N7-methylguanosine, in the aging process with an emphasis on cardiovascular aging. We also summarize the currently available methods to detect RNA modifications and the bioinformatic tools to study RNA modifications. More importantly, we discussed the specific implication of the RNA modifications on mRNAs and non-coding RNAs in the pathogenesis of aging-associated CVDs, including atherosclerosis, hypertension, coronary heart diseases, congestive heart failure, atrial fibrillation, peripheral artery disease, venous insufficiency, and stroke.
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Abstract
Nucleotide modifications can markedly influence mRNA processing and metabolism. This Primer explores two new studies, one in PLOS Biology, showing that ~130 yeast mRNAs contain dihydrouridine, a derivative of uridine. Functional studies show that dihydrouridine, in some cases, can affect mRNA splicing.
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Affiliation(s)
- Sameer Dixit
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, New York, United States of America
| | - Samie R. Jaffrey
- Department of Pharmacology, Weill-Cornell Medical College, Cornell University, New York, New York, United States of America
- * E-mail:
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Petrov DP, Kaiser S, Kaiser S, Jung K. Opportunities and challenges to profile mRNA modifications in Escherichia coli. Chembiochem 2022; 23:e202200270. [PMID: 35822398 PMCID: PMC9542048 DOI: 10.1002/cbic.202200270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/12/2022] [Indexed: 11/23/2022]
Abstract
mRNA methylation is an important regulator of many physiological processes in eukaryotes but has not been studied in depth in prokaryotes. Working with bacterial mRNA is challenging because it lacks a poly(A)‐tail. However, methods for detecting RNA modifications, both sequencing and mass spectrometry, rely on efficient preparation of mRNA. Here, we compared size‐dependent separation by electrophoresis and rRNA depletion for enrichment of Escherichia coli mRNA. The purification success was monitored by qRT‐PCR and RNA sequencing. Neither method allowed complete removal of rRNA. Nevertheless, we were able to quantitatively analyze several modified nucleosides in the different RNA types. We found evidence for stress dependent RNA modification reprofiling in rRNA, but also several modified nucleosides in the mRNA enriched fractions showed significant changes.
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Affiliation(s)
| | - Steffen Kaiser
- Goethe-Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Pharmacy, GERMANY
| | - Stefanie Kaiser
- Goethe-Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Pharmacy, GERMANY
| | - Kirsten Jung
- Ludwig-Maximilians-Universitat Munchen, Biology, Grosshaderner Str. 2-4, 82152, Martinsried, GERMANY
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Murakami S, Jaffrey SR. Hidden codes in mRNA: Control of gene expression by m 6A. Mol Cell 2022; 82:2236-2251. [PMID: 35714585 DOI: 10.1016/j.molcel.2022.05.029] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022]
Abstract
Information in mRNA has largely been thought to be confined to its nucleotide sequence. However, the advent of mapping techniques to detect modified nucleotides has revealed that mRNA contains additional information in the form of chemical modifications. The most abundant modified nucleotide is N6-methyladenosine (m6A), a methyl modification of adenosine. Although early studies viewed m6A as a dynamic and tissue-specific modification, it is now clear that the mRNAs that contain m6A and the location of m6A in those transcripts are largely universal and are influenced by gene architecture, i.e., the size and location of exons and introns. m6A can affect nuclear processes such as splicing and epigenetic regulation, but the major effect of m6A on mRNAs is to promote degradation in the cytoplasm. m6A marks a functionally related cohort of mRNAs linked to certain biological processes, including cell differentiation and cell fate determination. m6A is also enriched in other cohorts of mRNAs and can therefore affect their respective cellular processes and pathways. Future work will focus on understanding how the m6A pathway is regulated to achieve control of m6A-containing mRNAs.
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Affiliation(s)
- Shino Murakami
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.
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36
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Johnson Z, Xu X, Pacholec C, Xie H. Systematic evaluation of parameters in RNA bisulfite sequencing data generation and analysis. NAR Genom Bioinform 2022; 4:lqac045. [PMID: 35669236 PMCID: PMC9164272 DOI: 10.1093/nargab/lqac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/05/2022] [Accepted: 05/23/2022] [Indexed: 12/26/2022] Open
Abstract
The presence of 5-methylcytosine (m5C) in RNA molecules has been known for decades and its importance in regulating RNA metabolism has gradually become appreciated. Despite recent advances made in the functional and mechanistic understanding of RNA m5C modifications, the detection and quantification of methylated RNA remains a challenge. In this study, we compared four library construction procedures for RNA bisulfite sequencing and implemented an analytical pipeline to assess the key parameters in the process of m5C calling. We found that RNA fragmentation after bisulfite conversion increased the yield significantly, and an additional high temperature treatment improved bisulfite conversion efficiency especially for sequence reads mapped to the mitochondrial transcriptome. Using Unique Molecular Identifiers (UMIs), we observed that PCR favors the amplification of unmethylated templates. The low sequencing quality of bisulfite-converted bases is a major contributor to the methylation artifacts. In addition, we found that mitochondrial transcripts are frequently resistant to bisulfite conversion and no p-m5C sites with high confidence could be identified on mitochondrial mRNAs. Taken together, this study reveals the various sources of artifacts in RNA bisulfite sequencing data and provides an improved experimental procedure together with analytical methodology.
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Affiliation(s)
- Zachary Johnson
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
| | - Christina Pacholec
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine; Virginia Tech, Blacksburg, VA 24061, USA
- Translational Biology, Medicine and Health Program, Virginia Tech, Blacksburg, VA 24061, USA
- School of Neuroscience, Virginia Tech, Blacksburg, VA 24061, USA
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Jin H, Huo C, Zhou T, Xie S. m1A RNA Modification in Gene Expression Regulation. Genes (Basel) 2022; 13:genes13050910. [PMID: 35627295 PMCID: PMC9141559 DOI: 10.3390/genes13050910] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/31/2023] Open
Abstract
N1-methyladenosine (m1A) is a prevalent and reversible post-transcriptional RNA modification that decorates tRNA, rRNA and mRNA. Recent studies based on technical advances in analytical chemistry and high-throughput sequencing methods have revealed the crucial roles of m1A RNA modification in gene regulation and biological processes. In this review, we focus on progress in the study of m1A methyltransferases, m1A demethylases and m1A-dependent RNA-binding proteins and highlight the biological mechanisms and functions of m1A RNA modification, as well as its association with human disease. We also summarize the current understanding of detection approaches for m1A RNA modification.
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Affiliation(s)
- Hao Jin
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Chunxiao Huo
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Tianhua Zhou
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China;
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Correspondence: (T.Z.); (S.X.)
| | - Shanshan Xie
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China;
- Correspondence: (T.Z.); (S.X.)
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Liu J, Huang T, Chen W, Ding C, Zhao T, Zhao X, Cai B, Zhang Y, Li S, Zhang L, Xue M, He X, Ge W, Zhou C, Xu Y, Zhang R. Developmental mRNA m 5C landscape and regulatory innovations of massive m 5C modification of maternal mRNAs in animals. Nat Commun 2022; 13:2484. [PMID: 35513466 PMCID: PMC9072368 DOI: 10.1038/s41467-022-30210-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 04/06/2022] [Indexed: 11/09/2022] Open
Abstract
m5C is one of the longest-known RNA modifications, however, its developmental dynamics, functions, and evolution in mRNAs remain largely unknown. Here, we generate quantitative mRNA m5C maps at different stages of development in 6 vertebrate and invertebrate species and find convergent and unexpected massive methylation of maternal mRNAs mediated by NSUN2 and NSUN6. Using Drosophila as a model, we reveal that embryos lacking maternal mRNA m5C undergo cell cycle delays and fail to timely initiate maternal-to-zygotic transition, implying the functional importance of maternal mRNA m5C. From invertebrates to the lineage leading to humans, two waves of m5C regulatory innovations are observed: higher animals gain cis-directed NSUN2-mediated m5C sites at the 5' end of the mRNAs, accompanied by the emergence of more structured 5'UTR regions; humans gain thousands of trans-directed NSUN6-mediated m5C sites enriched in genes regulating the mitotic cell cycle. Collectively, our studies highlight the existence and regulatory innovations of a mechanism of early embryonic development and provide key resources for elucidating the role of mRNA m5C in biology and disease. mRNAs are known to be decorated with m5C at a low-to-medium level. Here, the authors generate atlases of mRNA m5C during animal development in 6 species and identify convergent and unexpected massive methylation of maternal mRNAs by NSUN2 and NSUN6.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Tao Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanying Chen
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Chenhui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Xueni Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Song Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China
| | - Ling Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Maoguang Xue
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Xiuju He
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310006, China. .,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China. .,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Canquan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Yanwen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Center for Reproductive Medicine and Department of Gynecology & Obstetrics, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, PR China.
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China.
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Chen SY, Chen KL, Ding LY, Yu CH, Wu HY, Chou YY, Chang CJ, Chang CH, Wu YN, Wu SR, Hou YC, Lee CT, Chen PC, Shan YS, Huang PH. RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer. Oncogene 2022; 41:3162-3176. [PMID: 35501460 DOI: 10.1038/s41388-022-02325-7] [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: 09/07/2021] [Revised: 03/26/2022] [Accepted: 04/14/2022] [Indexed: 11/09/2022]
Abstract
Posttranscriptional modifications in RNA have been considered to contribute to disease pathogenesis and tumor progression. NOL1/NOP2/Sun domain family member 2 (NSUN2) is an RNA methyltransferase that promotes tumor progression in several cancers. Pancreatic cancer relapse inevitably occurs even in cases where primary tumors have been successfully treated. Associations of cancer progression due to reprogramming of the cancer methyl-metabolome and the cancer genome have been noted, but the effect of base modifications, namely 5-methylcytosine (m5C), in the transcriptome remains unclear. Aberrant regulation of 5-methylcytosine turnover in cancer may affect posttranscriptional modifications in coding and noncoding RNAs in disease pathogenesis. Mutations in NSUN2 have been reported as drivers of neurodevelopmental disorders in mice, and upregulated expression of NSUN2 in tumors of the breast, bladder, and pancreas has been reported. In this study, we conducted mRNA whole transcriptomic bisulfite sequencing to categorize NSUN2 target sites in the mRNA of human pancreatic cancer cells. We identified a total of 2829 frequent m5C sites in mRNA from pancreatic cancer cells. A total of 90.9% (2572/2829) of these m5C sites were mapped to annotated genes in autosomes and sex chromosomes X and Y. Immunohistochemistry staining confirmed that the NSUN2 expression was significantly upregulated in cancer lesions in the LSL-KrasG12D/+;Trp53fl/fl;Pdx1-Cre (KPC) spontaneous pancreatic cancer mouse model induced by Pdx1-driven Cre/lox system expressing mutant KrasG12D and p53 deletion. The in vitro phenotypic analysis of NSUN2 knockdown showed mild effects on pancreatic cancer cell 2D/3D growth, morphology and gemcitabine sensitivity in the early phase of tumorigenesis, but cumulative changes after multiple cell doubling passages over time were required for these mutations to accumulate. Syngeneic transplantation of NSUN2-knockdown KPC cells via subcutaneous injection showed decreased stromal fibrosis and restored differentiation of ductal epithelium in vivo. SIGNIFICANCE: Transcriptome-wide mRNA bisulfite sequencing identified candidate m5C sites of mRNAs in human pancreatic cancer cells. NSUN2-mediated m5C mRNA metabolism was observed in a mouse model of pancreatic cancer. NSUN2 regulates cancer progression and epithelial differentiation via mRNA methylation.
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Affiliation(s)
- Szu-Ying Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Lin Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Li-Yun Ding
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin-Yi Wu
- Instrumentation Center, College of Science, National Taiwan University, Tainan, Taiwan
| | - Ya-Yi Chou
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Jung Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Han Chang
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, Tainan, Taiwan
- Center for Corporate Relations and Technology Transfer, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Na Wu
- International Institute for Macromolecular Analysis and Nanomedicine Innovations, Tainan, Taiwan
| | - Shang-Rung Wu
- International Institute for Macromolecular Analysis and Nanomedicine Innovations, Tainan, Taiwan
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Chin Hou
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chung-Ta Lee
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Peng-Chieh Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Division of General Surgery, Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Po-Hsien Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Zuidhof HR, Calkhoven CF. Oncogenic and tumor-suppressive functions of the RNA demethylase FTO. Cancer Res 2022; 82:2201-2212. [PMID: 35303057 DOI: 10.1158/0008-5472.can-21-3710] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022]
Abstract
The epitranscriptome represents the more than 140 types of chemically varying and reversable RNA modifications affecting RNA fate. Among these, the most relevant for this review are the mRNA-modifications N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am). Epitranscriptomic mRNA biology involves RNA methyltransferases (so called "writers"), RNA demethylases ("erasers"), and RNA-binding proteins ("readers") that interact with methylation sites to determine the functional outcome of the modification. In this review, we discuss the role of a specific RNA demethylase encoded by the fat mass and obesity associated gene (FTO) in cancer. FTO initially became known as the strongest genetic link for human obesity. Only in 2010, 16 years after its discovery, was its enzymatic function as a demethylase clarified, and only recently has its role in the development of cancer been revealed. FTO functions are challenging to study and interpret because of its genome-wide effects on transcript turnover and translation. We review the discovery of FTO and its enzymatic function, the tumor-promoting and suppressive roles of FTO in selected cancer types, and its potential as a therapeutic target.
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41
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D’Aquila P, De Rango F, Paparazzo E, Mandalà M, Bellizzi D, Passarino G. Impact of Nutrition on Age-Related Epigenetic RNA Modifications in Rats. Nutrients 2022; 14:nu14061232. [PMID: 35334889 PMCID: PMC8955587 DOI: 10.3390/nu14061232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Nutrition plastically modulates the epigenetic landscape in various tissues of an organism during life via epigenetic changes. In the present study, to clarify whether this modulation involves RNA methylation, we evaluated global RNA methylation profiles and the expression of writer, reader, and eraser genes, encoding for enzymes involved in the RNA methylation. The study was carried out in the heart, liver, and kidney samples from rats of different ages in response to a low-calorie diet. We found that, although each tissue showed peculiar RNA methylation levels, a general increase in these levels was observed throughout the lifespan as well as in response to the six-month diet. Similarly, a prominent remodeling of the expression of writer, reader, and eraser genes emerged. Our data provide a comprehensive overview of the role exerted by diet on the tissue-specific epigenetic plasticity of RNA according to aging in rats, providing the first evidence that methylation of RNA, similarly to DNA methylation, can represent an effective biomarker of aging. What is more, the fact that it is regulated by nutrition provides the basis for the development of targeted approaches capable of guaranteeing the maintenance of a state of good health.
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Epigenetic MRI: Noninvasive imaging of DNA methylation in the brain. Proc Natl Acad Sci U S A 2022; 119:e2119891119. [PMID: 35235458 PMCID: PMC8915962 DOI: 10.1073/pnas.2119891119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dynamic epigenetic activity is a fundamental mechanism underpinning how the brain changes its function during development and aging and in response to environmental and disease stimuli. We developed a technology called epigenetic MRI (eMRI) that enables noninvasive imaging of DNA methylation in the brain, a major epigenetic mechanism. eMRI reveals strong regional differences in global DNA methylation in pig brains, a model with stronger resemblance to human brains than are rodents. Given the noninvasive nature of eMRI, our results pave the way for a DNA-methylation imaging paradigm for living human brains. We expect eMRI to enable many studies to unravel the molecular control of brain function and disease. Both neuronal and genetic mechanisms regulate brain function. While there are excellent methods to study neuronal activity in vivo, there are no nondestructive methods to measure global gene expression in living brains. Here, we present a method, epigenetic MRI (eMRI), that overcomes this limitation via direct imaging of DNA methylation, a major gene-expression regulator. eMRI exploits the methionine metabolic pathways for DNA methylation to label genomic DNA through 13C-enriched diets. A 13C magnetic resonance spectroscopic imaging method then maps the spatial distribution of labeled DNA. We validated eMRI using pigs, whose brains have stronger similarity to humans in volume and anatomy than rodents, and confirmed efficient 13C-labeling of brain DNA. We also discovered strong regional differences in global DNA methylation. Just as functional MRI measurements of regional neuronal activity have had a transformational effect on neuroscience, we expect that the eMRI signal, both as a measure of regional epigenetic activity and as a possible surrogate for regional gene expression, will enable many new investigations of human brain function, behavior, and disease.
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43
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Liu J. 5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m 5C formation catalyzed by RNA methyltransferase. BMC Res Notes 2022; 15:81. [PMID: 35197120 PMCID: PMC8867762 DOI: 10.1186/s13104-022-05968-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE 5-Methylcytosine (m5C) is a type of chemical modification on the nucleotides and is widespread in both DNA and RNA. Although the DNA m5C has been extensively studied over the past years, the distribution and biological function of RNA m5C still remain to be elucidated. Here, I explored the profiles of RNA m5C in four mouse tissues by applying a RNA cytosine methylation data analysis tool to public mouse RNA m5C data. RESULTS I found that the methylation rates of cytosine were the same with the averages of methylation level at single-nucleotide level. Furthermore, I gave a mathematical formula to describe the observed relationship and analyzed it deeply. The sufficient necessary condition for the given formula suggests that the methylation levels at most m5C sites are the same in four mouse tissues. Therefore, I proposed a hypothesis that the m5C formation catalyzed by RNA methyltransferase is random and with the same probability at most m5C sites, which is the methylation rate of cytosine. My hypothesis can be used to explain the observed profiles of RNA m5C in four mouse tissues and will be benefit to future studies of the distribution and biological function of RNA m5C in mammals.
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Affiliation(s)
- Junfeng Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,China National Center for Bioinformation, Beijing, 100101, China. .,Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
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Motorin Y, Helm M. RNA nucleotide methylation: 2021 update. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1691. [PMID: 34913259 DOI: 10.1002/wrna.1691] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 12/14/2022]
Abstract
Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core Facility, Nancy, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Mainz, Germany
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45
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Wang Y, Zhang X, Liu H, Zhou X. Chemical methods and advanced sequencing technologies for deciphering mRNA modifications. Chem Soc Rev 2021; 50:13481-13497. [PMID: 34792050 DOI: 10.1039/d1cs00920f] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNA modification, like other epigenetic modifications such as DNA modification and histone modification, is an emerging player in the field of the posttranscriptional regulation of gene expression. More than 160 kinds of RNA modifications have been identified, and they are widely distributed in different types of RNA. Recently, researchers have increasingly used advanced technologies to study modified nucleic acids in order to elucidate their biological functions and expand the understanding of the central laws of epigenetics. In this tutorial review, we comprehensively outline current advanced techniques for decoding RNA modifications, highlighting some of the bottlenecks in existing approaches as well as new opportunities that may lead to innovations. With this review, we expect to provide chemistry and biology students and researchers with ideas for solving some challenging problems, such as how to simultaneously detect multiple types of modifications within the same system. Moreover, some low-coverage modifications that may act as 'candidates' in important transcriptional processes need to be further explored. These novel approaches have the potential to lay a foundation for understanding the nuanced complexities of the biological functions of RNA modification.
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Affiliation(s)
- Yafen Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiong Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.
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Guo G, Pan K, Fang S, Ye L, Tong X, Wang Z, Xue X, Zhang H. Advances in mRNA 5-methylcytosine modifications: Detection, effectors, biological functions, and clinical relevance. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:575-593. [PMID: 34631286 PMCID: PMC8479277 DOI: 10.1016/j.omtn.2021.08.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-methylcytosine (m5C) post-transcriptional modifications affect the maturation, stability, and translation of the mRNA molecule. These modifications play an important role in many physiological and pathological processes, including stress response, tumorigenesis, tumor cell migration, embryogenesis, and viral replication. Recently, there has been a better understanding of the biological implications of m5C modification owing to the rapid development and optimization of detection technologies, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-BisSeq. Further, predictive models (such as PEA-m5C, m5C-PseDNC, and DeepMRMP) for the identification of potential m5C modification sites have also emerged. In this review, we summarize the current experimental detection methods and predictive models for mRNA m5C modifications, focusing on their advantages and limitations. We systematically surveyed the latest research on the effectors related to mRNA m5C modifications and their biological functions in multiple species. Finally, we discuss the physiological effects and pathological significance of m5C modifications in multiple diseases, as well as their therapeutic potential, thereby providing new perspectives for disease treatment and prognosis.
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Affiliation(s)
- Gangqiang Guo
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kan Pan
- First Clinical College, Wenzhou Medical University, Wenzhou, China
| | - Su Fang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinya Tong
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhibin Wang
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Wenzhou Collaborative Innovation Center of Gastrointestinal Cancer in Basic Research and Precision Medicine, Wenzhou Key Laboratory of Cancer-related Pathogens and Immunity, Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
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Cayir A. RNA modifications as emerging therapeutic targets. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1702. [PMID: 34816607 DOI: 10.1002/wrna.1702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022]
Abstract
The field of epitranscriptome, posttranscriptional modifications to RNAs, is still growing up and has presented substantial evidences for the role of RNA modifications in diseases. In terms of new drug development, RNA modifications have a great promise for therapy. For example, more than 170 type of modifications exist in various types of RNAs. Regulatory genes and their roles in critical biological process have been identified and they are associated with several diseases. Current data, for example, identification of inhibitors targeting RNA modifications regulatory genes, strongly support the idea that RNA modifications have potential as emerging therapeutic targets. Therefore, in this review, RNA modifications and regulatory genes were comprehensively documented in terms of drug development by summarizing the findings from previous studies. It was discussed how RNA modifications or regulatory genes can be targeted by altering molecular mechanisms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
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48
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Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library. Nat Methods 2021; 18:1213-1222. [PMID: 34594034 DOI: 10.1038/s41592-021-01280-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Recent years have witnessed rapid progress in the field of epitranscriptomics. Functional interpretation of the epitranscriptome relies on sequencing technologies that determine the location and stoichiometry of various RNA modifications. However, contradictory results have been reported among studies, bringing the biological impacts of certain RNA modifications into doubt. Here, we develop a synthetic RNA library resembling the endogenous transcriptome but without any RNA modification. By incorporating this modification-free RNA library into established mapping techniques as a negative control, we reveal abundant false positives resulting from sequence bias or RNA structure. After calibration, precise and quantitative mapping expands the understanding of two representative modification types, N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We propose that this approach provides a systematic solution for the calibration of various RNA-modification mappings and holds great promise in epitranscriptomic studies.
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Helm M, Schmidt-Dengler MC, Weber M, Motorin Y. General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents. Adv Biol (Weinh) 2021; 5:e2100866. [PMID: 34535986 DOI: 10.1002/adbi.202100866] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Indexed: 12/16/2022]
Abstract
Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Martina C Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität, Staudingerweg 5, D-55128, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UMS2008/US40 IBSLor, EpiRNA-Seq Core facility, Nancy, F-54000, France.,Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, F-54000, France
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50
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Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution. Nat Methods 2021; 18:1060-1067. [PMID: 34480159 DOI: 10.1038/s41592-021-01242-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent modification of messenger RNA in mammals. To interrogate its functions and dynamics, there is a critical need to quantify m6A at three levels: site, gene and sample. Current approaches address these needs in a limited manner. Here we develop m6A-seq2, relying on multiplexed m6A-immunoprecipitation of barcoded and pooled samples. m6A-seq2 allows a big increase in throughput while reducing technical variability, requirements of input material and cost. m6A-seq2 is furthermore uniquely capable of providing sample-level relative quantitations of m6A, serving as an orthogonal alternative to mass spectrometry-based approaches. Finally, we develop a computational approach for gene-level quantitation of m6A. We demonstrate that using this metric, roughly 30% of the variability in RNA half life in mouse embryonic stem cells can be explained, establishing m6A as a main driver of RNA stability. m6A-seq2 thus provides an experimental and analytic framework for dissecting m6A-mediated regulation at three different levels.
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