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Becker MA, Meiser N, Schmidt-Dengler M, Richter C, Wacker A, Schwalbe H, Hengesbach M. m 6A Methylation of Transcription Leader Sequence of SARS-CoV-2 Impacts Discontinuous Transcription of Subgenomic mRNAs. Chemistry 2024; 30:e202401897. [PMID: 38785102 DOI: 10.1002/chem.202401897] [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: 05/16/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/25/2024]
Abstract
The SARS-CoV-2 genome has been shown to be m6A methylated at several positions in vivo. Strikingly, a DRACH motif, the recognition motif for adenosine methylation, resides in the core of the transcriptional regulatory leader sequence (TRS-L) at position A74, which is highly conserved and essential for viral discontinuous transcription. Methylation at position A74 correlates with viral pathogenicity. Discontinuous transcription produces a set of subgenomic mRNAs that function as templates for translation of all structural and accessory proteins. A74 is base-paired in the short stem-loop structure 5'SL3 that opens during discontinuous transcription to form long-range RNA-RNA interactions with nascent (-)-strand transcripts at complementary TRS-body sequences. A74 can be methylated by the human METTL3/METTL14 complex in vitro. Here, we investigate its impact on the structural stability of 5'SL3 and the long-range TRS-leader:TRS-body duplex formation necessary for synthesis of subgenomic mRNAs of all four viral structural proteins. Methylation uniformly destabilizes 5'SL3 and long-range duplexes and alters their relative equilibrium populations, suggesting that the m6A74 modification acts as a regulator for the abundance of viral structural proteins due to this destabilization.
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Affiliation(s)
- Matthias A Becker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martina Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute of Pharmaceutical and Biomedical Sciences (IPBS), Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
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Li Y, Luo B, Lin X, Bai D, Li L, Gao D, Li X, Zhong X, Wei Y, Yang L, Zhu X, Han L, Tian H, Zhang R, Wang P. 20(R)-Panaxatriol enhances METTL3-mediated m 6A modification of STUB1 to inhibit autophagy and exert antitumor effects in Triple-Negative Breast Cancer cells. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 130:155537. [PMID: 38823344 DOI: 10.1016/j.phymed.2024.155537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/31/2024] [Accepted: 03/13/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Aberrant activation of autophagy in triple-negative breast cancer (TNBC) has led researchers to investigate potential therapeutic strategies targeting this process. The regulation of autophagy is significantly influenced by METTL3. Our previous research has shown that the Panax ginseng-derived compound, 20(R)-panaxatriol (PT), has potential as an anti-tumor agent. However, it remains unclear whether PT can modulate autophagy through METTL3 to exert its anti-tumor effects. OBJECTIVE Our objective is to investigate whether PT can regulate autophagy in TNBC cells and elucidate the molecular mechanisms. STUDY DESIGN For in vitro experiments, we employed SUM-159-PT and MDA-MB-231 cells. While in vivo experiments involved BALB/c nude mice and NOD/SCID mice. METHODS In vitro, TNBC cells were treated with PT, and cell lines with varying expression levels of METTL3 were established. We assessed the impact on tumor cell activity and autophagy by analyzing autophagic flux, Western Blot (WB), and methylation levels. In vivo, subcutaneous transplantation models were established in BALB/c nude and NOD/SCID mice to observe the effect of PT on TNBC growth. HE staining and immunofluorescence were employed to analyze histopathological changes in tumor tissues. MeRIP-seq and dual-luciferase reporter gene assays were used to identify key downstream targets. Additionally, the silencing of STIP1 Homology And U-Box Containing Protein 1 (STUB1) explored PT's effects. The mechanism of PT's action on STUB1 via METTL3 was elucidated through mRNA stability assays, mRNA alternative splicing analysis, and nuclear-cytoplasmic mRNA separation. RESULTS In both in vivo and in vitro experiments, it was discovered that PT significantly upregulates the expression of METTL3, leading to autophagy inhibition and therapeutic effects in TNBC. Simultaneously, through MeRIP-seq analysis and dual-luciferase reporter gene assays, we have demonstrated that PT modulates STUB1 via METTL3, influencing autophagy in TNBC cells. Furthermore, intriguingly, PT extends the half-life of STUB1 mRNA by enhancing its methylation modification, thereby enhancing its stability. CONCLUSION In summary, our research reveals that PT increases STUB1 m6A modification through a METTL3-mediated mechanism in TNBC cells, inhibiting autophagy and further accentuating its anti-tumor properties. Our study provides novel mechanistic insights into TNBC pathogenesis and potential drug targets for TNBC.
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Affiliation(s)
- Yan Li
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Bingjie Luo
- College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Xuan Lin
- The 8th Clinical Medical College of Guangzhou University of Chinese Medicine, Foshan 528000, PR China
| | - Donghui Bai
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Lingyu Li
- Cancer Research Institute, Jinan University, Guangzhou, Guangdong 510630, PR China; Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Jinan University, Guangzhou, Guangdong,510630, PR China; College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Duan Gao
- College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Xiaoyun Li
- College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Xianxun Zhong
- The 8th Clinical Medical College of Guangzhou University of Chinese Medicine, Foshan 528000, PR China
| | - Yaru Wei
- The 8th Clinical Medical College of Guangzhou University of Chinese Medicine, Foshan 528000, PR China
| | - Li Yang
- Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Jinan University, Guangzhou, Guangdong,510630, PR China; College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Xiaofeng Zhu
- College of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong 510630, PR China; Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Jinan University, Guangzhou, Guangdong,510630, PR China
| | - Li Han
- First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, PR China
| | - Huaqin Tian
- Foshan Hospital of Traditional Chinese Medicine, Foshan, Guangdong 528000, PR China.
| | - Ronghua Zhang
- Cancer Research Institute, Jinan University, Guangzhou, Guangdong 510630, PR China; Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Jinan University, Guangzhou, Guangdong,510630, PR China; College of Pharmacy, Jinan University, Guangzhou, Guangdong 510630, PR China.
| | - Panpan Wang
- Cancer Research Institute, Jinan University, Guangzhou, Guangdong 510630, PR China; Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Informatization, Jinan University, Guangzhou, Guangdong,510630, PR China; First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510630, PR China.
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Xue F, Zhang J, Wu D, Sun S, Fu M, Wang J, Searle I, Gao H, Liang W. m 6A demethylase OsALKBH5 is required for double-strand break formation and repair by affecting mRNA stability in rice meiosis. THE NEW PHYTOLOGIST 2024. [PMID: 39044689 DOI: 10.1111/nph.19976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 06/13/2024] [Indexed: 07/25/2024]
Abstract
N6-methyladenosine (m6A) RNA modification is the most prevalent messenger RNA (mRNA) modification in eukaryotes and plays critical roles in the regulation of gene expression. m6A is a reversible RNA modification that is deposited by methyltransferases (writers) and removed by demethylases (erasers). The function of m6A erasers in plants is highly diversified and their roles in cereal crops, especially in reproductive development essential for crop yield, are largely unknown. Here, we demonstrate that rice OsALKBH5 acts as an m6A demethylase required for the normal progression of male meiosis. OsALKBH5 is a nucleo-cytoplasmic protein, highly enriched in rice anthers during meiosis, that associates with P-bodies and exon junction complexes, suggesting that it is involved in regulating mRNA processing and abundance. Mutations of OsALKBH5 cause reduced double-strand break (DSB) formation, severe defects in DSB repair, and delayed meiotic progression, leading to complete male sterility. Transcriptome analysis and m6A profiling indicate that OsALKBH5-mediated m6A demethylation stabilizes the mRNA level of multiple meiotic genes directly or indirectly, including several genes that regulate DSB formation and repair. Our study reveals the indispensable role of m6A metabolism in post-transcriptional regulation of meiotic progression in rice.
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Affiliation(s)
- Feiyang Xue
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Wu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiyu Sun
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ming Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Wang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Iain Searle
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hongbo Gao
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, 572024, China
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Bao N, Wang Z, Fu J, Dong H, Jin Y. RNA structure in alternative splicing regulation: from mechanism to therapy. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034824 DOI: 10.3724/abbs.2024119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.
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Li F, Li W. Readers of RNA Modification in Cancer and Their Anticancer Inhibitors. Biomolecules 2024; 14:881. [PMID: 39062595 PMCID: PMC11275166 DOI: 10.3390/biom14070881] [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: 06/18/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.
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Affiliation(s)
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
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An TY, Hu QM, Ni P, Hua YQ, Wang D, Duan GC, Chen SY, Jia B. N6-methyladenosine modification of hypoxia-inducible factor-1α regulates Helicobacter pylori-associated gastric cancer via the PI3K/AKT pathway. World J Gastrointest Oncol 2024; 16:3270-3283. [PMID: 39072157 PMCID: PMC11271789 DOI: 10.4251/wjgo.v16.i7.3270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/09/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Helicobacter pylori (H. pylori) colonizes the human gastric mucosa and is implicated in the development of gastric cancer (GC). The tumor microenvironment is characterized by hypoxia, where hypoxia-inducible factor-1α (HIF-1α) plays a key role as a transcription factor, but the mechanisms underlying H. pylori-induced HIF-1α expression and carcinogenesis remain unclear. AIM To explore the underlying mechanism of H. pylori-induced HIF-1α expression in promoting the malignant biological behavior of gastric epithelial cells (GES-1). METHODS The study was conducted with human GES-1 cells in vitro. Relative protein levels of methyltransferase-like protein 14 (METTL14), HIF-1α, main proteins of the PI3K/AKT pathway, epithelial-mesenchymal transition (EMT) biomarkers, and invasion indicators were detected by Western blot. Relative mRNA levels of METTL14 and HIF-1α were detected by quantitative reverse transcription-polymerase chain reaction. mRNA stability was evaluated using actinomycin D, and the interaction between METTL14 and HIF-1α was confirmed by immunofluorescence staining. Cell proliferation and migration were evaluated by cell counting kit-8 assay and wound healing assay, respectively. RESULTS H. pylori promoted HIF-1α expression and activated the PI3K/AKT pathway. Notably, METTL14 was downregulated in H. pylori-infected gastric mucosal epithelial cells and positively regulated HIF-1α expression. Functional experiments showed that the overexpression of HIF-1α or knockdown of METTL14 enhanced the activity of the PI3K/AKT pathway, thereby driving a series of malignant transformation, such as EMT and cell proliferation, migration, and invasion. By contrast, the knockdown of HIF-1α or overexpression of METTL14 had an opposite effect. CONCLUSION H. pylori-induced underexpression of METTL14 promotes the translation of HIF-1α and accelerates tumor progression by activating the PI3K/AKT pathway. These results provide novel insights into the carcinogenesis of GC.
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Affiliation(s)
- Tong-Yan An
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Quan-Man Hu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Peng Ni
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Yan-Qiao Hua
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Di Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Guang-Cai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Shuai-Yin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan Province, China
| | - Bin Jia
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
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Chen Y, Liu M, Lu M, Luo L, Han Z, Liu X. Exploring the impact of m 6A modification on immune diseases: mechanisms and therapeutic implication. Front Immunol 2024; 15:1387582. [PMID: 39072324 PMCID: PMC11272477 DOI: 10.3389/fimmu.2024.1387582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
N6-methyladenosine (m6A) is a chemical modification of RNA and has become a widely discussed topic among scientific researchers in recent years. It is distributed in various organisms, including eukaryotes and bacteria. It has been found that m6A is composed of writers, erasers and readers and is involved in biological functions such as splicing, transport and translation of RNA. The balance of the human immune microenvironment is important for human health abnormalities. Increasing studies have found that m6A affects the development of immune diseases such as inflammatory enteritis and systemic lupus erythematosus (SLE) by participating in the homeostatic regulation of the immune microenvironment in vivo. In this manuscript, we introduce the composition, biological function, regulation of m6A in the immune microenvironment and its progression in various immune diseases, providing new targets and directions for the treatment of immune diseases in clinical practice.
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Affiliation(s)
- Yutong Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Min Liu
- Department of Traditional Chinese Medicine, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, Zhejiang, China
| | - Miao Lu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Linling Luo
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhongyu Han
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xide Liu
- Department of Traditional Chinese Medicine, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou, Zhejiang, China
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Shu G, Zhao Z, Zhao T, Deng C, Zhu J, Han Y, Chen M, Jing J, Bai G, Li D, Li F, He J, Fu W, Liu G. N 6-methyladenosine modification of circMARK2 enhances cytoplasmic export and stabilizes LIN28B, contributing to the progression of Wilms tumor. J Exp Clin Cancer Res 2024; 43:191. [PMID: 38987793 PMCID: PMC11238472 DOI: 10.1186/s13046-024-03113-9] [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: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The potential involvement of circular RNAs (circRNAs) and N6-methyladenosine (m6A) modification in the progression of Wilms tumor (WT) has not been fully elucidated. This study investigates the regulatory mechanisms and clinical significance of m6A-modified circMARK2 and its role in WT progression. METHODS We identified dysregulated circRNAs through deep sequencing and validated their expression by qRT-PCR in WT tissues. The biological functions of circMARK2 were assessed using clone formation, transwell migration, and orthotopic animal models. To dissect the underlying mechanisms, we employed RNA immunoprecipitation, RNA pull-down, dual-luciferase reporter assays, Western blotting, and immunofluorescence and immunohistochemical staining. RESULTS CircMARK2, upregulated in WT tissues, was found to be m6A-modified and promoted cytoplasmic export. It facilitated WT progression by stabilizing LIN28B mRNA through the circMARK2/IGF2BP2 interaction. In vitro and in vivo studies demonstrated that circMARK2 enhances the malignant behavior of WT cells. Clinically, higher circMARK2 levels in tumor tissues of WT patients were linked to increased tumor aggressiveness and reduced survival rates. CONCLUSIONS Our study provides the first comprehensive evidence that m6A-modified circMARK2 contributes to WT progression by enhancing LIN28B mRNA stability, promoting cellular aggressiveness. CircMARK2 emerges as a potential biomarker for prognosis and a promising target for therapeutic intervention in WT, underscoring the clinical relevance of m6A modification in pediatric renal cancer.
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Affiliation(s)
- Guannan Shu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Zhang Zhao
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Tianxin Zhao
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Changmi Deng
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Jiangquan Zhu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Yufeng Han
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Minyu Chen
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, Guangdong, China
| | - Jiajia Jing
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Gaochen Bai
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Dian Li
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China
| | - Feng Li
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China.
| | - Wen Fu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China.
| | - Guochang Liu
- Department of Urology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou Institute of Pediatrics, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, Guangdong, China.
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Liu Y, Zheng L, Li Y, Ma L, Zheng N, Liu X, Zhao Y, Yu L, Liu N, Liu S, Zhang K, Zhou J, Wei M, Yang C, Yang G. Neratinib impairs function of m6A recognition on AML1-ETO pre-mRNA and induces differentiation of t (8;21) AML cells by targeting HNRNPA3. Cancer Lett 2024; 594:216980. [PMID: 38797229 DOI: 10.1016/j.canlet.2024.216980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
Acute myeloid leukemia (AML) is frequently linked to genetic abnormalities, with the t (8; 21) translocation, resulting in the production of a fusion oncoprotein AML1-ETO (AE), being a prevalent occurrence. This protein plays a pivotal role in t (8; 21) AML's onset, advancement, and recurrence, making it a therapeutic target. However, the development of drug molecules targeting AML1-ETO are markedly insufficient, especially used in clinical treatment. In this study, it was uncovered that Neratinib could significantly downregulate AML1-ETO protein level, subsequently promoting differentiation of t (8; 21) AML cells. Based on "differentiated active" probes, Neratinib was identified as a functional inhibitor against HNRNPA3 through covalent binding. The further studies demonstrated that HNRNPA3 function as a putative m6A reader responsible for recognizing and regulating the alternative splicing of AML-ETO pre-mRNA. These findings not only contribute to a novel insight to the mechanism governing post-transcriptional modification of AML1-ETO transcript, but also suggest that Neratinib would be promising therapeutic potential for t (8; 21) AML treatment.
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MESH Headings
- Humans
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Quinolines/pharmacology
- Cell Differentiation/drug effects
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- RNA Precursors/metabolism
- RNA Precursors/genetics
- Heterogeneous-Nuclear Ribonucleoprotein Group A-B/metabolism
- Heterogeneous-Nuclear Ribonucleoprotein Group A-B/genetics
- Translocation, Genetic/drug effects
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adenosine/pharmacology
- Alternative Splicing/drug effects
- Cell Line, Tumor
- Animals
- Mice
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Affiliation(s)
- Yulin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Liting Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Ying Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lan Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Nan Zheng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Xinhua Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Yanli Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, PR China
| | - Ning Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Shuangwei Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Kun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Jingfeng Zhou
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, PR China.
| | - Mingming Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Cheng Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Guang Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
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Du B, Wang P, Wei L, Qin K, Pei Z, Zheng J, Wang J. Unraveling the independent role of METTL3 in m6A modification and tumor progression in esophageal squamous cell carcinoma. Sci Rep 2024; 14:15398. [PMID: 38965238 PMCID: PMC11224396 DOI: 10.1038/s41598-024-64517-3] [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: 01/17/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
METTL3 and METTL14 are traditionally posited to assemble the m6A methyltransferase complex in a stoichiometric 1:1 ratio, modulating mRNA fate via m6A modifications. Nevertheless, recent investigations reveal inconsistent expression levels and prognostic significance of METTL3 and METTL14 across various tumor types, challenging their consistent functional engagement in neoplastic contexts. A pan-cancer analysis leveraging The Cancer Genome Atlas (TCGA) data has identified pronounced disparities in the expression patterns, functional roles, and correlations with tumor burden between METTL3 and METTL14, particularly in esophageal squamous cell carcinoma (ESCC). Knockdown experiments of METTL3 in EC109 cells markedly suppress cell proliferation both in vitro and in vivo, whereas METTL14 knockdown shows a comparatively muted effect on proliferation and does not significantly alter METTL3 protein levels. mRNA sequencing indicates that METTL3 singularly governs the expression of 1615 genes, with only 776 genes co-regulated with METTL14. Additionally, immunofluorescence co-localization studies suggest discrepancies in cellular localization between METTL3 and METTL14. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analyses demonstrate that METTL3 uniquely associates with the Nop56p-linked pre-rRNA complex and mRNA splicing machinery, independent of METTL14. Preliminary bioinformatics and multi-omics investigations reveal that METTL3's autonomous role in modulating tumor cell proliferation and its involvement in mRNA splicing are potentially pivotal molecular mechanisms. Our study lays both experimental and theoretical groundwork for a deeper understanding of the m6A methyltransferase complex and the development of targeted tumor therapies focusing on METTL3.
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Affiliation(s)
- Bin Du
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Pu Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Lingyu Wei
- Central Laboratory of Clinical Research, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 047500, China
| | - Kai Qin
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Zhen Pei
- Department of Physiology, Changzhi Medical College, Changzhi, 047500, China
| | - Jinping Zheng
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China
| | - Jia Wang
- Center of Healthy Aging, Changzhi Medical College, Changzhi, 047500, China.
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61
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Skeparnias I, Bou-Nader C, Anastasakis DG, Fan L, Wang YX, Hafner M, Zhang J. Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol 2024:10.1038/s41594-024-01340-4. [PMID: 38956168 DOI: 10.1038/s41594-024-01340-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) has key roles in regulating transcription, splicing, tumorigenesis, etc. Its maturation and stabilization require precise processing by RNase P, which simultaneously initiates the biogenesis of a 3' cytoplasmic MALAT1-associated small cytoplasmic RNA (mascRNA). mascRNA was proposed to fold into a transfer RNA (tRNA)-like secondary structure but lacks eight conserved linking residues required by the canonical tRNA fold. Here we report crystal structures of human mascRNA before and after processing, which reveal an ultracompact, quasi-tRNA-like structure. Despite lacking all linker residues, mascRNA faithfully recreates the characteristic 'elbow' feature of tRNAs to recruit RNase P and ElaC homolog protein 2 (ELAC2) for processing, which exhibit distinct substrate specificities. Rotation and repositioning of the D-stem and anticodon regions preclude mascRNA from aminoacylation, avoiding interference with translation. Therefore, a class of metazoan lncRNA loci uses a previously unrecognized, unusually streamlined quasi-tRNA architecture to recruit select tRNA-processing enzymes while excluding others to drive bespoke RNA biogenesis, processing and maturation.
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Affiliation(s)
- Ilias Skeparnias
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Dimitrios G Anastasakis
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD, USA
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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Zou Z, He C. The YTHDF proteins display distinct cellular functions on m 6A-modified RNA. Trends Biochem Sci 2024; 49:611-621. [PMID: 38677920 PMCID: PMC11227416 DOI: 10.1016/j.tibs.2024.04.001] [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: 01/09/2024] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
YTHDF proteins are main cytoplasmic 'reader' proteins of RNA N6-methyladenosine (m6A) methylation in mammals. They are largely responsible for m6A-mediated regulation in the cell cytosol by controlling both mRNA translation and degradation. Recent functional and mechanistic investigations of the YTHDF proteins revealed that these proteins have different functions to enable versatile regulation of the epitranscriptome. Their divergent functions largely originate from their different amino acid sequences in the low-complexity N termini. Consequently, they have different phase separation propensities and possess distinct post-translational modifications (PTMs). Different PTMs, subcellular localizations, and competition among partner proteins have emerged as three major mechanisms that control the functions of these YTHDF proteins. We also summarize recent progress on critical roles of these YTHDF proteins in anticancer immunity and the potential for targeting these proteins for developing new anticancer therapies.
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Affiliation(s)
- Zhongyu Zou
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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63
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Yang J, Liang F, Zhang F, Zhao H, Gong Q, Gao N. Recent advances in the reciprocal regulation of m 6A modification with non-coding RNAs and its therapeutic application in acute myeloid leukemia. Pharmacol Ther 2024; 259:108671. [PMID: 38830387 DOI: 10.1016/j.pharmthera.2024.108671] [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: 03/08/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/05/2024]
Abstract
N6-methyladenosine (m6A) is one of the most common modifications of RNA in eukaryotic cells and is involved in mRNA metabolism, including stability, translation, maturation, splicing, and export. m6A also participates in the modification of multiple types of non-coding RNAs, such as microRNAs, long non-coding RNAs, and circular RNAs, thereby affecting their metabolism and functions. Increasing evidence has revealed that m6A regulators, such as writers, erasers, and readers, perform m6A-dependent modification of ncRNAs, thus affecting cancer progression. Moreover, ncRNAs modulate m6A regulators to affect cancer development and progression. In this review, we summarize recent advances in understanding m6A modification and ncRNAs and provide insights into the interaction between m6A modification and ncRNAs in cancer. We also discuss the potential clinical applications of the mechanisms underlying the interplay between m6A modifications and ncRNAs in acute myeloid leukemia (AML). Therefore, clarifying the mutual regulation between m6A modifications and ncRNAs is of great significance to identify novel therapeutic targets for AML and has great clinical application prospects.
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Affiliation(s)
- Jiawang Yang
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, Guizhou, China; Chinese Phramcological Society-Guizhou Province Joint Laboratory for Pharmacology, Zunyi 563000, Guizhou, China
| | - Feng Liang
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, Guizhou, China; Chinese Phramcological Society-Guizhou Province Joint Laboratory for Pharmacology, Zunyi 563000, Guizhou, China
| | - Fenglin Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, Guizhou, China; Chinese Phramcological Society-Guizhou Province Joint Laboratory for Pharmacology, Zunyi 563000, Guizhou, China
| | - Hailong Zhao
- Department of Pathophysiology, Zunyi Medical University, Zunyi 563000, Guizhou, China.
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, Guizhou, China; Chinese Phramcological Society-Guizhou Province Joint Laboratory for Pharmacology, Zunyi 563000, Guizhou, China.
| | - Ning Gao
- Key Laboratory of Basic Pharmacology of Ministry of Education, Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, Guizhou, China; Chinese Phramcological Society-Guizhou Province Joint Laboratory for Pharmacology, Zunyi 563000, Guizhou, China.
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64
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Zheng Y, Lin S, Chen M, Xu L, Huang H. Regulation of N 6-methyladenosine modification in erythropoiesis and thalassemia. Clin Genet 2024; 106:3-12. [PMID: 38488342 DOI: 10.1111/cge.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 06/04/2024]
Abstract
In eukaryotic RNA, N6-methyladenosine (m6A) is a prevalent form of methylation modification. The m6A modification process is reversible and dynamic, written by m6A methyltransferase complex, erased by m6A demethylase, and recognized by m6A binding proteins. Through mediating RNA stability, decay, alternative splicing, and translation processes, m6A modification regulates gene expression at the post-transcriptional level. Erythropoiesis is the process of hematopoietic stem cells undergoing proliferation, a series of differentiation and maturation to form red blood cells (RBCs). Thalassemia is a common monogenic disease characterized by excessive production of ineffective RBCs in the peripheral circulation, resulting in hemolytic anemia. Increasing evidence suggests that m6A modification plays a crucial role in erythropoiesis. In this review, we comprehensively summarize the function of m6A modification in erythropoiesis and further generalize the mechanism of m6A modification regulating ineffective erythropoiesis and fetal hemoglobin expression. The purpose is to improve the understanding of the pathogenesis of erythroid dysplasia and offer new perspectives for the diagnosis and treatment of thalassemia.
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Affiliation(s)
- Yanping Zheng
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
| | - Siyang Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
- The School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
- The School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- Fujian Clinical Research Center for Maternal-Fetal Medicine, Fuzhou, China
- National Key Obstetric Clinical Specialty Construction Institution of China, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
- The School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- Fujian Clinical Research Center for Maternal-Fetal Medicine, Fuzhou, China
- National Key Obstetric Clinical Specialty Construction Institution of China, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fujian Medical University, Fuzhou, China
- The School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- Fujian Clinical Research Center for Maternal-Fetal Medicine, Fuzhou, China
- National Key Obstetric Clinical Specialty Construction Institution of China, Fuzhou, China
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65
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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66
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Zhang L, Xia J. N6-Methyladenosine Methylation of mRNA in Cell Apoptosis. Mol Neurobiol 2024; 61:3934-3948. [PMID: 38040996 DOI: 10.1007/s12035-023-03813-x] [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: 11/24/2022] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
Apoptosis, a highly controlled homeostatic mechanism that eliminates single cells without destroying tissue function, occurs during growing development and senescence. N6-methyladenosine (m6A), as the most common internal modification of eukaryotic mRNA, fine-tunes gene expression by regulating many aspects of mRNA metabolism, such as splicing, nucleation, stability, translation, and degradation. Remarkably, recent reports have indicated that aberrant methylation of m6A-related RNA may directly or indirectly influence the expression of apoptosis-related genes, thus regulating the process of cell apoptosis. In this review, we summarized the relationship between m6A modification and cell apoptosis, especially its role in the nervous system, and analyzed the limitations of the current research.
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Affiliation(s)
- Lin Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, People's Republic of China.
- Clinical Research Center for Cerebrovascular Disease of Hunan Province, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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67
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Hasan M, Nishat ZS, Hasan MS, Hossain T, Ghosh A. Identification of m 6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli. Biochem Biophys Rep 2024; 38:101677. [PMID: 38511186 PMCID: PMC10950732 DOI: 10.1016/j.bbrep.2024.101677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.
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Affiliation(s)
| | | | - Md. Soyib Hasan
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Tanvir Hossain
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
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68
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Garbo S, D'Andrea D, Colantoni A, Fiorentino F, Mai A, Ramos A, Tartaglia GG, Tancredi A, Tripodi M, Battistelli C. m6A modification inhibits miRNAs' intracellular function, favoring their extracellular export for intercellular communication. Cell Rep 2024; 43:114369. [PMID: 38878288 DOI: 10.1016/j.celrep.2024.114369] [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: 10/13/2023] [Revised: 04/19/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
Epitranscriptomics represents a further layer of gene expression regulation. Specifically, N6-methyladenosine (m6A) regulates RNA maturation, stability, degradation, and translation. Regarding microRNAs (miRNAs), while it has been reported that m6A impacts their biogenesis, the functional effects on mature miRNAs remain unclear. Here, we show that m6A modification on specific miRNAs weakens their coupling to AGO2, impairs their function on target mRNAs, determines their delivery into extracellular vesicles (EVs), and provides functional information to receiving cells. Mechanistically, the intracellular functional impairment is caused by m6A-mediated inhibition of AGO2/miRNA interaction, the EV loading is favored by m6A-mediated recognition by the RNA-binding protein (RBP) hnRNPA2B1, and the EV-miRNA function in the receiving cell requires their FTO-mediated demethylation. Consequently, cells express specific miRNAs that do not impact endogenous transcripts but provide regulatory information for cell-to-cell communication. This highlights that a further level of complexity should be considered when relating cellular dynamics to specific miRNAs.
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Affiliation(s)
- Sabrina Garbo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy
| | - Daniel D'Andrea
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Alessio Colantoni
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Fiorentino
- Center for Life Nano- and Neuro-Science, RNA Systems Biology Lab, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies Sapienza University of Rome, Ple. Aldo Moro 5, 00185 Rome, Italy
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6XA, UK
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Andrea Tancredi
- Dipartimento Metodi e Modelli per l'Economia, il Territorio e la Finanza MEMOTEF, Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Tripodi
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
| | - Cecilia Battistelli
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
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69
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Wu Z, Ke Q, Jiang L, Hong H, Pan W, Chen W, Abudukeremu X, She F, Chen Y. TGF-β1 facilitates gallbladder carcinoma metastasis by regulating FOXA1 translation efficiency through m 6A modification. Cell Death Dis 2024; 15:422. [PMID: 38886389 PMCID: PMC11183149 DOI: 10.1038/s41419-024-06800-9] [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: 10/13/2023] [Revised: 05/22/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024]
Abstract
TGF-β1 plays a pivotal role in the metastatic cascade of malignant neoplasms. N6-methyladenosine (m6A) stands as one of the most abundant modifications on the mRNA transcriptome. However, in the metastasis of gallbladder carcinoma (GBC), the effect of TGF-β1 with mRNA m6A modification, especially the effect of mRNA translation efficiency associated with m6A modification, remains poorly elucidated. Here we demonstrated a negative correlation between FOXA1 and TGF-β1 expression in GBC. Overexpression of FOXA1 inhibited TGF-β1-induced migration and epithelial-mesenchymal transition (EMT) in GBC cells. Mechanistically, we confirmed that TGF-β1 suppressed the translation efficiency of FOXA1 mRNA through polysome profiling analysis. Importantly, both in vivo and in vitro experiments showed that TGF-β1 promoted m6A modification on the coding sequence (CDS) region of FOXA1 mRNA, which was responsible for the inhibition of FOXA1 mRNA translation by TGF-β1. We demonstrated through MeRIP and RIP assays, dual-luciferase reporter assays and site-directed mutagenesis that ALKBH5 promoted FOXA1 protein expression by inhibiting m6A modification on the CDS region of FOXA1 mRNA. Moreover, TGF-β1 inhibited the binding capacity of ALKBH5 to the FOXA1 CDS region. Lastly, our study confirmed that overexpression of FOXA1 suppressed lung metastasis and EMT in a nude mice lung metastasis model. In summary, our research findings underscore the role of TGF-β1 in regulating TGF-β1/FOXA1-induced GBC EMT and metastasis by inhibiting FOXA1 translation efficiency through m6A modification.
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Affiliation(s)
- Zhenheng Wu
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fujian Medical University, Fuzhou, Fujian, 350122, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, Fujian, 350122, China
| | - Qiming Ke
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fujian Medical University, Fuzhou, Fujian, 350122, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, Fujian, 350122, China
| | - Lei Jiang
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
| | - Haijie Hong
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
| | - Wei Pan
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
| | - Wen Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
| | - Xiahenazi Abudukeremu
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China
| | - Feifei She
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fujian Medical University, Fuzhou, Fujian, 350122, China.
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, Fujian, 350122, China.
| | - Yanling Chen
- Department of Hepatobiliary Surgery and Fujian Institute of Hepatobiliary Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China.
- Fujian Medical University Cancer Center, Fuzhou, Fujian, 350122, China.
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fujian Medical University, Fuzhou, Fujian, 350122, China.
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, Fujian, 350122, China.
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Chen A, Zhang VX, Zhang Q, Sze KMF, Tian L, Huang H, Wang X, Lee E, Lu J, Lyu X, Lee MFJ, Wong CM, Ho DWH, Ng IOL. Targeting the oncogenic m6A demethylase FTO suppresses tumourigenesis and potentiates immune response in hepatocellular carcinoma. Gut 2024:gutjnl-2024-331903. [PMID: 38839271 DOI: 10.1136/gutjnl-2024-331903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
OBJECTIVE Fat mass and obesity-associated protein (FTO), an eraser of N 6-methyadenosine (m6A), plays oncogenic roles in various cancers. However, its role in hepatocellular carcinoma (HCC) is unclear. Furthermore, small extracellular vesicles (sEVs, or exosomes) are critical mediators of tumourigenesis and metastasis, but the relationship between FTO-mediated m6A modification and sEVs in HCC is unknown. DESIGN The functions and mechanisms of FTO and glycoprotein non-metastatic melanoma protein B (GPNMB) in HCC progression were investigated in vitro and in vivo. Neutralising antibody of syndecan-4 (SDC4) was used to assess the significance of sEV-GPNMB. FTO inhibitor CS2 was used to examine the effects on anti-PD-1 and sorafenib treatment. RESULTS FTO expression was upregulated in patient HCC tumours. Functionally, FTO promoted HCC cell proliferation, migration and invasion in vitro, and tumour growth and metastasis in vivo. FTO knockdown enhanced the activation and recruitment of tumour-infiltrating CD8+ T cells. Furthermore, we identified GPNMB to be a downstream target of FTO, which reduced the m6A abundance of GPNMB, hence, stabilising it from degradation by YTH N 6-methyladenosine RNA binding protein F2. Of note, GPNMB was packaged into sEVs derived from HCC cells and bound to the surface receptor SDC4 of CD8+ T cells, resulting in the inhibition of CD8+ T cell activation. A potential FTO inhibitor, CS2, suppresses the oncogenic functions of HCC cells and enhances the sensitivity of anti-PD-1 and sorafenib treatment. CONCLUSION Targeting the FTO/m6A/GPNMB axis could significantly suppress tumour growth and metastasis, and enhance immune activation, highlighting the potential of targeting FTO signalling with effective inhibitors for HCC therapy.
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Affiliation(s)
- Ao Chen
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
- Department of Biology, Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei Province, China
| | - Vanilla Xin Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Qingyang Zhang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Karen Man-Fong Sze
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Lu Tian
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Hongyang Huang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xia Wang
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Eva Lee
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jingyi Lu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xueying Lyu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Man-Fong Joyce Lee
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chun Ming Wong
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
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Khan FA, Nsengimana B, Awan UA, Ji XY, Ji S, Dong J. Regulatory roles of N6-methyladenosine (m 6A) methylation in RNA processing and non-communicable diseases. Cancer Gene Ther 2024:10.1038/s41417-024-00789-1. [PMID: 38839892 DOI: 10.1038/s41417-024-00789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Post-transcriptional RNA modification is an emerging epigenetic control mechanism in cells that is important in many different cellular and organismal processes. N6-methyladenosine (m6A) is one of the most prevalent, prolific, and ubiquitous internal transcriptional alterations in eukaryotic mRNAs, making it an important topic in the field of Epigenetics. m6A methylation acts as a dynamical regulatory process that regulates the activity of genes and participates in multiple physiological processes, by supporting multiple aspects of essential mRNA metabolic processes, including pre-mRNA splicing, nuclear export, translation, miRNA synthesis, and stability. Extensive research has linked aberrations in m6A modification and m6A-associated proteins to a wide range of human diseases. However, the impact of m6A on mRNA metabolism and its pathological connection between m6A and other non-communicable diseases, including cardiovascular disease, neurodegenerative disorders, liver diseases, and cancer remains in fragmentation. Here, we review the existing understanding of the overall role of mechanisms by which m6A exerts its activities and address new discoveries that highlight m6A's diverse involvement in gene expression regulation. We discuss m6A deposition on mRNA and its consequences on degradation, translation, and transcription, as well as m6A methylation of non-coding chromosomal-associated RNA species. This study could give new information about the molecular process, early detection, tailored treatment, and predictive evaluation of human non-communicable diseases like cancer. We also explore more about new data that suggests targeting m6A regulators in diseases may have therapeutic advantages.
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Affiliation(s)
- Faiz Ali Khan
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan.
| | - Bernard Nsengimana
- Department of Hepatobiliary Surgery, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Usman Ayub Awan
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xin-Ying Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
| | - Shaoping Ji
- Center for Molecular Medicine, Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou, Henan, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Jingcheng Dong
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Institute of Integrative Medicine, Fudan University, Shanghai, China.
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Ni P, Xu J, Zhong Z, Luo F, Wang J. RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads. Bioinformatics 2024; 40:btae375. [PMID: 38889266 PMCID: PMC11211211 DOI: 10.1093/bioinformatics/btae375] [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: 01/26/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 06/20/2024] Open
Abstract
MOTIVATION Nanopore direct RNA sequencing (DRS) enables the detection of RNA N6-methyladenosine (m6A) without extra laboratory techniques. A number of supervised or comparative approaches have been developed to identify m6A from Nanopore DRS reads. However, existing methods typically utilize either statistical features of the current signals or basecalling-error features, ignoring the richer information of the raw signals of DRS reads. RESULTS Here, we propose RedNano, a deep-learning method designed to detect m6A from Nanopore DRS reads by utilizing both raw signals and basecalling errors. RedNano processes the raw-signal feature and basecalling-error feature through residual networks. We validated the effectiveness of RedNano using synthesized, Arabidopsis, and human DRS data. The results demonstrate that RedNano surpasses existing methods by achieving higher area under the ROC curve (AUC) and area under the precision-recall curve (AUPRs) in all three datasets. Furthermore, RedNano performs better in cross-species validation, demonstrating its robustness. Additionally, when detecting m6A from an independent dataset of Populus trichocarpa, RedNano achieves the highest AUC and AUPR, which are 3.8%-9.9% and 5.5%-13.8% higher than other methods, respectively. AVAILABILITY AND IMPLEMENTATION The source code of RedNano is freely available at https://github.com/Derryxu/RedNano.
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Affiliation(s)
- Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
- Xiangjiang Laboratory, Changsha 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China
| | - Jinrui Xu
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
- Xiangjiang Laboratory, Changsha 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China
| | - Zeyu Zhong
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
- Xiangjiang Laboratory, Changsha 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC 29634-0974, United States
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
- Xiangjiang Laboratory, Changsha 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha 410083, China
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Chen JJ, Lu TZ, Wang T, Yan WH, Zhong FY, Qu XH, Gong XC, Li JG, Tou FF, Jiang LP, Han XJ. The m6A reader HNRNPC promotes glioma progression by enhancing the stability of IRAK1 mRNA through the MAPK pathway. Cell Death Dis 2024; 15:390. [PMID: 38830885 PMCID: PMC11148022 DOI: 10.1038/s41419-024-06736-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024]
Abstract
Glioma is the most common and aggressive type of primary malignant brain tumor. The N6-methyladenosine (m6A) modification widely exists in eukaryotic cells and plays an important role in the occurrence and development of human tumors. However, the function and mechanism of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an RNA-binding protein and m6A reader in gliomas remains to be comprehensively and extensively explored. Herein, we found that HNRNPC mRNA and protein overexpression were associated with a poor prognosis for patients with gliomas, based on the data from TCGA, the CGGA, and the TMAs. Biologically, HNRNPC knockdown markedly repressed malignant phenotypes of glioma in vitro and in vivo, whereas ectopic HNRNPC expression had the opposite effect. Integrative RNA sequencing and MeRIP sequencing analyses identified interleukin-1 receptor-associated kinase 1 (IRAK1) as a downstream target of HNRNPC. The glioma public datasets and tissue microarrays (TMAs) data indicated that IRAK1 overexpression was associated with poor prognosis, and IRAK1 knockdown significantly repressed malignant biological behavior in vitro. Mechanistically, HNRNPC maintains the mRNA stability of IRAK1 in an m6A-dependent manner, resulting in activation of the mitogen-activated protein kinase (MAPK) signaling pathway, which was necessary for the malignant behavior of glioma. Our findings demonstrate the HNRNPC-IRAK1-MAPK axis as a crucial carcinogenic factor for glioma and the novel underlying mechanism of IRAK1 upregulation, which provides a rationale for therapeutically targeting epitranscriptomic modulators in glioma.
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Affiliation(s)
- Jun-Jun Chen
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Tian-Zhu Lu
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Tao Wang
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Wen-Hui Yan
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Fang-Yan Zhong
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Xin-Hui Qu
- The Second Department of Neurology, Jiangxi Provincial People's Hospital & the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Xiao-Chang Gong
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Jin-Gao Li
- NHC Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi, 330029, PR China
| | - Fang-Fang Tou
- Department of Oncology, Jiangxi Provincial People's Hospital & the First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China
| | - Li-Ping Jiang
- Department of Pharmacology, School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
- Key Laboratory of Drug Targets and Drug Screening of Jiangxi Province, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Xiao-Jian Han
- Institute of Geriatrics, Jiangxi Provincial People's Hospital & The First Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330006, PR China.
- Key Laboratory of Drug Targets and Drug Screening of Jiangxi Province, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China.
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Wang S, Yang Y, Jiang X, Zheng X, Wei Q, Dai W, Zhang X. Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier. Cell Death Discov 2024; 10:271. [PMID: 38830900 PMCID: PMC11148167 DOI: 10.1038/s41420-024-02043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
The intestinal lumen acts as a critical interface connecting the external environment with the body's internal state. It's essential to prevent the passage of harmful antigens and bacteria while facilitating nutrient and water absorption. The intestinal barriers encompass microbial, mechanical, immunological, and chemical elements, working together to maintain intestinal balance. Numerous studies have associated m6A modification with intestinal homeostasis. This review comprehensively outlines potential mechanisms through which m6A modification could initiate, exacerbate, or sustain barrier damage from an intestinal perspective. The pivotal role of m6A modification in preserving intestinal equilibrium provides new insights, guiding the exploration of m6A modification as a target for optimizing preventive and therapeutic strategies for intestinal homeostasis.
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Affiliation(s)
| | - Yuzhong Yang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Xiaohan Jiang
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Qiufang Wei
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China
| | - Wenbin Dai
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China.
| | - Xuemei Zhang
- Department of Pathology, Liuzhou People's Hospital Affiliated to Guangxi Medical University, Liuzhou, Guangxi, China.
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Jiang J, Duan M, Wang Z, Lai Y, Zhang C, Duan C. RNA epigenetics in pulmonary diseases: Insights into methylation modification of lncRNAs in lung cancer. Biomed Pharmacother 2024; 175:116704. [PMID: 38749181 DOI: 10.1016/j.biopha.2024.116704] [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: 03/15/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/03/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are pivotal controllers of gene expression through epigenetic mechanisms, Methylation, a prominent area of study in epigenetics, significantly impacts cellular processes. Various RNA base methylations, including m6A, m5C, m1A, and 2'-O-methylation, profoundly influence lncRNA folding, interactions, and stability, thereby shaping their functionality. LncRNAs and methylation significantly contribute to tumor development, especially in lung cancer. Their roles encompass cell differentiation, proliferation, the generation of cancer stem cells, and modulation of immune responses. Recent studies have suggested that dysregulation of lncRNA methylation can contribute to lung cancer development. Furthermore, methylation modifications of lncRNAs hold potential for clinical application in lung cancer. Dysregulated lncRNA methylation can promote lung cancer progression and may offer insights into potential biomarker or therapeutic target. This review summarizes the current knowledge of lncRNA methylation in lung cancer and its implications for RNA epigenetics and pulmonary diseases.
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Affiliation(s)
- Junjie Jiang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Minghao Duan
- Department of Public Health Laboratory Sciences, School of Public Health, Hengyang Medical School, University of South China, Hengyang, 412017, Hunan, People's Republic of China
| | - Zheng Wang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Yuwei Lai
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China
| | - Chaojun Duan
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, 410008, Hunan, People's Republic of China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha 410008, Hunan, People's Republic of China; National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China.
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024; 56:1235-1249. [PMID: 38871819 PMCID: PMC11263585 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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Feng Z, Xiao H, Wang X, Niu Y, Zhao D, Tian C, Wang S, Peng B, Yang F, Geng B, Guo M, Sheng X, Xia Y. Unraveling Key m 6A Modification Regulators Signatures in Postmenopausal Osteoporosis through Bioinformatics and Experimental Verification. Orthop Surg 2024; 16:1418-1433. [PMID: 38658320 PMCID: PMC11144519 DOI: 10.1111/os.14064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
OBJECTIVE Bone marrow mesenchymal stem cells (BMSCs) show significant potential for osteogenic differentiation. However, the underlying mechanisms of osteogenic capability in osteoporosis-derived BMSCs (OP-BMSCs) remain unclear. This study aims to explore the impact of YTHDF3 (YTH N6-methyladenosine RNA binding protein 3) on the osteogenic traits of OP-BMSCs and identify potential therapeutic targets to boost their bone formation ability. METHODS We examined microarray datasets (GSE35956 and GSE35958) from the Gene Expression Omnibus (GEO) to identify potential m6A regulators in osteoporosis (OP). Employing differential, protein interaction, and machine learning analyses, we pinpointed critical hub genes linked to OP. We further probed the relationship between these genes and OP using single-cell analysis, immune infiltration assessment, and Mendelian randomization. Our in vivo and in vitro experiments validated the expression and functionality of the key hub gene. RESULTS Differential analysis revealed seven key hub genes related to OP, with YTHDF3 as a central player, supported by protein interaction analysis and machine learning methodologies. Subsequent single-cell, immune infiltration, and Mendelian randomization studies consistently validated YTHDF3's significant link to osteoporosis. YTHDF3 levels are significantly reduced in femoral head tissue from postmenopausal osteoporosis (PMOP) patients and femoral bone tissue from PMOP mice. Additionally, silencing YTHDF3 in OP-BMSCs substantially impedes their proliferation and differentiation. CONCLUSION YTHDF3 may be implicated in the pathogenesis of OP by regulating the proliferation and osteogenic differentiation of OP-BMSCs.
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Affiliation(s)
- Zhi‐wei Feng
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Department of OrthopaedicsNanchong Central Hospital, The Second Clinical Institute of North Sichuan Medical CollegeNanchongChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - He‐fang Xiao
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Xing‐wen Wang
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Yong‐kang Niu
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Da‐cheng Zhao
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Cong Tian
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Sheng‐hong Wang
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Bo Peng
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Fei Yang
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Department of OrthopaedicsNanchong Central Hospital, The Second Clinical Institute of North Sichuan Medical CollegeNanchongChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Bin Geng
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Ming‐gang Guo
- Department of OrthopaedicsNanchong Central Hospital, The Second Clinical Institute of North Sichuan Medical CollegeNanchongChina
| | - Xiao‐yun Sheng
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
| | - Ya‐yi Xia
- Department of OrthopaedicsLanzhou University Second HospitalLanzhouChina
- Gansu Province Intelligent Orthopedics Industry Technology CenterLanzhouChina
- Gansu Province Orthopaedic Clinical Medicine Research CenterLanzhouChina
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78
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Lee K, Ku J, Ku D, Kim Y. Inverted Alu repeats: friends or foes in the human transcriptome. Exp Mol Med 2024; 56:1250-1262. [PMID: 38871814 PMCID: PMC11263572 DOI: 10.1038/s12276-024-01177-3] [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: 10/09/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 06/15/2024] Open
Abstract
Alu elements are highly abundant primate-specific short interspersed nuclear elements that account for ~10% of the human genome. Due to their preferential location in gene-rich regions, especially in introns and 3' UTRs, Alu elements can exert regulatory effects on the expression of both host and neighboring genes. When two Alu elements with inverse orientations are positioned in close proximity, their transcription results in the generation of distinct double-stranded RNAs (dsRNAs), known as inverted Alu repeats (IRAlus). IRAlus are key immunogenic self-dsRNAs and post-transcriptional cis-regulatory elements that play a role in circular RNA biogenesis, as well as RNA transport and stability. Recently, IRAlus dsRNAs have emerged as regulators of transcription and activators of Z-DNA-binding proteins. The formation and activity of IRAlus can be modulated through RNA editing and interactions with RNA-binding proteins, and misregulation of IRAlus has been implicated in several immune-associated disorders. In this review, we summarize the emerging functions of IRAlus dsRNAs, the regulatory mechanisms governing IRAlus activity, and their relevance in the pathogenesis of human diseases.
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Affiliation(s)
- Keonyong Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jayoung Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Doyeong Ku
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Yoosik Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea.
- KAIST Institute for BioCentury (KIB), Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology (KIHST), Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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79
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Li YJ, Qiu YL, Li MR, Shen M, Zhang F, Shao JJ, Xu XF, Zhang ZL, Zheng SZ. New horizons for the role of RNA N6-methyladenosine modification in hepatocellular carcinoma. Acta Pharmacol Sin 2024; 45:1130-1141. [PMID: 38195693 PMCID: PMC11130213 DOI: 10.1038/s41401-023-01214-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancy, presenting a formidable challenge to the medical community owing to its intricate pathogenic mechanisms. Although current prevention, surveillance, early detection, diagnosis, and treatment have achieved some success in preventing HCC and controlling overall disease mortality, the imperative to explore novel treatment modalities for HCC remains increasingly urgent. Epigenetic modification has emerged as pivotal factors in the etiology of cancer. Among these, RNA N6-methyladenosine (m6A) modification stands out as one of the most prevalent, abundant, and evolutionarily conserved post-transcriptional alterations in eukaryotes. The literature underscores that the dynamic and reversible nature of m6A modifications orchestrates the intricate regulation of gene expression, thereby exerting a profound influence on cell destinies. Increasing evidence has substantiated conspicuous fluctuations in m6A modification levels throughout the progression of HCC. The deliberate modulation of m6A modification levels through molecular biology and pharmacological interventions has been demonstrated to exert a discernible impact on the pathogenesis of HCC. In this review, we elucidate the multifaceted biological functions of m6A modifications in HCC, and concurrently advancing novel therapeutic strategies for the management of this malignancy.
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Affiliation(s)
- Yu-Jia Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yang-Ling Qiu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Meng-Ran Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Min Shen
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, China
| | - Feng Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiang-Juan Shao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xue-Fen Xu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zi-Li Zhang
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Shi-Zhong Zheng
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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80
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Zhao N, Wu T, Wang W, Zhang L, Gong X. Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure. Interdiscip Sci 2024; 16:261-288. [PMID: 38955920 DOI: 10.1007/s12539-024-00626-x] [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: 10/26/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 07/04/2024]
Abstract
Protein complexes perform diverse biological functions, and obtaining their three-dimensional structure is critical to understanding and grasping their functions. In many cases, it's not just two proteins interacting to form a dimer; instead, multiple proteins interact to form a multimer. Experimentally resolving protein complex structures can be quite challenging. Recently, there have been efforts and methods that build upon prior predictions of dimer structures to attempt to predict multimer structures. However, in comparison to monomeric protein structure prediction, the accuracy of protein complex structure prediction remains relatively low. This paper provides an overview of recent advancements in efficient computational models for predicting protein complex structures. We introduce protein-protein docking methods in detail and summarize their main ideas, applicable modes, and related information. To enhance prediction accuracy, other critical protein-related information is also integrated, such as predicting interchain residue contact, utilizing experimental data like cryo-EM experiments, and considering protein interactions and non-interactions. In addition, we comprehensively review computational approaches for end-to-end prediction of protein complex structures based on artificial intelligence (AI) technology and describe commonly used datasets and representative evaluation metrics in protein complexes. Finally, we analyze the formidable challenges faced in current protein complex structure prediction tasks, including the structure prediction of heteromeric complex, disordered regions in complex, antibody-antigen complex, and RNA-related complex, as well as the evaluation metrics for complex assessment. We hope that this work will provide comprehensive knowledge of complex structure predictions to contribute to future advanced predictions.
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Affiliation(s)
- Nan Zhao
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Tong Wu
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Wenda Wang
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China
- School of Mathematics, Renmin University of China, Beijing, 100872, China
| | - Lunchuan Zhang
- School of Mathematics, Renmin University of China, Beijing, 100872, China.
| | - Xinqi Gong
- Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China.
- School of Mathematics, Renmin University of China, Beijing, 100872, China.
- Beijing Academy of Artificial Intelligence, Beijing, 100084, China.
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81
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Vignolini T, Couble JEC, Doré GRG, Baumgarten S. Transcript tinkering: RNA modifications in protozoan parasites. Curr Opin Microbiol 2024; 79:102477. [PMID: 38663181 DOI: 10.1016/j.mib.2024.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 06/11/2024]
Abstract
Apicomplexan and trypanosomatid parasites have evolved a wide range of post-transcriptional processes that allow them to replicate, differentiate, and transmit within and among multiple different tissue, host, and vector environments. In this review, we highlight the recent advances that point toward the regulatory potential of RNA modifications in mediating these processes on the coding and noncoding transcriptome throughout the life cycle of protozoan parasites. We discuss the recent technical advancements enabling the study of the 'epitranscriptome' and how parasites evolved RNA modification-mediated mechanisms adapted to their unique lifestyles.
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Affiliation(s)
- Tiziano Vignolini
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Justine E C Couble
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Grégory R G Doré
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France
| | - Sebastian Baumgarten
- Institut Pasteur, Université Paris Cité, G5 Parasite RNA Biology, Department of Parasites and Insect Vectors, F-75015 Paris, France.
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82
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Mehmood R. Ramifications of m6A Modification on ncRNAs in Cancer. Curr Genomics 2024; 25:158-170. [PMID: 39087001 PMCID: PMC11288162 DOI: 10.2174/0113892029296712240405053201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 08/02/2024] Open
Abstract
N6-methyladenosine (m6A) is an RNA modification wherein the N6-position of adenosine is methylated. It is one of the most prevalent internal modifications of RNA and regulates various aspects of RNA metabolism. M6A is deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by reader proteins, which modulate splicing, export, translation, and stability of the modified mRNA. Recent evidence suggests that various classes of non- coding RNAs (ncRNAs), including microRNAs (miRNAs), circular RNAs (circRNAs), and long con-coding RNAs (lncRNAs), are also targeted by this modification. Depending on the ncRNA species, m6A may affect the processing, stability, or localization of these molecules. The m6A- modified ncRNAs are implicated in a number of diseases, including cancer. In this review, the author summarizes the role of m6A modification in the regulation and functions of ncRNAs in tumor development. Moreover, the potential applications in cancer prognosis and therapeutics are discussed.
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Affiliation(s)
- Rashid Mehmood
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
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83
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Zhang J, Yao S, Cheng X, Zhao Y, Yu W, Ren X, Ji K, Yu Q. Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora. Int J Mol Sci 2024; 25:5960. [PMID: 38892149 PMCID: PMC11173211 DOI: 10.3390/ijms25115960] [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: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid-liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.
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Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Sheng Yao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xiang Cheng
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yulu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wenya Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Xingyue Ren
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Kongshu Ji
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Qiong Yu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing 210037, China (K.J.)
- Key Open Laboratory of Forest Genetics and Gene Engineering of National Forestry & Grassland, Nanjing Forestry University, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Beijing National Laboratory for Molecular Sciences, Beijing 100190, China
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84
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Mansfield KD. RNA Binding by the m6A Methyltransferases METTL16 and METTL3. BIOLOGY 2024; 13:391. [PMID: 38927271 PMCID: PMC11200852 DOI: 10.3390/biology13060391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024]
Abstract
Methyltransferases are a wide-ranging, yet well-conserved, class of molecules that have been found to modify a wide variety of substrates. Interest in RNA methylation has surged in recent years with the identification of the major eukaryotic mRNA m6A methyltransferase METTL3. METTL16 has also been identified as an RNA m6A methyltransferase; however, much less is known about its targets and actions. Interestingly, in addition to their catalytic activities, both METTL3 and METTL16 also have "methylation-independent" functions, including translational regulation, which have been discovered. However, evidence suggests that METTL16's role as an RNA-binding protein may be more significant than is currently recognized. In this review, we will introduce RNA methylation, specifically m6A, and the enzymes responsible for its deposition. We will discuss the varying roles that these enzymes perform and delve deeper into their RNA targets and possible roles as methylation-independent RNA binding proteins. Finally, we will touch upon the many open questions still remaining.
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Affiliation(s)
- Kyle D Mansfield
- Biochemistry and Molecular Biology Department, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA
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85
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McCormick CA, Akeson S, Tavakoli S, Bloch D, Klink IN, Jain M, Rouhanifard SH. Multicellular, IVT-derived, unmodified human transcriptome for nanopore-direct RNA analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.06.535889. [PMID: 37066160 PMCID: PMC10104151 DOI: 10.1101/2023.04.06.535889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Nanopore direct RNA sequencing (DRS) enables measurements of RNA modifications. Modification-free transcripts are a practical and targeted control for DRS, providing a baseline measurement for canonical nucleotides within a matched and biologically derived sequence context. However, these controls can be challenging to generate and carry nanopore-specific nuances that can impact analysis. We produced DRS datasets using modification-free transcripts from in vitro transcription (IVT) of cDNA from six immortalized human cell lines. We characterized variation across cell lines and demonstrated how these may be interpreted. These data will serve as a versatile control and resource to the community for RNA modification analysis of human transcripts.
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Affiliation(s)
- Caroline A. McCormick
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Stuart Akeson
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Dylan Bloch
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Isabel N. Klink
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
- Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Sara H. Rouhanifard
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
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86
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Bujosa P, Reina O, Caballé A, Casas-Lamesa A, Torras-Llort M, Pérez-Roldán J, Nacht AS, Vicent GP, Bernués J, Azorín F. Linker histone H1 regulates homeostasis of heterochromatin-associated cRNAs. Cell Rep 2024; 43:114137. [PMID: 38662543 DOI: 10.1016/j.celrep.2024.114137] [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: 04/14/2023] [Revised: 12/23/2023] [Accepted: 04/08/2024] [Indexed: 06/01/2024] Open
Abstract
Chromatin-associated RNAs (cRNAs) are a poorly characterized fraction of cellular RNAs that co-purify with chromatin. Their full complexity and the mechanisms regulating their packaging and chromatin association remain poorly understood. Here, we address these questions in Drosophila. We find that cRNAs constitute a heterogeneous group of RNA species that is abundant in heterochromatic transcripts. We show that heterochromatic cRNAs interact with the heterogeneous nuclear ribonucleoproteins (hnRNP) hrp36/hrp48 and that depletion of linker histone dH1 impairs this interaction. dH1 depletion induces the accumulation of RNA::DNA hybrids (R-loops) in heterochromatin and, as a consequence, increases retention of heterochromatic cRNAs. These effects correlate with increased RNA polymerase II (RNAPII) occupancy at heterochromatin. Notably, impairing cRNA assembly by depletion of hrp36/hrp48 mimics heterochromatic R-loop accumulation induced by dH1 depletion. We also show that dH1 depletion alters nucleosome organization, increasing accessibility of heterochromatin. Altogether, these perturbations facilitate annealing of cRNAs to the DNA template, enhancing R-loop formation and cRNA retention at heterochromatin.
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Affiliation(s)
- Paula Bujosa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Mònica Torras-Llort
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Juan Pérez-Roldán
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ana Silvina Nacht
- Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guillermo P Vicent
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Centre de Regulació Genòmica (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, CSIC, Baldiri Reixac, 4, 08028 Barcelona, Spain; Institute for Research in Biomedicine, IRB Barcelona. The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
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87
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Ye H, Li T, Rigden DJ, Wei Z. m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq. Nucleic Acids Res 2024; 52:4830-4842. [PMID: 38634812 PMCID: PMC11109940 DOI: 10.1093/nar/gkae280] [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: 09/04/2023] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.
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Affiliation(s)
- Haokai Ye
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Tenglong Li
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK
| | - Zhen Wei
- Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
- Institute of Life Course and Medical Sciences, University of Liverpool, L7 8TX Liverpool, UK
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88
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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [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: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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89
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Huang E, Frydman C, Xiao X. Navigating the landscape of epitranscriptomics and host immunity. Genome Res 2024; 34:515-529. [PMID: 38702197 PMCID: PMC11146601 DOI: 10.1101/gr.278412.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2024]
Abstract
RNA modifications, also termed epitranscriptomic marks, encompass chemical alterations to individual nucleotides, including processes such as methylation and editing. These marks contribute to a wide range of biological processes, many of which are related to host immune system defense. The functions of immune-related RNA modifications can be categorized into three main groups: regulation of immunogenic RNAs, control of genes involved in innate immune response, and facilitation of adaptive immunity. Here, we provide an overview of recent research findings that elucidate the contributions of RNA modifications to each of these processes. We also discuss relevant methods for genome-wide identification of RNA modifications and their immunogenic substrates. Finally, we highlight recent advances in cancer immunotherapies that aim to reduce cancer cell viability by targeting the enzymes responsible for RNA modifications. Our presentation of these dynamic research avenues sets the stage for future investigations in this field.
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Affiliation(s)
- Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Clara Frydman
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, California 90095, USA;
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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90
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Bak M, van Nimwegen E, Kouzel IU, Gur T, Schmidt R, Zavolan M, Gruber AJ. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer. Nat Commun 2024; 15:4110. [PMID: 38750024 PMCID: PMC11096328 DOI: 10.1038/s41467-024-48046-1] [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: 06/12/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Maturation of eukaryotic pre-mRNAs via splicing and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although there exist over 1,500 RBPs in human cells, their binding motifs and functions still remain to be elucidated, especially in the complex environment of tissues and in the context of diseases. To overcome the lack of methods for the systematic and automated detection of sequence motif-guided pre-mRNA processing regulation from RNA sequencing (RNA-Seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing). Applying MAPP to RBP knock-down experiments reveals that many RBPs regulate both splicing and polyadenylation of nascent transcripts by acting on similar sequence motifs. MAPP not only infers these sequence motifs, but also unravels the position-dependent impact of the RBPs on pre-mRNA processing. Interestingly, all investigated RBPs that act on both splicing and 3' end processing exhibit a consistently repressive or activating effect on both processes, providing a first glimpse on the underlying mechanism. Applying MAPP to normal and malignant brain tissue samples unveils that the motifs bound by the PTBP1 and RBFOX RBPs coordinately drive the oncogenic splicing program active in glioblastomas demonstrating that MAPP paves the way for characterizing pre-mRNA processing regulators under physiological and pathological conditions.
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Affiliation(s)
- Maciej Bak
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Erik van Nimwegen
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ian U Kouzel
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Tamer Gur
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Ralf Schmidt
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Mihaela Zavolan
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany.
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91
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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [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: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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92
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Feng G, Wu Y, Hu Y, Shuai W, Yang X, Li Y, Ouyang L, Wang G. Small molecule inhibitors targeting m 6A regulators. J Hematol Oncol 2024; 17:30. [PMID: 38711100 PMCID: PMC11075261 DOI: 10.1186/s13045-024-01546-5] [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: 02/07/2024] [Accepted: 04/23/2024] [Indexed: 05/08/2024] Open
Abstract
As the most common form of epigenetic regulation by RNA, N6 methyladenosine (m6A) modification is closely involved in physiological processes, such as growth and development, stem cell renewal and differentiation, and DNA damage response. Meanwhile, its aberrant expression in cancer tissues promotes the development of malignant tumors, as well as plays important roles in proliferation, metastasis, drug resistance, immunity and prognosis. This close association between m6A and cancers has garnered substantial attention in recent years. An increasing number of small molecules have emerged as potential agents to target m6A regulators for cancer treatment. These molecules target the epigenetic level, enabling precise intervention in RNA modifications and efficiently disrupting the survival mechanisms of tumor cells, thus paving the way for novel approaches in cancer treatment. However, there is currently a lack of a comprehensive review on small molecules targeting m6A regulators for anti-tumor. Here, we have comprehensively summarized the classification and functions of m6A regulators, elucidating their interactions with the proliferation, metastasis, drug resistance, and immune responses in common cancers. Furthermore, we have provided a comprehensive overview on the development, mode of action, pharmacology and structure-activity relationships of small molecules targeting m6A regulators. Our aim is to offer insights for subsequent drug design and optimization, while also providing an outlook on future prospects for small molecule development targeting m6A.
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Affiliation(s)
- Guotai Feng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yongya Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yuan Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610041, China
| | - Wen Shuai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Xiao Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Yong Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and West China Second Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu, 610041, China.
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93
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Hao JD, Liu QL, Liu MX, Yang X, Wang LM, Su SY, Xiao W, Zhang MQ, Zhang YC, Zhang L, Chen YS, Yang YG, Ren J. DDX21 mediates co-transcriptional RNA m 6A modification to promote transcription termination and genome stability. Mol Cell 2024; 84:1711-1726.e11. [PMID: 38569554 DOI: 10.1016/j.molcel.2024.03.006] [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: 06/14/2023] [Revised: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 04/05/2024]
Abstract
N6-methyladenosine (m6A) is a crucial RNA modification that regulates diverse biological processes in human cells, but its co-transcriptional deposition and functions remain poorly understood. Here, we identified the RNA helicase DDX21 with a previously unrecognized role in directing m6A modification on nascent RNA for co-transcriptional regulation. DDX21 interacts with METTL3 for co-recruitment to chromatin through its recognition of R-loops, which can be formed co-transcriptionally as nascent transcripts hybridize onto the template DNA strand. Moreover, DDX21's helicase activity is needed for METTL3-mediated m6A deposition onto nascent RNA following recruitment. At transcription termination regions, this nexus of actions promotes XRN2-mediated termination of RNAPII transcription. Disruption of any of these steps, including the loss of DDX21, METTL3, or their enzymatic activities, leads to defective termination that can induce DNA damage. Therefore, we propose that the R-loop-DDX21-METTL3 nexus forges the missing link for co-transcriptional modification of m6A, coordinating transcription termination and genome stability.
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Affiliation(s)
- Jin-Dong Hao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian-Lan Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Meng-Xia Liu
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xing Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liu-Ming Wang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Yi Su
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Xiao
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meng-Qi Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Chang Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lan Zhang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yu-Sheng Chen
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jie Ren
- Key Laboratory of RNA Science and Engineering, CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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94
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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95
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Xu W, Huang Z, Xiao Y, Li W, Xu M, Zhao Q, Yi P. HNRNPC promotes estrogen receptor-positive breast cancer cell cycle by stabilizing WDR77 mRNA in an m6A-dependent manner. Mol Carcinog 2024; 63:859-873. [PMID: 38353359 DOI: 10.1002/mc.23693] [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: 10/30/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 04/13/2024]
Abstract
Breast cancer has become the most commonly diagnosed cancer. Heterogeneous nuclear ribonucleoprotein C (HNRNPC), a reader of N6-methyladenosine (m6A), has been observed to be upregulated in various types of cancer. Nevertheless, the role of HNRNPC in breast cancer and whether it is regulated by m6A modification deserve further investigation. The expression of HNRNPC in breast cancer was examined by quantitative real-time polymerase chain reaction and western blot analysis. RNA immunoprecipitation was performed to validate the binding relationships between HNRNPC and WD repeat domain 77 (WDR77). The effects of HNRNPC and m6A regulators on WDR77 were investigated by actinomycin D assay. The experiments in vivo were conducted in xenograft models. In this research, we found that HNRNPC was highly expressed in breast cancer, and played a crucial role in cell growth, especially in the luminal subtype. HNRNPC could combine and stabilize WDR77 mRNA. WDR77 successively drove the G1/S phase transition in the cell cycle and promoted cell proliferation. Notably, this regulation axis was closely tied to the m6A modification status of WDR77 mRNA. Overall, a critical regulatory mechanism was identified, as well as promising targets for potential treatment strategies for luminal breast cancer.
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Affiliation(s)
- Wenjie Xu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziwei Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yunxiao Xiao
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenhui Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Xu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiuyang Zhao
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengfei Yi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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96
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Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m 6As. Nat Microbiol 2024; 9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [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: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
Abstract
Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N6-methyladenosine (m6A) modifications near the 3' end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m6As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple of these m6As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Ga-Eun Lee
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Sarah Golconda
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Anastasios A Manganaris
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
- Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA
| | - Shuliang Chen
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Nagaraja Tirumuru
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Hannah Yu
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Christopher Kimmel
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sanggu Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA.
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA.
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA.
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, Ohio State University, Columbus, OH, USA.
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97
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Ferruzo PYM, Boell VK, Russo LC, Oliveira CC, Forti FL. DUSP3 modulates IRES-dependent translation of mRNAs through dephosphorylation of the HNRNPC protein in cells under genotoxic stimulus. Biol Cell 2024; 116:e2300128. [PMID: 38538536 DOI: 10.1111/boc.202300128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND INFORMATION The dual-specificity phosphatase 3 (DUSP3) regulates cell cycle progression, proliferation, senescence, and DNA repair pathways under genotoxic stress. This phosphatase interacts with HNRNPC protein suggesting an involvement in the regulation of HNRNPC-ribonucleoprotein complex stability. In this work, we investigate the impact of DUSP3 depletion on functions of HNRNPC aiming to suggest new roles for this enzyme. RESULTS The DUSP3 knockdown results in the tyrosine hyperphosphorylation state of HNRNPC increasing its RNA binding ability. HNRNPC is present in the cytoplasm where it interacts with IRES trans-acting factors (ITAF) complex, which recruits the 40S ribosome on mRNA during protein synthesis, thus facilitating the translation of mRNAs containing IRES sequence in response to specific stimuli. In accordance with that, we found that DUSP3 is present in the 40S, monosomes and polysomes interacting with HNRNPC, just like other previously identified DUSP3 substrates/interacting partners such as PABP and NCL proteins. By downregulating DUSP3, Tyr-phosphorylated HNRNPC preferentially binds to IRES-containing mRNAs within ITAF complexes preferentially in synchronized or stressed cells, as evidenced by the higher levels of proteins such as c-MYC and XIAP, but not their mRNAs such as measured by qPCR. Under DUSP3 absence, this increased phosphorylated-HNRNPC/RNA interaction reduces HNRNPC-p53 binding in presence of RNAs releasing p53 for specialized cellular responses. Similarly, to HNRNPC, PABP physically interacts with DUSP3 in an RNA-dependent manner. CONCLUSIONS AND SIGNIFICANCE Overall, DUSP3 can modulate cellular responses to genotoxic stimuli at the translational level by maintaining the stability of HNRNPC-ITAF complexes and regulating the intensity and specificity of RNA interactions with RRM-domain proteins.
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Affiliation(s)
- Pault Y M Ferruzo
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Viktor K Boell
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Lilian C Russo
- Laboratory of Genome Instability, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Carla C Oliveira
- Laboratory of Post-transcriptional Control of Gene Expression, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Fabio L Forti
- Laboratory of Signaling in Biomolecular Systems, Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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98
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Zacco E, Broglia L, Kurihara M, Monti M, Gustincich S, Pastore A, Plath K, Nagakawa S, Cerase A, Sanchez de Groot N, Tartaglia GG. RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding. Chem Rev 2024; 124:4734-4777. [PMID: 38579177 PMCID: PMC11046439 DOI: 10.1021/acs.chemrev.3c00575] [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: 08/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 04/07/2024]
Abstract
This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNA-mediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.
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Affiliation(s)
- Elsa Zacco
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Laura Broglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Misuzu Kurihara
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Michele Monti
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Stefano Gustincich
- Central
RNA Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Annalisa Pastore
- UK
Dementia Research Institute at the Maurice Wohl Institute of King’s
College London, London SE5 9RT, U.K.
| | - Kathrin Plath
- Department
of Biological Chemistry, David Geffen School
of Medicine at the University of California Los Angeles, Los Angeles, California 90095, United States
| | - Shinichi Nagakawa
- RNA
Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Andrea Cerase
- Blizard
Institute,
Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, U.K.
- Unit
of Cell and developmental Biology, Department of Biology, Università di Pisa, 56123 Pisa, Italy
| | - Natalia Sanchez de Groot
- Unitat
de Bioquímica, Departament de Bioquímica i Biologia
Molecular, Universitat Autònoma de
Barcelona, 08193 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- RNA
Systems Biology Lab, Center for Human Technologies, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152 Genova, Italy
- Catalan
Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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99
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Wei G. RNA m6A modification, signals for degradation or stabilisation? Biochem Soc Trans 2024; 52:707-717. [PMID: 38629637 PMCID: PMC11088905 DOI: 10.1042/bst20230574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/24/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The RNA modification N6-methyladenosine (m6A) is conserved across eukaryotes, and profoundly influences RNA metabolism, including regulating RNA stability. METTL3 and METTL14, together with several accessory components, form a 'writer' complex catalysing m6A modification. Conversely, FTO and ALKBH5 function as demethylases, rendering m6A dynamic. Key to understanding the functional significance of m6A is its 'reader' proteins, exemplified by YTH-domain-containing proteins (YTHDFs) canonical reader and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) non-canonical reader. These proteins play a crucial role in determining RNA stability: YTHDFs mainly promote mRNA degradation through different cytoplasmic pathways, whereas IGF2BPs function to maintain mRNA stability. Additionally, YTHDC1 functions within the nucleus to degrade or protect certain m6A-containing RNAs, and other non-canonical readers also contribute to RNA stability regulation. Notably, m6A regulates retrotransposon LINE1 RNA stability and/or transcription via multiple mechanisms. However, conflicting observations underscore the complexities underlying m6A's regulation of RNA stability depending upon the RNA sequence/structure context, developmental stage, and/or cellular environment. Understanding the interplay between m6A and other RNA regulatory elements is pivotal in deciphering the multifaceted roles m6A plays in RNA stability regulation and broader cellular biology.
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Affiliation(s)
- Guifeng Wei
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
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100
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Wang Y, Wang S, Meng Z, Liu XM, Mao Y. Determinant of m6A regional preference by transcriptional dynamics. Nucleic Acids Res 2024; 52:3510-3521. [PMID: 38452220 DOI: 10.1093/nar/gkae169] [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: 01/28/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3' terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing m6A-seq on chromatin-associated RNAs, we found that m6A regional preference arises during transcription. Nucleosome occupancy is remarkedly increased in the region downstream of m6A sites, suggesting an intricate interplay between m6A methylation and nucleosome-mediated transcriptional dynamics. Notably, we found a remarkable slowdown of Pol-II movement around m6A sites. In addition, inhibiting Pol-II movement increases nearby m6A methylation levels. By analyzing massively parallel assays for m6A, we found that RNA secondary structures inhibit m6A methylation. Remarkably, the m6A sites associated with Pol-II pausing tend to be embedded within RNA secondary structures. These results suggest that Pol-II pausing could affect the accessibility of m6A motifs to the methyltransferase complex and subsequent m6A methylation by mediating RNA secondary structure. Overall, our study reveals a crucial role of transcriptional dynamics in the formation of m6A regional preference.
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Affiliation(s)
- Yalan Wang
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Shen Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zhen Meng
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yuanhui Mao
- Department of Neurology of The Second Affiliated Hospital & Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
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