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Xu W, Shen H. m 6A regulates heterochromatin in mammalian embryonic stem cells. Curr Opin Genet Dev 2024; 86:102196. [PMID: 38669774 DOI: 10.1016/j.gde.2024.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/14/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024]
Abstract
As the most well-studied modification in mRNA, m6A has been shown to regulate multiple biological processes, including RNA degradation, processing, and translation. Recent studies showed that m6A modification is enriched in chromatin-associated RNAs and nascent RNAs, suggesting m6A might play regulatory roles in chromatin contexts. Indeed, in the past several years, a number of studies have clarified how m6A and its modulators regulate different types of chromatin states. Specifically, in the past 2-3 years, several studies discovered the roles of m6A and/or its modulators in regulating constitutive and facultative heterochromatin, shedding interesting lights on RNA-dependent heterochromatin formation in mammalian cells. This review will summarize and discuss the mechanisms underlying m6A's regulation in different types of heterochromatin, with a specific emphasis on the regulation in mammalian embryonic stem cells, which exhibit distinct features of multiple heterochromatin marks.
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Affiliation(s)
- Wenqi Xu
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Hongjie Shen
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, The Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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2
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Phillips S, Mishra T, Huang S, Wu L. Functional Impacts of Epitranscriptomic m 6A Modification on HIV-1 Infection. Viruses 2024; 16:127. [PMID: 38257827 PMCID: PMC10820791 DOI: 10.3390/v16010127] [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: 12/15/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Epitranscriptomic RNA modifications play a crucial role in the posttranscriptional regulation of gene expression. N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic RNA and plays a pivotal role in RNA fate. RNA m6A modification is regulated by a group of cellular proteins, methyltransferases (writers) and demethylases (erasers), which add and remove the methyl group from adenosine, respectively. m6A modification is recognized by a group of cellular RNA-binding proteins (readers) that specifically bind to m6A-modified RNA, mediating effects on RNA stability, splicing, transport, and translation. The functional significance of m6A modification of viral and cellular RNA is an active area of virology research. In this review, we summarize and analyze the current literature on m6A modification of HIV-1 RNA, the multifaceted functions of m6A in regulating HIV-1 replication, and the role of viral RNA m6A modification in evading innate immune responses to infection. Furthermore, we briefly discuss the future directions and therapeutic implications of mechanistic studies of HIV-1 epitranscriptomic modifications.
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Affiliation(s)
| | | | | | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA; (S.P.); (T.M.); (S.H.)
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3
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Höfler S, Duss O. Interconnections between m 6A RNA modification, RNA structure, and protein-RNA complex assembly. Life Sci Alliance 2024; 7:e202302240. [PMID: 37935465 PMCID: PMC10629537 DOI: 10.26508/lsa.202302240] [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: 06/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.
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Affiliation(s)
- Simone Höfler
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Olivier Duss
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
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4
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Wu X, Wu C, Zhou T. No significant change of N 6 -methyladenosine modification landscape in mouse brain after morphine exposure. Brain Behav 2024; 14:e3350. [PMID: 38376052 PMCID: PMC10757896 DOI: 10.1002/brb3.3350] [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: 08/26/2023] [Revised: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 02/21/2024] Open
Abstract
OBJECTIVES N6 -methyladenosine (m6 A) plays a crucial role in regulating neuroplasticity and different brain functions at the posttranscriptional level. However, it remains unknown whether m6 A modification is involved in acute and chronic morphine exposure. MATERIALS AND METHODS In this study, we conducted a direct comparison of m6 A levels and mRNA expression of m6 A-associated factors between morphine-treated and nontreated C57BL/6 wild-type mice. We established animal models of both acute and chronic morphine treatment and confirmed the rewarding effects of chronic morphine treatment using the conditioned place preference (CPP) assay. The activation status of different brain regions in response to morphine was assessed by c-fos staining. To assess overall m6 A modification levels, we employed the m6 A dot blot assay, while mRNA levels of m6 A-associated proteins were measured using a quantitative polymerase chain reaction (qPCR) assay. These analyses were performed to investigate whether and how m6 A modification and m6 A-associated protein expression will change following morphine exposure. RESULTS The overall m6 A methylation and mRNA levels of m6 A-associated proteins were not significantly altered in brain regions that were either activated or not activated during acute morphine stimulation. Similarly, the overall m6 A modification and mRNA levels of m6 A-associated proteins remained unaffected in several key brain regions associated with reward following chronic morphine exposure. CONCLUSION This study showed that the overall m6 A modification level and mRNA expression levels of m6 A-associated factors were not affected after acute and chronic morphine exposure in different brain regions, indicating m6 A modification may not be involved in brain response to morphine exposure.
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Affiliation(s)
- Xiaoli Wu
- Shenzhen Neher Neural Plasticity Laboratory, Shenzhen Key Laboratory of Drug Addiction, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- Shenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenChina
| | - Cuiting Wu
- Shenzhen Neher Neural Plasticity Laboratory, Shenzhen Key Laboratory of Drug Addiction, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- University of Chinese Academy of SciencesBeijingChina
- Shenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenChina
| | - Tao Zhou
- Shenzhen Neher Neural Plasticity Laboratory, Shenzhen Key Laboratory of Drug Addiction, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
- Shenzhen‐Hong Kong Institute of Brain Science‐Shenzhen Fundamental Research InstitutionsShenzhenChina
- CAS Key Laboratory of Brain Connectome and Manipulation, Faculty of Life and Health Sciences, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhenChina
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5
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Perlegos AE, Quan X, Donnelly KM, Shen H, Shields EJ, Elashal H, Fange Liu K, Bonini NM. dTrmt10A impacts Hsp70 chaperone m 6A levels and the stress response in the Drosophila brain. Sci Rep 2023; 13:22999. [PMID: 38155219 PMCID: PMC10754819 DOI: 10.1038/s41598-023-50272-4] [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: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Chronic cellular stress has a profound impact on the brain, leading to degeneration and accelerated aging. Recent work has revealed the vital role of RNA modifications, and the proteins responsible for regulating them, in the stress response. In our study, we defined the role of CG14618/dTrmt10A, the Drosophila counterpart of human TRMT10A a N1-methylguanosine methyltransferase, on m6A regulation and heat stress resilience in the Drosophila brain. By m6A-IP RNA sequencing on Drosophila head tissue, we demonstrated that manipulating dTrmt10A levels indirectly regulates m6A levels on polyA + RNA. dTrmt10A exerted its influence on m6A levels on transcripts enriched for neuronal signaling and heat stress pathways, similar to the m6A methyltransferase Mettl3. Intriguingly, its impact primarily targeted 3' UTR m6A, setting it apart from the majority of Drosophila m6A-modified transcripts which display 5' UTR enrichment. Upregulation of dTrmt10A led to increased resilience to acute heat stress, decreased m6A modification on heat shock chaperones, and coincided with decreased decay of chaperone transcripts and increased translation of chaperone proteins. Overall, these findings establish a potential mechanism by which dTrmt10A regulates the acute brain stress response through m6A modification.
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Affiliation(s)
- Alexandra E Perlegos
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xiuming Quan
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kirby M Donnelly
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hui Shen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Emily J Shields
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Heidi Elashal
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nancy M Bonini
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Sun MH, Jiang WJ, Li XH, Lee SH, Heo G, Zhou D, Guo J, Cui XS. High Temperature-Induced m6A Epigenetic Changes Affect Early Porcine Embryonic Developmental Competence in Pigs. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2174-2183. [PMID: 38066680 DOI: 10.1093/micmic/ozad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/11/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023]
Abstract
N6-methyladenosine (m6A), the most prevalent modification in eukaryotic messenger RNA (mRNA), plays a key role in various developmental processes in mammals. Three proteins that affect RNA m6A modification have been identified: methyltransferases, demethylases, and m6A-binding proteins, known as "writer," "eraser," and "reader" proteins, respectively. However, changes in the m6A modification when early porcine embryos are exposed to stress remain unclear. In this study, we exposed porcine oocytes to a high temperature (HT, 41°C) for 10 h, after which the mature oocytes were parthenogenetically activated and cultured for 7 days to the blastocyst stage. HT significantly decreased the rates of the first polar body extrusion and blastocyst formation. Further detection of m6A modification found that HT can lead to increased expression levels of "reader," YTHDF2, and "writer," METTL3, and decreased expression levels of "eraser," FTO, resulting in an increased level of m6A modification in the embryos. Additionally, heat shock protein 70 (HSP70) is upregulated under HT conditions. Our study demonstrated that HT exposure alters m6A modification levels, which further affects early porcine embryonic development.
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Affiliation(s)
- Ming-Hong Sun
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Wen-Jie Jiang
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Xiao-Han Li
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Song-Hee Lee
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Geun Heo
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Dongjie Zhou
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
| | - Jing Guo
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street 2888, Changchun, Jilin, 130118, China
| | - Xiang-Shun Cui
- Department of Animal Science, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju, Chungbuk, 28644, South Korea
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7
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Li Y, Yi Y, Lv J, Gao X, Yu Y, Babu S, Bruno I, Zhao D, Xia B, Peng W, Zhu J, Chen H, Zhang L, Cao Q, Chen K. Low RNA stability signifies increased post-transcriptional regulation of cell identity genes. Nucleic Acids Res 2023; 51:6020-6038. [PMID: 37125636 PMCID: PMC10325912 DOI: 10.1093/nar/gkad300] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/02/2023] Open
Abstract
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.
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Affiliation(s)
- Yanqiang Li
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yi
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jie Lv
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Yang Yu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sahana Suresh Babu
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Ivone Bruno
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Dongyu Zhao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Bo Xia
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Research Institute, The Methodist Hospital System, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
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8
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Perez-Pepe M, Desotell AW, Li H, Li W, Han B, Lin Q, Klein DE, Liu Y, Goodarzi H, Alarcón CR. 7SK methylation by METTL3 promotes transcriptional activity. SCIENCE ADVANCES 2023; 9:eade7500. [PMID: 37163588 PMCID: PMC10171809 DOI: 10.1126/sciadv.ade7500] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A fundamental feature of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. The small nuclear RNA 7SK prevents transcriptional elongation by sequestering the cyclin dependent kinase 9/cyclin T1 (CDK9/CCNT1) positive transcription elongation factor (P-TEFb) complex. We found that epidermal growth factor signaling induces phosphorylation of the enzyme methyltransferase 3 (METTL3), leading to METTL3-mediated methylation of 7SK. 7SK methylation enhanced its binding to heterogeneous nuclear ribonucleoproteins, causing the release of the HEXIM1 P-TEFb complex subunit1 (HEXIM1)/P-TEFb complex and inducing transcriptional elongation. Our findings establish the mechanism underlying 7SK activation and uncover a previously unknown function for the m6A modification in converting growth factor signaling events into a regulatory transcriptional response via an RNA methylation-dependent switch.
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Affiliation(s)
- Marcelo Perez-Pepe
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Anthony W Desotell
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hengyi Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Bing Han
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qishan Lin
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Daryl E Klein
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudio R Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
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9
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Wang L, Tang Y. N6-methyladenosine (m6A) in cancer stem cell: From molecular mechanisms to therapeutic implications. Biomed Pharmacother 2023; 163:114846. [PMID: 37167725 DOI: 10.1016/j.biopha.2023.114846] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023] Open
Abstract
The emergence of drug resistance and metastasis has long been a difficult problem for cancer treatment. Recent studies have shown that cancer stem cell populations are key factors in the regulation of cancer aggressiveness, relapse and drug resistance. Cancer stem cell (CSC) populations are highly plastic and self-renewing, giving them unique metabolic, metastatic, and chemotherapy resistance properties. N6-methyladenosine (m6A) is the most abundant internal modification of mRNA and is involved in a variety of cell growth and development processes, including RNA transcription, alternative splicing, degradation, and translation. It has also been linked to the development of various cancers. At present, the important role of m6A in tumour progression is gradually attracting attention, especially in the tumour stemness regulation process. Abnormal m6A modifications regulate tumour metastasis, recurrence and drug resistance. This paper aims to explore the regulatory mechanism of m6A in CSCs and clinical therapy, clarify its regulatory network, and provide theoretical guidance for the development of clinical targets and improvement of therapeutic effects.
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Affiliation(s)
- Liming Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China
| | - Yuanxin Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, P.R. China.
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10
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Yang Q, Al-Hendy A. The Functional Role and Regulatory Mechanism of FTO m 6A RNA Demethylase in Human Uterine Leiomyosarcoma. Int J Mol Sci 2023; 24:ijms24097957. [PMID: 37175660 PMCID: PMC10178470 DOI: 10.3390/ijms24097957] [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: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Uterine leiomyosarcoma (uLMS) is the most frequent subtype of uterine sarcoma that presents a poor prognosis and high rates of recurrence and metastasis. The origin and molecular mechanism underlying and driving its clinical and biological behavior remain largely unknown. Recently, we and others have revealed the role of microRNAs, DNA methylation, and histone modifications in contributing to the pathogenesis of uLMS. However, the connection between reversible m6A RNA methylation and uLMS pathogenesis remains unclear. In this study, we assessed the role and mechanism of FTO m6A RNA demethylase in the pathogenesis of uLMS. Immunohistochemistry analysis revealed that the levels of RNA demethylases FTO and ALKBH5 were aberrantly upregulated in uLMS tissues compared to adjacent myometrium with a significant change by histochemical scoring assessment (p < 0.01). Furthermore, the inhibition of FTO demethylase with its small, potent inhibitor (Dac51) significantly decreased the uLMS proliferation dose-dependently via cell cycle arrest. Notably, RNA-seq analysis revealed that the inhibition of FTO with Dac51 exhibited a significant decrease in cell-cycle-related genes, including several CDK members, and a significant increase in the expression of CDKN1A, which correlated with a Dac51-exerted inhibitory effect on cell proliferation. Moreover, Dac51 treatment allowed the rewiring of several critical pathways, including TNFα signaling, KRAS signaling, inflammation response, G2M checkpoint, and C-Myc signaling, among others, leading to the suppression of the uLMS phenotype. Moreover, transcription factor (TF) analyses suggested that epitranscriptional alterations by Dac51 may alter the cell cycle-related gene expression via TF-driven pathways and epigenetic networks in uLMS cells. This intersection of RNA methylation and other epigenetic controls and pathways provides a framework to better understand uterine diseases, particularly uLMS pathogenesis with a dysregulation of RNA methylation machinery. Therefore, targeting the vulnerable epitranscriptome may provide an additional regulatory layer for a promising and novel strategy for treating patients with this aggressive uterine cancer.
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Affiliation(s)
- Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
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11
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Abstract
Characterization of RNA modifications has identified their distribution features and molecular functions. Dynamic changes in RNA modification on various forms of RNA are essential for the development and function of the immune system. In this review, we discuss the value of innovative RNA modification profiling technologies to uncover the function of these diverse, dynamic RNA modifications in various immune cells within healthy and diseased contexts. Further, we explore our current understanding of the mechanisms whereby aberrant RNA modifications modulate the immune milieu of the tumor microenvironment and point out outstanding research questions.
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Affiliation(s)
- Dali Han
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
| | - Meng Michelle Xu
- Institute for Immunology, Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing, China;
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12
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Liu Y, Yang D, Liu T, Chen J, Yu J, Yi P. N6-methyladenosine-mediated gene regulation and therapeutic implications. Trends Mol Med 2023; 29:454-467. [PMID: 37068987 DOI: 10.1016/j.molmed.2023.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation is the most abundant form of mRNA modification in eukaryotes and is at the front line of biological and biomedical research. This dynamic and reversible m6A RNA modification determines the fates of modified RNA molecules at the post-transcriptional level, affecting almost all important biological processes. Notably, m6A is also involved in chromatin and transcriptional regulation, while m6A dysregulation is implicated in various diseases. Here, we review current knowledge of post-transcriptional and transcriptional regulatory mechanisms involving m6A modification. We also discuss their involvement in the occurrence and development of diseases, including cancer, as well as potential theranostic targets, in hope of facilitating the translation of preclinical findings to the clinic.
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Affiliation(s)
- Yujiao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Dan Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Tao Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA
| | - Jianhua Yu
- Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA.
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing 401120, China.
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13
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Auf der Maur P, Trefny MP, Baumann Z, Vulin M, Correia AL, Diepenbruck M, Kramer N, Volkmann K, Preca BT, Ramos P, Leroy C, Eichlisberger T, Buczak K, Zilli F, Okamoto R, Rad R, Jensen MR, Fritsch C, Zippelius A, Stadler MB, Bentires-Alj M. N-acetylcysteine overcomes NF1 loss-driven resistance to PI3Kα inhibition in breast cancer. Cell Rep Med 2023; 4:101002. [PMID: 37044095 PMCID: PMC10140479 DOI: 10.1016/j.xcrm.2023.101002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 04/14/2023]
Abstract
A genome-wide PiggyBac transposon-mediated screen and a resistance screen in a PIK3CAH1047R-mutated murine tumor model reveal NF1 loss in mammary tumors resistant to the phosphatidylinositol 3-kinase α (PI3Kα)-selective inhibitor alpelisib. Depletion of NF1 in PIK3CAH1047R breast cancer cell lines and a patient-derived organoid model shows that NF1 loss reduces sensitivity to PI3Kα inhibition and correlates with enhanced glycolysis and lower levels of reactive oxygen species (ROS). Unexpectedly, the antioxidant N-acetylcysteine (NAC) sensitizes NF1 knockout cells to PI3Kα inhibition and reverts their glycolytic phenotype. Global phospho-proteomics indicates that combination with NAC enhances the inhibitory effect of alpelisib on mTOR signaling. In public datasets of human breast cancer, we find that NF1 is frequently mutated and that such mutations are enriched in metastases, an indication for which use of PI3Kα inhibitors has been approved. Our results raise the attractive possibility of combining PI3Kα inhibition with NAC supplementation, especially in patients with drug-resistant metastases associated with NF1 loss.
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Affiliation(s)
- Priska Auf der Maur
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Marcel P Trefny
- Cancer Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Zora Baumann
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Milica Vulin
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ana Luisa Correia
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Maren Diepenbruck
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Nicolas Kramer
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Katrin Volkmann
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Bogdan-Tiberius Preca
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Pedro Ramos
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Cedric Leroy
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Federica Zilli
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ryoko Okamoto
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, München, Germany; Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, München, Germany; Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christine Fritsch
- Oncology Research, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alfred Zippelius
- Cancer Immunology, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Mohamed Bentires-Alj
- Tumor Heterogeneity Metastasis and Resistance, Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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14
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Waldbillig F, Bormann F, Neuberger M, Ellinger J, Erben P, Kriegmair MC, Michel MS, Nuhn P, Nientiedt M. An m6A-Driven Prognostic Marker Panel for Renal Cell Carcinoma Based on the First Transcriptome-Wide m6A-seq. Diagnostics (Basel) 2023; 13:diagnostics13050823. [PMID: 36899967 PMCID: PMC10001021 DOI: 10.3390/diagnostics13050823] [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: 01/31/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
To date, only a single transcriptome-wide m6A sequencing study of clear cell renal cell carcinoma (ccRCC) has been reported, with no validation so far. Herein, by TCGA analysis of the KIRC cohort (n = 530 ccRCC; n = 72 normal), an external expression validation of 35 preidentified m6A targets was performed. Further in-depth expression stratification enabled assessment of m6A-driven key targets. Overall survival (OS) analysis and gene set enrichment analyses (GSEA) were conducted to assess their clinical and functional impact on ccRCC. In the hyper-up cluster significant upregulation was confirmed for NDUFA4L2, NXPH4, SAA1, and PLOD2 (40%) and in the hypo-up cluster for FCHSD1 (10%). Significant downregulation was observed for UMOD, ANK3, and CNTFR (27.3%) in the hypo-down cluster and for CHDH (25%) in the hyper-down cluster. In-depth expression stratification showed consistent dysregulation in ccRCC only for 11.67%: NDUFA4L2, NXPH4, and UMOD (NNU-panel). Patients with strong NNU panel dysregulation had significantly poorer OS (p = 0.0075). GSEA identified 13 associated and significantly upregulated gene sets (all p-values < 0.5; FDR < 0.25). External validation of the only available m6A sequencing in ccRCC consistently reduced dysregulated m6A-driven targets on the NNU panel with highly significant effects on OS. Epitranscriptomics are a promising target for developing novel therapies and for identifying prognostic markers for daily clinical practice.
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Affiliation(s)
- Frank Waldbillig
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | | | - Manuel Neuberger
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Jörg Ellinger
- Department of Urology & Pediatric Urology, University Medical Centre Bonn, University of Bonn, 53127 Bonn, Germany
| | - Philipp Erben
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Maximilian C. Kriegmair
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Maurice Stephan Michel
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Philipp Nuhn
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Malin Nientiedt
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Correspondence: ; Tel.: +49-(0)621-383-2201
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15
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Sendinc E, Shi Y. RNA m6A methylation across the transcriptome. Mol Cell 2023; 83:428-441. [PMID: 36736310 DOI: 10.1016/j.molcel.2023.01.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/05/2023]
Abstract
Since the early days of foundational studies of nucleic acids, many chemical moieties have been discovered to decorate RNA and DNA in diverse organisms. In mammalian cells, one of these chemical modifications, N6-methyl adenosine (m6A), is unique in a way that it is highly abundant not only on RNA polymerase II (RNAPII) transcribed, protein-coding transcripts but also on non-coding RNAs, such as ribosomal RNAs and snRNAs, mediated by distinct, evolutionarily conserved enzymes. Here, we review RNA m6A modification in the light of the recent appreciation of nuclear roles for m6A in regulating chromatin states and gene expression, as well as the recent discoveries of the evolutionarily conserved methyltransferases, which catalyze methylation of adenosine on diverse sets of RNAs. Considering that the substrates of these enzymes are involved in many important biological processes, this modification warrants further research to understand the molecular mechanisms and functions of m6A in health and disease.
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Affiliation(s)
- Erdem Sendinc
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Shi
- Ludwig Institute for Cancer Research, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7DQ, UK.
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16
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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Affiliation(s)
- Kalina Timcheva
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Solenne Dufour
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Leila Touat-Todeschini
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Callum Burnard
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marie-Christine Carpentier
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Florent Chuffart
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Rémy Merret
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Marion Helsmoortel
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabrina Ferré
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aude Grézy
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Yohann Couté
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Sophie Rousseaux
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Saadi Khochbin
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Claire Vourc'h
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Cécile Bousquet-Antonelli
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Rosemary Kiernan
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daphné Seigneurin-Berny
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
| | - André Verdel
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
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17
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Hong J, Xu K, Lee JH. Biological roles of the RNA m 6A modification and its implications in cancer. Exp Mol Med 2022; 54:1822-1832. [PMID: 36446846 PMCID: PMC9722703 DOI: 10.1038/s12276-022-00897-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022] Open
Abstract
The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
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Affiliation(s)
- Juyeong Hong
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Kexin Xu
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Ji Hoon Lee
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
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18
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Li Y, He X, Lu X, Gong Z, Li Q, Zhang L, Yang R, Wu C, Huang J, Ding J, He Y, Liu W, Chen C, Cao B, Zhou D, Shi Y, Chen J, Wang C, Zhang S, Zhang J, Ye J, You H. METTL3 acetylation impedes cancer metastasis via fine-tuning its nuclear and cytosolic functions. Nat Commun 2022; 13:6350. [PMID: 36289222 PMCID: PMC9605963 DOI: 10.1038/s41467-022-34209-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The methyltransferase like 3 (METTL3) has been generally recognized as a nuclear protein bearing oncogenic properties. We find predominantly cytoplasmic METTL3 expression inversely correlates with node metastasis in human cancers. It remains unclear if nuclear METTL3 is functionally distinct from cytosolic METTL3 in driving tumorigenesis and, if any, how tumor cells sense oncogenic insults to coordinate METTL3 functions within these intracellular compartments. Here, we report an acetylation-dependent regulation of METTL3 localization that impacts on metastatic dissemination. We identify an IL-6-dependent positive feedback axis to facilitate nuclear METTL3 functions, eliciting breast cancer metastasis. IL-6, whose mRNA transcript is subjected to METTL3-mediated m6A modification, promotes METTL3 deacetylation and nuclear translocation, thereby inducing global m6A abundance. This deacetylation-mediated nuclear shift of METTL3 can be counterbalanced by SIRT1 inhibition, a process that is further enforced by aspirin treatment, leading to ablated lung metastasis via impaired m6A methylation. Intriguingly, acetylation-mimetic METTL3 mutant reconstitution results in enhanced translation and compromised metastatic potential. Our study identifies an acetylation-dependent regulatory mechanism determining the subcellular localization of METTL3, which may provide mechanistic clues for developing therapeutic strategies to combat breast cancer metastasis.
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Affiliation(s)
- Yuanpei Li
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Xiaoniu He
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Xiao Lu
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Zhicheng Gong
- grid.459328.10000 0004 1758 9149Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, 214062 Wuxi, China
| | - Qing Li
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Lei Zhang
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Ronghui Yang
- grid.24696.3f0000 0004 0369 153XDepartment of Biochemistry and Molecular Biology, Capital Medical University, 100069 Beijing, China
| | - Chengyi Wu
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Jialiang Huang
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Jiancheng Ding
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, 361102 Xiamen, China
| | - Yaohui He
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, 361102 Xiamen, China
| | - Wen Liu
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, 361102 Xiamen, China
| | - Ceshi Chen
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Bin Cao
- grid.12955.3a0000 0001 2264 7233Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, 361102 Xiamen, China
| | - Dawang Zhou
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
| | - Yufeng Shi
- grid.24516.340000000123704535Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, 200092 Shanghai, China
| | - Juxiang Chen
- grid.73113.370000 0004 0369 1660Department of Neurosurgery, Shanghai Changhai Hospital, Naval Medical University, 200433 Shanghai, China
| | - Chuangui Wang
- grid.412509.b0000 0004 1808 3414The Biomedical Translational Research Institute, School of Life Sciences, Shandong University of Technology, 255049 Zibo, China
| | - Shengping Zhang
- grid.16821.3c0000 0004 0368 8293Translational Medicine Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 201620 Shanghai, China
| | - Jian Zhang
- grid.233520.50000 0004 1761 4404The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 710032 Xi’an, China
| | - Jing Ye
- grid.233520.50000 0004 1761 4404Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University, 710032 Xi’an, China
| | - Han You
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, 361102 Xiamen, China
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19
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Perlegos AE, Shields EJ, Shen H, Liu KF, Bonini NM. Mettl3-dependent m 6A modification attenuates the brain stress response in Drosophila. Nat Commun 2022; 13:5387. [PMID: 36104353 PMCID: PMC9474545 DOI: 10.1038/s41467-022-33085-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
N6-methyladenosine (m6A), the most prevalent internal modification on eukaryotic mRNA, plays an essential role in various stress responses. The brain is uniquely vulnerable to cellular stress, thus defining how m6A sculpts the brain's susceptibility may provide insight to brain aging and disease-related stress. Here we investigate the impact of m6A mRNA methylation in the adult Drosophila brain with stress. We show that m6A is enriched in the adult brain and increases with heat stress. Through m6A-immunoprecipitation sequencing, we show 5'UTR Mettl3-dependent m6A is enriched in transcripts of neuronal processes and signaling pathways that increase upon stress. Mettl3 knockdown results in increased levels of m6A targets and confers resilience to stress. We find loss of Mettl3 results in decreased levels of nuclear m6A reader Ythdc1, and knockdown of Ythdc1 also leads to stress resilience. Overall, our data suggest that m6A modification in Drosophila dampens the brain's biological response to stress.
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Affiliation(s)
- Alexandra E Perlegos
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Emily J Shields
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nancy M Bonini
- Neuroscience Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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20
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Akinlalu AO, Njoku PC, Nzekwe CV, Oni RO, Fojude T, Faniyi AJ, Olagunju AS. Recent developments in the significant effect of mRNA modification (M6A) in glioblastoma and esophageal cancer. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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21
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The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Mol Cell 2022; 82:2370-2384.e10. [PMID: 35512709 PMCID: PMC9807187 DOI: 10.1016/j.molcel.2022.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 01/05/2022] [Accepted: 04/06/2022] [Indexed: 01/04/2023]
Abstract
The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in in vivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.
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22
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Wu L, Quan W, Zhang Y, Wang M, Ou X, Mao S, Sun D, Yang Q, Wu Y, Wei Y, Jia R, Chen S, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Gao Q, Tian B, Cheng A. Attenuated Duck Hepatitis A Virus Infection Is Associated With High mRNA Maintenance in Duckling Liver via m6A Modification. Front Immunol 2022; 13:839677. [PMID: 35757688 PMCID: PMC9218207 DOI: 10.3389/fimmu.2022.839677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/05/2022] [Indexed: 11/15/2022] Open
Abstract
Host translation is generally modulated by viral infection, including duck hepatitis A virus (DHAV) infection. Previously, we reported that cellular protein synthesis in a cell model of duck embryo fibroblasts is significantly inhibited by DHAV infection but not viral proteins, suggesting that an important viral-host interaction occurs at the translational level. In this study, we aim to further understand the impact of DHAV virulence on cellular N6-methyladenosine (m6A) modification, which is essential to a wide variety of RNA biological processes, such as mRNA stabilization and translation. Using m6A antibody-based immunoprecipitation, m6A-seq, and LC–MS/MS, we observed that m6A-modified mRNA exists in both virulent and attenuated DHAV-infected duckling livers. Importantly, m6A levels in mRNA were much higher in attenuated DHAV-infected livers compared with virulent DHAV-infected livers, suggesting virulence-dependent regulation of m6A modification. Analysis of modification motifs indicated that GAAGAAG is the most enriched motif. Combined m6A-seq and RNA-seq data analysis indicated a generally positive correlation between m6A and mRNA expression levels in DHAV-infected duckling livers. GO analysis of genes with decreased or increased m6A levels showed that these genes were enriched in various terms, including oxidation–reduction processes and antiviral immune responses. Collectively, our work reveals DHAV virulence-dependent coordination between m6A modification and mRNA expression in duckling livers.
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Affiliation(s)
- Liping Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife, Inc., Wuhan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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23
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Xu Z, Xie T, Sui X, Xu Y, Ji L, Zhang Y, Zhang A, Chen J. Crosstalk Between Histone and m6A Modifications and Emerging Roles of m6A RNA Methylation. Front Genet 2022; 13:908289. [PMID: 35783260 PMCID: PMC9240596 DOI: 10.3389/fgene.2022.908289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
RNA, like DNA and proteins, has been discovered to undergo dynamic and reversible chemical alterations, increasing the diversity and functional complexity of the molecule. N-6-methyladenosine (m6A) RNA methylation serves as a bridge between transcription and translation and is critical for many diseases’ progression. There is a complex interrelationship between m6A modifications and other epigenetic modifications. Their crosstalk significantly affects transcriptional outputs, translation, recruitment of chromatin modifiers, as well as the deployment of the m6A methyltransferase complex at target sites. This article outlines the potential function of m6A RNA methylation in epigenetics and summarizes its interactions with histone modifications.
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Affiliation(s)
- Zibin Xu
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Tingfei Xie
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Xiaolu Sui
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yunpeng Xu
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lecai Ji
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Yanzi Zhang
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Aisha Zhang
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jihong Chen
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Jihong Chen,
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RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
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25
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Zhu Y, Wu W, Chen S, Zhang Z, Zhang G, Li J, Jiang M. Mettl3 downregulation in germinal vesicle oocytes inhibits mRNA decay and the 1st polar body extrusion during maturation. Biol Reprod 2022; 107:765-778. [PMID: 35639638 DOI: 10.1093/biolre/ioac112] [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: 12/14/2021] [Revised: 04/18/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
In oocytes, mRNA decay is essential for maturation and subsequent events, such as maternal-zygotic transition, zygotic genomic activation, and embryo development. Reversible N6-methyladenosine RNA methylation directly regulates transcription, pre-mRNA splicing, mRNA export, mRNA stability, and translation. Here, we identified that downregulation of N6-methyladenosine modification by microinjecting a methyltransferase-like 3 (Mettl3)-specific small interfering RNA into mouse germinal vesicle oocytes led to defects in meiotic spindles and the 1st polar body extrusion during maturation in vitro. By further quantitative real-time polymerase chain reaction and Poly(A)-tail assay analysis, we found that N6-methyladenosine methylation mainly acts by reducing deadenylation of mRNAs mediated by the Carbon catabolite repression 4 (CCR4)- negative on TATA less-(NOT) system, thereby causing mRNA accumulation in oocytes. Meanwhile, transcriptome analysis of germinal vesicle oocytes revealed the downregulation of transcripts of several genes encoding ribosomal subunits proteins in the Mettl3 small interfering RNA treated group, suggesting that N6-methyladenosine modification might affect translation. Together, our results indicate that RNA methylation accelerates mRNA decay, confirming the critical role of RNA clearance in oocyte maturation.
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Affiliation(s)
- Yan Zhu
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Wenjiao Wu
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Shaoqing Chen
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Zhen Zhang
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Guangli Zhang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Jie Li
- Medical Experiment Center, Guangdong Second Provincial General Hospital, Guangdong, PR China
| | - Manxi Jiang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangdong, PR China
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Gao M, Su S, Cao J, Xiang S, Huang Y, Shu X, Ma J, Liu J. Targeted Manipulation of Cellular RNA m 6A Methylation at the Single-Base Level. ACS Chem Biol 2022; 17:854-863. [PMID: 35294178 DOI: 10.1021/acschembio.1c00895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of tools for precise manipulation of cellular mRNA m6A methylation at the base level is highly required. Here, we report an RNA-guided RNA modification strategy using a fusion protein containing deactivated nuclease Cas13b and m6A methyltransferase METTL14, namely, dCas13b-M14, which is designedly positioned in the cytoplasm. dCas13b-M14 naturally heterodimerizes with endogenous METTL3 to form a catalytic complex to methylate specific cytoplasmic mRNA under a guide RNA (gRNA). We developed assays to screen and validate the guiding specificity of varied gRNAs at single-base resolution. With an optimum combination of dCas13b-M14 and gRNAs inside cells, we have successfully tuned methylation levels of several selected mRNA m6A sites. The off-target effect was evaluated by whole transcriptome m6A sequencing, and a very minor perturbation on the methylome was revealed. Finally, we successfully utilized the editing tool to achieve de novo methylations on five selected mRNA sites. Together, this study paves the way for studying position-dependent roles of m6A methylation in a particular transcript.
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Affiliation(s)
- Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Ye Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, China
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27
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Gonzalo L, Tossolini I, Gulanicz T, Cambiagno DA, Kasprowicz-Maluski A, Smolinski DJ, Mammarella MF, Ariel FD, Marquardt S, Szweykowska-Kulinska Z, Jarmolowski A, Manavella PA. R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants. NATURE PLANTS 2022; 8:402-418. [PMID: 35449404 PMCID: PMC9023350 DOI: 10.1038/s41477-022-01125-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/08/2022] [Indexed: 05/03/2023]
Abstract
In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.
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Affiliation(s)
- Lucia Gonzalo
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Ileana Tossolini
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
- Unidad de Estudios Agropecuarios (UDEA), INTA-CONICET, Córdoba, Argentina
| | - Anna Kasprowicz-Maluski
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dariusz Jan Smolinski
- Department of Cellular and Molecular Biology, Nicolaus Copernicus University, Torun, Poland
- Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - María Florencia Mammarella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.
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28
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Xu W, He C, Kaye EG, Li J, Mu M, Nelson GM, Dong L, Wang J, Wu F, Shi YG, Adelman K, Lan F, Shi Y, Shen H. Dynamic control of chromatin-associated m 6A methylation regulates nascent RNA synthesis. Mol Cell 2022; 82:1156-1168.e7. [PMID: 35219383 PMCID: PMC8969783 DOI: 10.1016/j.molcel.2022.02.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 11/02/2021] [Accepted: 02/01/2022] [Indexed: 12/12/2022]
Abstract
N6-methyladenosine (m6A) methylation is co-transcriptionally deposited on mRNA, but a possible role of m6A on transcription remains poorly understood. Here, we demonstrate that the METTL3/METTL14/WTAP m6A methyltransferase complex (MTC) is localized to many promoters and enhancers and deposits the m6A modification on nascent transcripts, including pre-mRNAs, promoter upstream transcripts (PROMPTs), and enhancer RNAs. PRO-seq analyses demonstrate that nascent RNAs originating from both promoters and enhancers are significantly decreased in the METTL3-depleted cells. Furthermore, genes targeted by the Integrator complex for premature termination are depleted of METTL3, suggesting a potential antagonistic relationship between METTL3 and Integrator. Consistently, we found the Integrator complex component INTS11 elevated at promoters and enhancers upon loss of MTC or nuclear m6A binders. Taken together, our findings suggest that MTC-mediated m6A modification protects nascent RNAs from Integrator-mediated termination and promotes productive transcription, thus unraveling an unexpected layer of gene regulation imposed by RNA m6A modification.
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Affiliation(s)
- Wenqi Xu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Chenxi He
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Emily G Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jiahui Li
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Mandi Mu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Li Dong
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Jiahua Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Feizhen Wu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China
| | - Yujiang Geno Shi
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Fei Lan
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China.
| | - Yang Shi
- Ludwig Institute for Cancer Research, Oxford Branch, Oxford University, Oxford OX3 7DQ, UK.
| | - Hongjie Shen
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 201399, China.
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29
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Dang Y, Dong Q, Wu B, Yang S, Sun J, Cui G, Xu W, Zhao M, Zhang Y, Li P, Li L. Global Landscape of m6A Methylation of Differently Expressed Genes in Muscle Tissue of Liaoyu White Cattle and Simmental Cattle. Front Cell Dev Biol 2022; 10:840513. [PMID: 35359442 PMCID: PMC8960853 DOI: 10.3389/fcell.2022.840513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
Liaoyu white cattle (LYWC) is a local breed in Liaoning Province, China. It has the advantages of grow quickly, high slaughter ratew, high meat quality and strong anti-stress ability. N6 methyladenosine (m6A) is a methylation modification of N6 position of RNA adenine, which is an important modification mechanism affecting physiological phenomena. In this study, we used the longissimus dorsi muscle of LYWC and SIMC for m6A-seq and RNA-seq high-throughput sequencing, and identified the key genes involved in muscle growth and m6A modification development by bioinformatics analysis. There were 31532 m6A peaks in the whole genome of LYWC and 47217 m6A peaks in the whole genome of SIMC. Compared with Simmental cattle group, LYWC group had 17,351 differentially expressed genes: 10,697 genes were up-regulated, 6,654 genes were down regulated, 620 differentially expressed genes were significant, while 16,731 differentially expressed genes were not significant. Among the 620 significantly differentially expressed genes, 295 genes were up-regulated and 325 genes were down regulated. In order to explore the relationship between m6A and mRNA expression in the muscles of LYWC and SIMC, the combined analysis of MeRIP-seq and RNA-seq revealed that 316 genes were m6A modified with mRNA expression. To identify differentially methylated genes related to muscle growth, four related genes were selected for quantitative verification in LYWC and SIMC. GO enrichment and KEGG analysis showed that the differentially expressed genes modified by m6A are mainly involved in skeletal muscle contraction, steroid biosynthesis process, redox process, PPAR pathway and fatty acid metabolism, and galactose metabolism. These results provide a theoretical basis for further research on the role of m6A in muscle growth and development.
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Affiliation(s)
- Yunlong Dang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qiao Dong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Bowei Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Shuhua Yang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiaming Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Gengyuan Cui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Weixiang Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Meiling Zhao
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yunxuan Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Peng Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
- *Correspondence: Peng Li, ; Lin Li,
| | - Lin Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Ruminant Infectious Disease Prevention and Control (East), Ministry of Agriculture and Rural Affairs, Beijing, China
- *Correspondence: Peng Li, ; Lin Li,
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30
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Driving Chromatin Organisation through N6-methyladenosine Modification of RNA: What Do We Know and What Lies Ahead? Genes (Basel) 2022; 13:genes13020340. [PMID: 35205384 PMCID: PMC8871937 DOI: 10.3390/genes13020340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, there has been an increase in research efforts surrounding RNA modification thanks to key breakthroughs in NGS-based whole transcriptome mapping methods. More than 100 modifications have been reported in RNAs, and some have been mapped at single-nucleotide resolution in the mammalian transcriptome. This has opened new research avenues in fields such as neurobiology, developmental biology, and oncology, among others. To date, we know that the RNA modification machinery finely tunes many diverse mechanisms involved in RNA processing and translation to regulate gene expression. However, it appears obvious to the research community that we have only just begun the process of understanding the several functions of the dynamic web of RNA modification, or the “epitranscriptome”. To expand the data generated so far, recently published studies revealed a dual role for N6-methyladenosine (m6A), the most abundant mRNA modification, in driving both chromatin dynamics and transcriptional output. These studies showed that the m6A-modified, chromatin-associated RNAs could act as molecular docks, recruiting histone modification proteins and thus contributing to the regulation of local chromatin structure. Here, we review these latest exciting findings and outline outstanding research questions whose answers will help to elucidate the biological relevance of the m6A modification of chromatin-associated RNAs in mammalian cells.
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Qi S, Mota J, Chan SH, Villarreal J, Dai N, Arya S, Hromas RA, Rao MK, Corrêa IR, Gupta YK. RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro. eLife 2022; 11:67150. [PMID: 35060905 PMCID: PMC8828048 DOI: 10.7554/elife.67150] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 01/20/2022] [Indexed: 11/28/2022] Open
Abstract
Methyltransferase like-3 (METTL3) and METTL14 complex transfers a methyl group from S-adenosyl-L-methionine to N6 amino group of adenosine bases in RNA (m6A) and DNA (m6dA). Emerging evidence highlights a role of METTL3-METTL14 in the chromatin context, especially in processes where DNA and RNA are held in close proximity. However, a mechanistic framework about specificity for substrate RNA/DNA and their interrelationship remain unclear. By systematically studying methylation activity and binding affinity to a number of DNA and RNA oligos with different propensities to form inter- or intra-molecular duplexes or single-stranded molecules in vitro, we uncover an inverse relationship for substrate binding and methylation and show that METTL3-METTL14 preferentially catalyzes the formation of m6dA in single-stranded DNA (ssDNA), despite weaker binding affinity to DNA. In contrast, it binds structured RNAs with high affinity, but methylates the target adenosine in RNA (m6A) much less efficiently than it does in ssDNA. We also show that METTL3-METTL14-mediated methylation of DNA is largely restricted by structured RNA elements prevalent in long noncoding and other cellular RNAs.
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Affiliation(s)
- Shan Qi
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio
| | - Javier Mota
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio
| | | | - Johanna Villarreal
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio
| | - Nan Dai
- RNA Biology, New England Biolabs
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio
| | - Robert A Hromas
- Department of Medicine, The University of Texas Health Science Center at San Antonio
| | - Manjeet K Rao
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio
| | | | - Yogesh K Gupta
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio
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Song T, Lv S, Li N, Zhao X, Ma X, Yan Y, Wang W, Sun L. OUP accepted manuscript. J Mol Cell Biol 2022; 14:6536920. [PMID: 35212732 PMCID: PMC9264158 DOI: 10.1093/jmcb/mjac011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/01/2022] Open
Abstract
m6A, a conserved and abundant modification on RNA, regulates RNA processing and function. RNA m6A machinery, including writers, erasers, and readers of m6A, is indispensable for m6A installation and function. Intriguingly, recent studies have revealed that m6A machinery can be recruited to chromatin by pleiotropic factors, including nascent RNA, transcription factors, regulatory RNA, histone modifications, and epigenetic machinery. Consequently, recruitment of m6A machinery can directly regulate chromatin biology, such as transcription, DNA damage repair, and DNA recombination beyond installation of m6A on nascent mRNA. Here, we discuss recent evidence showing that m6A machinery is targeted to chromatin and the direct biological consequences along with the underlying mechanisms.
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Affiliation(s)
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Neng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianyun Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingying Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weixia Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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m 6A RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N 6-Methyladenosine. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2404:355-362. [PMID: 34694619 DOI: 10.1007/978-1-0716-1851-6_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) in eukaryotes. It influences gene expression by regulating RNA processing, nuclear export, mRNA decay, and translation. Hence, m6A controls fundamental cellular processes, and dysregulated deposition of m6A has been acknowledged to play a role in a broad range of human diseases, including cancer. m6A RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq or m6A-seq) is a powerful technique to map m6A in a transcriptome-wide level. After immunoprecipitation of fragmented polyadenylated (poly(A)+) rich RNA by using specific anti-m6A antibodies, both the immunoprecipitated RNA fragments together with the input control are subjected to massively parallel sequencing. The generation of such comprehensive methylation profiles of signal enrichment relative to input control is necessary in order to better comprehend the pathogenesis behind aberrant m6A deposition.
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34
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Wang L, Qi H, Li D, Liu L, Chen D, Gao X. METTL3 is a key regulator of milk synthesis in mammary epithelial cells. Cell Biol Int 2021; 46:359-369. [PMID: 34865263 DOI: 10.1002/cbin.11733] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/31/2021] [Accepted: 11/28/2021] [Indexed: 12/15/2022]
Abstract
The enzyme m6 A methyltransferase-like 3 (METTL3) catalyzes N6 -methyladenosine (m6 A) modification in eukaryotic messenger RNAs (mRNAs). However, the physiological function and molecular mechanism of METTL3 in mammalian cells have not been fully understood. Here we showed that METTL3 was highly expressed in mouse mammary gland of the lactation period. METTL3 was located in the nucleus of bovine mammary epithelial cells (MECs), and methionine (Met) and β-estrodial (E2) upregulated METTL3 protein level. METTL3 knockdown decreased milk protein and fat synthesis, whereas its overexpression had the opposite effects. METTL3 overexpression stimulated mRNA expression and protein phosphorylation of the mechanistic target of rapamycin (mTOR) and mRNA and protein expression of sterol regulatory element binding protein 1 (SREBP1), whereas METTL3 knockdown blocked the stimulatory effects of Met and E2 on these processes. Furthermore, METTL3 overexpression led to increased mRNA m6 A methylation of mTOR and SREBP1, whereas METTL3 knockdown suppressed the stimulatory effects of Met and E2 on these processes. The interaction between METTL3 and glycyl-tRNA synthetase (GlyRS) was confirmed by Co-immunoprecipitation and fluorescence resonance energy transfer approaches, and colocalization observation further showed that Met and E2 treatment increased this interaction. GlyRS knockdown abolished METTL3 protein levels upregulated by Met and E2, and METTL3 knockdown markedly decreased the effects of GlyRS overexpression on mTOR expression and phosphorylation and SREBP1 expression. In summary, we demonstrate that METTL3 is a key positive regulator of Met and E2-stimulated and GlyRS-mediated mTOR and SREBP1 signaling pathways and milk protein and fat synthesis in mammary epithelial cells.
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Affiliation(s)
- Lulu Wang
- College of Animal Science, Yangtze University, Jingzhou, China.,College of Life Science, Northeast Agricultural University, Harbin, China
| | - Hao Qi
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Dong Li
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Lijie Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Dongying Chen
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xuejun Gao
- College of Animal Science, Yangtze University, Jingzhou, China
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35
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Balancing of mitochondrial translation through METTL8-mediated m 3C modification of mitochondrial tRNAs. Mol Cell 2021; 81:4810-4825.e12. [PMID: 34774131 DOI: 10.1016/j.molcel.2021.10.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 02/08/2023]
Abstract
Mitochondria contain a specific translation machinery for the synthesis of mitochondria-encoded respiratory chain components. Mitochondrial tRNAs (mt-tRNAs) are also generated from the mitochondrial DNA and, similar to their cytoplasmic counterparts, are post-transcriptionally modified. Here, we find that the RNA methyltransferase METTL8 is a mitochondrial protein that facilitates 3-methyl-cytidine (m3C) methylation at position C32 of the mt-tRNASer(UCN) and mt-tRNAThr. METTL8 knockout cells show a reduction in respiratory chain activity, whereas overexpression increases activity. In pancreatic cancer, METTL8 levels are high, which correlates with lower patient survival and an enhanced respiratory chain activity. Mitochondrial ribosome profiling uncovered mitoribosome stalling on mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons. Further analysis of the respiratory chain complexes using mass spectrometry revealed reduced incorporation of the mitochondrially encoded proteins ND6 and ND1 into complex I. The well-balanced translation of mt-tRNASer(UCN)- and mt-tRNAThr-dependent codons through METTL8-mediated m3C32 methylation might, therefore, facilitate the optimal composition and function of the mitochondrial respiratory chain.
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Covelo-Molares H, Obrdlik A, Poštulková I, Dohnálková M, Gregorová P, Ganji R, Potěšil D, Gawriyski L, Varjosalo M, Vaňáčová Š. The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features. Nucleic Acids Res 2021; 49:10895-10910. [PMID: 34634806 PMCID: PMC8565353 DOI: 10.1093/nar/gkab900] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) and N6,2′-O-dimethyladenosine (m6Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.
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Affiliation(s)
- Helena Covelo-Molares
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ales Obrdlik
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ivana Poštulková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Michaela Dohnálková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Pavlína Gregorová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Ranjani Ganji
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
| | - Lisa Gawriyski
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology & HiLIFE - Helsinki Institute of Life Science, University of Helsinki, Helsinki 00014, Finland
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 62500, Czech Republic
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37
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Wang H, Song X, Song C, Wang X, Cao H. m 6A-seq analysis of microRNAs reveals that the N6-methyladenosine modification of miR-21-5p affects its target expression. Arch Biochem Biophys 2021; 711:109023. [PMID: 34480914 DOI: 10.1016/j.abb.2021.109023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 12/11/2022]
Abstract
In eukaryotes, N6-methyladenosine (m6A) is one of the most abundant modifications on RNAs, and it plays important roles in many biological processes and diseases such as cancer. While most m6A researches focus on message RNAs and long non-coding RNAs, recent studies have reported the presence of m6A in small RNAs. Nevertheless, current knowledge about m6A prevalence in mature microRNAs (miRNA) is extremely limited and the functional significance of m6A methylation in miRNAs remains to be elucidated. Here, we demonstrated cell-specific m6A profiles of miRNAs in A549 human non-small cell lung cancer (NSCLC) cells and HEK293A cells by using miRNA m6A immunoprecipitation sequencing and constructed the consensus motif in m6A-enriched miRNAs de novo. We found that miR-21-5p, an oncogenic miRNA, showed the highest m6A enrichment in NSCLC cells. Depletion of the demethylase ALKBH5 did not change the expression level of miR-21-5p, but altered the m6A abundance of miR-21-5p, thereby changing the expression levels of its target gene. We further synthesized m6A modified miR-21-5p mimics in vitro and demonstrated that in NSCLC cells, m6A marks in mature miR-21-5p could directly affect its silencing potency towards target genes, which finally impaired its promotion to proliferation and motility. Together, our findings reveal the landscape of m6A modification in mature miRNAs, and provide the first evidence that it may contribute to the mRNA responses to cancer-related miRNAs.
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Affiliation(s)
- Hanming Wang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xinyun Song
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Chun Song
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xiaoxia Wang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Huiqing Cao
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
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38
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Cross-Talk between Oxidative Stress and m 6A RNA Methylation in Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:6545728. [PMID: 34484567 PMCID: PMC8416400 DOI: 10.1155/2021/6545728] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/03/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
Oxidative stress is a state of imbalance between oxidation and antioxidation. Excessive ROS levels are an important factor in tumor development. Damage stimulation and excessive activation of oncogenes cause elevated ROS production in cancer, accompanied by an increase in the antioxidant capacity to retain redox homeostasis in tumor cells at an increased level. Although moderate concentrations of ROS produced in cancer cells contribute to maintaining cell survival and cancer progression, massive ROS accumulation can exert toxicity, leading to cancer cell death. RNA modification is a posttranscriptional control mechanism that regulates gene expression and RNA metabolism, and m6A RNA methylation is the most common type of RNA modification in eukaryotes. m6A modifications can modulate cellular ROS levels through different mechanisms. It is worth noting that ROS signaling also plays a regulatory role in m6A modifications. In this review, we concluded the effects of m6A modification and oxidative stress on tumor biological functions. In particular, we discuss the interplay between oxidative stress and m6A modifications.
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39
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Zhang W, Qian Y, Jia G. The detection and functions of RNA modification m 6A based on m 6A writers and erasers. J Biol Chem 2021; 297:100973. [PMID: 34280435 PMCID: PMC8350415 DOI: 10.1016/j.jbc.2021.100973] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
N6-methyladenosine (m6A) is the most frequent chemical modification in eukaryotic mRNA and is known to participate in a variety of physiological processes, including cancer progression and viral infection. The reversible and dynamic m6A modification is installed by m6A methyltransferase (writer) enzymes and erased by m6A demethylase (eraser) enzymes. m6A modification recognized by m6A binding proteins (readers) regulates RNA processing and metabolism, leading to downstream biological effects such as promotion of stability and translation or increased degradation. The m6A writers and erasers determine the abundance of m6A modifications and play decisive roles in its distribution and function. In this review, we focused on m6A writers and erasers and present an overview on their known functions and enzymatic molecular mechanisms, showing how they recognize substrates and install or remove m6A modifications. We also summarize the current applications of m6A writers and erasers for m6A detection and highlight the merits and drawbacks of these available methods. Lastly, we describe the biological functions of m6A in cancers and viral infection based on research of m6A writers and erasers and introduce new assays for m6A functionality via programmable m6A editing tools.
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Affiliation(s)
- Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yang Qian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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40
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Affiliation(s)
- Chenxi He
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Lan
- Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
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41
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Duda KJ, Ching RW, Jerabek L, Shukeir N, Erikson G, Engist B, Onishi-Seebacher M, Perrera V, Richter F, Mittler G, Fritz K, Helm M, Knuckles P, Bühler M, Jenuwein T. m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin. Nucleic Acids Res 2021; 49:5568-5587. [PMID: 33999208 PMCID: PMC8191757 DOI: 10.1093/nar/gkab364] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin has essential functions in maintaining chromosome structure, in protecting genome integrity and in stabilizing gene expression programs. Heterochromatin is often nucleated by underlying DNA repeat sequences, such as major satellite repeats (MSR) and long interspersed nuclear elements (LINE). In order to establish heterochromatin, MSR and LINE elements need to be transcriptionally competent and generate non-coding repeat RNA that remain chromatin associated. We explored whether these heterochromatic RNA, similar to DNA and histones, may be methylated, particularly for 5-methylcytosine (5mC) or methyl-6-adenosine (m6A). Our analysis in mouse ES cells identifies only background level of 5mC but significant enrichment for m6A on heterochromatic RNA. Moreover, MSR transcripts are a novel target for m6A RNA modification, and their m6A RNA enrichment is decreased in ES cells that are mutant for Mettl3 or Mettl14, which encode components of a central RNA methyltransferase complex. Importantly, MSR transcripts that are partially deficient in m6A RNA methylation display impaired chromatin association and have a reduced potential to form RNA:DNA hybrids. We propose that m6A modification of MSR RNA will enhance the functions of MSR repeat transcripts to stabilize mouse heterochromatin.
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Affiliation(s)
- Katarzyna J Duda
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Reagan W Ching
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Lisa Jerabek
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Nicholas Shukeir
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Galina Erikson
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Bettina Engist
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Valentina Perrera
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Florian Richter
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Katharina Fritz
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg - University, Mainz 55128, Germany
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland and University of Basel, Basel 4051, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland and University of Basel, Basel 4051, Switzerland
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
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Wang D, Qu X, Lu W, Wang Y, Jin Y, Hou K, Yang B, Li C, Qi J, Xiao J, Che X, Liu Y. N 6-Methyladenosine RNA Demethylase FTO Promotes Gastric Cancer Metastasis by Down-Regulating the m6A Methylation of ITGB1. Front Oncol 2021; 11:681280. [PMID: 34277426 PMCID: PMC8282183 DOI: 10.3389/fonc.2021.681280] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/21/2021] [Indexed: 01/27/2023] Open
Abstract
Abnormal RNA m6A methylation is known to lead to the occurrence and progression of multiple cancers including gastric cancer (GC). However, the integrative effects of all m6A methylation regulators on GC prognosis are unclear. Our research aimed to globally analyze the prognosis values of all 33 m6A RNA methylation regulators in GC by univariate and multivariate Cox regression analyses. Among all 33 m6A RNA methylation regulators, fat mass and obesity-associated protein (FTO), an m6A demethylase, was identified as a key prognostic risk factor on overall survival (OS) of GC patients. It was found that FTO could promote GC cell migration and invasion abilities, and we predicted that ITGB1 was a demethylated target of FTO. Knockdown (KD) of FTO significantly down-regulated ITGB1 expression at both mRNA and protein levels and augmented ITGB1 mRNA m6A modification level. Moreover, overexpression (OE) of ITGB1 could partially reverse FTO-KD-inhibited migration and invasion of GC cells. Our study found that FTO was an independent risk factor for overall survival (OS) of GC patients and FTO could promote GC metastasis by upregulating the expression of Integrin β1(ITGB1) via decreasing its m6A level. These results indicated that FTO can be a potent GC biomarker for prognosis prediction as well as a potential target in GC treatment.
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Affiliation(s)
- Duo Wang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Wenqing Lu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Yizhe Wang
- Department of Respiratory and Infectious Disease of Geriatrics, The First Hospital of China Medical University, Shenyang, China
| | - Yue Jin
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Kezuo Hou
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Bowen Yang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Ce Li
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Jianfei Qi
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Shenyang, China
| | - Xiaofang Che
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, Shenyang, China.,Liaoning Province Clinical Research Center for Cancer, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, China
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43
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Gui Y, Yuan S. Epigenetic regulations in mammalian spermatogenesis: RNA-m 6A modification and beyond. Cell Mol Life Sci 2021; 78:4893-4905. [PMID: 33835194 PMCID: PMC11073063 DOI: 10.1007/s00018-021-03823-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/04/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Emerging evidence shows that m6A, one of the most abundant RNA modifications in mammals, is involved in the entire process of spermatogenesis, including mitosis, meiosis, and spermiogenesis. "Writers" catalyze m6A formation on stage-specific transcripts during male germline development, while "erasers" remove m6A modification to maintain a balance between methylation and demethylation. The different functions of RNA-m6A transcripts depend on their recognition by "readers". m6A modification mediates RNA metabolism, including mRNA splicing, translation, and degradation, as well as the maturity and biosynthesis of non-coding RNAs. Sperm RNA profiles are easily affected by environmental exposure and can even be inherited for several generations, similar to epigenetic inheritance. Here, we review and summarize the critical role of m6A in different developmental stages of male germ cells, to understand of the mechanisms and epigenetic regulation of m6A modifications. In addition, we also outline and discuss the important role of non-coding RNAs in spermatogenesis and RNA modifications in epigenetic inheritance.
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Affiliation(s)
- Yiqian Gui
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, 518057, China.
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44
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Jing FY, Zhou LM, Ning YJ, Wang XJ, Zhu YM. The Biological Function, Mechanism, and Clinical Significance of m6A RNA Modifications in Head and Neck Carcinoma: A Systematic Review. Front Cell Dev Biol 2021; 9:683254. [PMID: 34136491 PMCID: PMC8201395 DOI: 10.3389/fcell.2021.683254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers, yet the molecular mechanisms underlying its onset and development have not yet been fully elucidated. Indeed, an in-depth understanding of the potential molecular mechanisms underlying HNSCC oncogenesis may aid the development of better treatment strategies. Recent epigenetic studies have revealed that the m6A RNA modification plays important roles in HNSCC. In this review, we summarize the role of m6A modification in various types of HNSCC, including thyroid, nasopharyngeal, hypopharyngeal squamous cell, and oral carcinoma. In addition, we discuss the regulatory roles of m6A in immune cells within the tumor microenvironment, as well as the potential molecular mechanisms. Finally, we review the development of potential targets for treating cancer based on the regulatory functions of m6A, with an aim to improving targeted therapies for HNSCC. Together, this review highlights the important roles that m6A modification plays in RNA synthesis, transport, and translation, and demonstrates that the regulation of m6A-related proteins can indirectly affect mRNA and ncRNA function, thus providing a novel strategy for reengineering intrinsic cell activity and developing simpler interventions to treat HNSCC.
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Affiliation(s)
- Feng-Yang Jing
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital & College, Anhui Medical University, Hefei, China
| | - Li-Ming Zhou
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital & College, Anhui Medical University, Hefei, China
| | - Yu-Jie Ning
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital & College, Anhui Medical University, Hefei, China
| | - Xiao-Juan Wang
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital & College, Anhui Medical University, Hefei, China
| | - You-Ming Zhu
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital & College, Anhui Medical University, Hefei, China
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45
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The m 6A-epitranscriptome in brain plasticity, learning and memory. Semin Cell Dev Biol 2021; 125:110-121. [PMID: 34053866 DOI: 10.1016/j.semcdb.2021.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
Activity-dependent gene expression and protein translation underlie the ability of neurons to dynamically adjust their synaptic strength in response to sensory experience and during learning. The emerging field of epitranscriptomics (RNA modifications) has rapidly shifted our views on the mechanisms that regulate gene expression. Among hundreds of biochemical modifications on RNA, N6-methyladenosine (m6A) is the most abundant reversible mRNA modification in the brain. Its dynamic nature and ability to regulate all aspects of mRNA processing have positioned m6A as an important and versatile regulator of nervous system functions, including neuronal plasticity, learning and memory. In this review, we summarise recent experimental evidence that supports the role of m6A signalling in learning and memory, as well as providing an overview of the underlying molecular mechanisms in neurons. We also discuss the consequences of perturbed m6A signalling and/or its regulatory networks which are increasingly being linked to various cognitive disorders in humans.
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46
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Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
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47
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Gehring NH, Roignant JY. Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends Genet 2021; 37:355-372. [DOI: 10.1016/j.tig.2020.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
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48
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Liu P, Li F, Lin J, Fukumoto T, Nacarelli T, Hao X, Kossenkov AV, Simon MC, Zhang R. m 6A-independent genome-wide METTL3 and METTL14 redistribution drives the senescence-associated secretory phenotype. Nat Cell Biol 2021; 23:355-365. [PMID: 33795874 PMCID: PMC8035315 DOI: 10.1038/s41556-021-00656-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023]
Abstract
Methyltransferase-like 3 (METTL3) and 14 (METTL14) are core subunits of the methyltransferase complex that catalyses messenger RNA N6-methyladenosine (m6A) modification. Despite the expanding list of m6A-dependent functions of the methyltransferase complex, the m6A-independent function of the METTL3 and METTL14 complex remains poorly understood. Here we show that genome-wide redistribution of METTL3 and METTL14 transcriptionally drives the senescence-associated secretory phenotype (SASP) in an m6A-independent manner. METTL14 is redistributed to the enhancers, whereas METTL3 is localized to the pre-existing NF-κB sites within the promoters of SASP genes during senescence. METTL3 and METTL14 are necessary for SASP. However, SASP is not regulated by m6A mRNA modification. METTL3 and METTL14 are required for both the tumour-promoting and immune-surveillance functions of senescent cells, which are mediated by SASP in vivo in mouse models. In summary, our results report an m6A-independent function of the METTL3 and METTL14 complex in transcriptionally promoting SASP during senescence.
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Affiliation(s)
- Pingyu Liu
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Fuming Li
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianhuang Lin
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Takeshi Fukumoto
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Timothy Nacarelli
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Xue Hao
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Andrew V. Kossenkov
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - M. Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- Immunology, Microenvironment and Metastasis Program, The Wistar Institute, Philadelphia, PA 19104, USA,Correspondence should be addressed to: Rugang Zhang, Ph.D.,
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49
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Lan Q, Liu PY, Bell JL, Wang JY, Hüttelmaier S, Zhang XD, Zhang L, Liu T. The Emerging Roles of RNA m 6A Methylation and Demethylation as Critical Regulators of Tumorigenesis, Drug Sensitivity, and Resistance. Cancer Res 2021; 81:3431-3440. [PMID: 34228629 DOI: 10.1158/0008-5472.can-20-4107] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
RNA N6 -methyladenosine (m6A) modification occurs in approximately 25% of mRNAs at the transcriptome-wide level. RNA m6A is regulated by the RNA m6A methyltransferases methyltransferase-like 3 (METTL3), METTL14, and METTL16 (writers), demethylases FTO and ALKBH5 (erasers), and binding proteins YTHDC1-2, YTHDF1-3, IGF2BP1-3, and SND1 (readers). These RNA m6A modification proteins are frequently upregulated or downregulated in human cancer tissues and are often associated with poor patient prognosis. By modulating pre-mRNA splicing, mRNA nuclear export, decay, stability, and translation of oncogenic and tumor suppressive transcripts, RNA m6A modification proteins regulate cancer cell proliferation, survival, migration, invasion, tumor initiation, progression, metastasis, and sensitivity to anticancer therapies. Importantly, small-molecule activators of METTL3, as well as inhibitors of METTL3, FTO, ALKBH5, and IGF2BP1 have recently been identified and have shown considerable anticancer effects when administered alone or in combination with other anticancer agents, both in vitro and in mouse models of human cancers. Future compound screening and design of more potent and selective RNA m6A modification protein inhibitors and activators are expected to provide novel anticancer agents, appropriate for clinical trials in patients with cancer tissues harboring aberrant RNA m6A modification protein expression or RNA m6A modification protein-induced resistance to cancer therapy.
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Affiliation(s)
- Qing Lan
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Pei Y Liu
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Jessica L Bell
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Jenny Y Wang
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia.,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University, Halle Saale, Germany
| | - Xu Dong Zhang
- School of Medicine and Public Health, Priority Research Centre for Cancer Research, University of Newcastle, Callaghan, New South Wales, Australia. .,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, P.R. China.
| | - Tao Liu
- Children's Cancer Institute Australia, Sydney, New South Wales, Australia. .,School of Women's and Children's Health, University of New South Wales Sydney, Sydney, New South Wales, Australia.,Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, P.R. China
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50
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Zhao Y, Chen Y, Jin M, Wang J. The crosstalk between m 6A RNA methylation and other epigenetic regulators: a novel perspective in epigenetic remodeling. Am J Cancer Res 2021; 11:4549-4566. [PMID: 33754077 PMCID: PMC7977459 DOI: 10.7150/thno.54967] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/07/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation involves a range of sophisticated processes which contribute to heritable alterations in gene expression without altering DNA sequence. Regulatory events predominantly include DNA methylation, chromatin remodeling, histone modifications, non-coding RNAs (ncRNAs), and RNA modification. As the most prevalent RNA modification in eukaryotic cells, N6-methyladenosine (m6A) RNA methylation actively participates in the modulation of RNA metabolism. Notably, accumulating evidence has revealed complicated interrelations occurring between m6A and other well-known epigenetic modifications. Their crosstalk conspicuously triggers epigenetic remodeling, further yielding profound impacts on a variety of physiological and pathological processes, especially tumorigenesis. Herein, we provide an up-to-date review of this emerging hot area of biological research, summarizing the interplay between m6A RNA methylation and other epigenetic regulators, and highlighting their underlying functions in epigenetic reprogramming.
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