351
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Li Y, Ge YZ, Xu L, Xu Z, Dou Q, Jia R. The Potential Roles of RNA N6-Methyladenosine in Urological Tumors. Front Cell Dev Biol 2020; 8:579919. [PMID: 33015074 PMCID: PMC7510505 DOI: 10.3389/fcell.2020.579919] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is regarded as the most abundant, prevalent and conserved internal mRNA modification in mammalian cells. M6A can be catalyzed by m6A methyltransferases METTL3, METTL14 and WTAP (writers), reverted by demethylases ALKBH5 and FTO (erasers), and recognized by m6A -binding proteins such as YTHDF1/2/3, IGF2BP1/2/3 and HNRNPA2B1 (readers). Emerging evidence suggests that m6A modification is significant for regulating many biological and cellular processes and participates in the pathological development of various diseases, including tumors. This article reviews recent studies on the biological function of m6A modification and the methylation modification of m6A in urological tumors.
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Affiliation(s)
- Yang Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Quanliang Dou
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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352
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Aoyama T, Yamashita S, Tomita K. Mechanistic insights into m6A modification of U6 snRNA by human METTL16. Nucleic Acids Res 2020; 48:5157-5168. [PMID: 32266935 PMCID: PMC7229813 DOI: 10.1093/nar/gkaa227] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 02/04/2023] Open
Abstract
The N6-methyladenosine modification at position 43 (m6A43) of U6 snRNA is catalyzed by METTL16, and is important for the 5'-splice site recognition by U6 snRNA during pre-mRNA splicing. Human METTL16 consists of the N-terminal methyltransferase domain (MTD) and the C-terminal vertebrate conserved region (VCR). While the MTD has an intrinsic property to recognize a specific sequence in the distinct structural context of RNA, the VCR functions have remained uncharacterized. Here, we present structural and functional analyses of the human METTL16 VCR. The VCR increases the affinity of METTL16 toward U6 snRNA, and the conserved basic region in VCR is important for the METTL16-U6 snRNA interaction. The VCR structure is topologically homologous to the C-terminal RNA binding domain, KA1, in U6 snRNA-specific terminal uridylyl transferase 1 (TUT1). A chimera of the N-terminal MTD of METTL16 and the C-terminal KA1 of TUT1 methylated U6 snRNA more efficiently than the MTD, indicating the functional conservation of the VCR and KA1 for U6 snRNA biogenesis. The VCR interacts with the internal stem-loop (ISL) within U6 snRNA, and this interaction would induce the conformational rearrangement of the A43-containing region of U6 snRNA, thereby modifying the RNA structure to become suitable for productive catalysis by the MTD. Therefore, the MTD and VCR in METTL16 cooperatively facilitate the m6A43 U6 snRNA modification.
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Affiliation(s)
- Tomohiko Aoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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353
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Ru W, Zhang X, Yue B, Qi A, Shen X, Huang Y, Lan X, Lei C, Chen H. Insight into m 6A methylation from occurrence to functions. Open Biol 2020; 10:200091. [PMID: 32898471 PMCID: PMC7536083 DOI: 10.1098/rsob.200091] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
RNA m6A methylation is a post-transcriptional modification that occurs at the nitrogen-6 position of adenine. This dynamically reversible modification is installed, removed and recognized by methyltransferases, demethylases and readers, respectively. This modification has been found in most eukaryotic mRNA, tRNA, rRNA and other non-coding RNA. Recent studies have revealed important regulatory functions of the m6A including effects on gene expression regulation, organism development and cancer development. In this review, we summarize the discovery and features of m6A, and briefly introduce the mammalian m6A writers, erasers and readers. Finally, we discuss progress in identifying additional functions of m6A and the outstanding questions about the regulatory effect of this widespread modification.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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354
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the "fifth" ribonucleotide in 1951. Since then, the ever-increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal-Hreidarsson syndrome, Bowen-Conradi syndrome, or Williams-Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Phillip J. McCown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Agnieszka Ruszkowska
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
- Present address:
Institute of Bioorganic ChemistryPolish Academy of SciencesPoznanPoland
| | - Charlotte N. Kunkler
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Kurtis Breger
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jacob P. Hulewicz
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew C. Wang
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Noah A. Springer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jessica A. Brown
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
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355
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Zeng C, Huang W, Li Y, Weng H. Roles of METTL3 in cancer: mechanisms and therapeutic targeting. J Hematol Oncol 2020; 13:117. [PMID: 32854717 PMCID: PMC7457244 DOI: 10.1186/s13045-020-00951-w] [Citation(s) in RCA: 286] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant mRNA modification and is catalyzed by the methyltransferase complex, in which methyltransferase-like 3 (METTL3) is the sole catalytic subunit. Accumulating evidence in recent years reveals that METTL3 plays key roles in a variety of cancer types, either dependent or independent on its m6A RNA methyltransferase activity. While the roles of m6A modifications in cancer have been extensively reviewed elsewhere, the critical functions of METTL3 in various types of cancer, as well as the potential targeting of METTL3 as cancer treatment, have not yet been highlighted. Here we summarize our current understanding both on the oncogenic and tumor-suppressive functions of METTL3, as well as the underlying molecular mechanisms. The well-documented protein structure of the METTL3/METTL14 heterodimer provides the basis for potential therapeutic targeting, which is also discussed in this review.
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Affiliation(s)
- Chengwu Zeng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.,Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China
| | - Wanxu Huang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.,The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Yangqiu Li
- Institute of Hematology, School of Medicine, Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, 510632, China.
| | - Hengyou Weng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China. .,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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356
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Karthiya R, Khandelia P. m6A RNA Methylation: Ramifications for Gene Expression and Human Health. Mol Biotechnol 2020; 62:467-484. [PMID: 32840728 DOI: 10.1007/s12033-020-00269-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
Cellular transcriptomes are frequently adorned by a variety of chemical modification marks, which in turn have a profound influence on its functioning. Of these modifications, the one which has invited a lot of attention in the recent years is m6A RNA methylation, leading to the development of RNA epigenetics or epitranscriptomics as a frontier research area. m6A RNA methylation is one of the most abundant reversible internal modification seen in cellular RNAs. Studies in the last few years have not only shed light on the molecular machinery involved in m6A RNA methylation but also on the impact of this modification in regulating gene expression and hence biological processes. In this review, we will emphasize the biological impact of this modification in normal organismal development and diseases.
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Affiliation(s)
- R Karthiya
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal District, Hyderabad, Telangana, 500078, India.
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357
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Wu S, Zhang S, Wu X, Zhou X. m 6A RNA Methylation in Cardiovascular Diseases. Mol Ther 2020; 28:2111-2119. [PMID: 32910911 DOI: 10.1016/j.ymthe.2020.08.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/01/2020] [Accepted: 08/13/2020] [Indexed: 01/01/2023] Open
Abstract
Cardiovascular diseases (CVDs) remain the leading cause of death and disability worldwide, despite marked improvements in prevention, diagnosis, and early intervention. There is an urgent need to discover more effective therapeutic strategies, which would be facilitated by a more in-depth understanding of CVDs and their underlying molecular mechanisms. Recent advances in knowledge about epigenetic mechanisms, especially RNA methylation, have revealed a close relationship between epigenetic modifications and CVDs and have brought to potential novel targets for diagnosis and treatment. Here, we provide a review of recent studies exploring RNA N6-methyladenosine (m6A) modification, with particular emphasis on its role in CVDs, such as coronary heart disease, hypertension, cardiac hypertrophy, and heart failure. We also introduce the "life cycle" of m6A and its dominant function in several biological processes. Finally, we highlight the prospects of treatment based on interfering with m6A, which could have a transformative effect on clinical medicine.
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Affiliation(s)
- Siyi Wu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China
| | - Shuchen Zhang
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China
| | - Xiaoguang Wu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, P.R. China.
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358
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Chen S, Li Y, Zhi S, Ding Z, Wang W, Peng Y, Huang Y, Zheng R, Yu H, Wang J, Hu M, Miao J, Li J. WTAP promotes osteosarcoma tumorigenesis by repressing HMBOX1 expression in an m 6A-dependent manner. Cell Death Dis 2020; 11:659. [PMID: 32814762 PMCID: PMC7438489 DOI: 10.1038/s41419-020-02847-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
N6-methyladenosine (m6A) regulators are involved in the progression of various cancers via regulating m6A modification. However, the potential role and mechanism of the m6A modification in osteosarcoma remains obscure. In this study, WTAP was found to be highly expressed in osteosarcoma tissue and it was an independent prognostic factor for overall survival in osteosarcoma. Functionally, WTAP, as an oncogene, was involved in the proliferation and metastasis of osteosarcoma in vitro and vivo. Mechanistically, M6A dot blot, RNA-seq and MeRIP-seq, MeRIP-qRT-PCR and luciferase reporter assays showed that HMBOX1 was identified as the target gene of WTAP, which regulated HMBOX1 stability depending on m6A modification at the 3′UTR of HMBOX1 mRNA. In addition, HMBOX1 expression was downregulated in osteosarcoma and was an independent prognostic factor for overall survival in osteosarcoma patients. Silenced HMBOX1 evidently attenuated shWTAP-mediated suppression on osteosarcoma growth and metastasis in vivo and vitro. Finally, WTAP/HMBOX1 regulated osteosarcoma growth and metastasis via PI3K/AKT pathway. In conclusion, this study demonstrated the critical role of the WTAP-mediated m6A modification in the progression of osteosarcoma, which could provide novel insights into osteosarcoma treatment.
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Affiliation(s)
- Shijie Chen
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuezhan Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Shuang Zhi
- Four Gynecological Wards, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315000, China
| | - Zhiyu Ding
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Weiguo Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yi Peng
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Yan Huang
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - Ruping Zheng
- School of Basic Medical Science, Central South University, Changsha, China
| | - Haiyang Yu
- School of Basic Medical Science, Central South University, Changsha, China
| | - Jianlong Wang
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China
| | - Minghua Hu
- Department of Anatomy, Histology and Embryology, Changsha Medical University, Changsha, China
| | - Jinglei Miao
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
| | - Jinsong Li
- Department of Orthopaedics, The Third Xiangya Hospital of Central South University, 138 Tongzipo Rd, Changsha, Hunan, 410013, China.
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359
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A novel N6-methyladenosine (m6A)-dependent fate decision for the lncRNA THOR. Cell Death Dis 2020; 11:613. [PMID: 32792482 PMCID: PMC7426843 DOI: 10.1038/s41419-020-02833-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022]
Abstract
Previous studies have revealed the critical roles of the N6-methyladenosine (m6A) modification of long non-coding RNAs (lncRNAs) in cancers, but the relationship between the oncogenic role of the lncRNA THOR (a representative of cancer/testis lncRNAs) and m6A modification remains unclear. Here, we show that the internal m6A modification of the lncRNA THOR via an m6A-reader-dependent modality regulates the proliferation of cancer cells. Our findings demonstrated that the loss of the lncRNA THOR inhibits the proliferation, migration, and invasion of cancer cells in vitro and in vivo. In addition, m6A is highly enriched on lncRNA THOR transcripts, which contain GA (m6A) CA, GG (m6A) CU, and UG (m6A) CU sequence motifs. RIP-qRT-PCR and RNA pull-down assay results revealed that the specific m6A readers YTHDF1 and YTHDF2 can read the m6A motifs and regulate the stability of the lncRNA THOR (stabilization and decay). These m6A-dependent RNA-protein interactions can maintain the oncogenic role of the lncRNA THOR. Collectively, these findings highlight the critical role of the m6A modification in oncogenic lncRNA THOR and reveal a novel long non-coding RNA regulatory mechanism, providing a new way to explore RNA epigenetic regulatory patterns in the future.
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360
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Reichel M, Köster T, Staiger D. Marking RNA: m6A writers, readers, and functions in Arabidopsis. J Mol Cell Biol 2020; 11:899-910. [PMID: 31336387 PMCID: PMC6884701 DOI: 10.1093/jmcb/mjz085] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) emerges as an important modification in eukaryotic mRNAs. m6A has first been reported in 1974, and its functional significance in mammalian gene regulation and importance for proper development have been well established. An arsenal of writer, eraser, and reader proteins accomplish deposition, removal, and interpretation of the m6A mark, resulting in dynamic function. This led to the concept of an epitranscriptome, the compendium of RNA species with chemical modification of the nucleobases in the cell, in analogy to the epigenome. While m6A has long been known to also exist in plant mRNAs, proteins involved in m6A metabolism have only recently been detected by mutant analysis, homology search, and mRNA interactome capture in the reference plant Arabidopsis thaliana. Dysregulation of the m6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive development. Furthermore, m6A modification affects viral infection. Here, we discuss recent progress in identifying m6A sites transcriptome-wide, in identifying the molecular players involved in writing, removing, and reading the mark, and in assigning functions to this RNA modification in A. thaliana. We highlight similarities and differences to m6A modification in mammals and provide an outlook on important questions that remain to be addressed.
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Affiliation(s)
- Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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361
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Asada K, Bolatkan A, Takasawa K, Komatsu M, Kaneko S, Hamamoto R. Critical Roles of N6-Methyladenosine (m 6A) in Cancer and Virus Infection. Biomolecules 2020; 10:biom10071071. [PMID: 32709063 PMCID: PMC7408378 DOI: 10.3390/biom10071071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Studies have shown that epigenetic abnormalities are involved in various diseases, including cancer. In particular, in order to realize precision medicine, the integrated analysis of genetics and epigenetics is considered to be important; detailed epigenetic analysis in the medical field has been becoming increasingly important. In the epigenetics analysis, DNA methylation and histone modification analyses have been actively studied for a long time, and many important findings were accumulated. On the other hand, recently, attention has also been focused on RNA modification in the field of epigenetics; now it is known that RNA modification is associated with various biological functions, such as regulation of gene expression. Among RNA modifications, functional analysis of N6-methyladenosine (m6A), the most abundant RNA modification found from humans to plants is actively progressing, and it has also been known that m6A abnormality is involved in cancer and other diseases. Importantly, recent studies have shown that m6A is related to viral infections. Considering the current world situation under threat of viral infections, it is important to deepen knowledge of RNA modification from the viewpoint of viral diseases. Hence, in this review, we have summarized the recent findings regarding the roles of RNA modifications in biological functions, cancer biology, and virus infection, particularly focusing on m6A in mRNA.
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Affiliation(s)
- Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
| | - Amina Bolatkan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ken Takasawa
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
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362
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Abstract
As a unique subpopulation of cancer cells, cancer stem cells (CSCs) acquire the resistance to conventional therapies and appear to be the prime cause of cancer recurrence. Like their normal counterparts, CSCs can renew themselves and generate differentiated progenies. Cancer stem cells are distinguished among heterogenous cancer cells by molecular markers and their capacity of efficiently forming new tumors composed of diverse and heterogenous cancer cells. Tumor heterogeneity can be inter- or intra-tumor, molecularly resulting from the accumulation of genetic and non-genetic alterations. Non-genetic alterations are mainly changes on epigenetic modifications of DNA and histone, and chromatin remodeling. As tumor-initiating cells and contributing to the tumor heterogeneity in the brain, glioblastoma stem cells (GSCs) attract extensive research interests. Epigenetic modifications confer on tumor cells including CSCs reversible and inheritable genomic changes and affect gene expression without alteration in DNA sequence. Here, we will review recent advances in histone demethylation, DNA methylation, RNA methylation and ubiquitination in glioblastomas and their impacts on tumorigenesis with a focus on CSCs.
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Affiliation(s)
- Kezhou Zhu
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States
| | - Victoria Xie
- M.D. Program, Baylor College of Medicine, Houston, TX, United States
| | - Suyun Huang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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363
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Atdjian C, Coelho D, Iannazzo L, Ethève-Quelquejeu M, Braud E. Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups. Molecules 2020; 25:molecules25143241. [PMID: 32708658 PMCID: PMC7397255 DOI: 10.3390/molecules25143241] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
More than 150 RNA chemical modifications have been identified to date. Among them, methylation of adenosine at the N-6 position (m6A) is crucial for RNA metabolism, stability and other important biological events. In particular, this is the most abundant mark found in mRNA in mammalian cells. The presence of a methyl group at the N-1 position of adenosine (m1A) is mostly found in ncRNA and mRNA and is mainly responsible for stability and translation fidelity. These modifications are installed by m6A and m1A RNA methyltransferases (RNA MTases), respectively. In human, deregulation of m6A RNA MTases activity is associated with many diseases including cancer. To date, the molecular mechanism involved in the methyl transfer, in particular substrate recognition, remains unclear. We report the synthesis of new SAM-adenosine conjugates containing a triazole linker branched at the N-1 or N-6 position of adenosine. Our methodology does not require protecting groups for the functionalization of adenosine at these two positions. The molecules described here were designed as potential bisubstrate analogues for m6A and m1A RNA MTases that could be further employed for structural studies. This is the first report of compounds mimicking the transition state of the methylation reaction catalyzed by m1A RNA MTases.
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364
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Wang J, Wang WA, Zhang A, Liu HB. Molecular mechanism of methyltransferase-like protein family: Relationship with gastric cancer. Shijie Huaren Xiaohua Zazhi 2020; 28:428-434. [DOI: 10.11569/wcjd.v28.i11.428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Methyltransferase-like proteins (METTL) are part of a large protein family, which is characterized by the presence of an S-adenosylmethionine (SAM; a common substrate for methylation reactions) binding domain. Although members of this protein family have been shown or predicted as methyltransferases of RNA, DNA, or proteins, most methyltransferases are still poorly characterized. Identifying the complexes where these potential enzymes work can help to understand their function and substrate specificity. The METTL protein family is closely related to the occurrence and development of gastric cancer (GC), and its relationship with GC is of great importance in the diagnosis, treatment, and prognosis of GC. Here we give a systematic and comprehensive review of the mechanism of METTL protein family and its relationship with GC, with an aim to provide important resources for further research on these potential new methyltransferases and the diagnosis and treatment of GC.
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Affiliation(s)
- Jing Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Wen-An Wang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - An Zhang
- Gansu University of Chinese Medicine, Lanzhou 730000, Gansu Province, China
| | - Hong-Bin Liu
- People's Liberation Army Joint Logistics Support Unit 940 Hospital, Lanzhou 730000, Gansu Province, China
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365
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Zhou Z, Lv J, Yu H, Han J, Yang X, Feng D, Wu Q, Yuan B, Lu Q, Yang H. Mechanism of RNA modification N6-methyladenosine in human cancer. Mol Cancer 2020; 19:104. [PMID: 32513173 PMCID: PMC7278081 DOI: 10.1186/s12943-020-01216-3] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/08/2023] Open
Abstract
Since the breakthrough discoveries of DNA and histone modifications, the field of RNA modifications has gained increasing interest in the scientific community. The discovery of N6-methyladenosine (m6A), a predominantly internal epigenetic modification in eukaryotes mRNA, heralded the creation of the field of epi-transcriptomics. This post-transcriptional RNA modification is dynamic and reversible, and is regulated by methylases, demethylases and proteins that preferentially recognize m6A modifications. Altered m6A levels affect RNA processing, degradation and translation, thereby disrupting gene expression and key cellular processes, ultimately resulting in tumor initiation and progression. Furthermore, inhibitors and regulators of m6A-related factors have been explored as therapeutic approaches for treating cancer. In the present review, the mechanisms of m6A RNA modification, the clinicopathological relevance of m6A alterations, the type and frequency of alterations and the multiple functions it regulates in different types of cancer are discussed.
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Affiliation(s)
- Zijian Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jiancheng Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Jie Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Dexiang Feng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Qikai Wu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Baorui Yuan
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China
| | - Qiang Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Haiwei Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
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366
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Hasler D, Meister G, Fischer U. Stabilize and connect: the role of LARP7 in nuclear non-coding RNA metabolism. RNA Biol 2020; 18:290-303. [PMID: 32401147 DOI: 10.1080/15476286.2020.1767952] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
La and La-related proteins (LARPs) are characterized by a common RNA interaction platform termed the La module. This structural hallmark allows LARPs to pervade various aspects of RNA biology. The metazoan LARP7 protein binds to the 7SK RNA as part of a 7SK small nuclear ribonucleoprotein (7SK snRNP), which inhibits the transcriptional activity of RNA polymerase II (Pol II). Additionally, recent findings revealed unanticipated roles of LARP7 in the assembly of other RNPs, as well as in the modification, processing and cellular transport of RNA molecules. Reduced levels of functional LARP7 have been linked to cancer and Alazami syndrome, two seemingly unrelated human diseases characterized either by hyperproliferation or growth retardation. Here, we review the intricate regulatory networks centered on LARP7 and assess how malfunction of these networks may relate to the etiology of LARP7-linked diseases.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
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367
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Liu S, Zhuo L, Wang J, Zhang Q, Li Q, Li G, Yan L, Jin T, Pan T, Sui X, Lv Q, Xie T. METTL3 plays multiple functions in biological processes. Am J Cancer Res 2020; 10:1631-1646. [PMID: 32642280 PMCID: PMC7339281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023] Open
Abstract
N6-methyladenosine (m6A) is the most common internal modification of mRNAs in higher eukaryotic. This process is performed by methyltransferase. Methyltransferase-like 3 (METTL3) is the best known m6A methyltransferase that functions in the reversible epi-transcriptome modulation of m6A modification. Besides acting as a m6A methyltransferase, METTL3 also regulates mRNA translation and other biological processes. In recent years, studies have identified numerous roles and molecular mechanisms associated with METTL3 in multiple biological processes. However, these findings have not been summarized. In this review, we have systematically summarized the most recent important roles of METTL3 in various biological processes, including cell cycle progression, cell proliferation, cell apoptosis, cell migration and invasion, cell differentiation and inflammatory response. In addition, we discuss the prospect of using a METTL3 as a new diagnostic biomarker and therapeutic target for human cancers.
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Affiliation(s)
- Shuiping Liu
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Lvjia Zhuo
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Jianjun Wang
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Qin Zhang
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Qiujie Li
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Guohua Li
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Lili Yan
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Ting Jin
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Ting Pan
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Xinbing Sui
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Qun Lv
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
| | - Tian Xie
- Holistic Integrative Pharmacy Institutes of Medicine School, Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province & Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province & Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, Hangzhou Normal UniversityHangzhou 311121, Zhejiang, China
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368
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Ruszkowska A, Ruszkowski M, Hulewicz JP, Dauter Z, Brown JA. Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples. Nucleic Acids Res 2020; 48:3304-3314. [PMID: 31930330 PMCID: PMC7102945 DOI: 10.1093/nar/gkz1222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023] Open
Abstract
Three-dimensional structures have been solved for several naturally occurring RNA triple helices, although all are limited to six or fewer consecutive base triples, hindering accurate estimation of global and local structural parameters. We present an X-ray crystal structure of a right-handed, U•A-U-rich RNA triple helix with 11 continuous base triples. Due to helical unwinding, the RNA triple helix spans an average of 12 base triples per turn. The double helix portion of the RNA triple helix is more similar to both the helical and base step structural parameters of A′-RNA rather than A-RNA. Its most striking features are its wide and deep major groove, a smaller inclination angle and all three strands favoring a C3′-endo sugar pucker. Despite the presence of a third strand, the diameter of an RNA triple helix remains nearly identical to those of DNA and RNA double helices. Contrary to our previous modeling predictions, this structure demonstrates that an RNA triple helix is not limited in length to six consecutive base triples and that longer RNA triple helices may exist in nature. Our structure provides a starting point to establish structural parameters of the so-called ‘ideal’ RNA triple helix, analogous to A-RNA and B-DNA double helices.
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Affiliation(s)
- Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL 60439 USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 USA
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369
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Chen Y, Lin Y, Shu Y, He J, Gao W. Interaction between N 6-methyladenosine (m 6A) modification and noncoding RNAs in cancer. Mol Cancer 2020; 19:94. [PMID: 32443966 PMCID: PMC7243333 DOI: 10.1186/s12943-020-01207-4] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
As a critical internal RNA modification in higher eukaryotes, N6-methyladenosine (m6A) has become the hotspot of epigenetics research in recent years. Extensive studies on messenger RNAs have revealed that m6A affects RNA fate and cell functions in various bioprocesses, such as RNA splicing, export, translation, and stability, some of which seem to be directly or indirectly regulated by noncoding RNAs. Intriguingly, abundant noncoding RNAs such as microRNAs, long noncoding RNAs, circular RNAs, small nuclear RNAs, and ribosomal RNAs are also highly modified with m6A and require m6A modification for their biogenesis and functions. Here, we discuss the interaction between m6A modification and noncoding RNAs by focusing on the functional relevance of m6A in cancer progression, metastasis, drug resistance, and immune response. Furthermore, the investigation of m6A regulatory proteins and its inhibitors provides new opportunities for early diagnosis and effective treatment of cancer, especially in combination with immunotherapy.
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Affiliation(s)
- Yi Chen
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yu Lin
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Jing He
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Wen Gao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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370
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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371
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Wang Q, Geng W, Guo H, Wang Z, Xu K, Chen C, Wang S. Emerging role of RNA methyltransferase METTL3 in gastrointestinal cancer. J Hematol Oncol 2020; 13:57. [PMID: 32429972 PMCID: PMC7238608 DOI: 10.1186/s13045-020-00895-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Gastrointestinal cancer, the most common solid tumor, has a poor prognosis. With the development of high-throughput sequencing and detection technology, recent studies have suggested that many chemical modifications of human RNA are involved in the development of human diseases, including cancer. m6A, the most abundant modification, was revealed to participate in a series of aspects of cancer progression. Recent evidence has shown that methyltransferase-like 3 (METTL3), the first identified and a critical methyltransferase, catalyzes m6A methylation on mRNA or non-coding RNA in mammals, affecting RNA metabolism. Abnormal m6A levels caused by METTL3 have been reported to be involved in different aspects of cancer development, including proliferation, apoptosis, and metastasis. In this review, we will shed light on recent findings regarding the biological function of METTL3 in gastrointestinal cancer and discuss future research directions and potential clinical applications of METTL3 for gastrointestinal cancer.
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Affiliation(s)
- Qiang Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China.
| | - Wei Geng
- The Affiliated Yancheng No. 1 People's Hospital of Nanjing University Medical School, Yancheng, Jiangsu Province, China
| | - Huimin Guo
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
| | - Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China
| | - Kaiyue Xu
- Department of Radiotherapy, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Chen Chen
- Department of Molecular Cell Biology and Toxicology, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, China. .,Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, China. .,Center for Public Health Research, Medical School of Nanjing University, Nanjing, Jiangsu Province, China.
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372
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Diverse molecular functions of m 6A mRNA modification in cancer. Exp Mol Med 2020; 52:738-749. [PMID: 32404927 PMCID: PMC7272606 DOI: 10.1038/s12276-020-0432-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/10/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A), the most prevalent chemical modification found on eukaryotic mRNA, is associated with almost all stages of mRNA metabolism and influences various human diseases. Recent research has implicated the aberrant regulation of m6A mRNA modification in many human cancers. An increasing number of studies have revealed that dysregulation of m6A-containing gene expression via the abnormal expression of m6A methyltransferases, demethylases, or reader proteins is closely associated with tumorigenicity. Notably, the molecular functions and cellular consequences of m6A mRNA modification often show opposite results depending on the degree of m6A modification in specific mRNA. In this review, we highlight the current progress on the underlying mechanisms of m6A modification in mRNA metabolism, particularly the functions of m6A writers, erasers, and readers in the context of tumorigenesis. A thorough investigation into the role and function of RNA modifications in cancers could yield novel therapies. The chemical modification of messenger RNA (mRNA), the molecule that carries code from DNA to synthesize proteins, is thought to play a role in influencing genetically inherited traits and diseases. A common modification found in mRNA is N6-methyladenosine (m6A). Disruption to the regulation of m6A modification has been linked with human cancers. Junho Choe and Seung Hun Han at Hanyang University in Seoul, South Korea, reviewed current understanding of the molecular mechanisms behind m6A modification, with particular reference to tumor formation. The researchers point out that abnormal expression of proteins associated with m6A may lead to heightened expression of cancer-related genes. More extensive m6A modification levels are also linked to tumor formation.
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373
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Wang T, Kong S, Tao M, Ju S. The potential role of RNA N6-methyladenosine in Cancer progression. Mol Cancer 2020; 19:88. [PMID: 32398132 PMCID: PMC7216508 DOI: 10.1186/s12943-020-01204-7] [Citation(s) in RCA: 550] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
N6-methyladenosine (m6A) is considered the most common, abundant, and conserved internal transcript modification, especially in eukaryotic messenger RNA (mRNA). m6A is installed by m6A methyltransferases (METTL3/14, WTAP, RBM15/15B, VIRMA and ZC3H13, termed “writers”), removed by demethylases (FTO, ALKBH5, and ALKBH3, termed “erasers”), and recognized by m6A-binding proteins (YTHDC1/2, YTHDF1/2/3, IGF2BP1/2/3, HNRNP, and eIF3, termed “readers”). Accumulating evidence suggests that m6A RNA methylation greatly impacts RNA metabolism and is involved in the pathogenesis of many kinds of diseases, including cancers. In this review, we focus on the physiological functions of m6A modification and its related regulators, as well as on the potential biological roles of these elements in human tumors.
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Affiliation(s)
- Tianyi Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shan Kong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Mei Tao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, NO.20, Xisi Road, Nantong, 226001, Jiangsu, China. .,School of Public Health, Nantong University, NO 9, Seyuan Road, Nantong, 226019, Jiangsu, China.
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374
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Chai RC, Wu F, Wang QX, Zhang S, Zhang KN, Liu YQ, Zhao Z, Jiang T, Wang YZ, Kang CS. m 6A RNA methylation regulators contribute to malignant progression and have clinical prognostic impact in gliomas. Aging (Albany NY) 2020; 11:1204-1225. [PMID: 30810537 PMCID: PMC6402513 DOI: 10.18632/aging.101829] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/12/2019] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) RNA methylation, associated with cancer initiation and progression, is dynamically regulated by the m6A RNA methylation regulators (“writers”, “erasers” and “readers”). Here, we demonstrate that most of the thirteen main m6A RNA methylation regulators are differentially expressed among gliomas stratified by different clinicopathological features in 904 gliomas. We identified two subgroups of gliomas (RM1/2) by applying consensus clustering to m6A RNA methylation regulators. Compared with the RM1 subgroup, the RM2 subgroup correlates with a poorer prognosis, higher WHO grade, and lower frequency of IDH mutation. Moreover, the hallmarks of epithelial-mesenchymal transition and TNFα signaling via NF-κB are also significantly enriched in the RM2 subgroup. This finding indicates that m6A RNA methylation regulators are closely associated with glioma malignancy. Based on this finding, we derived a risk signature, using seven m6A RNA methylation regulators, that is not only an independent prognostic marker but can also predict the clinicopathological features of gliomas. Moreover, m6A regulators are associated with the mesenchymal subtype and TMZ sensitivity in GBM. In conclusion, m6A RNA methylation regulators are crucial participants in the malignant progression of gliomas and are potentially useful for prognostic stratification and treatment strategy development.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Qi-Xue Wang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Shu Zhang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100160, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Chinese Glioma Genome Atlas Network (CGGA)
| | - Chun-Sheng Kang
- Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Department of Neurosurgery, Tianjin Medical University General Hospital and Key Laboratory of Neurotrauma, Variation, and Regeneration, Ministry of Education and Tianjin Municipal Government, Tianjin 300052, China.,Chinese Glioma Genome Atlas Network (CGGA).,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China
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375
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Begik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. Genome Biol 2020; 21:97. [PMID: 32375858 PMCID: PMC7204298 DOI: 10.1186/s13059-020-02009-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type. RESULTS Here, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers. CONCLUSIONS Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.
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Affiliation(s)
- Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Morghan C Lucas
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Huanle Liu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Jose Miguel Ramirez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- UNSW, Sydney, Sydney, NSW, 2052, Australia.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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376
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Selberg S, Blokhina D, Aatonen M, Koivisto P, Siltanen A, Mervaala E, Kankuri E, Karelson M. Discovery of Small Molecules that Activate RNA Methylation through Cooperative Binding to the METTL3-14-WTAP Complex Active Site. Cell Rep 2020; 26:3762-3771.e5. [PMID: 30917327 DOI: 10.1016/j.celrep.2019.02.100] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 10/19/2018] [Accepted: 02/22/2019] [Indexed: 12/22/2022] Open
Abstract
Chemical modifications of RNA provide an additional, epitranscriptomic, level of control over cellular functions. N-6-methylated adenosines (m6As) are found in several types of RNA, and their amounts are regulated by methyltransferases and demethylases. One of the most important enzymes catalyzing generation of m6A on mRNA is the trimer N-6-methyltransferase METTL3-14-WTAP complex. Its activity has been linked to such critical biological processes as cell differentiation, proliferation, and death. We used in silico-based discovery to identify small-molecule ligands that bind to METTL3-14-WTAP and determined experimentally their binding affinity and kinetics, as well as their effect on enzymatic function. We show that these ligands serve as activators of the METTL3-14-WTAP complex.
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Affiliation(s)
- Simona Selberg
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Daria Blokhina
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Maria Aatonen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pertti Koivisto
- Organic Residues Section, Laboratory and Research Division, Chemistry Unit, Finnish Food Authority, Helsinki, Finland
| | - Antti Siltanen
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Eero Mervaala
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Tartu, Estonia.
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377
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Zheng N, Su J, Hu H, Wang J, Chen X. Research Progress of N6-Methyladenosine in the Cardiovascular System. Med Sci Monit 2020; 26:e921742. [PMID: 32350237 PMCID: PMC7207004 DOI: 10.12659/msm.921742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
According to the World Health Organization cardiovascular disease risk charts, the mortality rate of cardiovascular diseases in people is still high. The medical expenses caused by cardiovascular diseases are increasing daily, and the medical burden is becoming heavier; as such, it is imperative to prevent and cure cardiovascular diseases. A large number of scholars are analyzing the pathogenesis of cardiovascular diseases from various perspectives. Recent findings suggest that N6-methyladenosine (m6A) plays a multifaceted role in the cardiovascular system. m6A is a methylated modification product on RNA molecules and exists on various RNA molecules. It is one of the most common epigenetic modifications discovered to date. It regulates the expression of genes and subsequent responses. The amount of m6A is determined by methylases (writers) and demethylases (erasers). The third type of proteins, readers, selectively bind to m6A to regulate RNA stability and gene expression. In this paper, the relationship between m6A and related enzymes and cardiovascular structure and function was reviewed based on recent research results regarding the cardiovascular system.
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Affiliation(s)
- Nan Zheng
- Department of Cardiovascular Medicine, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China (mainland)
| | - Jia Su
- Department of Cardiovascular Medicine, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China (mainland)
| | - Haochang Hu
- Department of Cardiovascular Medicine, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China (mainland)
| | - Jingqiao Wang
- Department of Cardiovascular Medicine, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China (mainland)
| | - Xiaomin Chen
- Department of Cardiovascular Medicine, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China (mainland)
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378
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Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 2020; 21:e49443. [PMID: 32350990 DOI: 10.15252/embr.201949443] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently emerged as an important layer of gene regulation. N6-methyladenosine (m6 A) is the most prominent modification on eukaryotic messenger RNA and has also been found on noncoding RNA, including ribosomal and small nuclear RNA. Recently, several m6 A methyltransferases were identified, uncovering the specificity of m6 A deposition by structurally distinct enzymes. In order to discover additional m6 A enzymes, we performed an RNAi screen to deplete annotated orthologs of human methyltransferase-like proteins (METTLs) in Drosophila cells and identified CG9666, the ortholog of human METTL5. We show that CG9666 is required for specific deposition of m6 A on 18S ribosomal RNA via direct interaction with the Drosophila ortholog of human TRMT112, CG12975. Depletion of CG9666 yields a subsequent loss of the 18S rRNA m6 A modification, which lies in the vicinity of the ribosome decoding center; however, this does not compromise rRNA maturation. Instead, a loss of CG9666-mediated m6 A impacts fly behavior, providing an underlying molecular mechanism for the reported human phenotype in intellectual disability. Thus, our work expands the repertoire of m6 A methyltransferases, demonstrates the specialization of these enzymes, and further addresses the significance of ribosomal RNA modifications in gene expression and animal behavior.
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Affiliation(s)
| | | | | | - Ludivine Wacheul
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Minh Anh Vu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Pablo Mier
- Faculty of Biology, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Marc Graille
- BIOC, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Denis Lj Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Mainz, Germany.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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379
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The emerging molecular mechanism of m 6A modulators in tumorigenesis and cancer progression. Biomed Pharmacother 2020; 127:110098. [PMID: 32299028 DOI: 10.1016/j.biopha.2020.110098] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/24/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification; m6A modifications are installed by methyltransferases, removed by demethylases and recognized by reader proteins. M6A plays crucial roles in a variety of biological processes by regulating target RNA translation, splicing, nuclear export, and decay. Since the establishment of methylated RNA immunoprecipitation-sequencing methodology, over three hundred articles about m6A modulators, including "writers", "erasers" and "readers", have been reported in the last four years. In addition, an increasing number of molecular mechanisms underlying m6A RNA methylation in human cancers have been comprehensively clarified. The recently emerged molecular mechanisms of m6A modulators in cancer cell proliferation, cell cycle progression, migration and invasion, apoptosis, and autophagy remain to be summarized. Hence, this review specifically summarizes these recent advances in the understanding of m6A molecular mechanisms in tumorigenesis and cancer progression. In addition, we discuss the prospect of using an m6A methylation modulator as a new diagnostic biomarker and therapeutic target for human cancers.
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380
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Zhao Y, Shi Y, Shen H, Xie W. m 6A-binding proteins: the emerging crucial performers in epigenetics. J Hematol Oncol 2020; 13:35. [PMID: 32276589 PMCID: PMC7146974 DOI: 10.1186/s13045-020-00872-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022] Open
Abstract
N6-methyladenosine (m6A) is a well-known post-transcriptional modification that is the most common type of methylation in eukaryotic mRNAs. The regulation of m6A is dynamic and reversible, which is erected by m6A methyltransferases ("writers") and removed by m6A demethylases ("erasers"). Notably, the effects on targeted mRNAs resulted by m6A predominantly depend on the functions of different m6A-binding proteins ("readers") including YT521-B homology (YTH) domain family, heterogeneous nuclear ribonucleoproteins (HNRNPs), and insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs). Indeed, m6A readers not only participate in multiple procedures of RNA metabolism, but also are involved in a variety of biological processes. In this review, we summarized the specific functions and underlying mechanisms of m6A-binding proteins in tumorigenesis, hematopoiesis, virus replication, immune response, and adipogenesis.
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Affiliation(s)
- Yanchun Zhao
- Department of Hematology, the First Affiliated Hospital of Medical School of Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Yuanfei Shi
- Department of Hematology, the First Affiliated Hospital of Medical School of Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Huafei Shen
- Department of Hematology, the First Affiliated Hospital of Medical School of Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Wanzhuo Xie
- Department of Hematology, the First Affiliated Hospital of Medical School of Zhejiang University, No. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
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381
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Bujnowska M, Zhang J, Dai Q, Heideman EM, Fei J. Deoxyribozyme-based method for absolute quantification of N 6-methyladenosine fractions at specific sites of RNA. J Biol Chem 2020; 295:6992-7000. [PMID: 32269077 DOI: 10.1074/jbc.ra120.013359] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/06/2020] [Indexed: 11/06/2022] Open
Abstract
N 6-Methyladenosine (m6A) is the most prevalent modified base in eukaryotic mRNA and long noncoding RNA. Although candidate sites for the m6A modification are identified at the transcriptomic level, methods for site-specific quantification of absolute m6A modification levels are still limited. Herein, we present a facile method implementing a deoxyribozyme, VMC10, which preferentially cleaves the unmodified RNA. We leveraged reverse transcription and real-time quantitative PCR along with key control experiments to quantify the methylation fraction of specific m6A sites. We validated the accuracy of this method with synthetic RNA in which methylation fractions ranged from 0 to 100% and applied our method to several endogenous sites that were previously identified in sequencing-based studies. This method provides a time- and cost-effective approach for absolute quantification of the m6A fraction at specific loci, with the potential for multiplexed quantifications, expanding the current toolkit for studying RNA modifications.
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Affiliation(s)
- Magda Bujnowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jiacheng Zhang
- Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637
| | - Emily M Heideman
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637 .,Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637
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382
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Liu S, Li G, Li Q, Zhang Q, Zhuo L, Chen X, Zhai B, Sui X, Chen K, Xie T. The roles and mechanisms of YTH domain-containing proteins in cancer development and progression. Am J Cancer Res 2020; 10:1068-1084. [PMID: 32368386 PMCID: PMC7191095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 03/20/2020] [Indexed: 06/11/2023] Open
Abstract
Evolutionarily conserved YT521-B homology (YTH) domain-containing proteins, including YTHDF1-3 and YTHDC1-2, are known to confer m6A-dependent RNA-binding activity. The YTH domain-containing proteins participate in numerous RNA processes, such as mRNA splicing, nuclear export, translation and decay in post-transcriptional regulation. Most recently, it has been found that YTH domain-containing proteins play important roles in post-transcriptional modification process hence modulate the expression of genes involved in cancer and other processes including cell cycle progression, cell proliferation, migration and invasion, inflammatory, immunity and autophagy. In this review, we summarize the roles and molecular mechanisms of YTH domain-containing proteins in cancer development and progression. In addition, we discuss the prospect of using YTH domain-containing proteins as a new diagnostic biomarkers and therapeutic targets for cancers.
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Affiliation(s)
- Shuiping Liu
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Zhejiang Chinese Medical UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Guohua Li
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Qiujie Li
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Qin Zhang
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Lvjia Zhuo
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Xiaying Chen
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Bingtao Zhai
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Xinbing Sui
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
| | - Ke Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang UniversityHangzhou, Zhejiang, China
| | - Tian Xie
- Holistic Integrative Pharmacy Institutes, School of Medicine, Hangzhou Normal UniversityHangzhou, Zhejiang, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang ProvinceHangzhou, Zhejiang, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang ProvinceHangzhou, Zhejiang, China
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383
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Yang X, Liu M, Li M, Zhang S, Hiju H, Sun J, Mao Z, Zheng M, Feng B. Epigenetic modulations of noncoding RNA: a novel dimension of Cancer biology. Mol Cancer 2020; 19:64. [PMID: 32209098 PMCID: PMC7092482 DOI: 10.1186/s12943-020-01159-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Empowered by recent advances of sequencing techniques, transcriptome-wide studies have characterized over 150 different types of post-transcriptional chemical modifications of RNA, ranging from methylations of single base to complex installing reactions catalyzed by coordinated actions of multiple modification enzymes. These modifications have been shown to regulate the function and fate of RNAs and further affecting various cellular events. However, the current understanding of their biological functions in human diseases, especially in cancers, is still limited. Once regarded as “junk” or “noise” of the transcriptome, noncoding RNA (ncRNA) has been proved to be involved in a plethora of cellular signaling pathways especially those regulating cancer initiation and progression. Accumulating evidence has demonstrated that ncRNAs manipulate multiple phenotypes of cancer cells including proliferation, metastasis and chemoresistance and may become promising biomarkers and targets for diagnosis and treatment of cancer. Importantly, recent studies have mapped plenty of modified residues in ncRNA transcripts, indicating the existence of epigenetic modulation of ncRNAs and the potential effects of RNA modulation on cancer progression. In this review, we briefly introduced the characteristics of several main epigenetic marks on ncRNAs and summarized their consecutive effects on cancer cells. We found that ncRNAs could act both as regulators and targets of epigenetic enzymes, which indicated a cross-regulating network in cancer cells and unveil a novel dimension of cancer biology. Moreover, by epitomizing the knowledge of RNA epigenetics, our work may pave the way for the design of patient-tailored therapeutics of cancers.
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Affiliation(s)
- Xiao Yang
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China
| | - Ming Liu
- Department of genecology and obstetrics, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China
| | - Mengmeng Li
- Shanghai tenth People's Hospital, Medical School of Tongji University, Shanghai, 200205, China
| | - Sen Zhang
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China
| | - Hong Hiju
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China
| | - Jing Sun
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China
| | - Zhihai Mao
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China.
| | - Minhua Zheng
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China.
| | - Bo Feng
- Department of General Surgery, Division of gastrointestinal and colorectal Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200205, China.
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384
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He RZ, Jiang J, Luo DX. The functions of N6-methyladenosine modification in lncRNAs. Genes Dis 2020; 7:598-605. [PMID: 33335959 PMCID: PMC7729116 DOI: 10.1016/j.gendis.2020.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/05/2020] [Accepted: 03/08/2020] [Indexed: 01/08/2023] Open
Abstract
Increasing evidence indicates that mRNAs are often subject to posttranscriptional modifications. Among them, N6-methyladenosine (m6A), which has been shown to play key roles in RNA splicing, stability, nuclear export, and translation, is the most abundant modification of RNA. Extensive studies of m6A modification of mRNAs have been carried out, while little is known about m6A modification of long non-coding RNAs (lncRNAs). Recently, several studies reported m6A modification of lncRNAs. In this review, we focus on these m6A-modified lncRNAs and discuss possible functions of m6A modification.
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Affiliation(s)
- Rong-Zhang He
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China.,Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China
| | - Jing Jiang
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
| | - Di-Xian Luo
- Translational Medicine Institute, National & Local Joint Engineering Laboratory for High-through Molecular Diagnosis Technology, Collaborative Research Center for Post-doctoral Mobile Stations of Central South University, Affiliated the First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China.,Center for Clinical Pathology, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, People's Republic of China
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385
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Pinto R, Vågbø CB, Jakobsson ME, Kim Y, Baltissen MP, O'Donohue MF, Guzmán UH, Małecki JM, Wu J, Kirpekar F, Olsen JV, Gleizes PE, Vermeulen M, Leidel SA, Slupphaug G, Falnes PØ. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res 2020; 48:830-846. [PMID: 31799605 PMCID: PMC6954407 DOI: 10.1093/nar/gkz1147] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023] Open
Abstract
RNA methylations are essential both for RNA structure and function, and are introduced by a number of distinct methyltransferases (MTases). In recent years, N6-methyladenosine (m6A) modification of eukaryotic mRNA has been subject to intense studies, and it has been demonstrated that m6A is a reversible modification that regulates several aspects of mRNA function. However, m6A is also found in other RNAs, such as mammalian 18S and 28S ribosomal RNAs (rRNAs), but the responsible MTases have remained elusive. 28S rRNA carries a single m6A modification, found at position A4220 (alternatively referred to as A4190) within a stem–loop structure, and here we show that the MTase ZCCHC4 is the enzyme responsible for introducing this modification. Accordingly, we found that ZCCHC4 localises to nucleoli, the site of ribosome assembly, and that proteins involved in RNA metabolism are overrepresented in the ZCCHC4 interactome. Interestingly, the absence of m6A4220 perturbs codon-specific translation dynamics and shifts gene expression at the translational level. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.
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Affiliation(s)
- Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Yeji Kim
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Ulises H Guzmán
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Jie Wu
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen 6500 HB, The Netherlands
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway.,Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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386
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Huang H, Weng H, Chen J. m 6A Modification in Coding and Non-coding RNAs: Roles and Therapeutic Implications in Cancer. Cancer Cell 2020; 37:270-288. [PMID: 32183948 PMCID: PMC7141420 DOI: 10.1016/j.ccell.2020.02.004] [Citation(s) in RCA: 702] [Impact Index Per Article: 175.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/30/2020] [Accepted: 02/11/2020] [Indexed: 12/24/2022]
Abstract
N6-Methyladenosine (m6A) RNA modification has emerged in recent years as a new layer of regulatory mechanism controlling gene expression in eukaryotes. As a reversible epigenetic modification found not only in messenger RNAs but also in non-coding RNAs, m6A affects the fate of the modified RNA molecules and plays important roles in almost all vital bioprocesses, including cancer development. Here we review the up-to-date knowledge of the pathological roles and underlying molecular mechanism of m6A modifications (in both coding and non-coding RNAs) in cancer pathogenesis and drug response/resistance, and discuss the therapeutic potential of targeting m6A regulators for cancer therapy.
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Affiliation(s)
- Huilin Huang
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Hengyou Weng
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA; Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Jianjun Chen
- Department of Systems Biology & the Gehr Family Center for Leukemia Research, the Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA.
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387
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Role of m 6A in Embryonic Stem Cell Differentiation and in Gametogenesis. EPIGENOMES 2020; 4:epigenomes4010005. [PMID: 34968239 PMCID: PMC8594681 DOI: 10.3390/epigenomes4010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 12/11/2022] Open
Abstract
The rising field of RNA modifications is stimulating massive research nowadays. m6A, the most abundant mRNA modification is highly conserved during evolution. Through the last decade, the essential components of this dynamic mRNA modification machinery were found and classified into writer, eraser and reader proteins. m6A modification is now known to take part in diverse biological processes such as embryonic development, cell circadian rhythms and cancer stem cell proliferation. In addition, there is already firm evidence for the importance of m6A modification in stem cell differentiation and gametogenesis, both in males and females. This review attempts to summarize the important results of recent years studying the mechanism underlying stem cell differentiation and gametogenesis processes.
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388
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Jabs S, Biton A, Bécavin C, Nahori MA, Ghozlane A, Pagliuso A, Spanò G, Guérineau V, Touboul D, Giai Gianetto Q, Chaze T, Matondo M, Dillies MA, Cossart P. Impact of the gut microbiota on the m 6A epitranscriptome of mouse cecum and liver. Nat Commun 2020; 11:1344. [PMID: 32165618 PMCID: PMC7067863 DOI: 10.1038/s41467-020-15126-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/17/2020] [Indexed: 12/28/2022] Open
Abstract
The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. Here we examine whether host epitranscriptomic marks are affected by the gut microbiota. We use methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to identify N6-methyladenosine (m6A) modifications in mRNA of mice carrying conventional, modified, or no microbiota. We find that variations in the gut microbiota correlate with m6A modifications in the cecum, and to a lesser extent in the liver, affecting pathways related to metabolism, inflammation and antimicrobial responses. We analyze expression levels of several known writer and eraser enzymes, and find that the methyltransferase Mettl16 is downregulated in absence of a microbiota, and one of its target mRNAs, encoding S-adenosylmethionine synthase Mat2a, is less methylated. We furthermore show that Akkermansia muciniphila and Lactobacillus plantarum affect specific m6A modifications in mono-associated mice. Our results highlight epitranscriptomic modifications as an additional level of interaction between commensal bacteria and their host.
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Affiliation(s)
- Sabrina Jabs
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France.
| | - Anne Biton
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Christophe Bécavin
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Marie-Anne Nahori
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Alessandro Pagliuso
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Giulia Spanò
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France
| | - Vincent Guérineau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Quentin Giai Gianetto
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Thibault Chaze
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Mariette Matondo
- Unité de spectrométrie de masse et Protéomique, CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, F-75015, Paris, France
| | - Marie-Agnès Dillies
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 rue du Dr Roux, F-75015, Paris, France
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, U604 Institut National de la Santé et de la Recherche Médicale, USC 2020 Institut National de la Recherche Agronomique, 25 rue du Dr Roux, F-75015, Paris, France.
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389
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Liu L, Wang Y, Wu J, Liu J, Qin Z, Fan H. N 6-Methyladenosine: A Potential Breakthrough for Human Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:804-813. [PMID: 31958696 PMCID: PMC7005339 DOI: 10.1016/j.omtn.2019.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Among more than 100 types of identified RNA modification, N6-methyladenosine (m6A) modification is the predominant mRNA modification, which regulates RNA splicing, translocation, stability, and translation. m6A modification plays critical roles in the growth, differentiation, and metabolism of cells. As a dynamic and reversible modification, m6A is catalyzed by "writers" (RNA methyltransferases), removed by "erasers" (demethylases), and interacts with "readers" (m6A-binding proteins). With more advanced technology applied to research, the molecular mechanisms of RNA methyltransferase, demethylase, and m6A-binding protein have been revealed. An increasing number of studies have implicated the correlation between m6A modification and human cancers. In this review, we summarize that the occurrence and development of various human cancers are associated with aberrant m6A modification. We also discuss the progress in research related to m6A modification, providing novel therapeutic insight and potential breakthrough in anticancer therapy.
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Affiliation(s)
- Lina Liu
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China
| | - Yuwei Wang
- School of Stomatology, Qingdao University, Qingdao 266071, P.R. China
| | - Jie Wu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China.
| | - Zongchang Qin
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
| | - Hong Fan
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
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390
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Yan G, Yuan Y, He M, Gong R, Lei H, Zhou H, Wang W, Du W, Ma T, Liu S, Xu Z, Gao M, Yu M, Bian Y, Pang P, Li X, Yu S, Yang F, Cai B, Yang L. m 6A Methylation of Precursor-miR-320/RUNX2 Controls Osteogenic Potential of Bone Marrow-Derived Mesenchymal Stem Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:421-436. [PMID: 31896070 PMCID: PMC6940653 DOI: 10.1016/j.omtn.2019.12.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 01/13/2023]
Abstract
Methyltransferase-like 3 (METTL3) is the main enzyme for N6-methyladenosine (m6A)-based methylation of RNAs and it has been implicated in many biological and pathophysiological processes. In this study, we aimed to explore the potential involvement of METTL3 in osteoblast differentiation and decipher the underlying cellular and molecular mechanisms. We demonstrated that METTL3 is downregulated in human osteoporosis and the ovariectomized (OVX) mouse model, as well as during the osteogenic differentiation. Silence of METTL3 by short interfering RNA (siRNA) decreased m6A methylation levels and inhibited osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) and reduced bone mass, and similar effects were observed in METTL3+/- knockout mice. In contrast, adenovirus-mediated overexpression of METTL3 produced the opposite effects. In addition, METTL3 enhanced, whereas METTL3 silence or knockout suppressed, the m6A methylations of runt-related transcription factor 2 (RUNX2; a key transcription factor for osteoblast differentiation and bone formation) and precursor (pre-)miR-320. Moreover, downregulation of mature miR-320 rescued the decreased bone mass caused by METTL3 silence or METTL3+/- knockout. Therefore, METTL3-based m6A modification favors osteogenic differentiation of BMSCs through m6A-based direct and indirect regulation of RUNX2, and abnormal downregulation of METTL3 is likely one of the mechanisms underlying osteoporosis in patients and mice. Thus, METTL3 overexpression might be considered a new approach of replacement therapy for the treatment of human osteoporosis.
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Affiliation(s)
- Gege Yan
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Ye Yuan
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China.
| | - Mingyu He
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Rui Gong
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Hong Lei
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Hongbao Zhou
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Wenbo Wang
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Weijie Du
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Tianshuai Ma
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Shenzhen Liu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Zihang Xu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Manqi Gao
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Meixi Yu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Yu Bian
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Ping Pang
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Xin Li
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Shuting Yu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Fan Yang
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China
| | - Benzhi Cai
- Department of Pharmacy, The Second Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin 150081, China.
| | - Lei Yang
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China.
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391
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Abstract
Like DNA and proteins, RNA is subject to numerous (over 160) covalent modifications which play critical roles to regulate RNA metabolism. Among these modifications, N-methyladenosine (mA) is the most prevalent RNA methylation on mRNA which occurs on around 25% of transcripts. The recent studies demonstrated that mA participates in many aspects of RNA processing, including splicing, nuclear exporting, translation, stabilization, etc. Therefore, it revealed a new layer of regulatory mechanism for gene expression and has been termed "RNA Epigenetics" or "Epitranscriptomics". RNA mA is regulated and exerts its functions by three groups of "mA RNA modifiers" including mA methyltransferases (writers), mA demethylases (erasers), and mA binding proteins (readers). In this review, we would summarize and discuss the current understandings of the roles of the conventional mA RNA modifiers in human cancers.
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Affiliation(s)
- Yanwen Liang
- Department of Life Sciences and Institute of Genomic Sciences, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Guankai Zhan
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kao-Jung Chang
- Institute of clinical medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Yi-Ping Yang
- Institute of clinical medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Lingfang Wang
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiebo Lin
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chih-Hung Hsu
- Department of Public Health, and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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392
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Li Y, Wang J, Huang C, Shen M, Zhan H, Xu K. RNA N6-methyladenosine: a promising molecular target in metabolic diseases. Cell Biosci 2020; 10:19. [PMID: 32110378 PMCID: PMC7035649 DOI: 10.1186/s13578-020-00385-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine is a prevalent and abundant transcriptome modification, and its methylation regulates the various aspects of RNAs, including transcription, translation, processing and metabolism. The methylation of N6-methyladenosine is highly associated with numerous cellular processes, which plays important roles in the development of physiological process and diseases. The high prevalence of metabolic diseases poses a serious threat to human health, but its pathological mechanisms remain poorly understood. Recent studies have reported that the progression of metabolic diseases is closely related to the expression of RNA N6-methyladenosine modification. In this review, we aim to summarize the biological and clinical significance of RNA N6-methyladenosine modification in metabolic diseases, including obesity, type 2 diabetes, non-alcoholic fatty liver disease, hypertension, cardiovascular diseases, osteoporosis and immune-related metabolic diseases.
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Affiliation(s)
- Yan Li
- 1Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072 Sichuan China
| | - Jiawen Wang
- 1Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072 Sichuan China
| | - Chunyan Huang
- Houjie Hospital of Dongguan, Dongguan, 523945 Guangdong China
| | - Meng Shen
- Chengdu Tumor Hospital, Chengdu, 610041 Sichuan China
| | - Huakui Zhan
- 1Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072 Sichuan China
| | - Keyang Xu
- 4Hangzhou Xixi Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, 310023 Zhejiang China
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393
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Abstract
RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as 'riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.
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Affiliation(s)
- Magdalena Büscher
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Rastislav Horos
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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394
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Uddin MB, Wang Z, Yang C. Dysregulations of Functional RNA Modifications in Cancer, Cancer Stemness and Cancer Therapeutics. Theranostics 2020; 10:3164-3189. [PMID: 32194861 PMCID: PMC7053189 DOI: 10.7150/thno.41687] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
More than a hundred chemical modifications in coding and non-coding RNAs have been identified so far. Many of the RNA modifications are dynamic and reversible, playing critical roles in gene regulation at the posttranscriptional level. The abundance and functions of RNA modifications are controlled mainly by the modification regulatory proteins: writers, erasers and readers. Modified RNA bases and their regulators form intricate networks which are associated with a vast array of diverse biological functions. RNA modifications are not only essential for maintaining the stability and structural integrity of the RNA molecules themselves, they are also associated with the functional outcomes and phenotypic attributes of cells. In addition to their normal biological roles, many of the RNA modifications also play important roles in various diseases particularly in cancer as evidenced that the modified RNA transcripts and their regulatory proteins are aberrantly expressed in many cancer types. This review will first summarize the most commonly reported RNA modifications and their regulations, followed by discussing recent studies on the roles of RNA modifications in cancer, cancer stemness as wells as functional RNA modification machinery as potential cancer therapeutic targets. It is concluded that, while advanced technologies have uncovered the contributions of many of RNA modifications in cancer, the underlying mechanisms are still poorly understood. Moreover, whether and how environmental pollutants, important cancer etiological factors, trigger abnormal RNA modifications and their roles in environmental carcinogenesis remain largely unknown. Further studies are needed to elucidate the mechanism of how RNA modifications promote cell malignant transformation and generation of cancer stem cells, which will lead to the development of new strategies for cancer prevention and treatment.
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Affiliation(s)
| | | | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536-0305, USA
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395
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Wang X, Li ZT, Yan Y, Lin P, Tang W, Hasler D, Meduri R, Li Y, Hua MM, Qi HT, Lin DH, Shi HJ, Hui J, Li J, Li D, Yang JH, Lin J, Meister G, Fischer U, Liu MF. LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice. Mol Cell 2020; 77:999-1013.e6. [PMID: 32017896 DOI: 10.1016/j.molcel.2020.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/19/2019] [Accepted: 12/26/2019] [Indexed: 12/13/2022]
Abstract
U6 snRNA, as an essential component of the catalytic core of the pre-mRNA processing spliceosome, is heavily modified post-transcriptionally, with 2'-O-methylation being most common. The role of these modifications in pre-mRNA splicing as well as their physiological function in mammals have remained largely unclear. Here we report that the La-related protein LARP7 functions as a critical cofactor for 2'-O-methylation of U6 in mouse male germ cells. Mechanistically, LARP7 promotes U6 loading onto box C/D snoRNP, facilitating U6 2'-O-methylation by box C/D snoRNP. Importantly, ablation of LARP7 in the male germline causes defective U6 2'-O-methylation, massive alterations in pre-mRNA splicing, and spermatogenic failure in mice, which can be rescued by ectopic expression of wild-type LARP7 but not an U6-loading-deficient mutant LARP7. Our data uncover a novel role of LARP7 in regulating U6 2'-O-methylation and demonstrate the functional requirement of such modification for splicing fidelity and spermatogenesis in mice.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Tong Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yue Yan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Penghui Lin
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Tang
- Animal Core Facility, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Daniele Hasler
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | | | - Ye Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Min-Min Hua
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China; NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai 200032, China
| | - Hui-Tao Qi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Di-Hang Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui-Juan Shi
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Pharmacy School, Fudan University, Shanghai 200032, China
| | - Jingyi Hui
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Dangsheng Li
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Gunter Meister
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Utz Fischer
- Department of Biochemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences - University of Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China.
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396
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RNA N 6-Methyladenosine Modifications and the Immune Response. J Immunol Res 2020; 2020:6327614. [PMID: 32411802 PMCID: PMC7204177 DOI: 10.1155/2020/6327614] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/13/2019] [Accepted: 12/24/2019] [Indexed: 01/09/2023] Open
Abstract
N6-methyladenosine (m6A) is the most important modification of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) in higher eukaryotes. Modulation of m6A modifications relies on methyltransferases and demethylases. The discovery of binding proteins confirms that the m6A modification has a wide range of biological effects and significance at the molecular, cellular, and physiological levels. In recent years, techniques for investigating m6A modifications of RNA have developed rapidly. This article reviews the biological significance of RNA m6A modifications in the innate immune response, adaptive immune response, and viral infection.
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397
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Nance DJ, Satterwhite ER, Bhaskar B, Misra S, Carraway KR, Mansfield KD. Characterization of METTL16 as a cytoplasmic RNA binding protein. PLoS One 2020; 15:e0227647. [PMID: 31940410 PMCID: PMC6961929 DOI: 10.1371/journal.pone.0227647] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/23/2019] [Indexed: 12/17/2022] Open
Abstract
mRNA modification by N6-methyladenosine (m6A) is involved in many post-transcriptional regulation processes including mRNA stability, splicing and promotion of translation. Accordingly, the recently identified mRNA methylation complex containing METTL3, METTL14, and WTAP has been the subject of intense study. However, METTL16 (METT10D) has also been identified as an RNA m6A methyltransferase that can methylate both coding and noncoding RNAs, but its biological role remains unclear. While global studies have identified many potential RNA targets of METTL16, only a handful, including the long noncoding RNA MALAT1, the snRNA U6, as well as the mRNA MAT2A have been verified and/or studied to any great extent. In this study we identified/verified METTL16 targets by immunoprecipitation of both endogenous as well as exogenous FLAG-tagged protein. Interestingly, exogenously overexpressed METTL16 differed from the endogenous protein in its relative affinity for RNA targets which prompted us to investigate METTL16's localization within the cell. Surprisingly, biochemical fractionation revealed that a majority of METTL16 protein resides in the cytoplasm of a number of cells. Furthermore, siRNA knockdown of METTL16 resulted in expression changes of a few mRNA targets suggesting that METTL16 may play a role in regulating gene expression. Thus, while METTL16 has been reported to be a nuclear protein, our findings suggest that METTL16 is also a cytoplasmic methyltransferase that may alter its RNA binding preferences depending on its cellular localization. Future studies will seek to confirm differences between cytoplasmic and nuclear RNA targets in addition to exploring the physiological role of METTL16 through long-term knockdown.
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Affiliation(s)
- Daniel J. Nance
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Emily R. Satterwhite
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Brinda Bhaskar
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Sway Misra
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Kristen R. Carraway
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Kyle D. Mansfield
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail:
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398
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Wu J, Frazier K, Zhang J, Gan Z, Wang T, Zhong X. Emerging role of m 6 A RNA methylation in nutritional physiology and metabolism. Obes Rev 2020; 21:e12942. [PMID: 31475777 PMCID: PMC7427634 DOI: 10.1111/obr.12942] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/15/2019] [Indexed: 12/12/2022]
Abstract
N6 -methyladenine (m6 A) is the most prevalent type of internal RNA methylation in eukaryotic mRNA and plays critical roles in regulating gene expression for fundamental cellular processes and diverse physiological functions. Recent evidence indicates that m6 A methylation regulates physiology and metabolism, and m6 A has been increasingly implicated in a variety of human diseases, including obesity, diabetes, metabolic syndrome and cancer. Conversely, nutrition and diet can modulate or reverse m6 A methylation patterns on gene expression. In this review, we summarize the recent progress in the study of the m6 A methylation mechanisms and highlight the crosstalk between m6 A modification, nutritional physiology and metabolism.
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Affiliation(s)
- Jiamin Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Katya Frazier
- Department of Medicine, University of Chicago. Chicago, IL 60637, USA
| | - Jingfei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Zhending Gan
- College of Animal Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Tian Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
| | - Xiang Zhong
- College of Animal Science and Technology, Nanjing Agricultural University, Jiangsu, Nanjing, 210095, PR China
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399
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Arribas-Hernández L, Brodersen P. Occurrence and Functions of m 6A and Other Covalent Modifications in Plant mRNA. PLANT PHYSIOLOGY 2020; 182:79-96. [PMID: 31748418 PMCID: PMC6945878 DOI: 10.1104/pp.19.01156] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 05/07/2023]
Abstract
Posttranscriptional control of gene expression is indispensable for the execution of developmental programs and environmental adaptation. Among the many cellular mechanisms that regulate mRNA fate, covalent nucleotide modification has emerged as a major way of controlling the processing, localization, stability, and translatability of mRNAs. This powerful mechanism is conserved across eukaryotes and controls the cellular events that lead to development and growth. As in other eukaryotes, N 6-methylation of adenosine is the most abundant and best studied mRNA modification in flowering plants. It is essential for embryonic and postembryonic plant development and it affects growth rate and stress responses, including susceptibility to plant RNA viruses. Although the mRNA modification field is young, the intense interest triggered by its involvement in stem cell differentiation and cancer has led to rapid advances in understanding how mRNA modifications control gene expression in mammalian systems. An equivalent effort from plant molecular biologists has been lagging behind, but recent work in Arabidopsis (Arabidopsis thaliana) and other plant species is starting to give insights into how this essential layer of posttranscriptional regulation works in plants, and both similarities and differences with other eukaryotes are emerging. In this Update, we summarize, connect, and evaluate the experimental work that supports our current knowledge of the biochemistry, molecular mechanisms, and biological functions of mRNA modifications in plants. We devote particular attention to N 6-methylation of adenosine and attempt to place the knowledge gained from plant studies within the context of a more general framework derived from studies in other eukaryotes.
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Affiliation(s)
| | - Peter Brodersen
- University of Copenhagen, Department of Biology, DK-2200 Copenhagen N, Denmark
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400
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Yu S, Li X, Liu S, Yang R, Liu X, Wu S. N 6-Methyladenosine: A Novel RNA Imprint in Human Cancer. Front Oncol 2019; 9:1407. [PMID: 31921664 PMCID: PMC6930912 DOI: 10.3389/fonc.2019.01407] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022] Open
Abstract
N6-Methyladenosine (m6A), a pervasive posttranscriptional modification which is reversible, has been among hotspot issues in the past several years. The balance of intracellular m6A levels is dynamically maintained by methyltransferase complex and demethylases. Meanwhile, m6A reader proteins specifically recognize modified residues and convey messages so as to set up an efficient and orderly network of m6A regulation. The m6A mark has proved to affect every step of RNA life cycle, from processing in nucleus to translation or degradation in cytoplasm. Subsequently, disorders in m6A methylation are directly related to aberrant RNA metabolism, which results in tumorigenesis and altered drug response. Therefore, uncovering the underlying mechanism of m6A in oncogenic transformation and tumor progression seeks opportunities for novel targets in cancer therapy. In this review, we conclude the extensive impact of m6A on RNA metabolism and highlight its relevance with human cancer, implicating the far-reaching value in clinical application.
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Affiliation(s)
- Sihui Yu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shiyun Liu
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Yang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiangnan Liu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sufang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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