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Li T, Wang H, Zhang Y, Wang H, Zhang Z, Liu X, Zhang Z, Liu K, Yang D, Zhang H, Gu L. Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots. PLANT PHYSIOLOGY 2023; 191:1017-1035. [PMID: 36417282 PMCID: PMC9922427 DOI: 10.1093/plphys/kiac525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 05/13/2023]
Abstract
The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
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Affiliation(s)
- Tao Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huihui Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaxin Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeyu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Amentoflavone and methyl hesperidin, novel lead molecules targeting epitranscriptomic modulator in acute myeloid leukemia: in silico drug screening and molecular dynamics simulation approach. J Mol Model 2023; 29:9. [DOI: 10.1007/s00894-022-05407-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
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3
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Gu L, Zhang S, Li B, Jiang Q, Xu T, Huang Y, Lin D, Xing M, Huang L, Zheng X, Wang F, Chao Z, Sun W. m6A and miRNA jointly regulate the development of breast muscles in duck embryonic stages. Front Vet Sci 2022; 9:933850. [PMID: 36353255 PMCID: PMC9637736 DOI: 10.3389/fvets.2022.933850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/28/2022] [Indexed: 12/01/2022] Open
Abstract
N6-methyladenosine (m6A) is an abundant internal mRNA modification and plays a crucial regulatory role in animal growth and development. In recent years, m6A modification has been found to play a key role in skeletal muscles. However, whether m6A modification contributes to embryonic breast muscle development of Pekin ducks has not been explored. To explore the role of m6A in embryonic breast muscle development of ducks, we performed m6A sequencing and miRNA sequencing for the breast muscle of duck embryos on the 19th (E19) and 27th (E27) days. A total of 12,717 m6A peaks were identified at E19, representing a total of 7,438 gene transcripts. A total of 14,703 m6A peaks were identified, which overlapped with the transcripts of 7,753 genes at E27. Comparing E19 and E27, we identified 2,347 differential m6A peaks, which overlapped with 1,605 m6A-modified genes (MMGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that MMGs were enriched in multiple muscle- or fat-related pathways, which was also revealed from our analysis of differentially expressed genes (DEGs). Conjoint analysis of m6A-seq and RNA-seq data showed that pathways related to β-oxidation of fatty acids and skeletal muscle development were significantly enriched, suggesting that m6A modification is involved in the regulation of fat deposition and skeletal muscle development. There were 90 upregulated and 102 downregulated miRNAs identified between the E19 and E27 stages. Through overlapping analysis of genes shared by MMGs and DEGs and the targets of differentially expressed miRNAs (DEMs), we identified six m6A-mRNA-regulated miRNAs. Finally, we found that m6A modification can regulate fat deposition and skeletal muscle development. In conclusion, our results suggest that m6A modification is a key regulator for embryonic breast muscle development and fat deposition of ducks by affecting expressions of mRNAs and miRNAs. This is the first study to comprehensively characterize the m6A patterns in the duck transcriptome. These data provide a solid basis for future work aimed at determining the potential functional roles of m6A modification in adipose deposition and muscle growth.
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Affiliation(s)
- Lihong Gu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Boling Li
- The Hainan Animal Husbandry Technology Promotion Station, Haikou, China
| | - Qicheng Jiang
- School of Life Science, Hainan University, Haikou, China
| | - Tieshan Xu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Tieshan Xu
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Dajie Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Manping Xing
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Lili Huang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Xinli Zheng
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Feng Wang
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China
- Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou, China
| | - Weiping Sun
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Han X, Shi Q, He Z, Song W, Chen Q, Qi Z. Transcriptome-wide N 6-methyladenosine (m 6A) methylation in soybean under Meloidogyne incognita infection. ABIOTECH 2022; 3:197-211. [PMID: 36313932 PMCID: PMC9590533 DOI: 10.1007/s42994-022-00077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/30/2022] [Indexed: 02/02/2023]
Abstract
N6-methyladenosine (m6A) is a reversible epigenetic modification of mRNA and other RNAs that plays a significant role in regulating gene expression and biological processes. However, m6A abundance, dynamics, and transcriptional regulatory mechanisms remain unexplored in the context of soybean resistance to Meloidogyne incognita. In this study, we performed a comparative analysis of transcriptome-wide m6A and metabolome profiles of soybean root tissues with and without M. incognita infection. Global m6A hypermethylation was widely induced in response to M. incognita infection and was enriched around the 3' end of coding sequences and in 3' UTR regions. There were 2069 significantly modified m6A sites, 594 differentially expressed genes, and 103 differentially accumulated metabolites between infected and uninfected roots, including coumestrol, psoralidin, and 2-hydroxyethylphosphonate. Among 101 m6A-modified DEGs, 34 genes were hypomethylated and upregulated, and 39 genes were hypermethylated and downregulated, indicating a highly negative correlation between m6A methylation and gene transcript abundance. A number of these m6A-modified DEGs, including WRKY70, ERF60, POD47 and LRR receptor-like serine/threonine-protein kinases, were involved in plant defense responses. Our study provides new insights into the critical role of m6A modification in early soybean responses to M. incognita. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00077-2.
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Affiliation(s)
- Xue Han
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Qianqian Shi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Ziyi He
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Wenwen Song
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109 China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
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Abbas Z, Tayara H, Chong KT. ZayyuNet - A Unified Deep Learning Model for the Identification of Epigenetic Modifications Using Raw Genomic Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:2533-2544. [PMID: 34038365 DOI: 10.1109/tcbb.2021.3083789] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Epigenetic modifications have a vital role in gene expression and are linked to cellular processes such as differentiation, development, and tumorigenesis. Thus, the availability of reliable and accurate methods for identifying and defining these changes facilitates greater insights into the regulatory mechanisms that rely on epigenetic modifications. The current experimental methods provide a genome-wide identification of epigenetic modifications; however, they are expensive and time-consuming. To date, several machine learning methods have been proposed for identifying modifications such as DNA N6-Methyladenine (6mA), RNA N6-Methyladenosine (m6A), DNA N4-methylcytosine (4mC), and RNA pseudouridine ( Ψ). However, these methods are task-specific computational tools and require different encoding representations of DNA/RNA sequences. In this study, we propose a unified deep learning model, called ZayyuNet, for the identification of various epigenetic modifications. The proposed model is based on an architecture called, SpinalNet, inspired by the human somatosensory system that can efficiently receive large inputs and achieve better performance. The proposed model has been evaluated on various epigenetic modifications such as 6mA, m6A, 4mC, and Ψ and the results achieved outperform current state-of-the-art models. A user-friendly web server has been built and made freely available at http://nsclbio.jbnu.ac.kr/tools/ZayyuNet/.
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Tang X, Zheng P, Li X, Wu H, Wei DQ, Liu Y, Huang G. Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species. Methods 2022; 204:142-150. [PMID: 35477057 DOI: 10.1016/j.ymeth.2022.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
DNA N6-methyladenine (6mA) is a key DNA modification, which plays versatile roles in the cellular processes, including regulation of gene expression, DNA repair, and DNA replication. DNA 6mA is closely associated with many diseases in the mammals and with growth as well as development of plants. Precisely detecting DNA 6mA sites is of great importance to exploration of 6mA functions. Although many computational methods have been presented for DNA 6mA prediction, there is still a wide gap in the practical application. We presented a convolution neural network (CNN) and bi-directional long-short term memory (Bi-LSTM)-based deep learning method (Deep6mAPred) for predicting DNA 6mA sites across plant species. The Deep6mAPred stacked the CNNs and the Bi-LSTMs in a paralleling manner instead of a series-connection manner. The Deep6mAPred also employed the attention mechanism for improving the representations of sequences. The Deep6mAPred reached an accuracy of 0.9556 over the independent rice dataset, far outperforming the state-of-the-art methods. The tests across plant species showed that the Deep6mAPred is of a remarkable advantage over the state of the art methods. We developed a user-friendly web application for DNA 6mA prediction, which is freely available at http://106.13.196.152:7001/ for all the scientific researchers. The Deep6mAPred would enrich tools to predict DNA 6mA sites and speed up the exploration of DNA modification.
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Affiliation(s)
- Xingyu Tang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Xueyong Li
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Hongyan Wu
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dong-Qing Wei
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha, Hunan 410081, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China.
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7
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Cui J, Liu J, Li J, Cheng D, Dai C. Genome-wide sequence identification and expression analysis of N6 -methyladenosine demethylase in sugar beet ( Beta vulgaris L.) under salt stress. PeerJ 2022; 10:e12719. [PMID: 35036097 PMCID: PMC8742538 DOI: 10.7717/peerj.12719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/09/2021] [Indexed: 01/11/2023] Open
Abstract
In eukaryotes, N6 -methyladenosine (m6A) is the most abundant and highly conserved RNA modification. In vivo, m6A demethylase dynamically regulates the m6A level by removing the m6A marker where it plays an important role in plant growth, development and response to abiotic stress. The confirmed m6A demethylases in Arabidopsis thaliana include ALKBH9B and ALKBH10B, both belonging to the ALKB family. In this study, BvALKB family members were identified in sugar beet genome-wide database, and their conserved domains, gene structures, chromosomal locations, phylogeny, conserved motifs and expression of BvALKB genes were analyzed. Almost all BvALKB proteins contained the conserved domain of 2OG-Fe II-Oxy. Phylogenetic analysis suggested that the ten proteins were clustered into five groups, each of which had similar motifs and gene structures. Three Arabidopsis m6A demethylase-homologous proteins (BvALKBH6B, BvALKBH8B and BvALKBH10B) were of particular interest in our study. Expression profile analysis showed that almost all genes were up-regulated or down-regulated to varying degrees under salt stress. More specifically, BvALKBH10B homologous to AtALKBH10B was significantly up-regulated, suggesting that the transcriptional activity of this gene is responsive to salt stress. This study provides a theoretical basis for further screening of m6A demethylase in sugar beet, and also lays a foundation for studying the role of ALKB family proteins in growth, development and response to salinity stress.
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Affiliation(s)
- Jie Cui
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Junli Liu
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Junliang Li
- Harbin Institute of Technology, Harbin, Heilongjiang, China,College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, China
| | - Dayou Cheng
- Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Cuihong Dai
- Harbin Institute of Technology, Harbin, Heilongjiang, China
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Qi Z, Li J, Li M, Du X, Zhang L, Wang S, Xu B, Liu W, Xu Z, Deng Y. The Essential Role of Epigenetic Modifications in Neurodegenerative Diseases with Dyskinesia. Cell Mol Neurobiol 2021; 42:2459-2472. [PMID: 34383231 DOI: 10.1007/s10571-021-01133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/18/2021] [Indexed: 12/20/2022]
Abstract
Epigenetics play an essential role in the occurrence and improvement of many diseases. Evidence shows that epigenetic modifications are crucial to the regulation of gene expression. DNA methylation is closely linked to embryonic development in mammalian. In recent years, epigenetic drugs have shown unexpected therapeutic effects on neurological diseases, leading to the study of the epigenetic mechanism in neurodegenerative diseases. Unlike genetics, epigenetics modify the genome without changing the DNA sequence. Research shows that epigenetics is involved in all aspects of neurodegenerative diseases. The study of epigenetic will provide valuable insights into the molecular mechanism of neurodegenerative diseases, which may lead to new treatments and diagnoses. This article reviews the role of epigenetic modifications neurodegenerative diseases with dyskinesia, and discusses the therapeutic potential of epigenetic drugs in neurodegenerative diseases.
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Affiliation(s)
- Zhipeng Qi
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Jiashuo Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Minghui Li
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Xianchao Du
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Lei Zhang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Shuang Wang
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Bin Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Wei Liu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Zhaofa Xu
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China
| | - Yu Deng
- Department of Environmental Health, School of Public Health, China Medical University, No. 77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, People's Republic of China.
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9
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Qin Z, Wang W, Ali MA, Wang Y, Zhang Y, Zhang M, Zhou G, Yang JD, Zeng C. Transcriptome-wide m 6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation. BMC Genomics 2021; 22:588. [PMID: 34344298 PMCID: PMC8335898 DOI: 10.1186/s12864-021-07904-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N6-methyladenosine (m6A) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces m6A modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability. Results The mRNA and protein expression of m6A modification enzymes were significantly dysregulated in sperm after cryopreservation. Furthermore, m6A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. The mRNAs containing highly methylated m6A peaks (fts vs. fs) were significantly associated with metabolism and gene expression, while the genes with less methylated m6A peaks were primarily involved in processes regulating RNA metabolism and transcription. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis. Conclusions Our study is the first to reveal the dynamic m6A modification of mRNAs in boar sperm during cryopreservation. These epigenetic modifications may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism, which will provide novel insights into understanding of the cryoinjuries or freezability of boar sperm during cryopreservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07904-8.
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Affiliation(s)
- Ziyue Qin
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Wencan Wang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Malik Ahsan Ali
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China.,Department of Theriogenology, Riphah College of Veterinary Sciences, 54000, Lahore, Pakistan
| | - Yihan Wang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Yan Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Ming Zhang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Guangbin Zhou
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Jian-Dong Yang
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China
| | - Changjun Zeng
- College of Animal Sciences and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China. .,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 611130, Chengdu, Sichuan Province, China.
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10
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Gu C, Shi X, Qiu W, Huang Z, Yu Y, Shen F, Chen Y, Pan X. Comprehensive Analysis of the Prognostic Role and Mutational Characteristics of m6A-Related Genes in Lung Squamous Cell Carcinoma. Front Cell Dev Biol 2021; 9:661792. [PMID: 33842487 PMCID: PMC8027321 DOI: 10.3389/fcell.2021.661792] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There have been limited treatment therapies for lung squamous cell carcinoma (LUSC). M6A-related genes may be the next therapeutic targets for LUSC. In this study, we explored the prognostic role and mutational characteristics of m6A-related genes in LUSC. METHODS LUSC gene expression data, mutational data, and corresponding clinical information were extracted from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) were identified, and the mutation characteristics of LUSC patients were explored. Then, m6A-related genes were extracted and the correlations among the genes were detected. Finally, the prognostic roles of the genes were investigated and the nomogram model was developed. Besides, the protein-protein interaction (PPI) network was used to explore the potential interactions among the genes. RESULTS In total, there are 551 LUSC samples enrolled in our study, containing 502 LUSC tumor samples and 49 adjacent normal LUSC samples, respectively. There were 2970 upregulated DEGs and 1806 downregulated DEGs were further explored. IGF2BP1 and RBM15 had significant co-occurrence frequency (p < 0.05). Besides, METTL14 and ZC3H13 or YTHDF3 also had significant co-occurrence frequency (p < 0.05). All the m6A-related genes represent the positive correlation. WTAP was identified as a prognostic gene in the TCGA database while YTHDC1 and YTHDF1 were identified as prognostic genes. In multivariate Cox analysis, YTHDF1, age, pN stage, pTNM stage, and smoking were all identified as significant prognostic factors for OS. CONCLUSION We investigated the expression patterns and mutational characteristics of LUSC patients and identified three potential independent prognostic m6A-related genes (WTAP, YTHDC1, and YTHDF1) for OS in LUSC patients.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenli Qiu
- Department of Lab Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhenyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Colorectal Cancer Research Center, Shanghai, China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yumei Chen
- Department of Nuclear Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xufeng Pan
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
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11
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Chen J, Tian Y, Zhang Q, Ren D, Zhang Q, Yan X, Wang L, He Z, Zhang W, Zhang T, Yuan X. Novel Insights Into the Role of N6-Methyladenosine RNA Modification in Bone Pathophysiology. Stem Cells Dev 2020; 30:17-28. [PMID: 33231507 DOI: 10.1089/scd.2020.0157] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Thus far, there are more than known 150 modifications to RNA, in which common internal modifications of mRNA include N6-methyladenosine (m6A), N1-methyladenosine, and 5-methylcytosine. Among them, m6A RNA modification is one of the highest abundance modifications in eukaryotes, regulating mechanisms controlling gene expression at the post-transcription level. As an invertible and dynamic epigenetic marker, m6A base modification influences almost all vital biological processes, cellular components, and molecular functions. Once the m6A modification process is abnormal, a series of diseases-including cancer, neurological diseases, and growth disorders-will be caused. Besides, several base modification activities also have been created by noncoding RNAs (ncRNAs), for instance, microRNAs, and circular RNAs, long ncRNAs, which were dynamically regulated during bone and cartilage pathophysiology processes. Therefore, it has now been clear that dynamic modification on coding RNAs and ncRNAs represents a completely new way to modulate genetic information. In this review, we highlight up-to-date progress and applications of m6A RNA modification in bone and cartilage pathophysiology, and we discuss the pathological roles and underlying molecular mechanism of m6A modifications in osteoarthritis and osteoporosis and osteosarcoma pathogenesis.
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Affiliation(s)
- Junbo Chen
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Yihong Tian
- School of Stomatology, Qingdao University, Qingdao, China
| | - Qi Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Dapeng Ren
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qiang Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiao Yan
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lingzhi Wang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Zijing He
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Wei Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Tianzhen Zhang
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
| | - Xiao Yuan
- Department of Orthodontics, The Affiliated Hospital of Qingdao University, Qingdao, China.,School of Stomatology, Qingdao University, Qingdao, China
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12
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Gu C, Shi X, Dai C, Shen F, Rocco G, Chen J, Huang Z, Chen C, He C, Huang T, Chen C. RNA m 6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications. Innovation (N Y) 2020; 1:100066. [PMID: 34557726 PMCID: PMC8454620 DOI: 10.1016/j.xinn.2020.100066] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
N6-Methyladenosine (m6A) RNA modification brings a new dawn for RNA modification researches in recent years. This posttranscriptional RNA modification is dynamic and reversible, and is regulated by methylases ("writers"), demethylases ("erasers"), and proteins that preferentially recognize m6A modifications ("readers"). The change of RNA m6A modification regulates RNA metabolism in eucaryon, including translation, splicing, exporting, decay, and processing. Thereby the dysregulation of m6A may lead to tumorigenesis and progression. Given the tumorigenic role of abnormal m6A expression, m6A regulators may function as potential clinical therapeutic targets for cancers. In this review, we emphasize on the underlying mechanisms of m6A modifications in tumorigenesis and further introduce the potential m6A regulators-associated therapeutic targets for tumor therapy.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zhengyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chunji Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA,Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA,Corresponding author
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China,Corresponding author
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China,Corresponding author
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13
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Prediction of N6-methyladenosine sites using convolution neural network model based on distributed feature representations. Neural Netw 2020; 129:385-391. [PMID: 32593932 DOI: 10.1016/j.neunet.2020.05.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/21/2020] [Accepted: 05/24/2020] [Indexed: 01/24/2023]
Abstract
N6-methyladenosine (m6A) is a well-studied and most common interior messenger RNA (mRNA) modification that plays an important function in cell development. N6A is found in all kingdoms of life and many other cellular processes such as RNA splicing, immune tolerance, regulatory functions, RNA processing, and cancer. Despite the crucial role of m6A in cells, it was targeted computationally, but unfortunately, the obtained results were unsatisfactory. It is imperative to develop an efficient computational model that can truly represent m6A sites. In this regard, an intelligent and highly discriminative computational model namely: m6A-word2vec is introduced for the discrimination of m6A sites. Here, a concept of natural language processing in the form of word2vec is used to represent the motif of the target class automatically. These motifs (numerical descriptors) are automatically targeted from the human genome without any clear definition. Further, the extracted feature space is then forwarded to the convolution neural network model as input for prediction. The developed computational model obtained 83.17%, 92.69%, and 90.50% accuracy for benchmark datasets S1, S2, and S3, respectively, using a 10-fold cross-validation test. The predictive outcomes validate that the developed intelligent computational model showed better performance compared to existing computational models. It is thus greatly estimated that the introduced computational model "m6A-word2vec" may be a supportive and practical tool for elementary and pharmaceutical research such as in drug design along with academia.
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14
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Zhu X, He J, Zhao S, Tao W, Xiong Y, Bi S. A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae. Brief Funct Genomics 2020; 18:367-376. [PMID: 31609411 DOI: 10.1093/bfgp/elz018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) modification, as one of the commonest post-transcription modifications in RNAs, has been reported to be highly related to many biological processes. Over the past decade, several tools for m6A sites prediction of Saccharomyces cerevisiae have been developed and are freely available online. However, the quality of predictions by these tools is difficult to quantify and compare. In this study, an independent dataset M6Atest6540 was compiled to systematically evaluate nine publicly available m6A prediction tools for S. cerevisiae. The experimental results indicate that RAM-ESVM achieved the best performance on M6Atest6540; however, most models performed substantially worse than their performances reported in the original papers. The benchmark dataset Met2614, which was used as the training dataset for the nine methods, were further analyzed by using a position bias index. The results demonstrated the significantly different bias of dataset Met2614 compared with the RNA segments around m6A sites recorded in RMBase. Moreover, newMet2614 was collected by randomly selecting RNA segments from non-redundant data recorded in RMBase, and three different kinds of features were extracted. The performances of the models built on Met2614 and newMet2614 with the features were compared, which shows the better generalization of models built on newMet2614. Our results also indicate the position-specific propensity-based features outperform other features, although they are also easily over-fitted on a biased dataset.
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Affiliation(s)
- Xiaolei Zhu
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China.,School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Jingjing He
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Shihao Zhao
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Tao
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yi Xiong
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shoudong Bi
- School of Sciences, Anhui Agricultural University, Hefei, Anhui 230036, China
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15
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MTA, an RNA m 6A Methyltransferase, Enhances Drought Tolerance by Regulating the Development of Trichomes and Roots in Poplar. Int J Mol Sci 2020; 21:ijms21072462. [PMID: 32252292 PMCID: PMC7177244 DOI: 10.3390/ijms21072462] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes, where it is present within both coding and noncoding regions. In mammals, methylation requires the catalysis of a multicomponent m6A methyltransferase complex. Proposed biological functions for m6A modification include pre-mRNA splicing, RNA stability, cell fate regulation, and embryonic development. However, few studies have been conducted on m6A modification in trees. In particular, the regulation mechanism of RNA m6A in Populus development remains to be further elucidated. Here, we show that PtrMTA (Populus trichocarpa methyltransferase) was colocalized with PtrFIP37 in the nucleus. Importantly, the PtrMTA-overexpressing plants significantly increased the density of trichomes and exhibited a more developed root system than that of wild-type controls. Moreover, we found that PtrMTA-overexpressing plants had better tolerance to drought stress. We also found PtrMTA was a component of the m6A methyltransferase complex, which participated in the formation of m6A methylation in poplar. Taken together, these results demonstrate that PtrMTA is involved in drought resistance by affecting the development of trichomes and roots, which will provide new clues for the study of RNA m6A modification and expand our understanding of the epigenetic molecular mechanism in woody plants.
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16
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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: 696] [Impact Index Per Article: 174.0] [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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17
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Rajecka V, Skalicky T, Vanacova S. The role of RNA adenosine demethylases in the control of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:343-355. [PMID: 30550773 DOI: 10.1016/j.bbagrm.2018.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 01/21/2023]
Abstract
RNA modifications are being recognized as an essential factor in gene expression regulation. They play essential roles in germ line development, differentiation and disease. In eukaryotic mRNAs, N6-adenosine methylation (m6A) is the most prevalent internal chemical modification identified to date. The m6A pathway involves factors called writers, readers and erasers. m6A thus offers an interesting concept of dynamic reversible modification with implications in fine-tuning the cellular metabolism. In mammals, FTO and ALKBH5 have been initially identified as m6A erasers. Recently, FTO m6A specificity has been debated as new reports identify FTO targeting N6,2'-O-dimethyladenosine (m6Am). The two adenosine demethylases have diverse roles in the metabolism of mRNAs and their activity is involved in key processes, such as embryogenesis, disease or infection. In this article, we review the current knowledge of their function and mechanisms and discuss the existing contradictions in the field. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Veronika Rajecka
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 625 00, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 625 00, Czech Republic
| | - Stepanka Vanacova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno 625 00, Czech Republic.
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18
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Huang Y, He N, Chen Y, Chen Z, Li L. BERMP: a cross-species classifier for predicting m 6A sites by integrating a deep learning algorithm and a random forest approach. Int J Biol Sci 2018; 14:1669-1677. [PMID: 30416381 PMCID: PMC6216033 DOI: 10.7150/ijbs.27819] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 11/12/2022] Open
Abstract
N6-methyladenosine (m6A) is a prevalent RNA methylation modification involved in several biological processes. Hundreds or thousands of m6A sites identified from different species using high-throughput experiments provides a rich resource to construct in-silico approaches for identifying m6A sites. The existing m6A predictors are developed using conventional machine-learning (ML) algorithms and most are species-centric. In this paper, we develop a novel cross-species deep-learning classifier based on bidirectional Gated Recurrent Unit (BGRU) for the prediction of m6A sites. In comparison with conventional ML approaches, BGRU achieves outstanding performance for the Mammalia dataset that contains over fifty thousand m6A sites but inferior for the Saccharomyces cerevisiae dataset that covers around a thousand positives. The accuracy of BGRU is sensitive to the data size and the sensitivity is compensated by the integration of a random forest classifier with a novel encoding of enhanced nucleic acid content. The integrated approach dubbed as BGRU-based Ensemble RNA Methylation site Predictor (BERMP) has competitive performance in both cross-validation test and independent test. BERMP also outperforms existing m6A predictors for different species. Therefore, BERMP is a novel multi-species tool for identifying m6A sites with high confidence. This classifier is freely available at http://www.bioinfogo.org/bermp.
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Affiliation(s)
- Yu Huang
- School of Data Science and Software Engineering, Qingdao University, 266021, Qingdao, China
| | - Ningning He
- School of Basic Medicine, Qingdao University, 266021, Qingdao, China
| | - Yu Chen
- School of Data Science and Software Engineering, Qingdao University, 266021, Qingdao, China
| | - Zhen Chen
- School of Basic Medicine, Qingdao University, 266021, Qingdao, China
| | - Lei Li
- School of Data Science and Software Engineering, Qingdao University, 266021, Qingdao, China.,School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266061, China.,Qingdao Cancer Institute, Qingdao, Shandong 266061, China
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19
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Akbar S, Hayat M. iMethyl-STTNC: Identification of N 6-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences. J Theor Biol 2018; 455:205-211. [PMID: 30031793 DOI: 10.1016/j.jtbi.2018.07.018] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 11/17/2022]
Abstract
N6- methyladenosine (m6A) is a vital post-transcriptional modification, which adds another layer of epigenetic regulation at RNA level. It chemically modifies mRNA that effects protein expression. RNA sequence contains many genetic code motifs (GAC). Among these codes, identification of methylated or not methylated GAC motif is highly indispensable. However, with a large number of RNA sequences generated in post-genomic era, it becomes a challenging task how to accurately and speedily characterize these sequences. In view of this, the concept of an intelligent is incorporated with a computational model that truly and fast reflects the motif of the desired classes. An intelligent computational model "iMethyl-STTNC" model is proposed for identification of methyladenosine sites in RNA. In the proposed study, four feature extraction techniques, such as; Pseudo-dinucleotide-composition, Pseudo-trinucleotide-composition, split-trinucleotide-composition, and split-tetra-nucleotides-composition (STTNC) are utilized for genuine numerical descriptors. Three different classification algorithms including probabilistic neural network, Support vector machine (SVM), and K-nearest neighbor are adopted for prediction. After examining the outcomes of prediction model on each feature spaces, SVM using STTNC feature space reported the highest accuracy of 69.84%, 91.84% on dataset1 and dataset2, respectively. The reported results show that our proposed predictor has achieved encouraging results compared to the present approaches, so far in the research. It is finally reckoned that our developed model might be beneficial for in-depth analysis of genomes and drug development.
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Affiliation(s)
- Shahid Akbar
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan
| | - Maqsood Hayat
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan.
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20
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m6A RNA Methylation Controls Neural Development and Is Involved in Human Diseases. Mol Neurobiol 2018; 56:1596-1606. [DOI: 10.1007/s12035-018-1138-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/18/2018] [Indexed: 12/31/2022]
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21
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Wang X, Yan R. RFAthM6A: a new tool for predicting m 6A sites in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2018; 96:327-337. [PMID: 29340952 DOI: 10.1007/s11103-018-0698-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
We curated a reliable dataset of m6A sites in Arabidopsis thaliana, built competitive models for predicting m6A sites, extracted predominant rules from the prediction models and analyzed the most important features. In biological RNA, approximately 150 chemical modifications have been discovered, of which N6-methyladenine (m6A) is the most prevalent and abundant. This modification plays an essential role in a myriad of biological mechanisms and regulates RNA localization, nuclear export, translation, stability, alternative splicing, and other processes. However, m6A-seq and other wet-lab techniques do not easily facilitate accurate and complete determination of m6A sites across the transcriptome. Therefore, the use of computational methods to establish accurate models for predicting m6A sites is essential. In this work, we manually curated a reliable dataset of m6A sites and non-m6A sites and developed a new tool called RFAthM6A for predicting m6A sites in Arabidopsis thaliana. Briefly, RFAthM6A consists of four independent models named RFPSNSP, RFPSDSP, RFKSNPF and RFKNF and strict benchmarks show that the AUC values of the four models reached 0.894, 0.914, 0.920 and 0.926, respectively in a fivefold cross validation and the prediction performance of RFPSDSP, RFKSNPF and RFKNF exceeded that of three previously reported models (AthMethPre, M6ATH and RAM-NPPS). Linear combination of the prediction scores of RFPSDSP, RFKSNPF and RFKNF improved the prediction performance. We also extracted several predominant rules that underlie the m6A site identification from the trained models. Furthermore, the most important features of the predictors for the m6A site identification were also analyzed in depth. To facilitate use of our proposed models by interested researchers, all the source codes and datasets are publicly deposited at https://github.com/nongdaxiaofeng/RFAthM6A .
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Affiliation(s)
- Xiaofeng Wang
- College of Mathematics and Computer Science, Shanxi Normal University, Linfen, 041004, China.
| | - Renxiang Yan
- Institute of Applied Genomics, School of Biological Sciences and Engineering, Fuzhou University, Fuzhou, 350002, China.
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22
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Visvanathan A, Somasundaram K. mRNA Traffic Control Reviewed: N6-Methyladenosine (m 6 A) Takes the Driver's Seat. Bioessays 2017; 40. [PMID: 29205437 DOI: 10.1002/bies.201700093] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/11/2017] [Indexed: 12/31/2022]
Abstract
Messenger RNA is a flexible tool box that plays a key role in the dynamic regulation of gene expression. RNA modifications variegate the message conveyed by the mRNA. Similar to DNA and histone modifications, mRNA modifications are reversible and play a key role in the regulation of molecular events. Our understanding about the landscape of RNA modifications is still rudimentary in contrast to DNA and histone modifications. The major obstacle has been the lack of sensitive detection methods since they are non-editing events. However, with the advent of next-generation sequencing techniques, RNA modifications are being identified precisely at single nucleotide resolution. In recent years, methylation at the N6 position of adenine (m6 A) has gained the attention of RNA biologists. The m6 A modification has a set of writers (methylases), erasers (demethylases), and readers. Here, we provide a summary of interesting facts, conflicting findings, and recent advances in the technical and functional aspects of the m6 A epitranscriptome.
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Affiliation(s)
- Abhirami Visvanathan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
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23
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Kan L, Grozhik AV, Vedanayagam J, Patil DP, Pang N, Lim KS, Huang YC, Joseph B, Lin CJ, Despic V, Guo J, Yan D, Kondo S, Deng WM, Dedon PC, Jaffrey SR, Lai EC. The m 6A pathway facilitates sex determination in Drosophila. Nat Commun 2017; 8:15737. [PMID: 28675155 PMCID: PMC5500889 DOI: 10.1038/ncomms15737] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/29/2022] Open
Abstract
The conserved modification N6-methyladenosine (m6A) modulates mRNA processing and activity. Here, we establish the Drosophila system to study the m6A pathway. We first apply miCLIP to map m6A across embryogenesis, characterize its m6A ‘writer’ complex, validate its YTH ‘readers’ CG6422 and YT521-B, and generate mutants in five m6A factors. While m6A factors with additional roles in splicing are lethal, m6A-specific mutants are viable but present certain developmental and behavioural defects. Notably, m6A facilitates the master female determinant Sxl, since multiple m6A components enhance female lethality in Sxl sensitized backgrounds. The m6A pathway regulates Sxl processing directly, since miCLIP data reveal Sxl as a major intronic m6A target, and female-specific Sxl splicing is compromised in multiple m6A pathway mutants. YT521-B is a dominant m6A effector for Sxl regulation, and YT521-B overexpression can induce female-specific Sxl splicing. Overall, our transcriptomic and genetic toolkit reveals in vivo biologic function for the Drosophila m6A pathway. N6-methyladenosine (m6A) is a conserved RNA modification that has recently emerged as an important regulator of messenger RNA processing and activity. Here, the authors provide evidence that m6A pathway facilitates female-specific splicing of Sxl, regulating sex determination in Drosophila.
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Affiliation(s)
- Lijuan Kan
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Anya V Grozhik
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Deepak P Patil
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Nan Pang
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Kok-Seong Lim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yi-Chun Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Brian Joseph
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Ching-Jung Lin
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Vladimir Despic
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
| | - Jian Guo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Yan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shu Kondo
- Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York City, New York 10065, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York City, New York 10065, USA
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24
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Wu R, Jiang D, Wang Y, Wang X. N (6)-Methyladenosine (m(6)A) Methylation in mRNA with A Dynamic and Reversible Epigenetic Modification. Mol Biotechnol 2017; 58:450-9. [PMID: 27179969 DOI: 10.1007/s12033-016-9947-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
N (6)-methyladenosine (m(6)A) is the most abundant and reversible internal modification ubiquitously occurring in eukaryotic mRNA, albeit the significant biological roles of m(6)A methylation have remained largely unclear. The well-known DNA and histone methylations play crucial roles in epigenetic modification of biologic processes in eukaryotes. Analogously, the dynamic and reversible m(6)A RNA modification, which is installed by methyltransferase (METTL3, METTL14, and WTAP), reversed by demethylases (FTO, ALKBH5) and mediated by m(6)A-binding proteins (YTHDF1-3, YTHDC1), may also have a profound impact on gene expression regulation. Recent discoveries of the distributions, functions, and mechanisms of m(6)A modification suggest that this methylation functionally modulates the eukaryotic transcriptome to influence mRNA transcription, splicing, nuclear export, localization, translation, and stability. This reversible mRNA methylation shed light on a new dimension of post-transcriptional regulation of gene expression at the RNA level. m(6)A methylation also plays significant and broad roles in various physiological processes, such as development, fertility, carcinogenesis, stemness, early mortality, meiosis and circadian cycle, and links to obesity, cancer, and other human diseases. This review mainly describes the current knowledge of m(6)A and perspectives on future investigations.
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Affiliation(s)
- Ruifan Wu
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Denghu Jiang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Key Laboratory of Animal Nutrition & Feed Sciences, Ministry of Agriculture, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China. .,Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
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25
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He S, Wang H, Liu R, He M, Che T, Jin L, Deng L, Tian S, Li Y, Lu H, Li X, Jiang Z, Li D, Li M. mRNA N6-methyladenosine methylation of postnatal liver development in pig. PLoS One 2017; 12:e0173421. [PMID: 28267806 PMCID: PMC5340393 DOI: 10.1371/journal.pone.0173421] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification that plays an important role in the regulation of post-transcriptional protein coding gene expression. Liver is a vital organ and plays a major role in metabolism with numerous functions. Information concerning the dynamic patterns of mRNA m6A methylation during postnatal development of liver has been long overdue and elucidation of this information will benefit for further deciphering a multitude of functional outcomes of mRNA m6A methylation. Here, we profile transcriptome-wide m6A in porcine liver at three developmental stages: newborn (0 day), suckling (21 days) and adult (2 years). About 33% of transcribed genes were modified by m6A, with 1.33 to 1.42 m6A peaks per modified gene. m6A was distributed predominantly around stop codons. The consensus motif sequence RRm6ACH was observed in 78.90% of m6A peaks. A negative correlation (average Pearson's r = -0.45, P < 10-16) was found between levels of m6A methylation and gene expression. Functional enrichment analysis of genes consistently modified by m6A methylation at all three stages showed genes relevant to important functions, including regulation of growth and development, regulation of metabolic processes and protein catabolic processes. Genes with higher m6A methylation and lower expression levels at any particular stage were associated with the biological processes required for or unique to that stage. We suggest that differential m6A methylation may be important for the regulation of nutrient metabolism in porcine liver.
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Affiliation(s)
- Shen He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hong Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lamei Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Novogene Bioinformatics Institute, Beijing, China
| | - Yan Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
- * E-mail: (ML); (DL); (ZJ)
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (ML); (DL); (ZJ)
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail: (ML); (DL); (ZJ)
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26
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Abstract
The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N6-methyladenosine (m6A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine, together with m6A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis.
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Affiliation(s)
- Boxuan Simen Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ian A Roundtree
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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27
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Wang Y, Zhao JC. Update: Mechanisms Underlying N 6-Methyladenosine Modification of Eukaryotic mRNA. Trends Genet 2016; 32:763-773. [PMID: 27793360 DOI: 10.1016/j.tig.2016.09.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNA undergoes chemical modification both at the 5' cap and internally. Among internal modifications, N6-methyladensone (m6A), by far the most abundant, is present in all eukaryotes examined so far, including mammals, flies, plants, and yeast. m6A modification has an essential role in diverse biological processes. Over the past few years, our knowledge relevant to the establishment and function of this modification has grown rapidly. In this review, we focus on technologies that have facilitated m6A detection in mRNAs, the identification of m6A methylation enzymes and binding proteins, and potential functions of the modification at the molecular level.
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Affiliation(s)
- Yang Wang
- Tumor Initiation And Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jing Crystal Zhao
- Tumor Initiation And Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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28
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Shen L, Liang Z, Gu X, Chen Y, Teo ZWN, Hou X, Cai WM, Dedon PC, Liu L, Yu H. N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis. Dev Cell 2016; 38:186-200. [PMID: 27396363 DOI: 10.1016/j.devcel.2016.06.008] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/28/2016] [Accepted: 06/07/2016] [Indexed: 01/07/2023]
Abstract
N(6)-Methyladenosine (m(6)A) represents the most prevalent internal modification on mRNA and requires a multicomponent m(6)A methyltransferase complex in mammals. How their plant counterparts determine the global m(6)A modification landscape and its molecular link to plant development remain unknown. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m(6)A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m(6)A RNA modifications. We further demonstrate that FIP37 mediates m(6)A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m(6)A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Zhe Liang
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ying Chen
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Zhi Wei Norman Teo
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Xingliang Hou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weiling Maggie Cai
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore 138602, Singapore
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise (CREATE), Singapore 138602, Singapore
| | - Lu Liu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore.
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29
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Chen W, Feng P, Ding H, Lin H, Chou KC. iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition. Anal Biochem 2015; 490:26-33. [DOI: 10.1016/j.ab.2015.08.021] [Citation(s) in RCA: 254] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/13/2015] [Accepted: 08/16/2015] [Indexed: 10/23/2022]
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30
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Li Y, Wang X, Li C, Hu S, Yu J, Song S. Transcriptome-wide N⁶-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification. RNA Biol 2015; 11:1180-8. [PMID: 25483034 PMCID: PMC5155352 DOI: 10.4161/rna.36281] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
N(6)-methyladenosine (m(6)A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m(6)A modification becomes feasible. Here we present a transcriptome-wide m(6)A modification profiling effort for rice transcriptomes of differentiated callus and leaf, which yields 8,138 and 14,253 m(6)A-modified genes, respectively. The m(6)A peak (m(6)A-modified nucleotide position on mRNAs) distribution exhibits preference toward both translation termination and initiation sites. The m(6)A peak enrichment is negatively correlated with gene expression and weakly positively correlated with certain gene features, such as exon length and number. By comparing m(6)A-modified genes between the 2 samples, we define 1,792 and 6,508 tissue-specific m(6)A-modified genes (TSMGs) in callus and leaf, respectively. Among which, 626 and 5,509 TSMGs are actively expressed in both tissues but are selectively m(6)A-modified (SMGs) only in one of the 2 tissues. Further analyses reveal characteristics of SMGs: (1) Most SMGs are differentially expressed between callus and leaf. (2) Two conserved RNA-binding motifs, predicted to be recognized by PUM and RNP4F, are significantly over-represented in SMGs. (3) GO enrichment analysis shows that SMGs in callus mainly participate in transcription regulator/factor activity whereas SMGs in leaf are mainly involved in plastid and thylakoid. Our results suggest the presence of tissue-specific competitors involved in SMGs. These findings provide a resource for plant RNA epitranscriptomic studies and further enlarge our knowledge on the function of RNA m(6)A modification.
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Affiliation(s)
- Yuli Li
- a CAS Key Laboratory of Genome Sciences and Information ; Beijing Institute of Genomics; Chinese Academy of Sciences ; Beijing , P.R. China
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31
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Unique features of the m6A methylome in Arabidopsis thaliana. Nat Commun 2014; 5:5630. [PMID: 25430002 PMCID: PMC4248235 DOI: 10.1038/ncomms6630] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/21/2014] [Indexed: 12/27/2022] Open
Abstract
Recent discoveries of reversible N6-methyladenosine (m6A) methylation on messenger RNA (mRNA) and mapping of m6A methylomes in mammals and yeast have revealed potential regulatory functions of this RNA modification. In plants, defects in m6A methyltransferase cause an embryo-lethal phenotype, suggesting a critical role of m6A in plant development. Here, we profile m6A transcriptome-wide in two accessions of Arabidopsis thaliana and reveal that m6A is a highly conserved modification of mRNA in plants. Distinct from mammals, m6A in A. thaliana is enriched not only around the stop codon and within 3′ untranslated regions (3′ UTRs), but also around the start codon. Gene ontology analysis indicates that the unique distribution pattern of m6A in A. thaliana is associated with plant-specific pathways involving the chloroplast. We also discover a positive correlation between m6A deposition and the mRNA abundance, suggesting a regulatory role of m6A in plant gene expression.
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32
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Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, Adhikari S, Shi Y, Lv Y, Chen YS, Zhao X, Li A, Yang Y, Dahal U, Lou XM, Liu X, Huang J, Yuan WP, Zhu XF, Cheng T, Zhao YL, Wang X, Danielsen JMR, Liu F, Yang YG. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res 2014; 24:177-89. [PMID: 24407421 PMCID: PMC3915904 DOI: 10.1038/cr.2014.3] [Citation(s) in RCA: 1594] [Impact Index Per Article: 159.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/21/2022] Open
Abstract
The methyltransferase like 3 (METTL3)-containing methyltransferase complex catalyzes the N6-methyladenosine (m6A) formation, a novel epitranscriptomic marker; however, the nature of this complex remains largely unknown. Here we report two new components of the human m6A methyltransferase complex, Wilms' tumor 1-associating protein (WTAP) and methyltransferase like 14 (METTL14). WTAP interacts with METTL3 and METTL14, and is required for their localization into nuclear speckles enriched with pre-mRNA processing factors and for catalytic activity of the m6A methyltransferase in vivo. The majority of RNAs bound by WTAP and METTL3 in vivo represent mRNAs containing the consensus m6A motif. In the absence of WTAP, the RNA-binding capability of METTL3 is strongly reduced, suggesting that WTAP may function to regulate recruitment of the m6A methyltransferase complex to mRNA targets. Furthermore, transcriptomic analyses in combination with photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) illustrate that WTAP and METTL3 regulate expression and alternative splicing of genes involved in transcription and RNA processing. Morpholino-mediated knockdown targeting WTAP and/or METTL3 in zebrafish embryos caused tissue differentiation defects and increased apoptosis. These findings provide strong evidence that WTAP may function as a regulatory subunit in the m6A methyltransferase complex and play a critical role in epitranscriptomic regulation of RNA metabolism.
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Affiliation(s)
- Xiao-Li Ping
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Bao-Fa Sun
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Xiao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Jia Wang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Samir Adhikari
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Shi
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Lv
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Sheng Chen
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xu Zhao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ang Li
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ujwal Dahal
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Min Lou
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xi Liu
- Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Zhejiang 310058, China
| | - Wei-Ping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Xiao-Fan Zhu
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Tianjin 300041, China
| | - Yong-Liang Zhao
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinquan Wang
- Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jannie M Rendtlew Danielsen
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- The Novo Nordisk Foundation Center for Protein Research, Ubiquitin Signalling Group, Faculty of Health Sciences, Copenhagen, Denmark
| | - Feng Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- Center For Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
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33
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Liu J, Jia G. Methylation modifications in eukaryotic messenger RNA. J Genet Genomics 2013; 41:21-33. [PMID: 24480744 DOI: 10.1016/j.jgg.2013.10.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/09/2013] [Accepted: 10/20/2013] [Indexed: 10/26/2022]
Abstract
RNA methylation modifications have been found for decades of years, which occur at different RNA types of numerous species, and their distribution is species-specific. However, people rarely know their biological functions. There are several identified methylation modifications in eukaryotic messenger RNA (mRNA), such as N(7)-methylguanosine (m(7)G) at the cap, N(6)-methyl-2'-O-methyladenosine (m(6)Am), 2'-O-methylation (Nm) within the cap and the internal positions, and internal N(6)-methyladenosine (m(6)A) and 5-methylcytosine (m(5)C). Among them, m(7)G cap was studied more clearly and found to have vital roles in several important mRNA processes like mRNA translation, stability and nuclear export. m(6)A as the most abundant modification in mRNA was found in the 1970s and has been proposed to function in mRNA splicing, translation, stability, transport and so on. m(6)A has been discovered as the first RNA reversible modification which is demethylated directly by human fat mass and obesity associated protein (FTO) and its homolog protein, alkylation repair homolog 5 (ALKBH5). FTO has a special demethylation mechanism that demethylases m(6)A to A through two over-oxidative intermediate states: N(6)-hydroxymethyladenosine (hm(6)A) and N(6)-formyladenosine (f(6)A). The two newly discovered m(6)A demethylases, FTO and ALKBH5, significantly control energy homeostasis and spermatogenesis, respectively, indicating that the dynamic and reversible m(6)A, analogous to DNA and histone modifications, plays broad roles in biological kingdoms and brings us an emerging field "RNA Epigenetics". 5-methylcytosine (5mC) as an epigenetic mark in DNA has been studied widely, but m(5)C in mRNA is seldom explored. The bisulfide sequencing showed m(5)C is another abundant modification in mRNA, suggesting that it might be another RNA epigenetic mark. This review focuses on the main methylation modifications in mRNA to describe their formation, distribution, function and demethylation from the current knowledge and to provide future perspectives on functional studies.
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Affiliation(s)
- Jun Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Sibbritt T, Patel HR, Preiss T. Mapping and significance of the mRNA methylome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:397-422. [PMID: 23681756 DOI: 10.1002/wrna.1166] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 12/25/2022]
Abstract
Internal methylation of eukaryotic mRNAs in the form of N6-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high-throughput sequencing-based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m(6)A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m(5)C and m(6)A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post-transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA-binding proteins and microRNAs. The methyltransferase (MTase) METTL3 'writes' m(6)A marks on mRNA, whereas the demethylase FTO can 'erase' them. The RNA:m(5)C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics.
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Affiliation(s)
- Tennille Sibbritt
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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35
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Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG. N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 11:8-17. [PMID: 23453015 PMCID: PMC4357660 DOI: 10.1016/j.gpb.2012.12.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/02/2022]
Abstract
N6-methyl-adenosine (m6A) is one of the most common and abundant modifications on RNA molecules present in eukaryotes. However, the biological significance of m6A methylation remains largely unknown. Several independent lines of evidence suggest that the dynamic regulation of m6A may have a profound impact on gene expression regulation. The m6A modification is catalyzed by an unidentified methyltransferase complex containing at least one subunit methyltransferase like 3 (METTL3). m6A modification on messenger RNAs (mRNAs) mainly occurs in the exonic regions and 3′-untranslated region (3′-UTR) as revealed by high-throughput m6A-seq. One significant advance in m6A research is the recent discovery of the first two m6A RNA demethylases fat mass and obesity-associated (FTO) gene and ALKBH5, which catalyze m6A demethylation in an α-ketoglutarate (α-KG)- and Fe2+-dependent manner. Recent studies in model organisms demonstrate that METTL3, FTO and ALKBH5 play important roles in many biological processes, ranging from development and metabolism to fertility. Moreover, perturbation of activities of these enzymes leads to the disturbed expression of thousands of genes at the cellular level, implicating a regulatory role of m6A in RNA metabolism. Given the vital roles of DNA and histone methylations in epigenetic regulation of basic life processes in mammals, the dynamic and reversible chemical m6A modification on RNA may also serve as a novel epigenetic marker of profound biological significances.
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Affiliation(s)
- Yamei Niu
- Disease Genomics and Individualized Medicine Laboratory, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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Jia G, Fu Y, He C. Reversible RNA adenosine methylation in biological regulation. Trends Genet 2012; 29:108-15. [PMID: 23218460 DOI: 10.1016/j.tig.2012.11.003] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/01/2012] [Accepted: 11/05/2012] [Indexed: 01/20/2023]
Abstract
N(6)-methyladenosine (m(6)A) is a ubiquitous modification in mRNA and other RNAs across most eukaryotes. For many years, however, the exact functions of m(6)A were not clearly understood. The discovery that the fat mass and obesity-associated protein (FTO) is an m(6)A demethylase indicates that this modification is reversible and dynamically regulated, suggesting that it has regulatory roles. In addition, it has been shown that m(6)A affects cell fate decisions in yeast and plant development. Recent affinity-based m(6)A profiling in mouse and human cells further showed that this modification is a widespread mark in coding and noncoding RNA (ncRNA) transcripts and is likely dynamically regulated throughout developmental processes. Therefore, reversible RNA methylation, analogous to reversible DNA and histone modifications, may affect gene expression and cell fate decisions by modulating multiple RNA-related cellular pathways, which potentially provides rapid responses to various cellular and environmental signals, including energy and nutrient availability in mammals.
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Affiliation(s)
- Guifang Jia
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol 2012; 13:175. [PMID: 23113984 PMCID: PMC3491402 DOI: 10.1186/gb-2012-13-10-175] [Citation(s) in RCA: 322] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2012] [Indexed: 01/28/2023] Open
Abstract
Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3' UTR. We present a perspective on current work and new single-molecule sequencing methods for detecting RNA base modifications.
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Affiliation(s)
- Yogesh Saletore
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY10065, USA
| | - Kate Meyer
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jonas Korlach
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, CA 94025, USA
| | - Igor D Vilfan
- Pacific Biosciences, 1380 Willow Rd, Menlo Park, CA 94025, USA
| | - Samie Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
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Dong H, Chang DC, Hua MHC, Lim SP, Chionh YH, Hia F, Lee YH, Kukkaro P, Lok SM, Dedon PC, Shi PY. 2'-O methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathog 2012; 8:e1002642. [PMID: 22496660 PMCID: PMC3320599 DOI: 10.1371/journal.ppat.1002642] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 02/27/2012] [Indexed: 01/20/2023] Open
Abstract
RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro. We report that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant proteins of NS5 and its N-terminal methyltransferase domain of West Nile virus and Dengue virus (DENV) specifically methylates polyA, but not polyG, polyC, or polyU. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis confirmed that the internal methylation product is 2′-O-methyladenosine. Furthermore, the 2′-O-methyladenosine could also be detected in DENV genomic RNA. The 2′-O methylation of internal adenosine does not require specific RNA sequence context because the DENV methyltransferase can methylate RNAs spanning different regions of viral genome and host ribosomal RNAs at equal efficiencies. Mutagenesis analysis showed that K61-D146-K181-E217 motif of the DENV methyltransferase forms the active site of internal methylation activity; in addition, distinct residues on the surface of the enzyme are critical for the internal methylation activity. Functional analysis showed that internal methylation attenuated viral RNA translation and replication. Overall, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNA in vitro. Such 2′-O-methyladenosine modification may modulate virus-host interaction.
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Affiliation(s)
- Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | | | - Maggie Ho Chia Hua
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | | | - Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | - Fabian Hia
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | - Yie Hou Lee
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
| | | | | | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Pei-Yong Shi
- Novartis Institute for Tropical Diseases, Singapore
- Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- * E-mail:
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Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, May S, Fray RG. Adenosine Methylation in Arabidopsis mRNA is Associated with the 3' End and Reduced Levels Cause Developmental Defects. FRONTIERS IN PLANT SCIENCE 2012; 3:48. [PMID: 22639649 PMCID: PMC3355605 DOI: 10.3389/fpls.2012.00048] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/27/2012] [Indexed: 05/19/2023]
Abstract
We previously showed that the N6-methyladenosine (m(6)A) mRNA methylase is essential during Arabidopsis thaliana embryonic development. We also demonstrated that this modification is present at varying levels in all mature tissues. However, the requirement for the m(6)A in the mature plant was not tested. Here we show that a 90% reduction in m(6)A levels during later growth stages gives rise to plants with altered growth patterns and reduced apical dominance. The flowers of these plants commonly show defects in their floral organ number, size, and identity. The global analysis of gene expression from reduced m(6)A plants show that a significant number of down-regulated genes are involved in transport, or targeted transport, and most of the up-regulated genes are involved in stress and stimulus response processes. An analysis of m(6)A distribution in fragmented mRNA suggests that the m(6)A is predominantly positioned toward the 3' end of transcripts in a region 100-150 bp before the poly(A) tail. In addition to the analysis of the phenotypic changes in the low methylation Arabidopsis plants we will review the latest advances in the field of mRNA internal methylation.
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Affiliation(s)
- Zsuzsanna Bodi
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Silin Zhong
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Surbhi Mehra
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Jie Song
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Neil Graham
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Hongying Li
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Sean May
- School of Biosciences, University of NottinghamLoughborough, UK
| | - Rupert George Fray
- School of Biosciences, University of NottinghamLoughborough, UK
- *Correspondence: Rupert George Fray, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK. e-mail:
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O'hare K, Levis R, Rubin GM. Transcription of the white locus in Drosophila melanogaster. Proc Natl Acad Sci U S A 2010; 80:6917-21. [PMID: 16593390 PMCID: PMC390097 DOI: 10.1073/pnas.80.22.6917] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetic studies of the white locus have shown that it has a distal region where structural mutations occur and a proximal region where regulatory mutations occur. To better understand the molecular basis of this genetic organization we have analyzed white locus transcription. A 2.7-kilobase transcript comprising 0.0005% of poly(A)-RNA was detected in RNA prepared from pupae or adults. The structure of this transcript helps clarify some unusual genetic properties of the locus. There is a small 5' exon separated from the majority of the sequences found in the mature RNA by an intron of approximately 2.8 kilobases. This 5' exon is from the proximal region of the locus, whereas the main body of the RNA maps to the distal region. The mutationally silent region between the proximal and distal regions corresponds to the large intron. We have identified the family and determined the exact location of a number of transposable element insertions within the locus. These results show that transposable element insertions within introns can be without phenotypic effect. We have also investigated the effect on the white transcript of the zeste mutation, which represses white locus expression as judged by eye color phenotype. The RNA was unchanged in size or abundance in poly(A)-RNA from adult flies. This demonstrates that the zeste-white interaction does not occur by simply repressing transcription of the white locus in all tissues.
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Affiliation(s)
- K O'hare
- Department of Embryology, Carnegie Institution of Washington, 115 West University Parkway, Baltimore, MD 21210
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Abstract
N6-Methyladenosine (m6A) is a modified base present in the mRNA of all higher eukaryotes and in Saccharomyces cerevisiae, where there is an increase in m6A levels during sporulation. The methyltransferase, Ime4, is responsible for this modification and has a role in the initiation of meiosis. However, neither the function, nor the extent of distribution of this nucleotide modification is established. We demonstrate that in S. cerevisiae, substantial levels of internal adenosine methylation are present in the GpA context in mRNA from sporulating cells, which is consistent with the preferred methylation consensus of higher eukaryotes. Based upon our quantification data, every second transcript could contain one m6A during meiosis. As methylation is distributed across all mRNA size ranges, it is likely that m6A is not limited to a small population of messages. We developed a new antibody based method for identifying m6A containing messages, and using this method the transcripts of three key, early regulators of meiosis, IME1, IME2 and IME4 itself, were identified as being methylated. The position of m6A in IME2 was narrowed down to a region in the 3′-end. Methylation of these and other targets suggests mechanisms by which IME4 could control developmental choices leading to meiosis.
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Affiliation(s)
- Zsuzsanna Bodi
- School of Biosciences, Plant Sciences Division, University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, UK
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Zhong S, Li H, Bodi Z, Button J, Vespa L, Herzog M, Fray RG. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. THE PLANT CELL 2008; 20:1278-88. [PMID: 18505803 PMCID: PMC2438467 DOI: 10.1105/tpc.108.058883] [Citation(s) in RCA: 442] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 04/23/2008] [Accepted: 05/12/2008] [Indexed: 05/18/2023]
Abstract
N6-Methyladenosine is a ubiquitous modification identified in the mRNA of numerous eukaryotes, where it is present within both coding and noncoding regions. However, this base modification does not alter the coding capacity, and its biological significance remains unclear. We show that Arabidopsis thaliana mRNA contains N6-methyladenosine at levels similar to those previously reported for animal cells. We further show that inactivation of the Arabidopsis ortholog of the yeast and human mRNA adenosine methylase (MTA) results in failure of the developing embryo to progress past the globular stage. We also demonstrate that the arrested seeds are deficient in mRNAs containing N6-methyladenosine. Expression of MTA is strongly associated with dividing tissues, particularly reproductive organs, shoot meristems, and emerging lateral roots. Finally, we show that MTA interacts in vitro and in vivo with At FIP37, a homolog of the Drosophila protein FEMALE LETHAL2D and of human WILMS' TUMOUR1-ASSOCIATING PROTEIN. The results reported here provide direct evidence for an essential function for N6-methyladenosine in a multicellular eukaryote, and the interaction with At FIP37 suggests possible RNA processing events that might be regulated or altered by this base modification.
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Affiliation(s)
- Silin Zhong
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
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Narayan P, Rottman FM. Methylation of mRNA. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 65:255-85. [PMID: 1315118 DOI: 10.1002/9780470123119.ch7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- P Narayan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, Ohio
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The biosynthesis and functional roles of methylated nucleosides in eukaryotic mRNA. FINE-TUNING OF RNA FUNCTIONS BY MODIFICATION AND EDITING 2005. [DOI: 10.1007/b106365] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Clancy MJ, Shambaugh ME, Timpte CS, Bokar JA. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res 2002; 30:4509-18. [PMID: 12384598 PMCID: PMC137137 DOI: 10.1093/nar/gkf573] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
N6-methyladenosine (m6A) is present at internal sites in mRNA isolated from all higher eukaryotes, but has not previously been detected in the mRNA of the yeast Saccharomyces cerevisiae. This nucleoside modification occurs only in a sequence- specific context that appears to be conserved across diverse species. The function of this modification is not fully established, but there is some indirect evidence that m6A may play a role in the efficiency of mRNA splicing, transport or translation. The S.cerevisiae gene IME4, which is important for induction of sporulation, is very similar to the human gene MT-A70, which has been shown to be a critical subunit of the human mRNA [N6-adenosine]-methyltransferase. This observation led to the hypothesis that yeast sporulation may be dependent upon methylation of yeast mRNA, mediated by Ime4p. In this study we show that induction of sporulation leads to the appearance of low levels of m6A in yeast mRNA and that this modification requires IME4. Moreover, single amino acid substitutions in the putative catalytic residues of Ime4p lead to severe sporulation defects in a strain whose sporulation ability is completely dependent on this protein. Collectively, these data suggest very strongly that the activation of sporulation by Ime4p is the result of its proposed methyltransferase activity and provide the most direct evidence to date of a physiologic role of m6A in a gene regulatory pathway.
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Affiliation(s)
- Mary J Clancy
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
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Aiello LP, Robinson GS, Lin YW, Nishio Y, King GL. Identification of multiple genes in bovine retinal pericytes altered by exposure to elevated levels of glucose by using mRNA differential display. Proc Natl Acad Sci U S A 1994; 91:6231-5. [PMID: 8016144 PMCID: PMC44172 DOI: 10.1073/pnas.91.13.6231] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Loss of capillary pericytes, a characteristic finding in diabetic retinopathy, is strongly associated with hyperglycemia. The pathologic aberrations associated with diabetic retinopathy are localized primarily in the retinal capillaries and are only poorly reversed by subsequent euglycemic control. Since hyperglycemia significantly inhibits pericyte growth in culture, we investigated the regulation of gene expression in retinal pericytes exposed to physiologic (5.5mM) and pathologic (20 mM) glucose concentrations. By utilizing modifications of the mRNA differential display technique, over 14,000 mRNA species were screened, and 35 candidate clones were obtained. Partial DNA sequence demonstrated that 25 of these were distinct genes, including 7 known, 16 previously unreported, and 2 sequences with known homologues. Northern blot analysis demonstrated altered gene expression in 10 (40%), undetectable signals in 12 (48%), and nonregulation in 3 (12%). Genes with glucose-regulated expression included those encoding fibronectin (51% +/- 15%, P = 0.003; mean percentage of control +/- SD), caldesmon (68% +/- 18%; P = 0.026), two ribosomal proteins (201% +/- 72%, P = 0.011; 136% +/- 16%, P = 0.036), Rieske FeS reductase (66% +/- 17%; P = 0.029), three previously unreported sequences (57%, 167%, 271%), and molecules homologous to autoantigens (213%) and tyrosine kinases (down 16- to 33-fold). Caldesmon protein concentrations in pericytes and smooth muscle cells demonstrated decreases by Western blot analysis concordant with mRNA levels. These studies identify genes whose expression is significantly altered after 7 days of exposure to elevated glucose levels and provide new targets for understanding the adverse effects of hyperglycemia on vascular cells. In addition, this study provides strong support for the use of differential mRNA display as a method to rapidly isolate differentially expressed genes in metabolic systems.
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MESH Headings
- Amino Acid Sequence
- Animals
- Autoantigens/biosynthesis
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Calmodulin-Binding Proteins/biosynthesis
- Capillaries/cytology
- Capillaries/drug effects
- Capillaries/metabolism
- Cattle
- Cells, Cultured
- Endothelium, Vascular/cytology
- Endothelium, Vascular/metabolism
- Fibronectins/biosynthesis
- Gene Expression
- Glucose/pharmacology
- Humans
- Iron-Sulfur Proteins/biosynthesis
- Molecular Sequence Data
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Polymerase Chain Reaction
- Protein-Tyrosine Kinases/biosynthesis
- RNA, Messenger/biosynthesis
- Retina
- Retinal Vessels/cytology
- Retinal Vessels/metabolism
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- L P Aiello
- Beetham Eye Institute, Joslin Diabetes Center, Boston, MA 02215
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BERRY SPENCERJ. Insect Nucleic Acids. Biochemistry 1985. [DOI: 10.1016/b978-0-08-030811-1.50013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Heterogeneous nuclear RNA is normally complexed with a specific set of proteins, forming ribonucleoprotein particles termed hnRNP. These particles are likely to be involved in mRNA processing. We have found that the structure of hnRNP is profoundly altered during the heat shock response in Drosophila cultured cells. Although hnRNA continues to be synthesized at a near-normal rate during heat shock, its assembly into hnRNP is incomplete, as evidenced by a greatly decreased protein content of the particles in Cs2SO4 density gradients. RNA-protein cross-linking conducted in vivo (Mayrand and Pederson, Proc. Natl. Acad. Sci. U.S.A. 78:2208-2212, 1981) also reveals that hnRNA made during heat shock is complexed with greatly reduced amounts of protein. The block of hnRNP assembly occurs immediately upon heat shock, even before the onset of heat shock protein synthesis. Additional experiments reveal that hnRNP assembled normally at 25 degrees C subsequently disassembles during heat shock. The capacity for normal hnRNP assembly is gradually restored after heat-shocked cells are returned to 25 degrees C. Heat-shocked mammalian cells also show a similar block in hnRNP assembly. We suggest that incomplete assembly of hnRNP during heat shock leads to abortive processing of most mRNA precursors and favors the processing or export (or both) of others whose pathway of nuclear maturation is less dependent on, or even independent of, normal hnRNP particle structure. This hypothesis is compatible with a large number of previous observations.
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Abstract
Heterogeneous nuclear RNA is normally complexed with a specific set of proteins, forming ribonucleoprotein particles termed hnRNP. These particles are likely to be involved in mRNA processing. We have found that the structure of hnRNP is profoundly altered during the heat shock response in Drosophila cultured cells. Although hnRNA continues to be synthesized at a near-normal rate during heat shock, its assembly into hnRNP is incomplete, as evidenced by a greatly decreased protein content of the particles in Cs2SO4 density gradients. RNA-protein cross-linking conducted in vivo (Mayrand and Pederson, Proc. Natl. Acad. Sci. U.S.A. 78:2208-2212, 1981) also reveals that hnRNA made during heat shock is complexed with greatly reduced amounts of protein. The block of hnRNP assembly occurs immediately upon heat shock, even before the onset of heat shock protein synthesis. Additional experiments reveal that hnRNP assembled normally at 25 degrees C subsequently disassembles during heat shock. The capacity for normal hnRNP assembly is gradually restored after heat-shocked cells are returned to 25 degrees C. Heat-shocked mammalian cells also show a similar block in hnRNP assembly. We suggest that incomplete assembly of hnRNP during heat shock leads to abortive processing of most mRNA precursors and favors the processing or export (or both) of others whose pathway of nuclear maturation is less dependent on, or even independent of, normal hnRNP particle structure. This hypothesis is compatible with a large number of previous observations.
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50
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Flavell AJ, Levis R, Simon MA, Rubin GM. The 5' termini of RNAs encoded by the transposable element copia. Nucleic Acids Res 1981; 9:6279-91. [PMID: 6275356 PMCID: PMC327603 DOI: 10.1093/nar/9.23.6279] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The 5' termini of copia-specific RNAs in Drosophila melanogaster tissue culture cells were determined by S1 nuclease mapping and cap analysis. Both major copia RNAs share an identical set of heterogeneous 5' ends. Three major cap 1 structures M7GpppCmpUp, M7GpppCmpCp and M7GpppGmpUp together with several other minor caps were found. Almost all the 5' termini, as judged by S-1 nuclease mapping, were located either in a pyrimidine-rich part of the terminal direct repeat or apparently outside of the copia element, suggesting that a proportion of copia transcripts derive from promoters external to the genetic element.
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