1
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Tan L, Guo Z, Shao Y, Ye L, Wang M, Deng X, Chen S, Li R. Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Res 2024:gkae601. [PMID: 39011882 DOI: 10.1093/nar/gkae601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Affiliation(s)
- Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yanwen Shao
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Miaomiao Wang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Deng
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China
| | - Runsheng Li
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, 518057, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
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2
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Chen H, Liu H, Zhang C, Xiao N, Li Y, Zhao X, Zhang R, Gu H, Kang Q, Wan J. RNA methylation-related inhibitors: Biological basis and therapeutic potential for cancer therapy. Clin Transl Med 2024; 14:e1644. [PMID: 38572667 PMCID: PMC10993167 DOI: 10.1002/ctm2.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/05/2024] Open
Abstract
RNA methylation is widespread in nature. Abnormal expression of proteins associated with RNA methylation is strongly associated with a number of human diseases including cancer. Increasing evidence suggests that targeting RNA methylation holds promise for cancer treatment. This review specifically describes several common RNA modifications, such as the relatively well-studied N6-methyladenosine, as well as 5-methylcytosine and pseudouridine (Ψ). The regulatory factors involved in these modifications and their roles in RNA are also comprehensively discussed. We summarise the diverse regulatory functions of these modifications across different types of RNAs. Furthermore, we elucidate the structural characteristics of these modifications along with the development of specific inhibitors targeting them. Additionally, recent advancements in small molecule inhibitors targeting RNA modifications are presented to underscore their immense potential and clinical significance in enhancing therapeutic efficacy against cancer. KEY POINTS: In this paper, several important types of RNA modifications and their related regulatory factors are systematically summarised. Several regulatory factors related to RNA modification types were associated with cancer progression, and their relationships with cancer cell migration, invasion, drug resistance and immune environment were summarised. In this paper, the inhibitors targeting different regulators that have been proposed in recent studies are summarised in detail, which is of great significance for the development of RNA modification regulators and cancer treatment in the future.
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Affiliation(s)
- Huanxiang Chen
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Hongyang Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Chenxing Zhang
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Nan Xiao
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Li
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | | | - Ruike Zhang
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Huihui Gu
- Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Qiaozhen Kang
- School of Life ScienceZhengzhou UniversityZhengzhouChina
| | - Junhu Wan
- Department of Clinical LaboratoryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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3
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Wang H, Huang T, Wang D, Zeng W, Sun Y, Zhang L. MSCAN: multi-scale self- and cross-attention network for RNA methylation site prediction. BMC Bioinformatics 2024; 25:32. [PMID: 38233745 PMCID: PMC10795237 DOI: 10.1186/s12859-024-05649-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory mechanisms. However, wet experimental methods are often costly and time-consuming, limiting their wide range of applications. Therefore, recent research has focused on developing computational methods, particularly deep learning (DL). Bidirectional long short-term memory (BiLSTM), convolutional neural network (CNN), and the transformer have demonstrated achievements in modification site prediction. However, BiLSTM cannot achieve parallel computation, leading to a long training time, CNN cannot learn the dependencies of the long distance of the sequence, and the Transformer lacks information interaction with sequences at different scales. This insight underscores the necessity for continued research and development in natural language processing (NLP) and DL to devise an enhanced prediction framework that can effectively address the challenges presented. RESULTS This study presents a multi-scale self- and cross-attention network (MSCAN) to identify the RNA methylation site using an NLP and DL way. Experiment results on twelve RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) reveal that the area under the receiver operating characteristic of MSCAN obtains respectively 98.34%, 85.41%, 97.29%, 96.74%, 99.04%, 79.94%, 76.22%, 65.69%, 92.92%, 92.03%, 95.77%, 89.66%, which is better than the state-of-the-art prediction model. This indicates that the model has strong generalization capabilities. Furthermore, MSCAN reveals a strong association among different types of RNA modifications from an experimental perspective. A user-friendly web server for predicting twelve widely occurring human RNA modification sites (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um) is available at http://47.242.23.141/MSCAN/index.php . CONCLUSIONS A predictor framework has been developed through binary classification to predict RNA methylation sites.
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Affiliation(s)
- Honglei Wang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
- School of Information Engineering, Xuzhou College of Industrial Technology, Xuzhou, 221400, China
| | - Tao Huang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Dong Wang
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 221116, China
| | - Wenliang Zeng
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Yanjing Sun
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.
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4
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Shi X, Bu X, Zhou X, Shen N, Chang Y, Yu W, Wu Y. Prognostic analysis and risk assessment based on RNA editing in hepatocellular carcinoma. J Appl Genet 2024:10.1007/s13353-023-00819-y. [PMID: 38217666 DOI: 10.1007/s13353-023-00819-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/15/2024]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality, and prognosis assessment is crucial for guiding treatment decisions. In this study, we aimed to develop a personalized prognostic model for HCC based on RNA editing. RNA editing is a post-transcriptional process that can affect gene expression and, in some cases, play a role in cancer development. By analyzing RNA editing sites in HCC, we sought to identify a set of sites associated with patient prognosis and use them to create a prognostic model. We gathered RNA editing data from the Synapse database, comprising 9990 RNA editing sites and 250 HCC samples. Additionally, we collected clinical data for 377 HCC patients from the Cancer Genome Atlas (TCGA) database. We employed a multi-step approach to identify prognosis-related RNA editing sites (PR-RNA-ESs). We assessed how patients in the high-risk and low-risk groups, as defined by the model, fared in terms of survival. A nomogram was developed to predict the precise survival prognosis of HCC patients and assessed the prognostic model's utility through a receiver operating characteristic (ROC) analysis and decision curve analysis (DCA). Our analysis identified 33 prognosis-related RNA editing sites (PR-RNA-ESs) associated with HCC patient prognosis. Using a combination of LASSO regression and cross-validation, we constructed a prognostic model based on 13 PR-RNA-ESs. Survival analysis demonstrated significant differences in the survival outcomes of patients in the high-risk and low-risk groups defined by this model. Additionally, the differential expression of the 13 PR-RNA-ESs played a role in shaping patient survival. Risk-prognostic investigations further distinguished patients based on their risk levels. The nomogram enabled precise survival prognosis prediction. Our study has successfully developed a highly personalized and accurate prognostic model for individuals with HCC, leveraging RNA editing data. This model has the potential to revolutionize clinical evaluation and medical management by providing individualized prognostic information. The identification of specific RNA editing sites associated with HCC prognosis and their incorporation into a predictive model holds promise for improving the precision of treatment strategies and ultimately enhancing patient outcomes in HCC.
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Affiliation(s)
- Xintong Shi
- Department of Biliary Surgery, the Third Affiliated Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaoyuan Bu
- The Department of Respiratory Medicine, the Third Affiliated Hospital of the Naval Military Medical University, Shanghai, China
| | - Xinyu Zhou
- The Fifth Ward, Shanghai Mental Health Center, Shanghai, China
| | - Ningjia Shen
- Department of Biliary Surgery, the Third Affiliated Hospital, Naval Military Medical University, Shanghai, China
| | - Yanxin Chang
- Department of Biliary Surgery, the Third Affiliated Hospital, Naval Military Medical University, Shanghai, China
| | - Wenlong Yu
- Department of Biliary Surgery, the Third Affiliated Hospital, Naval Military Medical University, Shanghai, China
| | - Yingjun Wu
- Department of Biliary Surgery, the Third Affiliated Hospital, Naval Military Medical University, Shanghai, China.
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5
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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6
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Xu J, He J, Hu B, Hou N, Guo J, Wang C, Li X, Li Z, Zhai J, Zhang T, Ma C, Ma F, Guan Q. Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting. PLANT PHYSIOLOGY 2023; 193:2513-2537. [PMID: 37648253 PMCID: PMC10663141 DOI: 10.1093/plphys/kiad470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
Grafting can facilitate better scion performance and is widely used in plants. Numerous studies have studied the involvement of mRNAs, small RNAs, and epigenetic regulations in the grafting process. However, it remains unclear whether the mRNA N6-methyladenosine (m6A) modification participates in the apple (Malus x domestica Borkh.) grafting process. Here, we decoded the landscape of m6A modification profiles in 'Golden delicious' (a cultivar, Gd) and Malus prunifolia 'Fupingqiuzi' (a unique rootstock with resistance to environmental stresses, Mp), as well as their heterografted and self-grafted plants. Interestingly, global hypermethylation of m6A occurred in both heterografted scion and rootstock compared with their self-grafting controls. Gene Ontology (GO) term enrichment analysis showed that grafting-induced differentially m6A-modified genes were mainly involved in RNA processing, epigenetic regulation, stress response, and development. Differentially m6A-modified genes harboring expression alterations were mainly involved in various stress responses and fatty acid metabolism. Furthermore, grafting-induced mobile mRNAs with m6A and gene expression alterations mainly participated in ABA synthesis and transport (e.g. carotenoid cleavage dioxygenase 1 [CCD1] and ATP-binding cassette G22 [ABCG22]) and abiotic and biotic stress responses, which might contribute to the better performance of heterografted plants. Additionally, the DNA methylome analysis also demonstrated the DNA methylation alterations during grafting. Downregulated expression of m6A methyltransferase gene MdMTA (ortholog of METTL3) in apples induced the global m6A hypomethylation and distinctly activated the expression level of DNA demethylase gene MdROS1 (REPRESSOR OF SILENCING 1) showing the possible association between m6A and 5mC methylation in apples. Our results reveal the m6A modification profiles in the apple grafting process and enhance our understanding of the m6A regulatory mechanism in plant biological processes.
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Affiliation(s)
- Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Bichun Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jingjing Zhai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ting Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
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Song B, Huang D, Zhang Y, Wei Z, Su J, Pedro de Magalhães J, Rigden DJ, Meng J, Chen K. m6A-TSHub: Unveiling the Context-specific m 6A Methylation and m 6A-affecting Mutations in 23 Human Tissues. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:678-694. [PMID: 36096444 PMCID: PMC10787194 DOI: 10.1016/j.gpb.2022.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats.
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Affiliation(s)
- Bowen Song
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daiyun Huang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
| | - Yuxin Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Zhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jionglong Su
- School of AI and Advanced Computing, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - João Pedro de Magalhães
- Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Jia Meng
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China; AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Kunqi Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China.
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8
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Zhang Y, Yu L, Jing R, Han B, Luo J. Fast and Efficient Design of Deep Neural Networks for Predicting N 7-Methylguanosine Sites Using autoBioSeqpy. ACS OMEGA 2023; 8:19728-19740. [PMID: 37305295 PMCID: PMC10249100 DOI: 10.1021/acsomega.3c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023]
Abstract
N7-Methylguanosine (m7G) is a crucial post-transcriptional RNA modification that plays a pivotal role in regulating gene expression. Accurately identifying m7G sites is a fundamental step in understanding the biological functions and regulatory mechanisms associated with this modification. While whole-genome sequencing is the gold standard for RNA modification site detection, it is a time-consuming, expensive, and intricate process. Recently, computational approaches, especially deep learning (DL) techniques, have gained popularity in achieving this objective. Convolutional neural networks and recurrent neural networks are examples of DL algorithms that have emerged as versatile tools for modeling biological sequence data. However, developing an efficient network architecture with superior performance remains a challenging task, requiring significant expertise, time, and effort. To address this, we previously introduced a tool called autoBioSeqpy, which streamlines the design and implementation of DL networks for biological sequence classification. In this study, we utilized autoBioSeqpy to develop, train, evaluate, and fine-tune sequence-level DL models for predicting m7G sites. We provided detailed descriptions of these models, along with a step-by-step guide on their execution. The same methodology can be applied to other systems dealing with similar biological questions. The benchmark data and code utilized in this study can be accessed for free at http://github.com/jingry/autoBioSeeqpy/tree/2.0/examples/m7G.
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Affiliation(s)
- Yonglin Zhang
- Department
of Pharmacy, Affiliated Hospital of North
Sichuan Medical College, Nanchong 637000, China
| | - Lezheng Yu
- School
of Chemistry and Materials Science, Guizhou
Education University, Guiyang 550024, China
| | - Runyu Jing
- School
of Cyber Science and Engineering, Sichuan
University, Chengdu 610017, China
| | - Bin Han
- GCP
Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong 637503, China
| | - Jiesi Luo
- Basic
Medical College, Southwest Medical University, Luzhou 646099, Sichuan, China
- Key
Medical
Laboratory of New Drug Discovery and Druggability Evaluation, Luzhou
Key Laboratory of Activity Screening and Druggability Evaluation for
Chinese Materia Medica, Southwest Medical
University, Luzhou 646099, China
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9
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Acera Mateos P, Zhou Y, Zarnack K, Eyras E. Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning. Brief Bioinform 2023; 24:7150742. [PMID: 37139545 DOI: 10.1093/bib/bbad163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/03/2023] [Indexed: 05/05/2023] Open
Abstract
The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. In recent years, the development of new high-throughput experimental and computational techniques has been a key driving force in discovering the properties of RNA modifications. Machine learning applications, such as for classification, clustering or de novo identification, have been critical in these advances. Nonetheless, various challenges remain before the full potential of machine learning for epitranscriptomics can be leveraged. In this review, we provide a comprehensive survey of machine learning methods to detect RNA modifications using diverse input data sources. We describe strategies to train and test machine learning methods and to encode and interpret features that are relevant for epitranscriptomics. Finally, we identify some of the current challenges and open questions about RNA modification analysis, including the ambiguity in predicting RNA modifications in transcript isoforms or in single nucleotides, or the lack of complete ground truth sets to test RNA modifications. We believe this review will inspire and benefit the rapidly developing field of epitranscriptomics in addressing the current limitations through the effective use of machine learning.
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Affiliation(s)
- Pablo Acera Mateos
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - You Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt a.M., Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt a.M., Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt a.M., Germany
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt a.M., Germany
| | - Eduardo Eyras
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, Australia
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Soylu NN, Sefer E. BERT2OME: Prediction of 2'-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2177-2189. [PMID: 37819796 DOI: 10.1109/tcbb.2023.3237769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Recent work on language models has resulted in state-of-the-art performance on various language tasks. Among these, Bidirectional Encoder Representations from Transformers (BERT) has focused on contextualizing word embeddings to extract context and semantics of the words. On the other hand, post-transcriptional 2'-O-methylation (Nm) RNA modification is important in various cellular tasks and related to a number of diseases. The existing high-throughput experimental techniques take longer time to detect these modifications, and costly in exploring these functional processes. Here, to deeply understand the associated biological processes faster, we come up with an efficient method Bert2Ome to infer 2'-O-methylation RNA modification sites from RNA sequences. Bert2Ome combines BERT-based model with convolutional neural networks (CNN) to infer the relationship between the modification sites and RNA sequence content. Unlike the methods proposed so far, Bert2Ome assumes each given RNA sequence as a text and focuses on improving the modification prediction performance by integrating the pretrained deep learning-based language model BERT. Additionally, our transformer-based approach could infer modification sites across multiple species. According to 5-fold cross-validation, human and mouse accuracies were 99.15% and 94.35% respectively. Similarly, ROC AUC scores were 0.99, 0.94 for the same species. Detailed results show that Bert2Ome reduces the time consumed in biological experiments and outperforms the existing approaches across different datasets and species over multiple metrics. Additionally, deep learning approaches such as 2D CNNs are more promising in learning BERT attributes than more conventional machine learning methods.
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11
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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12
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Yang X, Patil S, Joshi S, Jamla M, Kumar V. Exploring epitranscriptomics for crop improvement and environmental stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:56-71. [PMID: 35567875 DOI: 10.1016/j.plaphy.2022.04.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/27/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change and stressful environmental conditions severely hamper crop growth, development and yield. Plants respond to environmental perturbations, through their plasticity provided by key-genes, governed at post-/transcriptional levels. Gene-regulation in plants is a multilevel process controlled by diverse cellular entities that includes transcription factors (TF), epigenetic regulators and non-coding RNAs beside others. There are successful studies confirming the role of epigenetic modifications (DNA-methylation/histone-modifications) in gene expression. Recent years have witnessed emergence of a highly specialized field the "Epitranscriptomics". Epitranscriptomics deals with investigating post-transcriptional RNA chemical-modifications present across the life forms that change structural, functional and biological characters of RNA. However, deeper insights on of epitranscriptomic modifications, with >140 types known so far, are to be understood fully. Researchers have identified epitranscriptome marks (writers, erasers and readers) and mapped the site-specific RNA modifications (m6A, m5C, 3' uridylation, etc.) responsible for fine-tuning gene expression in plants. Simultaneous advancement in sequencing platforms, upgraded bioinformatic tools and pipelines along with conventional labelled techniques have further given a statistical picture of these epitranscriptomic modifications leading to their potential applicability in crop improvement and developing climate-smart crops. We present herein the insights on epitranscriptomic machinery in plants and how epitranscriptome and epitranscriptomic modifications underlying plant growth, development and environmental stress responses/adaptations. Third-generation sequencing technology, advanced bioinformatics tools and databases being used in plant epitranscriptomics are also discussed. Emphasis is given on potential exploration of epitranscriptome engineering for crop-improvement and developing environmental stress tolerant plants covering current status, challenges and future directions.
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Affiliation(s)
- Xiangbo Yang
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, PR China.
| | - Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India.
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13
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Li XY, Wang SL, Chen DH, Liu H, You JX, Su LX, Yang XT. Construction and Validation of a m7G-Related Gene-Based Prognostic Model for Gastric Cancer. Front Oncol 2022; 12:861412. [PMID: 35847903 PMCID: PMC9281447 DOI: 10.3389/fonc.2022.861412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/26/2022] [Indexed: 12/14/2022] Open
Abstract
Background Gastric cancer (GC) is one of the most common malignant tumors of the digestive system. Chinese cases of GC account for about 40% of the global rate, with approximately 1.66 million people succumbing to the disease each year. Despite the progress made in the treatment of GC, most patients are diagnosed at an advanced stage due to the lack of obvious clinical symptoms in the early stages of GC, and their prognosis is still very poor. The m7G modification is one of the most common forms of base modification in post-transcriptional regulation, and it is widely distributed in the 5′ cap region of tRNA, rRNA, and eukaryotic mRNA. Methods RNA sequencing data of GC were downloaded from The Cancer Genome Atlas. The differentially expressed m7G-related genes in normal and tumour tissues were determined, and the expression and prognostic value of m7G-related genes were systematically analysed. We then built models using the selected m7G-related genes with the help of machine learning methods.The model was then validated for prognostic value by combining the receiver operating characteristic curve (ROC) and forest plots. The model was then validated on an external dataset. Finally, quantitative real-time PCR (qPCR) was performed to detect gene expression levels in clinical gastric cancer and paraneoplastic tissue. Results The model is able to determine the prognosis of GC samples quantitatively and accurately. The ROC analysis of model has an AUC of 0.761 and 0.714 for the 3-year overall survival (OS) in the training and validation sets, respectively. We determined a correlation between risk scores and immune cell infiltration and concluded that immune cell infiltration affects the prognosis of GC patients. NUDT10, METTL1, NUDT4, GEMIN5, EIF4E1B, and DCPS were identified as prognostic hub genes and potential therapeutic agents were identified based on these genes. Conclusion The m7G-related gene-based prognostic model showed good prognostic discrimination. Understanding how m7G modification affect the infiltration of the tumor microenvironment (TME) cells will enable us to better understand the TME’s anti-tumor immune response, and hopefully guide more effective immunotherapy methods.
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Affiliation(s)
- Xin-yu Li
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Shou-lian Wang
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - De-hu Chen
- Department of Gastrointestinal Surgery, Hospital Affiliated 5 to Nantong University (Taizhou People's Hospital), Taizhou, China
| | - Hui Liu
- Department of Clinical Medicine, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jian-Xiong You
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-xin Su
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-tao Yang
- Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xi-tao Yang,
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14
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Role of main RNA modifications in cancer: N 6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct Target Ther 2022; 7:142. [PMID: 35484099 PMCID: PMC9051163 DOI: 10.1038/s41392-022-01003-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the major diseases threatening human life and health worldwide. Epigenetic modification refers to heritable changes in the genetic material without any changes in the nucleic acid sequence and results in heritable phenotypic changes. Epigenetic modifications regulate many biological processes, such as growth, aging, and various diseases, including cancer. With the advancement of next-generation sequencing technology, the role of RNA modifications in cancer progression has become increasingly prominent and is a hot spot in scientific research. This review studied several common RNA modifications, such as N6-methyladenosine, 5-methylcytosine, and pseudouridine. The deposition and roles of these modifications in coding and noncoding RNAs are summarized in detail. Based on the RNA modification background, this review summarized the expression, function, and underlying molecular mechanism of these modifications and their regulators in cancer and further discussed the role of some existing small-molecule inhibitors. More in-depth studies on RNA modification and cancer are needed to broaden the understanding of epigenetics and cancer diagnosis, treatment, and prognosis.
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He Z, Xu J, Shi H, Wu S. m5CRegpred: Epitranscriptome Target Prediction of 5-Methylcytosine (m5C) Regulators Based on Sequencing Features. Genes (Basel) 2022; 13:genes13040677. [PMID: 35456483 PMCID: PMC9025882 DOI: 10.3390/genes13040677] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
5-methylcytosine (m5C) is a common post-transcriptional modification observed in a variety of RNAs. m5C has been demonstrated to be important in a variety of biological processes, including RNA structural stability and metabolism. Driven by the importance of m5C modification, many projects focused on the m5C sites prediction were reported before. To better understand the upstream and downstream regulation of m5C, we present a bioinformatics framework, m5CRegpred, to predict the substrate of m5C writer NSUN2 and m5C readers YBX1 and ALYREF for the first time. After features comparison, window lengths selection and algorism comparison on the mature mRNA model, our model achieved AUROC scores 0.869, 0.724 and 0.889 for NSUN2, YBX1 and ALYREF, respectively in an independent test. Our work suggests the substrate of m5C regulators can be distinguished and may help the research of m5C regulators in a special condition, such as substrates prediction of hyper- or hypo-expressed m5C regulators in human disease.
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Affiliation(s)
- Zhizhou He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; (Z.H.); (J.X.)
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jing Xu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; (Z.H.); (J.X.)
| | - Haoran Shi
- Research Center for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
- Correspondence: (H.S.); (S.W.)
| | - Shuxiang Wu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; (Z.H.); (J.X.)
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China
- Correspondence: (H.S.); (S.W.)
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16
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Zhang Y, Huang D, Wei Z, Chen K. Primary sequence-assisted prediction of m6A RNA methylation sites from Oxford nanopore direct RNA sequencing data. Methods 2022; 203:62-69. [DOI: 10.1016/j.ymeth.2022.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022] Open
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17
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Song J, Zhang L, Li C, Maimaiti M, Sun J, Hu J, Li L, Zhang X, Wang C, Hu H. m6A-mediated modulation coupled with transcriptional regulation shapes long noncoding RNA repertoire of the cGAS-STING signaling. Comput Struct Biotechnol J 2022; 20:1785-1797. [PMID: 35495108 PMCID: PMC9034016 DOI: 10.1016/j.csbj.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 11/22/2022] Open
Abstract
The cGAS-STING signaling plays pivotal roles not only in host antiviral defense but also in various noninfectious contexts. Compared with protein-coding genes, much less was known about long noncoding RNAs involved in this pathway. Here, we performed an integrative study to elucidate the lncRNA repertoire and the mechanisms modulating lncRNA’s expression following cGAS-STING signaling activation. We uncovered a reliable set of 672 lncRNAs closely linked to cGAS-STING signaling activation (cs-lncRNA), which might be associated with type-I interferon response and infection-related phenotypes. The ChIP-seq analysis demonstrated that cs-lncRNA was strongly regulated at the transcriptional level. We further found N6-methyladenosine (m6A) regulatory machinery was indispensable for establishing cs-lncRNA repertoire via modulating m6A modification on cs-lncRNA transcripts and promoting the expression of signaling transduction key components, including IFNAR1. Loss of IFNAR1 led to the dysregulation of cs-lncRNAs resembled that of loss of an essential subunit of m6A writer METTL14. We also found m6A system affected transcriptional machinery to modulate cs-lncRNAs by targeting multiple crucial transcription factors. Inhibiting an m6A modification regulated transcription factor, EZH2, markedly enhanced the expression pattern of cs-lncRNAs. Taken together, our results uncovered the composition of the cs-lncRNAs and revealed m6A-mediated modulation coupled with transcriptional regulation significantly shaped cs-lncRNA repertoire.
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Affiliation(s)
- Jinyi Song
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Lele Zhang
- Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Corresponding authors.
| | - Chenhui Li
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Munire Maimaiti
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Jing Sun
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Jiameng Hu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Lu Li
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Xiang Zhang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
| | - Chen Wang
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
- Corresponding authors.
| | - Haiyang Hu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, China
- Corresponding authors.
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18
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Song P, Zhou S, Qi X, Jiao Y, Gong Y, Zhao J, Yang H, Qian Z, Qian J, Tang L. RNA modification writers influence tumor microenvironment in gastric cancer and prospects of targeted drug therapy. J Bioinform Comput Biol 2022; 20:2250004. [PMID: 35287562 DOI: 10.1142/s0219720022500044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: RNA adenosine modifications are crucial for regulating RNA levels. N6-methyladenosine (m6A), N1-methyladenosine (m1A), adenosine-to-inosine RNA editing, and alternative polyadenylation (APA) are four major RNA modification types. Methods: We evaluated the altered mRNA expression profiles of 27 RNA modification enzymes and compared the differences in tumor microenvironment (TME) and clinical prognosis between two RNA modification patterns using unsupervised clustering. Then, we constructed a scoring system, WM_score, and quantified the RNA modifications in patients of gastric cancer (GC), associating WM_score with TME, clinical outcomes, and effectiveness of targeted therapies. Results: RNA adenosine modifications strongly correlated with TME and could predict the degree of TME cell infiltration, genetic variation, and clinical prognosis. Two modification patterns were identified according to high and low WM_scores. Tumors in the WM_score-high subgroup were closely linked with survival advantage, CD4[Formula: see text] T-cell infiltration, high tumor mutation burden, and cell cycle signaling pathways, whereas those in the WM_score-low subgroup showed strong infiltration of inflammatory cells and poor survival. Regarding the immunotherapy response, a high WM_score showed a significant correlation with PD-L1 expression, predicting the effect of PD-L1 blockade therapy. Conclusion: The WM_scoring system could facilitate scoring and prediction of GC prognosis.
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Affiliation(s)
- Peng Song
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Sheng Zhou
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Xiaoyang Qi
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Yuwen Jiao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Yu Gong
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Jie Zhao
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Haojun Yang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Zhifen Qian
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Jun Qian
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
| | - Liming Tang
- Department of Gastrointestinal Surgery, The Affiliated Changzhou, No. 2 People's Hospital of Nanjing Medical University, Changzhou 213000, Jiangsu Province, P. R. China
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Quiles-Jiménez A, Dahl TB, Bjørås M, Alseth I, Halvorsen B, Gregersen I. Epitranscriptome in Ischemic Cardiovascular Disease: Potential Target for Therapies. Stroke 2022; 53:2114-2122. [PMID: 35240858 DOI: 10.1161/strokeaha.121.037581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The global risk of cardiovascular disease, including ischemic disease such as stroke, remains high, and cardiovascular disease is the cause of one-third of all deaths worldwide. The main subjacent cause, atherosclerosis, is not fully understood. To improve early diagnosis and therapeutic strategies, it is crucial to unveil the key molecular mechanisms that lead to atherosclerosis development. The field of epitranscriptomics is blossoming and quickly advancing in fields like cancer research, nevertheless, poorly understood in the context of cardiovascular disease. Epitranscriptomic modifications are shown to regulate the metabolism and function of RNA molecules, which are important for cell functions such as cell proliferation, a key aspect in atherogenesis. As such, epitranscriptomic regulatory mechanisms can serve as novel checkpoints in gene expression during disease development. In this review, we describe examples of the latest research investigating epitranscriptomic modifications, in particular A-to-I editing and the covalent modification N6-methyladenosine and their regulatory proteins, in the context of cardiovascular disease. We additionally discuss the potential of these mechanisms as therapeutic targets and novel treatment options.
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Affiliation(s)
- Ana Quiles-Jiménez
- Research Institute for Internal Medicine, Oslo University Hospital, Rikshospitalet, Norway. (A.Q.-J., T.B.D., B.H., I.G.).,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway (A.Q.-J., B.H.)
| | - Tuva B Dahl
- Research Institute for Internal Medicine, Oslo University Hospital, Rikshospitalet, Norway. (A.Q.-J., T.B.D., B.H., I.G.).,Division of Critical Care and Emergencies, Oslo University Hospital, Rikshospitalet, Norway. (T.B.D.)
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Norway. (M.B., I.A.).,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway (M.B.)
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Norway. (M.B., I.A.)
| | - Bente Halvorsen
- Research Institute for Internal Medicine, Oslo University Hospital, Rikshospitalet, Norway. (A.Q.-J., T.B.D., B.H., I.G.).,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway (A.Q.-J., B.H.)
| | - Ida Gregersen
- Research Institute for Internal Medicine, Oslo University Hospital, Rikshospitalet, Norway. (A.Q.-J., T.B.D., B.H., I.G.)
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20
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Liu J. 5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m 5C formation catalyzed by RNA methyltransferase. BMC Res Notes 2022; 15:81. [PMID: 35197120 PMCID: PMC8867762 DOI: 10.1186/s13104-022-05968-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE 5-Methylcytosine (m5C) is a type of chemical modification on the nucleotides and is widespread in both DNA and RNA. Although the DNA m5C has been extensively studied over the past years, the distribution and biological function of RNA m5C still remain to be elucidated. Here, I explored the profiles of RNA m5C in four mouse tissues by applying a RNA cytosine methylation data analysis tool to public mouse RNA m5C data. RESULTS I found that the methylation rates of cytosine were the same with the averages of methylation level at single-nucleotide level. Furthermore, I gave a mathematical formula to describe the observed relationship and analyzed it deeply. The sufficient necessary condition for the given formula suggests that the methylation levels at most m5C sites are the same in four mouse tissues. Therefore, I proposed a hypothesis that the m5C formation catalyzed by RNA methyltransferase is random and with the same probability at most m5C sites, which is the methylation rate of cytosine. My hypothesis can be used to explain the observed profiles of RNA m5C in four mouse tissues and will be benefit to future studies of the distribution and biological function of RNA m5C in mammals.
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Affiliation(s)
- Junfeng Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,China National Center for Bioinformation, Beijing, 100101, China. .,Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.
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21
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Mao X, Hou N, Liu Z, He J. Profiling of N 6-Methyladenosine (m 6A) Modification Landscape in Response to Drought Stress in Apple ( Malus prunifolia (Willd.) Borkh). PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010103. [PMID: 35009106 PMCID: PMC8747461 DOI: 10.3390/plants11010103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 05/26/2023]
Abstract
Drought stress is a significant environmental factor limiting crop growth worldwide. Malus prunifolia is an important apple species endemic to China and is used for apple cultivars and rootstocks with great drought tolerance. N6-methyladenosine (m6A) is a common epigenetic modification on messenger RNAs (mRNAs) in eukaryotes which is critical for various biological processes. However, there are no reports on m6A methylation in apple response to drought stress. Here, we assessed the m6A landscape of M. prunifolia seedlings in response to drought and analyzed the association between m6A modification and transcript expression. In total, we found 19,783 and 19,609 significant m6A peaks in the control and drought treatment groups, respectively, and discovered a UGUAH (H: A/U/C) motif. In M. prunifolia, under both control and drought conditions, peaks were highly enriched in the 3' untranslated region (UTR) and coding sequence (CDS). Among 4204 significant differential m6A peaks in drought-treated M. prunifolia compared to control-treated M. prunifolia, 4158 genes with m6A modification were identified. Interestingly, a large number of hypermethylated peaks (4069) were stimulated by drought treatment compared to hypomethylation. Among the hypermethylated peak-related genes, 972 and 1238 differentially expressed genes (DEGs) were up- and down-regulated in response to drought, respectively. Gene ontology (GO) analyses of differential m6A-modified genes revealed that GO slims related to RNA processing, epigenetic regulation, and stress tolerance were significantly enriched. The m6A modification landscape depicted in this study sheds light on the epigenetic regulation of M. prunifolia in response to drought stress and indicates new directions for the breeding of drought-tolerant apple trees.
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Affiliation(s)
- Xiushan Mao
- Shandong Transport Vocational College, 7369 Bohai Road, Weifang 261206, China;
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Xianyang 712100, China;
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhenzhong Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Xianyang 712100, China;
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Xianyang 712100, China;
- Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
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22
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Li J, He S, Guo F, Zou Q. HSM6AP: a high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching. RNA Biol 2021; 18:1882-1892. [PMID: 33446014 PMCID: PMC8583144 DOI: 10.1080/15476286.2021.1875180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/02/2020] [Accepted: 01/08/2021] [Indexed: 01/21/2023] Open
Abstract
Recent studies have shown that RNA methylation modification can affect RNA transcription, metabolism, splicing and stability. In addition, RNA methylation modification has been associated with cancer, obesity and other diseases. Based on information about human genome and machine learning, this paper discusses the effect of the fusion sequence and gene-level feature extraction on the accuracy of methylation site recognition. The significant limitation of existing computing tools was exposed by discovered of new features. (1) Most prediction models are based solely on sequence features and use SVM or random forest as classification methods. (2) Limited by the number of samples, the model may not achieve good performance. In order to establish a better prediction model for methylation sites, we must set specific weighting strategies for training samples and find more powerful and informative feature matrices to establish a comprehensive model. In this paper, we present HSM6AP, a high-precision predictor for the Homo sapiens N6-methyladenosine (m 6 A ) based on multiple weights and feature stitching. Compared with existing methods, HSM6AP samples were creatively weighted during training, and a wide range of features were explored. Max-Relevance-Max-Distance (MRMD) is employed for feature selection, and the feature matrix is generated by fusing a single feature. The extreme gradient boosting (XGBoost), an integrated machine learning algorithm based on decision tree, is used for model training and improves model performance through parameter adjustment. Two rigorous independent data sets demonstrated the superiority of HSM6AP in identifying methylation sites. HSM6AP is an advanced predictor that can be directly employed by users (especially non-professional users) to predict methylation sites. Users can access our related tools and data sets at the following website: http://lab.malab.cn/~lijing/HSM6AP.html The codes of our tool can be publicly accessible at https://github.com/lijingtju/HSm6AP.git.
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Affiliation(s)
- Jing Li
- Institute of computational biology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Shida He
- Institute of computational biology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Fei Guo
- Institute of computational biology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Quan Zou
- Bioinformatics Laboratory, Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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23
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Chen M, Zhou S, Shi H, Gu H, Wen Y, Chen L. Identification and validation of pivotal genes related to age-related meniscus degeneration based on gene expression profiling analysis and in vivo and in vitro models detection. BMC Med Genomics 2021; 14:237. [PMID: 34587952 PMCID: PMC8482591 DOI: 10.1186/s12920-021-01088-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/20/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The componential and structural change in the meniscus with aging would increase the tissue vulnerability of the meniscus, which would induce meniscus tearing. Here, we investigated the molecular mechanism of age-related meniscus degeneration with gene expression profiling analysis, and validate pivotal genes in vivo and in vitro models. METHODS The GSE45233 dataset, including 6 elderly meniscus samples and 6 younger meniscus samples, was downloaded from the Gene Expression Omnibus (GEO) database. To screen the differential expression of mRNAs and identify the miRNAs targeting hub genes, we completed a series of bioinformatics analyses, including functional and pathway enrichment, protein-protein interaction network, hub genes screening, and construction of a lncRNA-miRNA-mRNA network. Furthermore, crucial genes were examined in human senescent menisci, mouse senescent meniscus tissues and mouse meniscus cells stimulated by IL-1β. RESULTS In total, the most significant 4 hub genes (RRM2, AURKB, CDK1, and TIMP1) and 5 miRNAs (hsa-miR-6810-5p, hsa-miR-4676-5p, hsa-miR-6877-5p, hsa-miR-8085, and hsa-miR-6133) that regulated such 4 hub genes, were finally identified. Moreover, these hub genes were decreased in meniscus cells in vitro and meniscus tissues in vivo, which indicated that hub genes were related to meniscus senescence and could serve as potential biomarkers for age-related meniscus tearing. CONCLUSIONS In short, the integrated analysis of gene expression profile, co-expression network, and models detection identified pivotal genes, which elucidated the possible molecular basis underlying the senescence meniscus and also provided prognosis clues for early-onset age-related meniscus tearing.
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Affiliation(s)
- Ming Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Siqi Zhou
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.,Department of Orthopedics Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Huasong Shi
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Hanwen Gu
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Yinxian Wen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China. .,Joint Disease Research Center, Wuhan University, Wuhan, 430071, China.
| | - Liaobin Chen
- Division of Joint Surgery and Sports Medicine, Department of Orthopedics Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China. .,Joint Disease Research Center, Wuhan University, Wuhan, 430071, China.
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24
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Probiotics and Trained Immunity. Biomolecules 2021; 11:biom11101402. [PMID: 34680035 PMCID: PMC8533468 DOI: 10.3390/biom11101402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/09/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022] Open
Abstract
The characteristics of innate immunity have recently been investigated in depth in several research articles, and original findings suggest that innate immunity also has a memory capacity, which has been named “trained immunity”. This notion has revolutionized our knowledge of the innate immune response. Thus, stimulation of trained immunity represents a therapeutic alternative that is worth exploring. In this context, probiotics, live microorganisms which when administered in adequate amounts confer a health benefit on the host, represent attractive candidates for the stimulation of trained immunity; however, although numerous studies have documented the beneficial proprieties of these microorganisms, their mechanisms of action are not yet fully understood. In this review, we propose to explore the putative connection between probiotics and stimulation of trained immunity.
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25
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Huang D, Song B, Wei J, Su J, Coenen F, Meng J. Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. Bioinformatics 2021; 37:i222-i230. [PMID: 34252943 PMCID: PMC8336446 DOI: 10.1093/bioinformatics/btab278] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Motivation Increasing evidence suggests that post-transcriptional ribonucleic acid (RNA) modifications regulate essential biomolecular functions and are related to the pathogenesis of various diseases. Precise identification of RNA modification sites is essential for understanding the regulatory mechanisms of RNAs. To date, many computational approaches for predicting RNA modifications have been developed, most of which were based on strong supervision enabled by base-resolution epitranscriptome data. However, high-resolution data may not be available. Results We propose WeakRM, the first weakly supervised learning framework for predicting RNA modifications from low-resolution epitranscriptome datasets, such as those generated from acRIP-seq and hMeRIP-seq. Evaluations on three independent datasets (corresponding to three different RNA modification types and their respective sequencing technologies) demonstrated the effectiveness of our approach in predicting RNA modifications from low-resolution data. WeakRM outperformed state-of-the-art multi-instance learning methods for genomic sequences, such as WSCNN, which was originally designed for transcription factor binding site prediction. Additionally, our approach captured motifs that are consistent with existing knowledge, and visualization of the predicted modification-containing regions unveiled the potentials of detecting RNA modifications with improved resolution. Availability implementation The source code for the WeakRM algorithm, along with the datasets used, are freely accessible at: https://github.com/daiyun02211/WeakRM Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daiyun Huang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bowen Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jingjue Wei
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Frans Coenen
- Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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26
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Chantsalnyam T, Siraj A, Tayara H, Chong KT. ncRDense: A novel computational approach for classification of non-coding RNA family by deep learning. Genomics 2021; 113:3030-3038. [PMID: 34242708 DOI: 10.1016/j.ygeno.2021.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022]
Abstract
With the rapidly growing importance of biological research, non-coding RNAs (ncRNA) attract more attention in biology and bioinformatics. They play vital roles in biological processes such as transcription and translation. Classification of ncRNAs is essential to our understanding of disease mechanisms and treatment design. Many approaches to ncRNA classification have been developed, several of which use machine learning and deep learning. In this paper, we construct a novel deep learning-based architecture, ncRDense, to effectively classify and distinguish ncRNA families. In a comparative study, our model produces comparable results with existing state-of-the-art methods. Finally, we built a freely accessible web server for the ncRDense tool, which is available at http://nsclbio.jbnu.ac.kr/tools/ncRDense/.
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Affiliation(s)
- Tuvshinbayar Chantsalnyam
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Arslan Siraj
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea.
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea; Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea.
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27
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Song Z, Huang D, Song B, Chen K, Song Y, Liu G, Su J, Magalhães JPD, Rigden DJ, Meng J. Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. Nat Commun 2021; 12:4011. [PMID: 34188054 PMCID: PMC8242015 DOI: 10.1038/s41467-021-24313-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/07/2021] [Indexed: 02/08/2023] Open
Abstract
Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of RNAs. Here, we present MultiRM, a method for the integrated prediction and interpretation of post-transcriptional RNA modifications from RNA sequences. Built upon an attention-based multi-label deep learning framework, MultiRM not only simultaneously predicts the putative sites of twelve widely occurring transcriptome modifications (m6A, m1A, m5C, m5U, m6Am, m7G, Ψ, I, Am, Cm, Gm, and Um), but also returns the key sequence contents that contribute most to the positive predictions. Importantly, our model revealed a strong association among different types of RNA modifications from the perspective of their associated sequence contexts. Our work provides a solution for detecting multiple RNA modifications, enabling an integrated analysis of these RNA modifications, and gaining a better understanding of sequence-based RNA modification mechanisms. RNA modifications appear to play a role in determining RNA structure and function. Here, the authors develop a deep learning model that predicts the location of 12 RNA modifications using primary sequence, and show that several modifications are associated, which suggests dependencies between them.
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Affiliation(s)
- Zitao Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China
| | - Daiyun Huang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China. .,Department of Computer Sciences, University of Liverpool, Liverpool, United Kingdom.
| | - Bowen Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Kunqi Chen
- Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, PR China
| | - Yiyou Song
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China
| | - Gang Liu
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, PR China
| | | | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, PR China. .,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom. .,AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, PR China.
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28
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Zhang SY, Zhang SW, Zhang T, Fan XN, Meng J. Recent advances in functional annotation and prediction of the epitranscriptome. Comput Struct Biotechnol J 2021; 19:3015-3026. [PMID: 34136099 PMCID: PMC8175281 DOI: 10.1016/j.csbj.2021.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
RNA modifications, in particular N6-methyladenosine (m6A), participate in every stages of RNA metabolism and play diverse roles in essential biological processes and disease pathogenesis. Thanks to the advances in sequencing technology, tens of thousands of RNA modification sites can be identified in a typical high-throughput experiment; however, it remains a major challenge to decipher the functional relevance of these sites, such as, affecting alternative splicing, regulation circuit in essential biological processes or association to diseases. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, we review here recent progress in functional annotation and prediction of RNA modification sites from a bioinformatics perspective. The review covers naïve annotation with associated biological events, e.g., single nucleotide polymorphism (SNP), RNA binding protein (RBP) and alternative splicing, prediction of key sites and their regulatory functions, inference of disease association, and mining the diagnosis and prognosis value of RNA modification regulators. We further discussed the limitations of existing approaches and some future perspectives.
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Affiliation(s)
- Song-Yao Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Teng Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiao-Nan Fan
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
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29
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Status of Bioinformatics Education in South Asia: Past and Present. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568262. [PMID: 33997009 PMCID: PMC8096557 DOI: 10.1155/2021/5568262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022]
Abstract
Bioinformatics education has been a hot topic in South Asia, and the interest in this education peaks with the start of the 21st century. The governments of South Asian countries had a systematic effort for bioinformatics. They developed the infrastructures to provide maximum facility to the scientific community to gain maximum output in this field. This article renders bioinformatics, measures, and its importance of implementation in South Asia with proper ways of improving bioinformatics education flaws. It also addresses the problems faced in South Asia and proposes some recommendations regarding bioinformatics education. The information regarding bioinformatics education and institutes was collected from different existing research papers, databases, and surveys. The information was then confirmed by visiting each institution's website, while problems and solutions displayed in the article are mostly in line with South Asian bioinformatics conferences and institutions' objectives. Among South Asian countries, India and Pakistan have developed infrastructure and education regarding bioinformatics rapidly as compared to other countries, whereas Bangladesh, Sri Lanka, and Nepal are still in a progressing phase in this field. To advance in a different sector, the bioinformatics industry has to be revolutionized, and it will contribute to strengthening the pharmaceutical, agricultural, and molecular sectors in South Asia. To advance in bioinformatics, universities' infrastructure needs to be on a par with the current international standards, which will produce well-trained professionals with skills in multiple fields like biotechnology, mathematics, statistics, and computer science. The bioinformatics industry has revolutionized and strengthened the pharmaceutical, agricultural, and molecular sectors in South Asia, and it will serve as the standard of education increases in the South Asian countries. A framework for developing a centralized database is suggested after the literature review to collect and store the information on the current status of South Asian bioinformatics education. This will be named as the South Asian Bioinformatics Education Database (SABE). This will provide comprehensive information regarding the bioinformatics in South Asian countries by the country name, the experts of this field, and the university name to explore the top-ranked outputs relevant to queries.
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30
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Kuai L, Luo Y, Qu K, Ru Y, Luo Y, Ding X, Xing M, Liu L, Sun X, Li X, Li B. Transcriptomic Analysis of the Mechanisms for Alleviating Psoriatic Dermatitis Using Taodan Granules in an Imiquimod-Induced Psoriasis-like Mouse Model. Front Pharmacol 2021; 12:632414. [PMID: 33995034 PMCID: PMC8114823 DOI: 10.3389/fphar.2021.632414] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/11/2021] [Indexed: 01/04/2023] Open
Abstract
Taodan granules (TDGs) are clinically efficacious for treating psoriasis, buttheir specific mechanisms of action are unclear. In this study, we determined the concentrations of tanshinone IIA and curcumol using high-performance liquid chromatography (HPLC) to establish quality control parameters for assessing the mechanism of TDGs in treating psoriasis. Thereafter, a mouse model of psoriasis was treated with TDGs. TDGs attenuated imiquimod-induced typical erythema, scales, and thickening of the back and ear lesions in the psoriatic mouse model. Furthermore, PCNA and Ki67-positive cells were reduced in the epidermis of psoriatic lesions following TDG treatment. Finally, the sequencing results were verified using a multitude of methods, and the mechanism of action of TDGs against psoriasis was found to be via the upregulation of metabolic signaling pathways such as the Gly-Ser-Thr axis, the downregulation of immune and inflammatory pathways, and the decrease in Rac2 and Arhgdib concentrations. Overall, this study clarified the mechanism of TDG treatment for psoriasis and provided evidence for its clinical application.
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Affiliation(s)
- Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ying Luo
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Keshen Qu
- Department of Traditional Chinese Surgery, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Ru
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yue Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaojie Ding
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Meng Xing
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.,Department of Dermatology, Shaanxi Hospital of Traditional Chinese Medicine, Xi`an, China
| | - Liu Liu
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoying Sun
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Xin Li
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Bin Li
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Dermatology, Shaanxi Hospital of Traditional Chinese Medicine, Xi`an, China.,Shanghai Dermatology Hospital, Tongji University, Shanghai, China
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