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Zhang Y, Wang Z, Zhang Y, Li S, Guo Y, Song J, Yu DJ. Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. Bioinformatics 2023; 39:btad709. [PMID: 37995291 PMCID: PMC10697738 DOI: 10.1093/bioinformatics/btad709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/01/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
MOTIVATION RNA N6-methyladenosine (m6A) in Homo sapiens plays vital roles in a variety of biological functions. Precise identification of m6A modifications is thus essential to elucidation of their biological functions and underlying molecular-level mechanisms. Currently available high-throughput single-nucleotide-resolution m6A modification data considerably accelerated the identification of RNA modification sites through the development of data-driven computational methods. Nevertheless, existing methods have limitations in terms of the coverage of single-nucleotide-resolution cell lines and have poor capability in model interpretations, thereby having limited applicability. RESULTS In this study, we present CLSM6A, comprising a set of deep learning-based models designed for predicting single-nucleotide-resolution m6A RNA modification sites across eight different cell lines and three tissues. Extensive benchmarking experiments are conducted on well-curated datasets and accordingly, CLSM6A achieves superior performance than current state-of-the-art methods. Furthermore, CLSM6A is capable of interpreting the prediction decision-making process by excavating critical motifs activated by filters and pinpointing highly concerned positions in both forward and backward propagations. CLSM6A exhibits better portability on similar cross-cell line/tissue datasets, reveals a strong association between highly activated motifs and high-impact motifs, and demonstrates complementary attributes of different interpretation strategies. AVAILABILITY AND IMPLEMENTATION The webserver is available at http://csbio.njust.edu.cn/bioinf/clsm6a. The datasets and code are available at https://github.com/zhangying-njust/CLSM6A/.
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Affiliation(s)
- Ying Zhang
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhikang Wang
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Yiwen Zhang
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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Abbas Z, Tayara H, Zou Q, Chong KT. TS-m6A-DL: Tissue-specific identification of N6-methyladenosine sites using a universal deep learning model. Comput Struct Biotechnol J 2021; 19:4619-4625. [PMID: 34471503 PMCID: PMC8383060 DOI: 10.1016/j.csbj.2021.08.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 01/30/2023] Open
Abstract
The most communal post-transcriptional modification, N6-methyladenosine (m6A), is associated with a number of crucial biological processes. The precise detection of m6A sites around the genome is critical for revealing its regulatory function and providing new insights into drug design. Although both experimental and computational models for detecting m6A sites have been introduced, but these conventional methods are laborious and expensive. Furthermore, only a handful of these models are capable of detecting m6A sites in various tissues. Therefore, a more generic and optimized computational method for detecting m6A sites in different tissues is required. In this paper, we proposed a universal model using a deep neural network (DNN) and named it TS-m6A-DL, which can classify m6A sites in several tissues of humans (Homo sapiens), mice (Mus musculus), and rats (Rattus norvegicus). To extract RNA sequence features and to convert the input into numerical format for the network, we utilized one-hot-encoding method. The model was tested using fivefold cross-validation and its stability was measured using independent datasets. The proposed model, TS-m6A-DL, achieved accuracies in the range of 75-85% using the fivefold cross-validation method and 72-84% on the independent datasets. Finally, to authenticate the generalization of the model, we performed cross-species testing and proved the generalization ability by achieving state-of-the-art results.
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Affiliation(s)
- Zeeshan Abbas
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Institute of Avionics and Aeronautics (IAA), Air University, Islamabad 44000, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
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Dao FY, Lv H, Yang YH, Zulfiqar H, Gao H, Lin H. Computational identification of N6-methyladenosine sites in multiple tissues of mammals. Comput Struct Biotechnol J 2020; 18:1084-1091. [PMID: 32435427 PMCID: PMC7229270 DOI: 10.1016/j.csbj.2020.04.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) is the methylation of the adenosine at the nitrogen-6 position, which is the most abundant RNA methylation modification and involves a series of important biological processes. Accurate identification of m6A sites in genome-wide is invaluable for better understanding their biological functions. In this work, an ensemble predictor named iRNA-m6A was established to identify m6A sites in multiple tissues of human, mouse and rat based on the data from high-throughput sequencing techniques. In the proposed predictor, RNA sequences were encoded by physical-chemical property matrix, mono-nucleotide binary encoding and nucleotide chemical property. Subsequently, these features were optimized by using minimum Redundancy Maximum Relevance (mRMR) feature selection method. Based on the optimal feature subset, the best m6A classification models were trained by Support Vector Machine (SVM) with 5-fold cross-validation test. Prediction results on independent dataset showed that our proposed method could produce the excellent generalization ability. We also established a user-friendly webserver called iRNA-m6A which can be freely accessible at http://lin-group.cn/server/iRNA-m6A. This tool will provide more convenience to users for studying m6A modification in different tissues.
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Affiliation(s)
| | | | - Yu-He Yang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hasan Zulfiqar
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Gao
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Identification and Characterization of MiRNAs in Coccomyxa subellipsoidea C-169. Int J Mol Sci 2019; 20:ijms20143448. [PMID: 31337051 PMCID: PMC6678167 DOI: 10.3390/ijms20143448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/01/2023] Open
Abstract
Coccomyxa subellipsoidea C-169 (C-169) is an oleaginous microalga which is promising for renewable biofuel production. MicroRNAs (miRNAs), as the pivotal modulators of gene expression at post-transcriptional level, are prospective candidates for bioengineering practice. However, so far, no miRNA in C-169 has been reported and its potential impact upon CO2 supplementation remains unclear. High-throughput sequencing of small RNAs from C-169 cultured in air or 2% CO2 revealed 124 miRNAs in total, including 118 conserved miRNAs and six novel ones. In total, 384 genes were predicted as their potential target genes, 320 for conserved miRNAs and 64 for novel miRNAs. The annotated target genes were significantly enriched in six KEGG pathways, including pantothenate and CoA biosynthesis, C5-branched dibasic acid metabolism, 2-oxocarboxylic acid metabolism, butanoate metabolism, valine, leucine and isoleucine biosynthesis and alpha-linolenic acid metabolism. The miRNAs’ target genes were enriched in lipid metabolism as well as RNA-interacting proteins involved in translation, transcription and rRNA processing. The pioneering identification of C-169 miRNAs and analysis of their putative target genes lay the foundation for further miRNA research in eukaryotic algae and will contribute to the development of C-169 as an oleaginous microalga through bioengineering in the future.
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Razaviyan J, Hadavi R, Tavakoli R, Kamani F, Paknejad M, Mohammadi-Yeganeh S. Expression of miRNAs Targeting mTOR and S6K1 Genes of mTOR Signaling Pathway Including miR-96, miR-557, and miR-3182 in Triple-Negative Breast Cancer. Appl Biochem Biotechnol 2018; 186:1074-1089. [PMID: 29862445 DOI: 10.1007/s12010-018-2773-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/23/2018] [Indexed: 12/15/2022]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer. Aberrant expression of genes in mTOR pathway and their targeting miRNAs plays an important role in TNBC. The aim of this study was to determine the expression of mTOR and S6K1 and their targeting miRNAs in breast cancer cell lines and clinical samples. miRNAs targeting 3'-UTR of mTOR and S6K1 mRNAs were predicted using bioinformatic algorithms. MDA-MB-231, MCF-7, and MCF-10A as well as 20 TNBC samples were analyzed for gene and miRNA expression using quantitative real-time PCR (RT-qPCR). A receiver operating characteristic (ROC) curve analysis was performed for evaluation of candidate miRNAs as diagnostic biomarkers. miR-96 and miR-557 targeting mTOR and S6K1 mRNAs, respectively, were selected, and miR-3182 was selected as the miRNA targeting both genes. The miRNAs were down-regulated in cell lines, while their target mRNAs were up-regulated. Similar findings were observed in clinical samples. The ROC curve analysis revealed decline in expression of these miRNAs. We suggest that miR-96, miR-557, and miR-3182 can be used as inhibitory agents for mTOR and S6K1 in TNBC-targeted therapy.
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Affiliation(s)
- Javad Razaviyan
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Razie Hadavi
- Department of Biochemistry and Student Research Committee, Semnan University of Medical School, Semnan, Iran
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - Rezvan Tavakoli
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - Fereshteh Kamani
- Department of Surgery, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maliheh Paknejad
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Samira Mohammadi-Yeganeh
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Wang X, Liao Z, Bai Z, He Y, Duan J, Wei L. MiR-93-5p Promotes Cell Proliferation through Down-Regulating PPARGC1A in Hepatocellular Carcinoma Cells by Bioinformatics Analysis and Experimental Verification. Genes (Basel) 2018; 9:genes9010051. [PMID: 29361788 PMCID: PMC5793202 DOI: 10.3390/genes9010051] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PPARGC1A, formerly known as PGC-1a) is a transcriptional coactivator and metabolic regulator. Previous studies are mainly focused on the association between PPARGC1A and hepatoma. However, the regulatory mechanism remains unknown. A microRNA associated with cancer (oncomiR), miR-93-5p, has recently been found to play an essential role in tumorigenesis and progression of various carcinomas, including liver cancer. Therefore, this paper aims to explore the regulatory mechanism underlying these two proteins in hepatoma cells. Firstly, an integrative analysis was performed with miRNA–mRNA modules on microarray and The Cancer Genome Atlas (TCGA) data and obtained the core regulatory network and miR-93-5p/PPARGC1A pair. Then, a series of experiments were conducted in hepatoma cells with the results including miR-93-5p upregulated and promoted cell proliferation. Thirdly, the inverse correlation between miR-93-5p and PPARGC1A expression was validated. Finally, we inferred that miR-93-5p plays an essential role in inhibiting PPARGC1A expression by directly targeting the 3′-untranslated region (UTR) of its mRNA. In conclusion, these results suggested that miR-93-5p overexpression contributes to hepatoma development by inhibiting PPARGC1A. It is anticipated to be a promising therapeutic strategy for patients with liver cancer in the future.
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Affiliation(s)
- Xinrui Wang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital Affiliated to School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China.
| | - Zhijun Liao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.
| | - Zhimin Bai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.
- Department of Clinical Laboratory, Jinjiang Municipal Hospital, Jinjiang 362200, China.
| | - Yan He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.
| | - Juan Duan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China.
| | - Leyi Wei
- School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
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Liu B, Fang L. WITHDRAWN: Identification of microRNA precursor based on gapped n-tuple structure status composition kernel. Comput Biol Chem 2016:S1476-9271(16)30036-6. [PMID: 26935400 DOI: 10.1016/j.compbiolchem.2016.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Bin Liu
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China; Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
| | - Longyun Fang
- School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China.
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Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana). Interdiscip Sci 2015; 9:72-79. [PMID: 26496774 DOI: 10.1007/s12539-015-0130-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.
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Yang R, Zeng Y, Yi X, Zhao L, Zhang Y. Small RNA deep sequencing reveals the important role of microRNAs in the halophyte Halostachys caspica. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:395-408. [PMID: 25832169 DOI: 10.1111/pbi.12337] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 05/23/2023]
Abstract
MicroRNAs (miRNAs), an extensive class of small regulatory RNAs, play versatile roles in plant growth and development as well as stress responses. However, the regulatory mechanism is unclear on miRNA-mediated response to abiotic stress in plants. Halostachys caspica is a halophytic plant species and a great model for investigating plant response to salinity stress. However, no research has been performed on miRNAs in H. caspica. In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed H. caspica and its untreated control. Among the 13-19 million sequences generated from both treatments, a total of 170 conserved miRNAs, belonging to 151 miRNA families, were identified; among these miRNAs, 31 were significantly up-regulated and 48 were significantly down-regulated by salinity stress. We also identified 102 novel miRNAs from H. caspica; among them, 12 miRNAs were significantly up-regulated and 13 were significantly down-regulated by salinity. qRT-PCR expression analysis validated the deep sequencing results and also demonstrated that miRNAs and their targeted genes were responsive to high salt stress and existed a negative expression correlation between miRNAs and their targets. miRNA-target prediction, GO and KEGG analysis showed that miRNAs were involved in salt stress-related biological pathway, including calcium signalling pathway, MAPK signalling pathway, plant hormone signal transduction and flavonoid biosynthesis, etc. This suggests that miRNAs play an important role in plant salt stress tolerance in H. caspica. This result could be used to improve salt tolerance in crops and woods.
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Affiliation(s)
- Ruirui Yang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
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