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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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Chen Y, Fu X, Li Z, Peng L, Zhuo L. Prediction of lncRNA-Protein Interactions via the Multiple Information Integration. Front Bioeng Biotechnol 2021; 9:647113. [PMID: 33718346 PMCID: PMC7947871 DOI: 10.3389/fbioe.2021.647113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 01/19/2021] [Indexed: 01/09/2023] Open
Abstract
The long non-coding RNA (lncRNA)-protein interaction plays an important role in the post-transcriptional gene regulation, such as RNA splicing, translation, signaling, and the development of complex diseases. The related research on the prediction of lncRNA-protein interaction relationship is beneficial in the excavation and the discovery of the mechanism of lncRNA function and action occurrence, which are important. Traditional experimental methods for detecting lncRNA-protein interactions are expensive and time-consuming. Therefore, computational methods provide many effective strategies to deal with this problem. In recent years, most computational methods only use the information of the lncRNA-lncRNA or the protein-protein similarity and cannot fully capture all features to identify their interactions. In this paper, we propose a novel computational model for the lncRNA-protein prediction on the basis of machine learning methods. First, a feature method is proposed for representing the information of the network topological properties of lncRNA and protein interactions. The basic composition feature information and evolutionary information based on protein, the lncRNA sequence feature information, and the lncRNA expression profile information are extracted. Finally, the above feature information is fused, and the optimized feature vector is used with the recursive feature elimination algorithm. The optimized feature vectors are input to the support vector machine (SVM) model. Experimental results show that the proposed method has good effectiveness and accuracy in the lncRNA-protein interaction prediction.
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Affiliation(s)
- Yifan Chen
- College of Information Science and Engineering, Hunan University, Changsha, China
- School of Computer and Information Science, Hunan Institute of Technology, Hengyang, China
| | - Xiangzheng Fu
- College of Information Science and Engineering, Hunan University, Changsha, China
| | - Zejun Li
- School of Computer and Information Science, Hunan Institute of Technology, Hengyang, China
| | - Li Peng
- College of Computer Science and Engineering, Hunan University of Science and Technology, Xiangtan, China
| | - Linlin Zhuo
- Department of Mathematics and Information Engineering, Wenzhou University Oujiang College, Wenzhou, China
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Zhao J, Huang J, Geng X, Chu W, Li S, Chen ZJ, Du Y. Polycystic Ovary Syndrome: Novel and Hub lncRNAs in the Insulin Resistance-Associated lncRNA-mRNA Network. Front Genet 2019; 10:772. [PMID: 31507635 PMCID: PMC6715451 DOI: 10.3389/fgene.2019.00772] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a common metabolic and reproductive disorder with an increasing risk for type 2 diabetes. Insulin resistance is a common feature of women with PCOS, but the underlying molecular mechanism remains unclear. This study aimed to screen critical long non-coding RNAs (lncRNAs) that might play pivotal roles in insulin resistance, which could provide candidate biomarkers and potential therapeutic targets for PCOS. Gene expression profiles of the skeletal muscle in patients with PCOS accompanied by insulin resistance and healthy patients were obtained from the publicly available Gene Expression Omnibus (GEO) database. A global triple network including RNA-binding protein, mRNA, and lncRNAs was constructed based on the data from starBase. Then, we extracted an insulin resistance-associated lncRNA–mRNA network (IRLMN) by integrating the data from starBase and GEO. We also performed a weighted gene co-expression network analysis (WGCNA) on the differentially expressed genes between the women with and without PCOS, to identify hub lncRNAs. Additionally, the findings of key lncRNAs were examined in an independent GEO dataset. The expression level of lncRNA RP11-151A6.4 in ovarian granulosa cells was increased in patients with PCOS compared with that in control women. Levels were also increased in PCOS patients with higher BMI, hyperinsulinemia, and higher HOMA-IR values. As a result, RP11-151A6.4 was identified as a hub lncRNA based on IRLMN and WGCNA and was highly expressed in ovarian granulosa cells, skeletal muscle, and subcutaneous and omental adipose tissues of patients with insulin resistance. This study showed the differences between lncRNA and mRNA profiles from healthy women and women with PCOS and insulin resistance. Here, we demonstrated that RP11-151A6.4 might play a vital role in insulin resistance, androgen excess, and adipose dysfunction in patients with PCOS. Further study concerning RP11-151A6.4 could elucidate the underlying mechanisms of insulin resistance.
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Affiliation(s)
- Jun Zhao
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Jiayu Huang
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Xueying Geng
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Weiwei Chu
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Shang Li
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China.,Center for Reproductive Medicine, Shandong Provincial Hospital, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, The Key Laboratory for Reproductive Endocrinology, Ministry of Education, Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong Provincial Key Laboratory of Reproductive Medicine, China
| | - Yanzhi Du
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
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