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Li KX, Fan L, Wang H, Tian Y, Zhang S, Hu Q, Liu F, Chen H, Hou H. A synonymous mutation of rs1137070 cause the mice Maoa gene transcription and translation to decrease. Front Mol Neurosci 2024; 17:1406708. [PMID: 39359688 PMCID: PMC11446106 DOI: 10.3389/fnmol.2024.1406708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/03/2024] [Indexed: 10/04/2024] Open
Abstract
The Monoamine Oxidase-A (MAOA) EcoRV polymorphism (rs1137070) is a unique synonymous mutation (c.1409 T > C) within the MAOA gene, which plays a crucial role in Maoa gene expression and function. This study aimed to explore the relationship between the mouse Maoa rs1137070 genotype and differences in MAOA gene expression. Mice carrying the CC genotype of rs1137070 exhibited a significantly lower Maoa expression level, with an odds ratio of 2.44 compared to the T carriers. Moreover, the wild-type TT genotype of MAOA demonstrated elevated mRNA expression and a longer half-life. We also delved into the significant expression and structural disparities among genotypes. Furthermore, it was evident that different aspartic acid synonymous codons within Maoa influenced both MAOA expression and enzyme activity, highlighting the association between rs1137070 and MAOA. To substantiate these findings, a dual-luciferase reporter assay confirmed that GAC was more efficient than GAT binding. Conversely, the synonymous mutation altered Maoa gene expression in individual mice. An RNA pull-down assay suggested that this alteration could impact the interaction with RNA-binding proteins. In summary, our results illustrate that synonymous mutations can indeed regulate the downregulation of gene expression, leading to changes in MAOA function and their potential association with neurological-related diseases.
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Affiliation(s)
- Kai Xin Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Lei Fan
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Hongjuan Wang
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
| | - Yushan Tian
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
| | - Sen Zhang
- Department of Bioengineering, School of Chemical Engineering, Northwest University, Xi’an, China
| | - Qingyuan Hu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Fanglin Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
- Institute of Technical Biology and Agricultural Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Huan Chen
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, China
- Key Laboratory of Tobacco Biological Effects, Zhengzhou, China
- Beijing Life Science Academy, Beijing, China
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Yang W, Lyu Y, Xiang R, Yang J. Long Noncoding RNAs in the Pathogenesis of Insulin Resistance. Int J Mol Sci 2022; 23:ijms232416054. [PMID: 36555704 PMCID: PMC9785789 DOI: 10.3390/ijms232416054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Insulin resistance (IR), designated as the blunted response of insulin target tissues to physiological level of insulin, plays crucial roles in the development and progression of diabetes, nonalcoholic fatty liver disease (NAFLD) and other diseases. So far, the distinct mechanism(s) of IR still needs further exploration. Long non-coding RNA (lncRNA) is a class of non-protein coding RNA molecules with a length greater than 200 nucleotides. LncRNAs are widely involved in many biological processes including cell differentiation, proliferation, apoptosis and metabolism. More recently, there has been increasing evidence that lncRNAs participated in the pathogenesis of IR, and the dysregulated lncRNA profile played important roles in the pathogenesis of metabolic diseases including obesity, diabetes and NAFLD. For example, the lncRNAs MEG3, H19, MALAT1, GAS5, lncSHGL and several other lncRNAs have been shown to regulate insulin signaling and glucose/lipid metabolism in various tissues. In this review, we briefly introduced the general features of lncRNA and the methods for lncRNA research, and then summarized and discussed the recent advances on the roles and mechanisms of lncRNAs in IR, particularly focused on liver, skeletal muscle and adipose tissues.
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Affiliation(s)
- Weili Yang
- Beijing Key Laboratory of Diabetes Research and Care, Beijing Diabetes Institute, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yixiang Lyu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Rui Xiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
| | - Jichun Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Key Laboratory of Cardiovascular Science of the Ministry of Education, Center for Non-Coding RNA Medicine, Beijing 100191, China
- Correspondence:
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Qi Y, Zhang Y, Zheng G, Chen B, Zhang M, Li J, Peng T, Huang J, Wang X. In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum. Front Cell Infect Microbiol 2021; 11:673966. [PMID: 34079769 PMCID: PMC8166286 DOI: 10.3389/fcimb.2021.673966] [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: 02/28/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
It is widely accepted that the structure of RNA plays important roles in a number of biological processes, such as polyadenylation, splicing, and catalytic functions. Dynamic changes in RNA structure are able to regulate the gene expression programme and can be used as a highly specific and subtle mechanism for governing cellular processes. However, the nature of most RNA secondary structures in Plasmodium falciparum has not been determined. To investigate the genome-wide RNA secondary structural features at single-nucleotide resolution in P. falciparum, we applied a novel high-throughput method utilizing the chemical modification of RNA structures to characterize these structures. Structural data from parasites are in close agreement with the known 18S ribosomal RNA secondary structures of P. falciparum and can help to predict the in vivo RNA secondary structure of a total of 3,396 transcripts in the ring-stage and trophozoite-stage developmental cycles. By parallel analysis of RNA structures in vivo and in vitro during the Plasmodium parasite ring-stage and trophozoite-stage intraerythrocytic developmental cycles, we identified some key regulatory features. Recent studies have established that the RNA structure is a ubiquitous and fundamental regulator of gene expression. Our study indicate that there is a critical connection between RNA secondary structure and mRNA abundance during the complex biological programme of P. falciparum. This work presents a useful framework and important results, which may facilitate further research investigating the interactions between RNA secondary structure and the complex biological programme in P. falciparum. The RNA secondary structure characterized in this study has potential applications and important implications regarding the identification of RNA structural elements, which are important for parasite infection and elucidating host-parasite interactions and parasites in the environment.
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Affiliation(s)
- Yanwei Qi
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yuhong Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Guixing Zheng
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Bingxia Chen
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Mengxin Zhang
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Tao Peng
- Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jun Huang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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Wang L, Zhong X, Wang S, Zhang H, Liu Y. A novel end-to-end method to predict RNA secondary structure profile based on bidirectional LSTM and residual neural network. BMC Bioinformatics 2021; 22:169. [PMID: 33789581 PMCID: PMC8011163 DOI: 10.1186/s12859-021-04102-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/24/2021] [Indexed: 11/26/2022] Open
Abstract
Background Studies have shown that RNA secondary structure, a planar structure formed by paired bases, plays diverse vital roles in fundamental life activities and complex diseases. RNA secondary structure profile can record whether each base is paired with others. Hence, accurate prediction of secondary structure profile can help to deduce the secondary structure and binding site of RNA. RNA secondary structure profile can be obtained through biological experiment and calculation methods. Of them, the biological experiment method involves two ways: chemical reagent and biological crystallization. The chemical reagent method can obtain a large number of prediction data, but its cost is high and always associated with high noise, making it difficult to get results of all bases on RNA due to the limited of sequencing coverage. By contrast, the biological crystallization method can lead to accurate results, yet heavy experimental work and high costs are required. On the other hand, the calculation method is CROSS, which comprises a three-layer fully connected neural network. However, CROSS can not completely learn the features of RNA secondary structure profile since its poor network structure, leading to its low performance. Results In this paper, a novel end-to-end method, named as “RPRes, was proposed to predict RNA secondary structure profile based on Bidirectional LSTM and Residual Neural Network. Conclusions RPRes utilizes data sets generated by multiple biological experiment methods as the training, validation, and test sets to predict profile, which can compatible with numerous prediction requirements. Compared with the biological experiment method, RPRes has reduced the costs and improved the prediction efficiency. Compared with the state-of-the-art calculation method CROSS, RPRes has significantly improved performance.
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Affiliation(s)
- Linyu Wang
- College of Computer Science and Technology, Jilin University, Changchun, China
| | - Xiaodan Zhong
- Department of Pediatric Oncology, The First Hospital of Jilin University, Changchun, China
| | - Shuo Wang
- College of Computer Science and Technology, Jilin University, Changchun, China
| | - Hao Zhang
- College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yuanning Liu
- College of Computer Science and Technology, Jilin University, Changchun, China.
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [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: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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Abstract
The proper regulation of mRNA processing, localization, translation, and degradation occurs on mRNPs. However, the global principles of mRNP organization are poorly understood. We utilize the limited, but existing, information available to present a speculative synthesis of mRNP organization with the following key points. First, mRNPs form a compacted structure due to the inherent folding of RNA. Second, the ribosome is the principal mechanism by which mRNA regions are partially decompacted. Third, mRNPs are 50%-80% protein by weight, consistent with proteins modulating mRNP organization, but also suggesting the majority of mRNA sequences are not directly interacting with RNA-binding proteins. Finally, the ratio of mRNA-binding proteins to mRNAs is higher in the nucleus to allow effective RNA processing and limit the potential for nuclear RNA based aggregation. This synthesis of mRNP understanding provides a model for mRNP biogenesis, structure, and regulation with multiple implications.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Roy Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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Miladi M, Sokhoyan E, Houwaart T, Heyne S, Costa F, Grüning B, Backofen R. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering. Gigascience 2019; 8:giz150. [PMID: 31808801 PMCID: PMC6897289 DOI: 10.1093/gigascience/giz150] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/23/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function. With the advent of high-throughput sequencing techniques, experimental and genomic data are expanding to complement the predictive methods. However, the existing methods do not effectively utilize and cope with the immense amount of data becoming available. RESULTS Hundreds of thousands of non-coding RNAs have been detected; however, their annotation is lagging behind. Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities. GraphClust2 bridges the gap between high-throughput sequencing and structural RNA analysis and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner via the Galaxy framework. GraphClust2 can efficiently cluster and annotate large datasets of RNAs and supports structure-probing data. We demonstrate that the annotation performance of clustering functional RNAs can be considerably improved. Furthermore, an off-the-shelf procedure is introduced for identifying locally conserved structure candidates in long RNAs. We suggest the presence and the sparseness of phylogenetically conserved local structures for a collection of long non-coding RNAs. CONCLUSIONS By clustering data from 2 cross-linking immunoprecipitation experiments, we demonstrate the benefits of GraphClust2 for motif discovery under the presence of biological and methodological biases. Finally, we uncover prominent targets of double-stranded RNA binding protein Roquin-1, such as BCOR's 3' untranslated region that contains multiple binding stem-loops that are evolutionary conserved.
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Affiliation(s)
- Milad Miladi
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Eteri Sokhoyan
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Torsten Houwaart
- Institute of Medical Microbiology and Hospital Hygiene, University of Dusseldorf, Universitaetsstr. 1, 40225 Dusseldorf, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Stuebeweg 51, 79108 Freiburg, Germany
| | - Fabrizio Costa
- Department of Computer Science, University of Exeter, North Park Road, EX4 4QF Exeter, UK
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- ZBSA Centre for Biological Systems Analysis, University of Freiburg, Hauptstr. 1, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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Pharmacological screening of a new alpha-2 adrenergic receptor agonist, mafedine, in zebrafish. Neurosci Lett 2019; 701:234-239. [PMID: 30836120 DOI: 10.1016/j.neulet.2019.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/25/2019] [Accepted: 03/02/2019] [Indexed: 10/27/2022]
Abstract
Pharmacological agents acting at alpha-2 adrenergic receptors are widely used in physiology and neuroscience research. Mounting evidence of their potential utility in clinical and experimental psychopharmacology, necessitates new models and novel model organisms for their screening. Here, we characterize behavioral effects of mafedine (6-oxo-1-phenyl-2- (phenylamino)-1,6-dihydropyrimidine-4-sodium olate), a novel drug with alpha-2 adrenergic receptor agonistic effects, in adult zebrafish (Danio rerio) in the novel tank test of anxiety and activity. Following an acute 20-min exposure, mafedine at 60 mg/L produced a mild psychostimulant action with some anxiogenic-like effects. Repeated acute 20-min/day administration of mafedine for 7 consecutive days at 1, 5 and 10 mg/L had a similar action on fish behavior as an acute exposure to 60 mg/L. Since mafedine demonstrated robust behavioral effects in zebrafish - a sensitive vertebrate aquatic model, it is likely that it may modulate rodent and human behavior as well. Thus, further studies are needed to explore this possibility in detail, and whether it may foster clinical application of mafedine and related alpha-2 adrenergic agents.
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