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Liang X, Gong M, Wang Z, Wang J, Guo W, Cai A, Yang Z, Liu X, Xu F, Xiong W, Fu C, Wang X. LncRNA TubAR complexes with TUBB4A and TUBA1A to promote microtubule assembly and maintain myelination. Cell Discov 2024; 10:54. [PMID: 38769343 PMCID: PMC11106304 DOI: 10.1038/s41421-024-00667-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/13/2024] [Indexed: 05/22/2024] Open
Abstract
A long-standing hypothesis proposes that certain RNA(s) must exhibit structural roles in microtubule assembly. Here, we identify a long noncoding RNA (TubAR) that is highly expressed in cerebellum and forms RNA-protein complex with TUBB4A and TUBA1A, two tubulins clinically linked to cerebellar and myelination defects. TubAR knockdown in mouse cerebellum causes loss of oligodendrocytes and Purkinje cells, demyelination, and decreased locomotor activity. Biochemically, we establish the roles of TubAR in promoting TUBB4A-TUBA1A heterodimer formation and microtubule assembly. Intriguingly, different from the hypomyelination-causing mutations, the non-hypomyelination-causing mutation TUBB4A-R2G confers gain-of-function for an RNA-independent interaction with TUBA1A. Experimental use of R2G/A mutations restores TUBB4A-TUBA1A heterodimer formation, and rescues the neuronal cell death phenotype caused by TubAR knockdown. Together, we uncover TubAR as the long-elusive structural RNA for microtubule assembly and demonstrate how TubAR mediates microtubule assembly specifically from αβ-tubulin heterodimers, which is crucial for maintenance of cerebellar myelination and activity.
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Affiliation(s)
- Xiaolin Liang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Meng Gong
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Jie Wang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Neuroscience and Brain Diseases, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei, China
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Weiwei Guo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Aoling Cai
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zhenye Yang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China
| | - Fuqiang Xu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wei Xiong
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Chuanhai Fu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Science Center for Physical Sciences at Microscale & University of Science and Technology of China, School of Life Sciences/Division of Biomedical Sciences, Hefei, Anhui, China.
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Cao L, Zhou J, Ma W, Zhang H, Pan H, Xu M, Wang Y, Wang P, Xiang X, Liu Y, Qiu X, Zhou X, Wang X. Identification of lncRNA-based regulatory mechanisms of Takifugu rubripes growth traits in fast and slow-growing family lines. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101164. [PMID: 37976965 DOI: 10.1016/j.cbd.2023.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Family selection is an important method in fish aquaculture because growth is the most important economic trait. Fast-and slow-growing families of tiger puffer fish (Takifugu rubripes) have been established through family selection. The development of teleost fish is primarily controlled by the growth hormone (GH)-insulin-like growth factor 1 (IGF-1) axis that includes the hypothalamus-pituitary-liver. In this study, the molecular mechanisms underlying T. rubripes growth were analyzed by comparing transcriptomes from fast- and slow-growing families. The expressions of 214 lncRNAs were upregulated, and those of 226 were downregulated in the brain tissues of the fast-growing T. rubripes family compared to those of the slow-growing family. Differentially expressed lncRNAs centrally regulate mitogen-activated protein kinase (MAPK) and forkhead box O (FoxO) signaling pathways. Based on the results of lncRNA-gene network construction, we found that lncRNA3133.13, lncRNA23169.1, lncRNA23145.1, and lncRNA23141.3 regulated all four genes (igf1, mdm2, flt3, and cwf19l1). In addition, lncRNA7184.10 may be a negative regulator of rasgrp2 and a positive regulator of gadd45ga, foxo3b, and dusp5. These target genes are associated with the growth and development of organisms through the PI3K/AKT and MAPK/ERK pathways. Overall, transcriptomic analyses of fast- and slow-growing families of T. rubripes provided insights into the molecular mechanisms of teleost fish growth rates. Further, these analyses provide evidence for key genes related to growth regulation and the lncRNA expression regulatory network that will provide a framework for improving puffer fish germplasm resources.
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Affiliation(s)
- Lirong Cao
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Jinxu Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Wenchao Ma
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Huakun Zhang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Hanbai Pan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Mingjie Xu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Yusen Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Peiyang Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xuejian Xiang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Yang Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China
| | - Xiaoxu Zhou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
| | - Xiuli Wang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Pufferfish Breeding and Culture in Liaoning Province, Dalian Ocean University, Dalian 116023, China.
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Huang W, Zhong W, He Q, Xu Y, Lin J, Ding Y, Zhao H, Zheng X, Zheng Y. Time-series expression profiles of mRNAs and lncRNAs during mammalian palatogenesis. Oral Dis 2022. [PMID: 35506257 DOI: 10.1111/odi.14237] [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: 12/14/2021] [Revised: 03/12/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Mammalian palatogenesis is a highly regulated morphogenetic process to form the intact roof of the oral cavity. Long noncoding RNAs (lncRNAs) and mRNAs participate in numerous biological and pathological processes, but their roles in palatal development and causing orofacial clefts (OFC) remain to be clarified. METHODS Palatal tissues were separated from ICR mouse embryos at four stages (E10.5, E13.5, E15, and E17). Then, RNA sequencing (RNA-seq) was used. Various analyses were performed to explore the results. Finally, hub genes were validated via qPCR and in situ hybridization. RESULTS Starting from E10.5, the expression of cell adhesion genes escalated in the following stages. Cilium assembly and ossification genes were both upregulated at E15 compared with E13.5. Besides, the expression of cilium assembly genes was also increased at E17 compared with E15. Expression patterns of three lncRNAs (H19, Malat1, and Miat) and four mRNAs (Cdh1, Irf6, Grhl3, Efnb1) detected in RNA-seq were validated. CONCLUSIONS This study provides a time-series expression landscape of mRNAs and lncRNAs during palatogenesis, which highlights the importance of processes such as cell adhesion and ossification. Our results will facilitate a deeper understanding of the complexity of gene expression and regulation during palatogenesis.
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Affiliation(s)
- Wenbin Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and- 3 -Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
| | - Wenjie Zhong
- The Affiliated Stomatology Hospital, Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
| | - Qing He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Yizhu Xu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jiuxiang Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and- 3 -Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
| | - Yi Ding
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Huaxiang Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China.,Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaowen Zheng
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Disease, Shanghai, China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yunfei Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and- 3 -Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, China
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Chen X, Ren G, Li Y, Chao W, Chen S, Li X, Xue S. Level of LncRNA GAS5 and Hippocampal Volume are Associated with the Progression of Alzheimer’s Disease. Clin Interv Aging 2022; 17:745-753. [PMID: 35592641 PMCID: PMC9112342 DOI: 10.2147/cia.s363116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/29/2022] [Indexed: 01/09/2023] Open
Abstract
Purpose We evaluated the diagnostic value of long non-coding RNA growth arrest-specific transcript 5 (GAS5) and its relationship with hippocampal volume in Alzheimer’s disease (AD). Patients and Methods One hundred and eight patients with AD and 83 healthy controls were included, and demographic data, biochemical parameters, GAS5 levels, and hippocampal volume were recorded. Chi-squared tests or independent sample t-tests were used to compare the baseline characteristics, relative expression of GAS5, and hippocampal volume. Correlations between variables were determined using Spearman’s rank correlation test. Receiver operating characteristic (ROC) curves were generated to compare the diagnostic value of GAS5 and total hippocampal volume in AD. Results The levels of GAS5 were significantly upregulated in patients with AD compared with those in controls and were negatively correlated with MMSE score. There were differences in left hippocampal volume, right hippocampal volume, and total hippocampal volume between the two groups. Total hippocampal volume was positively correlated with MMSE score and negatively correlated with GAS5 expression in patients with AD. The area under the curve (AUC) of for GAS5 expression was 0.831, the sensitivity was 61.1%, and the specificity was 95.2%. The AUC of the combined total hippocampal volume was 0.891, the sensitivity was 74.1%, and the specificity was 92.8%. Conclusion The results suggested that GAS5 may be an excellent indicator of AD progression alone or in combination with hippocampal volume.
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Affiliation(s)
- Xiaopeng Chen
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Department of Neurology, the Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
| | - Guoqiang Ren
- Department of Radiology, the Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
| | - Yan Li
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Department of Neurology, the Taixing People’s Hospital, Taixing, Jiangsu, People’s Republic of China
| | - Wa Chao
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Siyuan Chen
- Department of Neurology, the Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
| | - Xuezhong Li
- Department of Neurology, the Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, People’s Republic of China
| | - Shouru Xue
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Correspondence: Shouru Xue, Department of Neurology, the First Affiliated Hospital of Soochow University, No. 188 Shizi Road, Suzhou, Jiangsu Province, 215006, People’s Republic of China, Tel +86-18962133036, Fax +86-512-65223637, Email
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Zhou H, Gao Y, Li X, Shang S, Wang P, Zhi H, Guo S, Sun D, Liu H, Li X, Zhang Y, Ning S. Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer. J Transl Med 2021; 19:509. [PMID: 34906173 PMCID: PMC8672572 DOI: 10.1186/s12967-021-03179-5] [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: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03179-5.
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Affiliation(s)
- Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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Marí-Beffa M, Mesa-Román AB, Duran I. Zebrafish Models for Human Skeletal Disorders. Front Genet 2021; 12:675331. [PMID: 34490030 PMCID: PMC8418114 DOI: 10.3389/fgene.2021.675331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
In 2019, the Nosology Committee of the International Skeletal Dysplasia Society provided an updated version of the Nosology and Classification of Genetic Skeletal Disorders. This is a reference list of recognized diseases in humans and their causal genes published to help clinician diagnosis and scientific research advances. Complementary to mammalian models, zebrafish has emerged as an interesting species to evaluate chemical treatments against these human skeletal disorders. Due to its versatility and the low cost of experiments, more than 80 models are currently available. In this article, we review the state-of-art of this “aquarium to bedside” approach describing the models according to the list provided by the Nosology Committee. With this, we intend to stimulate research in the appropriate direction to efficiently meet the actual needs of clinicians under the scope of the Nosology Committee.
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Affiliation(s)
- Manuel Marí-Beffa
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain.,Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
| | - Ana B Mesa-Román
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain
| | - Ivan Duran
- Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga, IBIMA, Málaga, Spain.,Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, Málaga, Spain
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Long noncoding RNA PM maintains cerebellar synaptic integrity and Cbln1 activation via Pax6/Mll1-mediated H3K4me3. PLoS Biol 2021; 19:e3001297. [PMID: 34111112 PMCID: PMC8219131 DOI: 10.1371/journal.pbio.3001297] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/22/2021] [Accepted: 05/24/2021] [Indexed: 01/30/2023] Open
Abstract
Recent studies have shown that long noncoding RNAs (lncRNAs) are critical regulators in the central nervous system (CNS). However, their roles in the cerebellum are currently unclear. In this work, we identified the isoform 204 of lncRNA Gm2694 (designated as lncRNA-Promoting Methylation (lncRNA-PM)) is highly expressed in the cerebellum and derived from the antisense strand of the upstream region of Cerebellin-1 (Cbln1), a well-known critical cerebellar synaptic organizer. LncRNA-PM exhibits similar spatiotemporal expression pattern as Cbln1 in the postnatal mouse cerebellum and activates the transcription of Cbln1 through Pax6/Mll1-mediated H3K4me3. In mouse cerebellum, lncRNA-PM, Pax6/Mll1, and H3K4me3 are all associated with the regulatory regions of Cbln1. Knockdown of lncRNA-PM in cerebellum causes deficiencies in Cbln1 expression, cerebellar synaptic integrity, and motor function. Together, our work reveals an lncRNA-mediated transcriptional activation of Cbln1 through Pax6-Mll1-H3K4me3 and provides novel insights of the essential roles of lncRNA in the cerebellum. The long non-coding RNA lncRNA-PM activates transcription of the cerebellar synaptic organizer Cbln1 by promoting Pax6-Mll1-mediated H3K4me3 methylation, thereby helping to maintain cerebellar synaptic integrity and motor function.
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Zhang B, Min S, Guo Q, Huang Y, Guo Y, Liang X, Wu LL, Yu GY, Wang X. 7SK Acts as an Anti-tumor Factor in Tongue Squamous Cell Carcinoma. Front Genet 2021; 12:642969. [PMID: 33868377 PMCID: PMC8047107 DOI: 10.3389/fgene.2021.642969] [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: 12/17/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Increasing evidence has shown the mechanistic insights about non-coding RNA 7SK in controlling the transcription. However, the biological function and mechanism of 7SK in cancer are largely unclear. Here, we show that 7SK is down-regulated in human tongue squamous carcinoma (TSCC) and acts as a TSCC suppressor through multiple cell-based assays including a migration assay and a xenograft mouse model. The expression level of 7SK was negatively correlated with the size of tumors in the 73 in-house collected TSCC patients. Through combined analysis of 7SK knockdown of RNA-Seq and available published 7SK ChIRP-seq data, we identified 27 of 7SK-regulated genes that were involved in tumor regulation and whose upstream regulatory regions were bound by 7SK. Motif analysis showed that the regulatory sequences of these genes were enriched for transcription factors FOXJ3 and THRA, suggesting a potential involvement of FOXJ3 and THRA in 7SK-regulated genes. Interestingly, the augmented level of FOXJ3 in TSCC patients and previous reports on THRA in other cancers have suggested that these two factors may promote TSCC progression. In support of this idea, we found that 21 out of 27 aforementioned 7SK-associated genes were regulated by FOXJ3 and THRA, and 12 of them were oppositely regulated by 7SK and FOXJ3/THRA. We also found that FOXJ3 and THRA dramatically promoted migration in SCC15 cells. Collectively, we identified 7SK as an antitumor factor and suggested a potential involvement of FOXJ3 and THRA in 7SK-mediated TSCC progression.
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Affiliation(s)
- Bowen Zhang
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Sainan Min
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Qi Guo
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Yan Huang
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Yuzhu Guo
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaolin Liang
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Li-Ling Wu
- Department of Physiology and Pathophysiology, Peking University School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Guang-Yan Yu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
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9
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Wang S, Ke S, Wu Y, Zhang D, Liu B, He YH, Liu W, Mu H, Song X. Functional Network of the Long Non-coding RNA Growth Arrest-Specific Transcript 5 and Its Interacting Proteins in Senescence. Front Genet 2021; 12:615340. [PMID: 33777096 PMCID: PMC7987947 DOI: 10.3389/fgene.2021.615340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 02/01/2021] [Indexed: 11/24/2022] Open
Abstract
Increasing studies show that long non-coding RNAs (lncRNAs) play essential roles in various fundamental biological processes. Long non-coding RNA growth arrest-specific transcript 5 (GAS5) showed differential expressions between young and old mouse brains in our previous RNA-Seq data, suggesting its potential role in senescence and brain aging. Examination using quantitative reverse transcription-polymerase chain reaction revealed that GAS5 had a significantly higher expression level in the old mouse brain hippocampus region than the young one. Cellular fractionation using hippocampus-derived HT22 cell line confirmed its nucleoplasm and cytoplasm subcellular localization. Overexpression or knockdown of GAS5 in HT22 cell line revealed that GAS5 inhibits cell cycle progression and promotes cell apoptosis. RNA-Seq analysis of GAS5-knockdown HT22 cells identified differentially expressed genes related to cell proliferation (e.g., DNA replication and nucleosome assembly biological processes). RNA pull-down assay using mouse brain hippocampus tissues showed that potential GAS5 interacting proteins could be enriched into several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and some of them are involved in senescence-associated diseases such as Parkinson’s and Alzheimer’s diseases. These results contribute to understand better the underlying functional network of GAS5 and its interacting proteins in senescence at brain tissue and brain-derived cell line levels. Our study may also provide a reference for developing diagnostic and clinic biomarkers of GAS5 in senescence and brain aging.
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Affiliation(s)
- Siqi Wang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shengwei Ke
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yueming Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Duo Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei, China
| | - Baowei Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yao-Hui He
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, China
| | - Huawei Mu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Brain Function and Disease, Division of Life Sciences and Medicine, School of Life Sciences, University of Science and Technology of China, Hefei, China
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10
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Tan L, Yu M, Li Y, Xue S, Chen J, Zhai Y, Fang X, Liu J, Liu J, Wu X, Xu H, Shen Q. Overexpression of Long Non-coding RNA 4933425B07 Rik Causes Urinary Malformations in Mice. Front Cell Dev Biol 2021; 9:594640. [PMID: 33681192 PMCID: PMC7933199 DOI: 10.3389/fcell.2021.594640] [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: 08/13/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) is a common birth defect and is the leading cause of end-stage renal disease in children. The etiology of CAKUT is complex and includes mainly genetic and environmental factors. However, these factors cannot fully explain the etiological mechanism of CAKUT. Recently, participation of long non-coding RNAs (lncRNAs) in the development of the circulatory and nervous systems was demonstrated; however, the role of lncRNAs in the development of the kidney and urinary tract system is unclear. In this study, we used the piggyBac (PB) transposon-based mutagenesis to construct a mouse with lncRNA 4933425B07Rik (Rik) PB insertion (RikPB/PB) and detected overexpression of Rik and a variety of developmental abnormalities in the urinary system after PB insertion, mainly including renal hypo/dysplasia. The number of ureteric bud (UB) branches in the RikPB/PB embryonic kidney was significantly decreased in embryonic kidney culture. Only bone morphogenetic protein 4 (Bmp4), a key molecule regulating UB branching, is significantly downregulated in RikPB/PB embryonic kidney, while the expression levels of other molecules involved in the regulation of UB branching were not significantly different according to the RNA-sequencing (RNA-seq) data, and the results were verified by quantitative real-time polymerase chain reaction (RT-PCR) and immunofluorescence assays. Besides, the expression of pSmad1/5/8, a downstream molecule of BMP4 signaling, decreased by immunofluorescence. These findings suggest that abnormal expression of Rik may cause a reduction in the UB branches by reducing the expression levels of the UB branching-related molecule Bmp4, thus leading to the development of CAKUT.
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Affiliation(s)
- Lihong Tan
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Minghui Yu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yaxin Li
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Shanshan Xue
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Chen
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yihui Zhai
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaoyan Fang
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jialu Liu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jiaojiao Liu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaohui Wu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
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