1
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de los Angeles Becerra Rodriguez M, Gonzalez Muñoz E, Moore T. Oligodendrocyte-specific expression of PSG8- AS1 suggests a role in myelination with prognostic value in oligodendroglioma. Noncoding RNA Res 2024; 9:1061-1068. [PMID: 39022681 PMCID: PMC11254506 DOI: 10.1016/j.ncrna.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
The segmentally duplicated Pregnancy-specific glycoprotein (PSG) locus on chromosome 19q13 may be one of the most rapidly evolving in the human genome. It comprises ten coding genes (PSG1-9, 11) and one predominantly non-coding gene (PSG10) that are expressed in the placenta and gut, in addition to several poorly characterized long non-coding RNAs. We report that long non-coding RNA PSG8-AS1 has an oligodendrocyte-specific expression pattern and is co-expressed with genes encoding key myelin constituents. PSG8-AS1 exhibits two peaks of expression during human brain development coinciding with the most active periods of oligodendrogenesis and myelination. PSG8-AS1 orthologs were found in the genomes of several primates but significant expression was found only in the human, suggesting a recent evolutionary origin of its proposed role in myelination. Additionally, because co-deletion of chromosomes 1p/19q is a genomic marker of oligodendroglioma, expression of PSG8-AS1 was examined in these tumors. PSG8-AS1 may be a promising diagnostic biomarker for glioma, with prognostic value in oligodendroglioma.
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Affiliation(s)
- Maria de los Angeles Becerra Rodriguez
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Genomics Data Science, University College Cork, Cork, Ireland
| | - Elena Gonzalez Muñoz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA Plataforma BIONAND, 29590, Málaga, Spain
- Universidad de Malaga, Dpto. Biología Celular, Genética y Fisiología, 29071, Málaga, Spain
| | - Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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2
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Sun Y, Liu X, Shan X, Wang Y, Zhong C, Lu C, Guan B, Yao S, Huo Y, Sun R, Wei M, Dong Z. Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis. Gene 2024; 911:148346. [PMID: 38452877 DOI: 10.1016/j.gene.2024.148346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.
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Affiliation(s)
- Yuyan Sun
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xuxiao Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xin Shan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Yiwo Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chongyu Zhong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chaofa Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Bin Guan
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Shun Yao
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Yujia Huo
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Runkai Sun
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Min Wei
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
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3
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Rey F, Esposito L, Maghraby E, Mauri A, Berardo C, Bonaventura E, Tonduti D, Carelli S, Cereda C. Role of epigenetics and alterations in RNA metabolism in leukodystrophies. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1854. [PMID: 38831585 DOI: 10.1002/wrna.1854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 06/05/2024]
Abstract
Leukodystrophies are a class of rare heterogeneous disorders which affect the white matter of the brain, ultimately leading to a disruption in brain development and a damaging effect on cognitive, motor and social-communicative development. These disorders present a great clinical heterogeneity, along with a phenotypic overlap and this could be partially due to contributions from environmental stimuli. It is in this context that there is a great need to investigate what other factors may contribute to both disease insurgence and phenotypical heterogeneity, and novel evidence are raising the attention toward the study of epigenetics and transcription mechanisms that can influence the disease phenotype beyond genetics. Modulation in the epigenetics machinery including histone modifications, DNA methylation and non-coding RNAs dysregulation, could be crucial players in the development of these disorders, and moreover an aberrant RNA maturation process has been linked to leukodystrophies. Here, we provide an overview of these mechanisms hoping to supply a closer step toward the analysis of leukodystrophies not only as genetically determined but also with an added level of complexity where epigenetic dysregulation is of key relevance. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNA RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
- Department of Biology and Biotechnology "L. Spallanzani" (DBB), University of Pavia, Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Eleonora Bonaventura
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Davide Tonduti
- Unit of Pediatric Neurology, COALA Center for Diagnosis and Treatment of Leukodystrophies, V. Buzzi Children's Hospital, Milan, Italy
- Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi," Department of Biomedical and Clinical Sciences, University of Milano, Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, Milan, Italy
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4
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Singh J, Narayan G, Dixit VK. The long intergenic non-coding RNA LINC01140 modulates gastric cancer phenotypes and cancer cell lines aggressiveness. Dig Liver Dis 2024:S1590-8658(24)00307-4. [PMID: 38556409 DOI: 10.1016/j.dld.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Long-intergenic non-protein coding gene 01140 (LINC01140) a long non-coding RNA is highly expressed in various cancers. However, its biological functions in gastric cancer progression is still unknown. METHOD To elucidate LINC01140 function, 70 GC tumor samples and 30 normal gastric tissues were collected. LINC01140 expression level were determined by qRT-PCR analysis and correlated with different clinico-pathological parameters. Then we tried to see the impact of LINC01140 on gastric cell line aggressiveness by knocking down the target gene and performing cell viability assay, migration assay and invasive capacity of the cell lines along with immunoblotting to check several protein levels. RESULT LINC01140 RNA is found to be positively correlated with FGF9 and significantly up regulated in GC tissues. LINC01140 knockdown inhibited the viability, migratory capacity and invasive capacity of AGS cells. LINC01140 targets miR-140-5p, while miR-140-5p targeted FGF9 to form lncRNA-miRNA-mRNA axis. The affect of miR-140-5p inhibition on gastric cancer cell aggressiveness were opposite to those of LINC01140 or FGF9 knockdown. Additionally, inhibition partially reversed the effects of LINC01140 knockdown on FGF9 protein levels, gastric cancer cell phenotypes. CONCLUSION LINC01140, miR-140-5p and FGF9 form a lncRNA-miRNA-mRNA axis that modulates the gastric cancer phenotypes and in turn affects gastric cancer cell aggressiveness.
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Affiliation(s)
- Juhi Singh
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Gopeshwar Narayan
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi, 221005, India
| | - Vinod Kumar Dixit
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India.
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5
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Bai Y, Ren H, Bian L, Zhou Y, Wang X, Xiong Z, Liu Z, Han B, Yao H. Regulation of Glial Function by Noncoding RNA in Central Nervous System Disease. Neurosci Bull 2023; 39:440-452. [PMID: 36161582 PMCID: PMC10043107 DOI: 10.1007/s12264-022-00950-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are a class of functional RNAs that play critical roles in different diseases. NcRNAs include microRNAs, long ncRNAs, and circular RNAs. They are highly expressed in the brain and are involved in the regulation of physiological and pathophysiological processes of central nervous system (CNS) diseases. Mounting evidence indicates that ncRNAs play key roles in CNS diseases. Further elucidating the mechanisms of ncRNA underlying the process of regulating glial function that may lead to the identification of novel therapeutic targets for CNS diseases.
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Affiliation(s)
- Ying Bai
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Hui Ren
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Liang Bian
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - You Zhou
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xinping Wang
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Zhongli Xiong
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Ziqi Liu
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Bing Han
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Honghong Yao
- Department of Pharmacology, Jiangsu Provincial Key Laboratory, School of Medicine, Southeast University, Nanjing, 210009, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210009, China.
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6
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Selcen I, Prentice E, Casaccia P. The epigenetic landscape of oligodendrocyte lineage cells. Ann N Y Acad Sci 2023; 1522:24-41. [PMID: 36740586 PMCID: PMC10085863 DOI: 10.1111/nyas.14959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The epigenetic landscape of oligodendrocyte lineage cells refers to the cell-specific modifications of DNA, chromatin, and RNA that define a unique gene expression pattern of functionally specialized cells. Here, we focus on the epigenetic changes occurring as progenitors differentiate into myelin-forming cells and respond to the local environment. First, modifications of DNA, RNA, nucleosomal histones, key principles of chromatin organization, topologically associating domains, and local remodeling will be reviewed. Then, the relationship between epigenetic modulators and RNA processing will be explored. Finally, the reciprocal relationship between the epigenome as a determinant of the mechanical properties of cell nuclei and the target of mechanotransduction will be discussed. The overall goal is to provide an interpretative key on how epigenetic changes may account for the heterogeneity of the transcriptional profiles identified in this lineage.
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Affiliation(s)
- Ipek Selcen
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA
| | - Emily Prentice
- Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA.,Graduate Program in Biology, The Graduate Center of The City University of New York, New York, New York, USA
| | - Patrizia Casaccia
- Graduate Program in Biochemistry, The Graduate Center of The City University of New York, New York, New York, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center of The City University of New York, New York, New York, USA.,Graduate Program in Biology, The Graduate Center of The City University of New York, New York, New York, USA
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7
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Tan Z, Li W, Cheng X, Zhu Q, Zhang X. Non-Coding RNAs in the Regulation of Hippocampal Neurogenesis and Potential Treatment Targets for Related Disorders. Biomolecules 2022; 13:biom13010018. [PMID: 36671403 PMCID: PMC9855933 DOI: 10.3390/biom13010018] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, circRNAs, and piRNAs, do not encode proteins. Nonetheless, they have critical roles in a variety of cellular activities-such as development, neurogenesis, degeneration, and the response to injury to the nervous system-via protein translation, RNA splicing, gene activation, silencing, modifications, and editing; thus, they may serve as potential targets for disease treatment. The activity of adult neural stem cells (NSCs) in the subgranular zone of the hippocampal dentate gyrus critically influences hippocampal function, including learning, memory, and emotion. ncRNAs have been shown to be involved in the regulation of hippocampal neurogenesis, including proliferation, differentiation, and migration of NSCs and synapse formation. The interaction among ncRNAs is complex and diverse and has become a major topic within the life science. This review outlines advances in research on the roles of ncRNAs in modulating NSC bioactivity in the hippocampus and discusses their potential applications in the treatment of illnesses affecting the hippocampus.
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Affiliation(s)
- Zhengye Tan
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Wen Li
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Xiang Cheng
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qing Zhu
- School of Pharmacy, Nantong University, Nantong 226001, China
- Key Laboratory of Inflammation and Molecular Drug Target of Jiangsu Province, Nantong 226001, China
| | - Xinhua Zhang
- Department of Anatomy, Institute of Neurobiology, Medical School, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
- Central Lab, Yancheng Third People’s Hospital, The Sixth Affiliated Hospital of Nantong University, Yancheng 224001, China
- Correspondence:
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8
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Cell-type-specific epigenetic effects of early life stress on the brain. Transl Psychiatry 2022; 12:326. [PMID: 35948532 PMCID: PMC9365848 DOI: 10.1038/s41398-022-02076-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/08/2023] Open
Abstract
Early life stress (ELS) induces long-term phenotypic adaptations that contribute to increased vulnerability to a host of neuropsychiatric disorders. Epigenetic mechanisms, including DNA methylation, histone modifications and non-coding RNA, are a proposed link between environmental stressors, alterations in gene expression, and phenotypes. Epigenetic modifications play a primary role in shaping functional differences between cell types and can be modified by environmental perturbations, especially in early development. Together with contributions from genetic variation, epigenetic mechanisms orchestrate patterns of gene expression within specific cell types that contribute to phenotypic variation between individuals. To date, many studies have provided insights into epigenetic changes resulting from ELS. However, most of these studies have examined heterogenous brain tissue, despite evidence of cell-type-specific epigenetic modifications in phenotypes associated with ELS. In this review, we focus on rodent and human studies that have examined epigenetic modifications induced by ELS in select cell types isolated from the brain or associated with genes that have cell-type-restricted expression in neurons, microglia, astrocytes, and oligodendrocytes. Although significant challenges remain, future studies using these approaches can enable important mechanistic insight into the role of epigenetic variation in the effects of ELS on brain function.
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9
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Ilieva M, Uchida S. Long Non-Coding RNAs in Cardiac and Pulmonary Fibroblasts and Fibrosis. Noncoding RNA 2022; 8:ncrna8040053. [PMID: 35893236 PMCID: PMC9326574 DOI: 10.3390/ncrna8040053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
The cardiopulmonary system delivers oxygen throughout the body via blood circulation. It is an essential part of the body to sustain the lives of organisms. The integral parts of the cardiopulmonary system—the heart and lungs—are constantly exposed to damaging agents (e.g., dust, viruses), and can be greatly affected by injuries caused by dysfunction in tissues (e.g., myocardial infarction). When damaged, mesenchymal cells, such as fibroblasts, are activated to become myofibroblasts to initiate fibrosis as part of a regenerative mechanism. In diseased states, the excess accumulation of extracellular matrices secreted by myofibroblasts results in further dysfunction in the damaged organs. These fibrotic tissues cannot easily be removed. Thus, there is a growing interest in understanding the fibrotic process, as well as finding biomolecules that can be targets for slowing down or potentially stopping fibrosis. Among these biomolecules, the interest in studying long non-coding RNAs (lncRNAs; any non-protein-coding RNAs longer than 200 nucleotides) has intensified in recent years. In this commentary, we summarize the current status of lncRNA research in the cardiopulmonary system by focusing on cardiac and pulmonary fibrosis.
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10
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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11
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Zhang J, Guan M, Zhou X, Berry K, He X, Lu QR. Long Noncoding RNAs in CNS Myelination and Disease. Neuroscientist 2022; 29:287-301. [PMID: 35373640 DOI: 10.1177/10738584221083919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Myelination by oligodendrocytes is crucial for neuronal survival and function, and defects in myelination or failure in myelin repair can lead to axonal degeneration and various neurological diseases. At present, the factors that promote myelination and overcome the remyelination block in demyelinating diseases are poorly defined. Although the roles of protein-coding genes in oligodendrocyte differentiation have been extensively studied, the majority of the mammalian genome is transcribed into noncoding RNAs, and the functions of these molecules in myelination are poorly characterized. Long noncoding RNAs (lncRNAs) regulate transcription at multiple levels, providing spatiotemporal control and robustness for cell type-specific gene expression and physiological functions. lncRNAs have been shown to regulate neural cell-type specification, differentiation, and maintenance of cell identity, and dysregulation of lncRNA function has been shown to contribute to neurological diseases. In this review, we discuss recent advances in our understanding of the functions of lncRNAs in oligodendrocyte development and myelination as well their roles in neurological diseases and brain tumorigenesis. A more systematic characterization of lncRNA functional networks will be instrumental for a better understanding of CNS myelination, myelin disorders, and myelin repair.
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Affiliation(s)
- Jing Zhang
- Laboratory of Nervous System Injuries and Diseases, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children at Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Menglong Guan
- Laboratory of Nervous System Injuries and Diseases, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children at Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xianyao Zhou
- Laboratory of Nervous System Injuries and Diseases, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children at Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Kalen Berry
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xuelian He
- Laboratory of Nervous System Injuries and Diseases, Center for Translational Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children at Sichuan University, Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Q Richard Lu
- Department of Pediatrics, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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12
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Wu X, Wei H, Wu JQ. Coding and long non-coding gene expression changes in the CNS traumatic injuries. Cell Mol Life Sci 2022; 79:123. [PMID: 35129669 PMCID: PMC8907010 DOI: 10.1007/s00018-021-04092-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 02/06/2023]
Abstract
Traumatic brain injury (TBI) and spinal cord injury (SCI) are two main central nervous system (CNS) traumas, caused by external physical insults. Both injuries have devastating effects on the quality of life, and there is no effective therapy at present. Notably, gene expression profiling using bulk RNA sequencing (RNA-Seq) and single-cell RNA-Seq (scRNA-Seq) have revealed significant changes in many coding and non-coding genes, as well as important pathways in SCI and TBI. Particularly, recent studies have revealed that long non-coding RNAs (lncRNAs) with lengths greater than 200 nucleotides and without protein-coding potential have tissue- and cell type-specific expression pattern and play critical roles in CNS injury by gain- and loss-of-function approaches. LncRNAs have been shown to regulate protein-coding genes or microRNAs (miRNAs) directly or indirectly, participating in processes including inflammation, glial activation, cell apoptosis, and vasculature events. Therefore, lncRNAs could serve as potential targets for the diagnosis, treatment, and prognosis of SCI and TBI. In this review, we highlight the recent progress in transcriptome studies of SCI and TBI and insights into molecular mechanisms.
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Affiliation(s)
- Xizi Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, 77030, USA.
- MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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13
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Senís E, Esgleas M, Najas S, Jiménez-Sábado V, Bertani C, Giménez-Alejandre M, Escriche A, Ruiz-Orera J, Hergueta-Redondo M, Jiménez M, Giralt A, Nuciforo P, Albà MM, Peinado H, Del Toro D, Hove-Madsen L, Götz M, Abad M. TUNAR lncRNA Encodes a Microprotein that Regulates Neural Differentiation and Neurite Formation by Modulating Calcium Dynamics. Front Cell Dev Biol 2022; 9:747667. [PMID: 35036403 PMCID: PMC8758570 DOI: 10.3389/fcell.2021.747667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are regulatory molecules which have been traditionally considered as “non-coding”. Strikingly, recent evidence has demonstrated that many non-coding regions, including lncRNAs, do in fact contain small-open reading frames that code for small proteins that have been called microproteins. Only a few of them have been characterized so far, but they display key functions in a wide variety of cellular processes. Here, we show that TUNAR lncRNA encodes an evolutionarily conserved microprotein expressed in the nervous system that we have named pTUNAR. pTUNAR deficiency in mouse embryonic stem cells improves their differentiation potential towards neural lineage both in vitro and in vivo. Conversely, pTUNAR overexpression impairs neuronal differentiation by reduced neurite formation in different model systems. At the subcellular level, pTUNAR is a transmembrane protein that localizes in the endoplasmic reticulum and interacts with the calcium transporter SERCA2. pTUNAR overexpression reduces cytoplasmatic calcium, consistent with a possible role of pTUNAR as an activator of SERCA2. Altogether, our results suggest that our newly discovered microprotein has an important role in neural differentiation and neurite formation through the regulation of intracellular calcium. From a more general point of view, our results provide a proof of concept of the role of lncRNAs-encoded microproteins in neural differentiation.
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Affiliation(s)
- Elena Senís
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Miriam Esgleas
- Physiological Genomics, Biomedical Center (BMC), Helmholtz Center Munich, Institute of Stem Cell Research, Großhaderner Str, SyNergy Excellence Cluster, Ludwig-Maximilians-Universitaet (LMU), Munich, Germany
| | - Sonia Najas
- Physiological Genomics, Biomedical Center (BMC), Helmholtz Center Munich, Institute of Stem Cell Research, Großhaderner Str, SyNergy Excellence Cluster, Ludwig-Maximilians-Universitaet (LMU), Munich, Germany
| | - Verónica Jiménez-Sábado
- Instituto de Investigación Biomédica Barcelona (IIBB-CSIC), Instituto de Investigación Biomédica Sant Pau (IIB-Sant Pau) and CIBERCV, Barcelona, Spain
| | - Camilla Bertani
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Giménez-Alejandre
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Alba Escriche
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marta Hergueta-Redondo
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Mireia Jiménez
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Albert Giralt
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Paolo Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Héctor Peinado
- Microenvironment and Metastasis Laboratory, Molecular Oncology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Daniel Del Toro
- Department of Biological Sciences, Institute of Neurosciences, IDIBAPS, CIBERNED, University of Barcelona, Barcelona, Spain
| | - Leif Hove-Madsen
- Instituto de Investigación Biomédica Barcelona (IIBB-CSIC), Instituto de Investigación Biomédica Sant Pau (IIB-Sant Pau) and CIBERCV, Barcelona, Spain
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center (BMC), Helmholtz Center Munich, Institute of Stem Cell Research, Großhaderner Str, SyNergy Excellence Cluster, Ludwig-Maximilians-Universitaet (LMU), Munich, Germany
| | - María Abad
- Cellular Plasticity and Cancer Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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14
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Mustafin RN. Relationship of Peptides and Long Non-Coding RNAs with Aging. ADVANCES IN GERONTOLOGY 2021. [DOI: 10.1134/s2079057021040081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Zhou Y, Yu F. Emerging roles of long non-coding RNAs in spinal cord injury. J Orthop Surg (Hong Kong) 2021; 29:23094990211030698. [PMID: 34323142 DOI: 10.1177/23094990211030698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Spinal cord injury (SCI) is the most serious complication of spinal injury and often leads to severe dysfunction of the limb below the injured segment. SCI causes not only serious physical and psychological harm to the patients, but imposes an enormous economic burden on the whole society. Great efforts have been made to improve the functional outcomes of patients with SCI; however, therapeutic advances have far been limited. Long non-coding RNA (lncRNA) is an important regulator of gene expression and has recently been characterized as a key regulator of central nervous system stabilization. Emerging evidence suggested that lncRNAs are significantly dysregulated and play a key role in the development of SCI. Our review summarizes current researches regarding the roles of deregulated lncRNAs in modulating apoptosis, inflammatory response, neuronal behavior in SCI. These studies suggest that specific regulation of lncRNA or its downstream targets may provide a new therapeutic approach for this desperate disease.
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Affiliation(s)
- Yiguang Zhou
- Queen Mary College of Nanchang University, Nanchang, People's Republic of China
| | - Feng Yu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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16
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Wu J, Yu H, Huang H, Shu P, Peng X. Functions of noncoding RNAs in glial development. Dev Neurobiol 2021; 81:877-891. [PMID: 34402590 DOI: 10.1002/dneu.22848] [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: 06/28/2021] [Revised: 08/01/2021] [Accepted: 08/15/2021] [Indexed: 12/27/2022]
Abstract
Glia are widely distributed in the central nervous system and are closely related to cell metabolism, signal transduction, support, cell migration, and other nervous system development processes and functions. Glial development is complex and essential, including the processes of proliferation, differentiation, and migration, and requires precise regulatory networks. Noncoding RNAs (ncRNAs) can be deeply involved in glial development through gene regulation. Here, we review the regulatory roles of ncRNAs in glial development. We briefly describe the classification and functions of noncoding RNAs and focus on microRNAs (miRNAs) and long ncRNAs (lncRNAs), which have been reported to participate extensively during glial formation. The highlight of this summary is that miRNAs and lncRNAs can participate in and regulate the signaling pathways of glial development. The review not only describes how noncoding RNAs participate in nervous system development but also explains the processes of glial development, providing a foundation for subsequent studies on glial development and new insights into the pathogeneses of related neurological diseases.
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Affiliation(s)
- Jiarui Wu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Haoyang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Hao Huang
- Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Pengcheng Shu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Chinese Institute for Brain Research, Beijing, China
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.,Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China
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17
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Wei H, Dong X, You Y, Hai B, Duran RCD, Wu X, Kharas N, Wu JQ. OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation. BMC Biol 2021; 19:132. [PMID: 34172044 PMCID: PMC8235854 DOI: 10.1186/s12915-021-01057-6] [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: 12/29/2019] [Accepted: 05/27/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Oligodendrocytes, responsible for axon ensheathment, are critical for central nervous system (CNS) development, function, and diseases. OLIG2 is an important transcription factor (TF) that acts during oligodendrocyte development and performs distinct functions at different stages. Previous studies have shown that lncRNAs (long non-coding RNAs; > 200 bp) have important functions during oligodendrocyte development, but their roles have not been systematically characterized and their regulation is not yet clear. RESULTS We performed an integrated study of genome-wide OLIG2 binding and the epigenetic modification status of both coding and non-coding genes during three stages of oligodendrocyte differentiation in vivo: neural stem cells (NSCs), oligodendrocyte progenitor cells (OPCs), and newly formed oligodendrocytes (NFOs). We found that 613 lncRNAs have OLIG2 binding sites and are expressed in at least one cell type, which can potentially be activated or repressed by OLIG2. Forty-eight of them have increased expression in oligodendrocyte lineage cells. Predicting lncRNA functions by using a "guilt-by-association" approach revealed that the functions of these 48 lncRNAs were enriched in "oligodendrocyte development and differentiation." Additionally, bivalent genes are known to play essential roles during embryonic stem cell differentiation. We identified bivalent genes in NSCs, OPCs, and NFOs and found that some bivalent genes bound by OLIG2 are dynamically regulated during oligodendrocyte development. Importantly, we unveiled a previously unknown mechanism that, in addition to transcriptional regulation via DNA binding, OLIG2 could self-regulate through the 3' UTR of its own mRNA. CONCLUSIONS Our studies have revealed the missing links in the mechanisms regulating oligodendrocyte development at the transcriptional level and after transcription. The results of our research have improved the understanding of fundamental cell fate decisions during oligodendrocyte lineage formation, which can enable insights into demyelination diseases and regenerative medicine.
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Affiliation(s)
- Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Xiaomin Dong
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Yanan You
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Bo Hai
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, N.L., Mexico
| | - Xizi Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | - Natasha Kharas
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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18
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Mishra P, Kumar S. Association of lncRNA with regulatory molecular factors in brain and their role in the pathophysiology of schizophrenia. Metab Brain Dis 2021; 36:849-858. [PMID: 33608830 DOI: 10.1007/s11011-021-00692-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023]
Abstract
Schizophrenia is one of the most agonizing neurodegenerative diseases of the brain. Research undertaken to understand the molecular mechanism of this disease has undergone a transition and currently more emphasis is put on long noncoding RNA (lncRNA). High expression level of lncRNA in the brain contributes to several molecular pathways essential for the proper functioning of neurons, neurotransmitters, and synapses, that are often found dysfunctional in Schizophrenia. Recently, the association of lncRNA with various molecular factors in the brain has been explored to a considerably large extent. This review comprehends the significance of lncRNA in causing profound regulatory effect in the brain and how any alterations to the association of lncRNA with regulatory proteins, enzymes and other noncoding RNA could contribute to the aetiology of Schizophrenia.
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Affiliation(s)
- Parinita Mishra
- Life Science Department, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- Life Science Department, National Institute of Technology, Rourkela, Odisha, 769008, India.
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19
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Zhou H, Shi P, Jia X, Xue Q. Long non-coding RNA LINC01018 inhibits the progression of acute myeloid leukemia by targeting miR-499a-5p to regulate PDCD4. Oncol Lett 2021; 22:541. [PMID: 34079594 PMCID: PMC8157334 DOI: 10.3892/ol.2021.12802] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous disease with a very high mortality rate. In recent years, an increasing number of studies have proven that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) may serve as useful biomarkers in various cancer types. However, the mechanism of LINC01018 and miR-499a-5p in AML requires further investigation. The mRNA expression of LINC01018, miR-499a-5p and PDCD4 in AML tissues and cells was detected using reverse transcription-quantitative polymerase chain reaction. Cell proliferation was measured using Cell Counting kit-8 and EdU assays. Cell apoptosis was monitored via a TUNEL staining assay. Protein expression of PDCD4, Bax and Bcl-2 was measured using western blot analysis. The interaction between PDCD4 and LINC01018 or miR-499a-5p was verified by RNA pull-down, RIP and dual-luciferase reporter assays. LINC01018 and PDCD4 were downregulated in AML, while miR-499a-5p was upregulated. LINC01018-overexpression suppressed AML cell proliferation and induced AML cell apoptosis, while miR-499a-5p transfection reversed these effects. LINC01018 acted as a sponge of miR-499a-5p, and PDCD4 was demonstrated to be targeted by miR-499a-5p. Knockdown of miR-499a-5p suppressed AML cell proliferation and promoted AML cell apoptosis, but silencing PDCD4 abolished this effect. LINC01018 inhibited AML cell growth by modulating PDCD4 through suppression of miR-499a-5p, providing a feasible theoretical basis for the treatment of AML.
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Affiliation(s)
- Hong Zhou
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Pengfei Shi
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaofeng Jia
- College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, P.R. China
| | - Qianfu Xue
- Department of Hematology, Yong Chuan Hospital of Chongqing Medical University, Chongqing 402160, P.R. China
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20
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Chen L, He M, Zhang M, Sun Q, Zeng S, Zhao H, Yang H, Liu M, Ren S, Meng X, Xu H. The Role of non-coding RNAs in colorectal cancer, with a focus on its autophagy. Pharmacol Ther 2021; 226:107868. [PMID: 33901505 DOI: 10.1016/j.pharmthera.2021.107868] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of malignant afflictions burdening people worldwide, mainly caused by shortages of effective medical intervention and poorly mechanistic understanding of the pathogenesis of CRC. Non-coding RNAs (ncRNAs) are a type of heterogeneous transcripts without the capability of coding protein, but have the potency of regulating protein-coding gene expression. Autophagy is an evolutionarily conserved catabolic process in which cytoplasmic contents are delivered to cellular lysosomes for degradation, resulting in the turnover of cellular components and producing energy for cell functions. A growing body of evidence reveals that ncRNAs, autophagy, and the crosstalks of ncRNAs and autophagy play intricate roles in the initiation, progression, metastasis, recurrence and therapeutic resistance of CRC, which confer ncRNAs and autophagy to serve as clinical biomarkers and therapeutic targets for CRC. In this review, we sought to delineate the complicated roles of ncRNAs, mainly including miRNAs, lncRNAs and circRNAs, in the pathogenesis of CRC, particularly focus on the regulatory role of ncRNAs in CRC-related autophagy, attempting to shed light on the complex pathological mechanisms, involving ncRNAs and autophagy, responsible for CRC tumorigenesis and development, so as to underpin the ncRNAs- and autophagy-based therapeutic strategies for CRC in clinical setting.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Man He
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Meng Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Qiang Sun
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Sha Zeng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hui Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Han Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Maolun Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shan Ren
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianli Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Haibo Xu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Department of Pharmacology, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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21
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Wei H, Wu X, You Y, Duran RCD, Zheng Y, Narayanan KL, Hai B, Li X, Tallapragada N, Prajapati TJ, Kim DH, Deneen B, Cao QL, Wu JQ. Systematic analysis of purified astrocytes after SCI unveils Zeb2os function during astrogliosis. Cell Rep 2021; 34:108721. [PMID: 33535036 PMCID: PMC7920574 DOI: 10.1016/j.celrep.2021.108721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/24/2020] [Accepted: 01/12/2021] [Indexed: 10/27/2022] Open
Abstract
Spinal cord injury (SCI) is one of the most devastating neural injuries without effective therapeutic solutions. Astrocytes are the predominant component of the scar. Understanding the complex contributions of reactive astrocytes to SCI pathophysiologies is fundamentally important for developing therapeutic strategies. We have studied the molecular changes in the injury environment and the astrocyte-specific responses by astrocyte purification from injured spinal cords from acute to chronic stages. In addition to protein-coding genes, we have systematically analyzed the expression profiles of long non-coding RNAs (lncRNAs) (>200 bp), which are regulatory RNAs that play important roles in the CNS. We have identified a highly conserved lncRNA, Zeb2os, and demonstrated using functional assays that it plays an important role in reactive astrogliosis through the Zeb2os/Zeb2/Stat3 axis. These studies provide valuable insights into the molecular basis of reactive astrogliosis and fill the knowledge gap regarding the function(s) of lncRNAs in astrogliosis and SCI.
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Affiliation(s)
- Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Xizi Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Yanan You
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, N.L. 64710, Mexico
| | - Yiyan Zheng
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - K Lakshmi Narayanan
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Bo Hai
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Xu Li
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | | | | | - Dong H Kim
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qi-Lin Cao
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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22
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Pruvost M, Moyon S. Oligodendroglial Epigenetics, from Lineage Specification to Activity-Dependent Myelination. Life (Basel) 2021; 11:62. [PMID: 33467699 PMCID: PMC7830029 DOI: 10.3390/life11010062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/08/2021] [Accepted: 01/10/2021] [Indexed: 12/25/2022] Open
Abstract
Oligodendroglial cells are the myelinating cells of the central nervous system. While myelination is crucial to axonal activity and conduction, oligodendrocyte progenitor cells and oligodendrocytes have also been shown to be essential for neuronal support and metabolism. Thus, a tight regulation of oligodendroglial cell specification, proliferation, and myelination is required for correct neuronal connectivity and function. Here, we review the role of epigenetic modifications in oligodendroglial lineage cells. First, we briefly describe the epigenetic modalities of gene regulation, which are known to have a role in oligodendroglial cells. We then address how epigenetic enzymes and/or marks have been associated with oligodendrocyte progenitor specification, survival and proliferation, differentiation, and finally, myelination. We finally mention how environmental cues, in particular, neuronal signals, are translated into epigenetic modifications, which can directly influence oligodendroglial biology.
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Affiliation(s)
| | - Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, CUNY, 85 St Nicholas Terrace, New York, NY 10031, USA;
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23
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Saba LM, Hoffman PL, Homanics GE, Mahaffey S, Daulatabad SV, Janga SC, Tabakoff B. A long non-coding RNA (Lrap) modulates brain gene expression and levels of alcohol consumption in rats. GENES BRAIN AND BEHAVIOR 2020; 20:e12698. [PMID: 32893479 PMCID: PMC7900948 DOI: 10.1111/gbb.12698] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 12/14/2022]
Abstract
LncRNAs are important regulators of quantitative and qualitative features of the transcriptome. We have used QTL and other statistical analyses to identify a gene coexpression module associated with alcohol consumption. The "hub gene" of this module, Lrap (Long non-coding RNA for alcohol preference), was an unannotated transcript resembling a lncRNA. We used partial correlation analyses to establish that Lrap is a major contributor to the integrity of the coexpression module. Using CRISPR/Cas9 technology, we disrupted an exon of Lrap in Wistar rats. Measures of alcohol consumption in wild type, heterozygous and knockout rats showed that disruption of Lrap produced increases in alcohol consumption/alcohol preference. The disruption of Lrap also produced changes in expression of over 700 other transcripts. Furthermore, it became apparent that Lrap may have a function in alternative splicing of the affected transcripts. The GO category of "Response to Ethanol" emerged as one of the top candidates in an enrichment analysis of the differentially expressed transcripts. We validate the role of Lrap as a mediator of alcohol consumption by rats, and also implicate Lrap as a modifier of the expression and splicing of a large number of brain transcripts. A defined subset of these transcripts significantly impacts alcohol consumption by rats (and possibly humans). Our work shows the pleiotropic nature of non-coding elements of the genome, the power of network analysis in identifying the critical elements influencing phenotypes, and the fact that not all changes produced by genetic editing are critical for the concomitant changes in phenotype.
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Affiliation(s)
- Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Paula L Hoffman
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Gregg E Homanics
- Departments of Anesthesiology, Neurobiology and Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Swapna Vidhur Daulatabad
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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24
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Fan B, Pan W, Wang X, Wei M, He A, Zhao A, Chopp M, Zhang ZG, Liu XS. Long noncoding RNA mediates stroke-induced neurogenesis. Stem Cells 2020; 38:973-985. [PMID: 32346940 PMCID: PMC11062764 DOI: 10.1002/stem.3189] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 03/18/2020] [Accepted: 04/01/2020] [Indexed: 01/11/2023]
Abstract
Neurogenesis contributes to poststroke recovery. Long noncoding RNAs (lncRNAs) participate in the regulation of stem cell self-renewal and differentiation. However, the role of lncRNAs in stroke-induced neurogenesis remains unknown. In this study, we found that H19 was the most highly upregulated lncRNA in neural stem cells (NSCs) of the subventricular zone (SVZ) of rats subjected to focal cerebral ischemia. Deletion of H19 suppressed cell proliferation, promoted cell death, and blocked NSC differentiation. RNA sequencing analysis revealed that genes deregulated by H19 knockdown were those that are involved in transcription, apoptosis, proliferation, cell cycle, and response to hypoxia. H19 knockdown significantly increased the transcription of cell cycle-related genes including p27, whereas overexpression of H19 substantially reduced expression of these genes through the interaction with chromatin remodeling proteins EZH2 and SUZ12. Moreover, H19 regulated neurogenesis-related miRNAs. Inactivation of H19 in NSCs of ischemic rats attenuated spontaneous functional recovery after stroke. Collectively, our data provide novel insights into the epigenetic regulation of lncRNAs in stroke-induced neurogenesis.
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Affiliation(s)
- Baoyan Fan
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Wanlong Pan
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Xinli Wang
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Min Wei
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Annie He
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Anna Zhao
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Michael Chopp
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
- Department of Physics, Oakland University, Rochester, Michigan
| | - Zheng Gang Zhang
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
| | - Xian Shuang Liu
- Department of Neurology, Henry Ford Health System, Detroit, Michigan
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25
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Xu YJ, Liu PP, Ng SC, Teng ZQ, Liu CM. Regulatory networks between Polycomb complexes and non-coding RNAs in the central nervous system. J Mol Cell Biol 2020; 12:327-336. [PMID: 31291646 PMCID: PMC7288736 DOI: 10.1093/jmcb/mjz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/26/2019] [Accepted: 06/11/2019] [Indexed: 01/29/2023] Open
Abstract
High-throughput sequencing has facilitated the identification of many types of non-coding RNAs (ncRNAs) involved in diverse cellular processes. NcRNAs as epigenetic mediators play key roles in neuronal development, maintenance, and dysfunction by controlling gene expression at multiple levels. NcRNAs may not only target specific DNA or RNA for gene silence but may also directly interact with chromatin-modifying proteins like Polycomb group (PcG) proteins to drive orchestrated transcriptional programs. Recent significant progress has been made in characterizing ncRNAs and PcG proteins involved in transcriptional, post-transcriptional, and epigenetic regulation. More importantly, dysregulation of ncRNAs, PcG proteins, and interplay among them is closely associated with the pathogenesis of central nervous system (CNS) disorders. In this review, we focus on the interplay between ncRNAs and PcG proteins in the CNS and highlight the functional roles of the partnership during neural development and diseases.
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Affiliation(s)
- Ya-Jie Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shyh-Chang Ng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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26
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Zhao Y, Liu H, Zhang Q, Zhang Y. The functions of long non-coding RNAs in neural stem cell proliferation and differentiation. Cell Biosci 2020; 10:74. [PMID: 32514332 PMCID: PMC7260844 DOI: 10.1186/s13578-020-00435-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/23/2020] [Indexed: 02/06/2023] Open
Abstract
The capacities for neural stem cells (NSCs) self-renewal with differentiation are need to be precisely regulated for ensuring brain development and homeostasis. Recently, increasing number of studies have highlighted that long non-coding RNAs (lncRNAs) are associated with NSC fate determination during brain development stages. LncRNAs are a class of non-coding RNAs more than 200 nucleotides without protein-coding potential and function as novel critical regulators in multiple biological processes. However, the correlation between lncRNAs and NSC fate decision still need to be explored in-depth. In this review, we will summarize the roles and molecular mechanisms of lncRNAs focusing on NSCs self-renewal, neurogenesis and gliogenesis over the course of neural development, still more, dysregulation of lncRNAs in all stage of neural development have closely relationship with development disorders or glioma. In brief, lncRNAs may be explored as effective modulators in NSCs related neural development and novel biomarkers for diagnosis and prognosis of neurological disorders in the future.
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Affiliation(s)
- Yanfang Zhao
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Hongliang Liu
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Qili Zhang
- Institute of Biomedical Research, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Zibo Key Laboratory of New Drug Development of Neurodegenerative Diseases, School for Life Science, Shandong University of Technology, Zibo, China
| | - Yuan Zhang
- Institute for Translational Medicine, Qingdao University, Qingdao, China
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27
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Kukharsky MS, Ninkina NN, An H, Telezhkin V, Wei W, Meritens CRD, Cooper-Knock J, Nakagawa S, Hirose T, Buchman VL, Shelkovnikova TA. Long non-coding RNA Neat1 regulates adaptive behavioural response to stress in mice. Transl Psychiatry 2020; 10:171. [PMID: 32467583 PMCID: PMC7256041 DOI: 10.1038/s41398-020-0854-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/10/2020] [Accepted: 05/18/2020] [Indexed: 12/18/2022] Open
Abstract
NEAT1 is a highly and ubiquitously expressed long non-coding RNA (lncRNA) which serves as an important regulator of cellular stress response. However, the physiological role of NEAT1 in the central nervous system (CNS) is still poorly understood. In the current study, we addressed this by characterising the CNS function of the Neat1 knockout mouse model (Neat1-/- mice), using a combination of behavioural phenotyping, electrophysiology and expression analysis. RNAscope® in situ hybridisation revealed that in wild-type mice, Neat1 is expressed across the CNS regions, with high expression in glial cells and low expression in neurons. Loss of Neat1 in mice results in an inadequate reaction to physiological stress manifested as hyperlocomotion and panic escape response. In addition, Neat1-/- mice display deficits in social interaction and rhythmic patterns of activity but retain normal motor function and memory. Neat1-/- mice do not present with neuronal loss, overt neuroinflammation or gross synaptic dysfunction in the brain. However, cultured Neat1-/- neurons are characterised by hyperexcitability and dysregulated calcium homoeostasis, and stress-induced neuronal activity is also augmented in Neat1-/- mice in vivo. Gene expression analysis showed that Neat1 may act as a weak positive regulator of multiple genes in the brain. Furthermore, loss of Neat1 affects alternative splicing of genes important for the CNS function and implicated in neurological diseases. Overall, our data suggest that Neat1 is involved in stress signalling in the brain and fine-tunes the CNS functions to enable adaptive behaviour in response to physiological stress.
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Affiliation(s)
- Michail S Kukharsky
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Institute of Physiologically Active Compounds of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Natalia N Ninkina
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Institute of Physiologically Active Compounds of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Haiyan An
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Vsevolod Telezhkin
- School of Dental Sciences, Newcastle University, Newcastle upon Tyne, NE2 4BW, UK
| | - Wenbin Wei
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | | | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Tetsuro Hirose
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Vladimir L Buchman
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
- Institute of Physiologically Active Compounds of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Tatyana A Shelkovnikova
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK.
- Institute of Physiologically Active Compounds of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation.
- Medicines Discovery Institute, Cardiff University, Cardiff, CF10 3AT, UK.
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28
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Verheijen BM. Expression Profile of Long Non-Coding RNAs during Early Postnatal Development of Mouse Spinal Cord. Noncoding RNA 2020; 6:ncrna6020018. [PMID: 32443580 DOI: 10.3390/ncrna6020018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 01/03/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that are >200 nucleotides long and lack significant protein-coding potential. LncRNAs are emerging as major regulators of gene expression networks in various physiological and pathological processes. Interestingly, many lncRNAs show tissue-specific expression, for example, in the nervous system. Although lncRNAs have been suggested to play key roles in the brain, most functions of neural lncRNAs remain poorly understood. In order to provide a catalog of lncRNA changes that occur in spinal cord during early postnatal development, RNA from mouse spinal cord was sequenced at different time points in the first week after birth (postnatal day 1 and postnatal day 7). Two hundred and ninty-six differentially expressed lncRNAs (FDR < 0.05) were identified in the resulting dataset. Altered transcripts were associated with several biological processes including myelination, neural differentiation, and glial cell development. PCR validation confirmed differential expression of select lncRNAs (i.e., Cerox1, lncOL3, Neat1, and Sox2ot). Additionally, analysis of circular RNAs (circRNAs), another class of non-coding RNA with regulatory potency, pointed out a number of circRNAs associated with spinal cord development. These data can be used as a resource for future studies on transcriptional changes during early postnatal nervous system development and studies of disorders that affect the spinal cord, e.g., spinal muscular atrophy.
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Affiliation(s)
- Bert M Verheijen
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
- Laboratory for Experimental Neurology, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
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29
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Samudyata, Castelo-Branco G, Liu J. Epigenetic regulation of oligodendrocyte differentiation: From development to demyelinating disorders. Glia 2020; 68:1619-1630. [PMID: 32154951 DOI: 10.1002/glia.23820] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/19/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022]
Abstract
The maintenance of progenitor states or the differentiation of progenitors into specific lineages requires epigenetic remodeling of the gene expression program. In the central nervous system, oligodendrocyte progenitors (OPCs) give rise to oligodendrocytes (OLs), whose main function has been thought to be to produce myelin, a lipid-rich structure insulating the axons. However, recent findings suggest diverse OL transcriptional states, which might imply additional functions. The differentiation of OPCs into postmitotic OLs is a highly regulated and sensitive process and requires temporal waves of gene expression through epigenetic remodeling of the genome. In this review, we will discuss recent advances in understanding the events shaping the chromatin landscape through histone modifications and long noncoding RNAs during OPC differentiation, in physiological and pathological conditions. We suggest that epigenetic regulation plays a fundamental role in governing the accessibility of transcriptional machinery to DNA sequences, which ultimately determines functional outcomes in OLs.
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Affiliation(s)
- Samudyata
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Jia Liu
- Advanced Science Research Center at the Graduate Center, Neuroscience Initiative, City University of New York, New York, New York, USA
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30
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Berry K, Wang J, Lu QR. Epigenetic regulation of oligodendrocyte myelination in developmental disorders and neurodegenerative diseases. F1000Res 2020; 9:F1000 Faculty Rev-105. [PMID: 32089836 PMCID: PMC7014579 DOI: 10.12688/f1000research.20904.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Oligodendrocytes are the critical cell types giving rise to the myelin nerve sheath enabling efficient nerve transmission in the central nervous system (CNS). Oligodendrocyte precursor cells differentiate into mature oligodendrocytes and are maintained throughout life. Deficits in the generation, proliferation, or differentiation of these cells or their maintenance have been linked to neurological disorders ranging from developmental disorders to neurodegenerative diseases and limit repair after CNS injury. Understanding the regulation of these processes is critical for achieving proper myelination during development, preventing disease, or recovering from injury. Many of the key factors underlying these processes are epigenetic regulators that enable the fine tuning or reprogramming of gene expression during development and regeneration in response to changes in the local microenvironment. These include chromatin remodelers, histone-modifying enzymes, covalent modifiers of DNA methylation, and RNA modification-mediated mechanisms. In this review, we will discuss the key components in each of these classes which are responsible for generating and maintaining oligodendrocyte myelination as well as potential targeted approaches to stimulate the regenerative program in developmental disorders and neurodegenerative diseases.
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Affiliation(s)
- Kalen Berry
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jiajia Wang
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Q. Richard Lu
- Department of Pediatrics, Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
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31
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Hezroni H, Perry RBT, Ulitsky I. Long Noncoding RNAs in Development and Regeneration of the Neural Lineage. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:165-177. [PMID: 31900326 DOI: 10.1101/sqb.2019.84.039347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are gathering increasing attention toward their roles in different biological systems. In mammals, the richest repertoires of lncRNAs are expressed in the brain and in the testis, and the diversity of lncRNAs in the nervous system is thought to be related to the diversity and the complexity of its cell types. Supporting this notion, many lncRNAs are differentially expressed between different regions of the brain or in particular cell types, and many lncRNAs are dynamically expressed during embryonic or postnatal neurogenesis. Less is known about the functions of these genes, if any, but they are increasingly implicated in diverse processes in health and disease. Here, we review the current knowledge about the roles and importance of lncRNAs in the central and peripheral nervous systems and discuss the specific niches within gene regulatory networks that might be preferentially occupied by lncRNAs.
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Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Liu X, Chen R, Liu L. SP1-DLEU1-miR-4429 feedback loop promotes cell proliferative and anti-apoptotic abilities in human glioblastoma. Biosci Rep 2019; 39:BSR20190994. [PMID: 31713587 PMCID: PMC6900472 DOI: 10.1042/bsr20190994] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Mounting studies have revealed that long non-coding RNA (lncRNA) deleted in lymphocytic leukemia 1 (DLEU1) positively regulated the initiation and development of various human malignant tumors. Nevertheless, the function and mechanism of DLEU1 in human glioblastoma multiforme (GBM) remain elusive and ill-defined. The current study was designed to highlight the functional role and disclose the underlying molecular mechanism by which DLEU1 regulated GBM development. We found that DLEU1 was up-regulated in GBM and DLEU1 knockdown significantly inhibited GBM cell proliferation and induced apoptosis. As predicted by bioinformatics analysis and validated in mechanistic assays, SP1 could bind to the promoter region of DLEU1 to activate DLEU1 transcription. Additionally, miR-4429 was verified as a target gene of DLEU1 and negatively modulated by DLEU1. More importantly, miR-4429 overexpression repressed the mRNA and protein levels of SP1 via binding to the 3'UTR of SP1. Overexpression of SP1 or miR-4429 inhibitor could partly abolish the effect of DLEU1 knockdown on cell viability and apoptosis in GBM. Accordingly, our experimental data revealed that SP1-DLEU1-miR-4429 formed a feedback loop to promote GBM development, providing a new evidence for the role of DLEU1 in GBM.
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Affiliation(s)
- Xiaolei Liu
- Department of Neurosurgery, Xianyang Hospital of Yan’an University, Xianyang City, Shaanxi Province 712000, P.R. China
| | - Ruwei Chen
- Department of Neurosurgery, Binzhou People’s Hospital, Shandong Province 256610, P.R. China
| | - Lijun Liu
- Department of Neurosurgery, Xiangyang No. 1 People’s Hospital Affiliated to Hubei University of Medicine, Xiangyang 441000, Hubei, P.R. China
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33
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Han Z, Hua J, Xue W, Zhu F. Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. Front Genet 2019; 10:1136. [PMID: 31781177 PMCID: PMC6861379 DOI: 10.3389/fgene.2019.01136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic fatal central nervous system (CNS) disease involving in complex immunity dysfunction. Recently, long noncoding RNAs (lncRNAs) were discovered as the important regulatory factors for the pathogenesis of MS. However, these findings often cannot be repeated and confirmed by the subsequent studies. We considered that the small-scale samples or the heterogeneity among various tissues may result in the divergence of the results. Currently, RNA-seq has become a powerful approach to quantify the abundances of lncRNA transcripts. Therefore, we comprehensively collected the MS-related RNA-seq data from a variety of previous studies, and integrated these data using an expression-based meta-analysis to identify the differentially expressed lncRNA between MS patients and controls in whole samples and subgroups. Then, we performed the Jensen-Shannon (JS) divergence and cluster analysis to explore the heterogeneity and expression specificity among various tissues. Finally, we investigated the potential function of identified lncRNAs for MS using weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA), and 5,420 MS-related lncRNAs specifically expressed in the brain tissue were identified. The subgroup analysis found a small heterogeneity of the lncRNA expression profiles between brain and blood tissues. The results of WGCNA and GSEA showed that a potential important function of lncRNAs in MS may be involved in the regulation of ribonucleoproteins and tumor necrosis factor cytokines receptors. In summary, this study provided a strategy to explore disease-related lncRNAs on genome-wide scale, and our findings will be benefit to improve the understanding of MS pathogenesis.
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Affiliation(s)
- Zhijie Han
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Jiao Hua
- School of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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Wang Y, Pan WY, Ge JS, Wang XD, Chen W, Luo X, Wang YL. A review of the relationship between long noncoding RNA and post-stroke injury repair. J Int Med Res 2019; 47:4619-4624. [PMID: 31526155 PMCID: PMC6833389 DOI: 10.1177/0300060519867493] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/12/2019] [Indexed: 11/15/2022] Open
Abstract
Stroke is a cerebrovascular circulation disorder with sudden onset, which causes disorder of ion balance, inflammation, and acidosis, and that in turn induces ischemia-reperfusion injury, influencing the prognosis of stroke patients. Long noncoding RNAs (lncRNAs) are regulatory sequences involved at the transcriptional, post-transcriptional, and epigenetic levels, have high specific expression in the central nervous system, and effectively regulate the development of the central nervous system and progression of diseases. Stroke induces changes in the expression of many lncRNAs. Therefore, lncRNAs play an important role in the complex pathological process of stroke. Exploring lncRNA could facilitate a comprehensive understanding of the pathological mechanism of stroke and the post-injury molecular regulatory network. However, there are few reports on the role of lncRNA in the pathological development of stroke. In the present review, we discuss the association of lncRNA with post-stroke injury repair.
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Affiliation(s)
- Yao Wang
- Department of Rehabilitation Medicine, Shenzhen Dapeng New District Nan’ao People’s Hospital, Shenzhen, China
| | - Wei-Yi Pan
- Department of Rehabilitation Medicine, Shenzhen Dapeng New District Nan’ao People’s Hospital, Shenzhen, China
| | - Jun-Sheng Ge
- Department of Rehabilitation Medicine, Shenzhen Dapeng New District Nan’ao People’s Hospital, Shenzhen, China
| | - Xiao-Dong Wang
- Department of Rehabilitation, Shenzhen Second People’s Hospital, The First Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, China
| | - Wei Chen
- Kerry Rehabilitation Medicine Research Institute, Shenzhen, Guangdong, China
| | - Xun Luo
- Kerry Rehabilitation Medicine Research Institute, Shenzhen, Guangdong, China
| | - Yu-Long Wang
- Department of Rehabilitation, Shenzhen Second People’s Hospital, The First Affiliated Hospital, Shenzhen University School of Medicine, Shenzhen, China
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Duran RCD, Wei H, Kim DH, Wu JQ. Invited Review: Long non-coding RNAs: important regulators in the development, function and disorders of the central nervous system. Neuropathol Appl Neurobiol 2019; 45:538-556. [PMID: 30636336 PMCID: PMC6626588 DOI: 10.1111/nan.12541] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Genome-wide transcriptional studies have demonstrated that tens of thousands of long non-coding RNAs (lncRNA) genes are expressed in the central nervous system (CNS) and that they exhibit tissue- and cell-type specificity. Their regulated and dynamic expression and their co-expression with protein-coding gene neighbours have led to the study of the functions of lncRNAs in CNS development and disorders. In this review, we describe the general characteristics, localization and classification of lncRNAs. We also elucidate the examples of the molecular mechanisms of nuclear and cytoplasmic lncRNA actions in the CNS and discuss common experimental approaches used to identify and unveil the functions of lncRNAs. Additionally, we provide examples of lncRNA studies of cell differentiation and CNS disorders including CNS injuries and neurodegenerative diseases. Finally, we review novel lncRNA-based therapies. Overall, this review highlights the important biological roles of lncRNAs in CNS functions and disorders.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Ave. Morones Prieto 3000, Monterrey, N.L., 64710, Mexico
| | - Haichao Wei
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
| | - Dong H. Kim
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX 77030, USA
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Fu Y, Yin Y, Peng S, Yang G, Yu Y, Guo C, Qin Y, Zhang X, Xu W, Qin Y. Small nucleolar RNA host gene 1 promotes development and progression of colorectal cancer through negative regulation of miR-137. Mol Carcinog 2019; 58:2104-2117. [PMID: 31469189 PMCID: PMC6852404 DOI: 10.1002/mc.23101] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/30/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022]
Abstract
Small nucleolar RNA host gene 1 (SNHG1) is critical in the progression of cancers. However, the mechanism by which SNHG1 regulates the progression of colorectal cancer (CRC) remains unclear. Expressions of SNHG1 and miR‐137 in CRC tissues and cell lines were evaluated by quantitative real‐time polymerase chain reaction. A luciferase reporter gene assay was conducted to investigate miR‐137 target. Additionally, RNA pull‐down assay was performed to explore the physical association between miR‐137, SNHG1, and RNA induced silencing complex (RISC). Cell cycling and invasion were examined by flow cytometry (FCM) and transwell assays. The in vivo carcinogenic activity of SNHG1 was examined using murine xenograft models. Expression of RICTOR, serine/threonine kinase 1 (AKT), serum and glucocorticoid‐inducible kinase 1 (SGK1), p70S6K1, and LC3II/LC3I ratio was examined by Western blot analysis. SNHG1 upregulation was observed in CRC tissues and cell lines, which was associated with the lymph node metastasis, advanced TNM stage and poorer prognosis. SNHG1 increased RICTOR level in CRC via sponging miR‐137. In addition, SNHG1 silencing inhibited CRC cell proliferation and migration in vitro and in vivo. SNHG1 regulated RICTOR expression by sponging miR‐137 and promoted tumorgenesis in CRC.
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Affiliation(s)
- Yang Fu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhan Yin
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Sanfei Peng
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ge Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Yu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Changqing Guo
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yanru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiefu Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wen Xu
- State Key Laboratory of Bioreactor Engineering & Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, Shanghai, China
| | - Yiyu Qin
- Research Centre of Biomedical Technology, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu, China
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Dong W, Qiu C, Gong D, Jiang X, Liu W, Liu W, Zhang L, Zhang W. Proteomics and bioinformatics approaches for the identification of plasma biomarkers to detect Parkinson's disease. Exp Ther Med 2019; 18:2833-2842. [PMID: 31572530 PMCID: PMC6755458 DOI: 10.3892/etm.2019.7888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/27/2019] [Indexed: 12/30/2022] Open
Abstract
The aim of the present study was to screen for biomarkers of Parkinson's disease (PD) using proteomics and bioinformatics approaches. PD patients were divided into three groups: Those without surgery (PD1 group); those who had undergone deep brain stimulation (DBS) surgery without electrode stimulation (PD2 group); and those who had undergone DBS surgery with 1 month of electrode stimulation (PD3 group). The non-Parkinson control group (CK group) was also involved. Quantitative proteomic analysis of human sera was performed through the use of tandem mass tag markers and liquid chromatography-mass spectrometry (LC-MS)-based techniques. For the proteins with quantitative information, a systematic bioinformatics analysis was then performed, including protein annotation, functional classification, functional enrichment and cluster analysis based on functional enrichment. Of the 739 proteins identified, quantitative information was available for 644. With regard to differential expression, 18 upregulated and 21 downregulated proteins were screened in the PD1/CK comparison group; 12 upregulated and 12 downregulated proteins in the PD2/PD1 comparison group; and 16 upregulated and 19 downregulated proteins in the PD3/PD2 comparison group. Coiled-coil domain-containing protein 154 (CCDC154) and tripartite motif-containing protein 3 (TRIM3) were key proteins involved in the molecular mechanisms of PD, participating in intracellular vesicle, ubiquitin protein ligase and transition metal ion-binding activities. After DBS surgery, desert hedgehog protein (DHH) was downregulated, whereas neuropilin-2 (NRP2) was upregulated; these participated in the ensheathment of neurons and the semaphorin receptor complex, respectively. The expression level of chloride intracellular channel protein 1 (CLIC1) was increased after 1 month of electrode stimulation following DBS. By combining proteomic approaches and LC-MS methods, significant proteins including CCDC154, TRIM3, DHH, NRP2 and CLIC1 were detected with high specificity and sensitivity. These may be used as novel biomarkers for early diagnosis of PD and the future development of treatments.
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Affiliation(s)
- Wenwen Dong
- Department of Functional Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Chang Qiu
- Department of Functional Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Dawei Gong
- Department of Functional Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Xu Jiang
- Department of Neurology, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wan Liu
- Department of Neurology, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Weiguo Liu
- Department of Neurology, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Li Zhang
- Department of Neurology, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Wenbin Zhang
- Department of Functional Neurosurgery, Nanjing Brain Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
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Han Z, Xue W, Tao L, Lou Y, Qiu Y, Zhu F. Genome-wide identification and analysis of the eQTL lncRNAs in multiple sclerosis based on RNA-seq data. Brief Bioinform 2019; 21:1023-1037. [PMID: 31323688 DOI: 10.1093/bib/bbz036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/29/2022] Open
Abstract
Abstract
The pathogenesis of multiple sclerosis (MS) is significantly regulated by long noncoding RNAs (lncRNAs), the expression of which is substantially influenced by a number of MS-associated risk single nucleotide polymorphisms (SNPs). It is thus hypothesized that the dysregulation of lncRNA induced by genomic variants may be one of the key molecular mechanisms for the pathology of MS. However, due to the lack of sufficient data on lncRNA expression and SNP genotypes of the same MS patients, such molecular mechanisms underlying the pathology of MS remain elusive. In this study, a bioinformatics strategy was applied to obtain lncRNA expression and SNP genotype data simultaneously from 142 samples (51 MS patients and 91 controls) based on RNA-seq data, and an expression quantitative trait loci (eQTL) analysis was conducted. In total, 2383 differentially expressed lncRNAs were identified as specifically expressing in brain-related tissues, and 517 of them were affected by SNPs. Then, the functional characterization, secondary structure changes and tissue and disease specificity of the cis-eQTL SNPs and lncRNA were assessed. The cis-eQTL SNPs were substantially and specifically enriched in neurological disease and intergenic region, and the secondary structure was altered in 17.6% of all lncRNAs in MS. Finally, the weighted gene coexpression network and gene set enrichment analyses were used to investigate how the influence of SNPs on lncRNAs contributed to the pathogenesis of MS. As a result, the regulation of lncRNAs by SNPs was found to mainly influence the antigen processing/presentation and mitogen-activated protein kinases (MAPK) signaling pathway in MS. These results revealed the effectiveness of the strategy proposed in this study and give insight into the mechanism (SNP-mediated modulation of lncRNAs) underlying the pathology of MS.
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Affiliation(s)
- Zhijie Han
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yunqing Qiu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Feng Zhu
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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LncRNA MRAK048635_P1 is critical for vascular smooth muscle cell function and phenotypic switching in essential hypertension. Biosci Rep 2019; 39:BSR20182229. [PMID: 30833363 PMCID: PMC6422888 DOI: 10.1042/bsr20182229] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Vascular remodeling caused by essential hypertension is a leading cause of death in patients, and vascular smooth muscle cell (VSMC) dysfunction and phenotypic switching result in vascular remodeling. Therefore, inhibiting cell dysfunction and phenotypic switching in VSMCs may be a new treatment strategy for essential hypertension. The aim of the current study is to explore the roles of long non-coding RNA (lncRNA) MRAK048635_P1 in VSMC function and phenotypic switching. The MRAK048635_P1 level was determined in spontaneously hypertensive rats (SHRs) and VSMCs isolated from SHRs. MRAK048635_P1 was knocked down using a specific siRNA in VSMCs isolated from the thoracic aorta of SHRs and Wistar–Kyoto rats. Then, the proliferation and migration of VSMCs were determined using a cell counting kit-8 (CCK-8), a 3H labeling method, a transwell assay, and a wound healing assay. Flow cytometry was used to test the effect of MRAK048635_P1 on VSMC apoptosis. The protein and mRNA levels of associated genes were measured through Western blotting, immunofluorescence, and Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR). MRAK048635_P1 showed low expression during hypertension in vivo and in vitro. Down-regulation of lncRNA MRAK048635_P1 promoted proliferation and migration and inhibited apoptosis in VSMCs isolated from healthy rat vascular tissue and SHR-derived VSMCs. Importantly, we also found that down-regulation of MRAK048635_P1 could induce VSMC phenotypic switching from a contractile to a secretory phenotype. In conclusion, our findings reveal that decreased MRAK048635_P1 is probably an important factor for vascular remodeling by affecting VSMC cell function and phenotypic switching in essential hypertension.
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Cuevas-Diaz Duran R, Wang CY, Zheng H, Deneen B, Wu JQ. Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases. eNeuro 2019; 6:ENEURO.0288-18.2019. [PMID: 30957015 PMCID: PMC6449165 DOI: 10.1523/eneuro.0288-18.2019] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 01/16/2019] [Accepted: 02/12/2019] [Indexed: 12/29/2022] Open
Abstract
Currently, there are no effective treatments for glioma or for neurodegenerative diseases because of, in part, our limited understanding of the pathophysiology and cellular heterogeneity of these diseases. Mounting evidence suggests that astrocytes play an active role in the pathogenesis of these diseases by contributing to a diverse range of pathophysiological states. In a previous study, five molecularly distinct astrocyte subpopulations from three different brain regions were identified. To further delineate the underlying diversity of these populations, we obtained mouse brain region-specific gene signatures for both protein-coding and long non-coding RNA and found that these astrocyte subpopulations are endowed with unique molecular signatures across diverse brain regions. Additional gene set and single-sample enrichment analyses revealed that gene signatures of different subpopulations are differentially correlated with glioma tumors that harbor distinct genomic alterations. To the best of our knowledge, this is the first study that links transcriptional profiles of astrocyte subpopulations with glioma genomic mutations. Furthermore, our results demonstrated that subpopulations of astrocytes in select brain regions are associated with specific neurodegenerative diseases. Overall, the present study provides a new perspective for understanding the pathophysiology of glioma and neurodegenerative diseases and highlights the potential contributions of diverse astrocyte populations to normal, malignant, and degenerative brain functions.
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Affiliation(s)
- Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, Texas 77030
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey NL 64710, Mexico
| | - Chih-Yen Wang
- Department of Life Sciences, National Cheng Kung University, Tainan City 70101, Taiwan
| | - Hui Zheng
- Huffington Center on Aging
- Medical Scientist Training Program
- Department of Molecular and Human Genetics
| | - Benjamin Deneen
- Center for Cell and Gene Therapy
- Department of Neuroscience
- Neurological Research Institute at Texas’ Children’s Hospital
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, Texas 77030
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Xiong W, Tan M, Tong Z, Yin C, He L, Liu L, Shen Y, Guan S, Ge H, Li G, Liang S, Gao Y. Effects of long non-coding RNA uc.48+ on pain transmission in trigeminal neuralgia. Brain Res Bull 2019; 147:92-100. [PMID: 30772439 DOI: 10.1016/j.brainresbull.2019.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/02/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
Trigeminal neuralgia (TN) is the most common neuropathic pain in the facial area, for which the effective therapy is unavailable. Long non-coding RNA (lncRNA) such as lncRNA uc.48+ is involved in diabetic neuropathic pain and may affect purinergic signaling in ganglia of diabetic rats. In this research, chronic constriction injury of the infraorbital nerve (CCI-ION) was applied to establish a rat model of TN. Five days after local injection of siRNA targeting the lncRNA uc.48+ in trigeminal ganglia (TGs), the upregulated uc.48+ expression and the reduced mechanical withdrawal threshold (MWT) in the TN rats were significantly reversed. The expression of P2X7 receptor in TGs was increased in the TN group compared with the sham group, but uc.48+ siRNA treatment mitigated this effect. The phosphorylation of ERK1/2 in TGs of TN rats was significantly enhanced compared with the sham group, while uc.48+ siRNA treatment reversed this change. In addition, injection of the lncRNA uc.48+ overexpression plasmid in TGs of control rats significantly reduced the MWT but elevated the expression of P2X7 in TGs; the phosphorylation of ERK1/2 in TGs in these uc.48+-overexpressed rats was significantly higher, similar to the observations in rats of TN model. The interaction between uc.48+ and the P2X7 receptor was detected by RNA binding protein immunoprecipitation (RIP), indicating that P2X7 receptor could specifically bind to uc.48 + . In summary, knockdown of lncRNA uc.48+ by siRNA could inhibit transduction of TN signals, whereas uc.48+ overexpression promoted TN signal transduction. LncRNA uc.48+ may interact with P2X7 receptor to upregulate expression of P2X7 receptor and furthermore enhance the phosphorylation of ERK1/2 in TGs, thereby participating in pain transmission in TN.
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Affiliation(s)
- Wei Xiong
- Affiliated Stomatological Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Provincial Key Laboratory of Oral Biomedicine, Nanchang, Jiangxi, 330006, PR China
| | - Mengxia Tan
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China; Department of Basic Medicine, Jiangxi Health Vocational College, Nanchang, Jiangxi, 330006, PR China
| | - Zhoujie Tong
- Queen Mary College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Cancan Yin
- Affiliated Stomatological Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Lingkun He
- Affiliated Stomatological Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Lijuan Liu
- Affiliated Stomatological Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Yulin Shen
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Shu Guan
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Huixiang Ge
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Guodong Li
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China; Department of Clinical Translational Research, Singapore General Hospital, Singapore, 169856, Singapore
| | - Shangdong Liang
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, PR China
| | - Yun Gao
- Department of Physiology, Basic Medical College, Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Provincial Key Laboratory of Autonomic Nervous Function and Disease, Nanchang, Jiangxi, 330006, PR China.
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Lu G, Zhang M, Wang J, Zhang K, Wu S, Zhao X. Epigenetic regulation of myelination in health and disease. Eur J Neurosci 2019; 49:1371-1387. [DOI: 10.1111/ejn.14337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/22/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Guozhen Lu
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
| | - Ming Zhang
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
| | - Jian Wang
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
| | - Kaixiang Zhang
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
| | - Shengxi Wu
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
| | - Xianghui Zhao
- Department of Neurobiology and Collaborative Innovation Center for Brain ScienceSchool of Basic MedicineFourth Military Medical University Xi'an China
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Prajapati B, Fatma M, Maddhesiya P, Sodhi MK, Fatima M, Dargar T, Bhagat R, Seth P, Sinha S. Identification and epigenetic analysis of divergent long non-coding RNAs in multilineage differentiation of human Neural Progenitor Cells. RNA Biol 2018; 16:13-24. [PMID: 30574830 DOI: 10.1080/15476286.2018.1553482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Long non-coding RNAs have emerged as an important regulatory layer in biological systems. Of the various types of lncRNAs, one class (designated as divergent RNAs/XH), which is in head-to-head overlap with the coding genes, has emerged as a critical biotype that regulates development and cellular differentiation. This work aimed to analyze previously published data on differential expression, epigenetic and network analysis in order to demonstrate the association of divergent lncRNAs, a specific biotype with the differentiation of human neural progenitor cells (hNPCs). We have analyzed various available RNAseq databases that address the neuronal and astrocytic differentiation of hNPCs and identified differentially expressed lncRNAs (DELs) during cell-fate determination. Key DELs identified from the databases were experimentally verified by us in our in-vitro hNPC differentiation system. We also analyzed the change in promoter activity using ChIP-seq datasets of the histone markers H3K4me3 (activation) and H3K27me3 (inactivation) of these DELs. Additionally, we explored the change in the euchromatinization state of DELs (by analyzing DNase-seq data) during lineage-specific differentiation of hNPCs and performed their network analysis. We were able to identify differences between neuronal and astrocytic differentiation of hNPCs at the level of divergent DELs epigenetic markers, DNAase hypersensitive sites and gene expression network. Divergent lncRNAs are more involved in neuronal rather than astrocytic differentiation, while the sense downstream lncRNA biotype appears to be more involved in astrocytic differentiation. By studying the lncRNA involvement of distinct biotypes, we have been able to indicate the preferential role of a particular biotype during lineage-specific differentiation.
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Affiliation(s)
- Bharat Prajapati
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Mena Fatma
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Priya Maddhesiya
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Manjot Kour Sodhi
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Mahar Fatima
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Tanushri Dargar
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Reshma Bhagat
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Pankaj Seth
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India
| | - Subrata Sinha
- a Cellular and Molecular Neuroscience , National Brain Research Centre , Manesar, Gurgaon , Haryana , India.,b Department of Biochemistry , All India Institute of Medical Sciences , New Delhi , India
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Zhao D, Zheng D. SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis. BMC Bioinformatics 2018; 19:544. [PMID: 30587107 PMCID: PMC6307164 DOI: 10.1186/s12859-018-2577-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Background Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ChIP-seq (chromatin immunoprecipitation and deep sequencing) libraries from small amount of DNA material, using the DNA SMART ChIP-seq Kit. The protocol adds Ts to the 3′ end of DNA templates, which is subsequently recognized and used by SMART poly(dA) primers for reverse transcription and then addition of PCR primers and sequencing adapters. The poly(dA) primers, however, can anneal to poly(T) sequences in a genome and amplify DNA fragments that are not enriched in the immunoprecipitated DNA templates. This off-target amplification results in false signals in the ChIP-seq data. Results Here, we show that the off-target ChIP-seq reads derived from false amplification of poly(T/A) genomic sequences have unique and strand-specific features. Accordingly, we develop a tool (called “SMARTcleaner”) that can exploit these features to remove SMART ChIP-seq artifacts. Application of SMARTcleaner to several SMART ChIP-seq datasets demonstrates that it can remove reads from off-target amplification effectively, leading to significantly improved ChIP-seq peaks and results. Conclusions SMARTcleaner could identify and clean the false signals in SMART-based ChIP-seq libraries, leading to improvement in peak calling, and downstream data analysis and interpretation. Electronic supplementary material The online version of this article (10.1186/s12859-018-2577-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, USA. .,Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, USA. .,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York, USA. .,Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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You Y, Cuevas-Diaz Duran R, Jiang L, Dong X, Zong S, Snyder M, Wu JQ. An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation. Integr Biol (Camb) 2018; 10:390-405. [PMID: 29892750 PMCID: PMC6047913 DOI: 10.1039/c8ib00059j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Systematic study of the regulatory mechanisms of Hematopoietic Stem Cell and Progenitor Cell (HSPC) self-renewal is fundamentally important for understanding hematopoiesis and for manipulating HSPCs for therapeutic purposes. Previously, we have characterized gene expression and identified important transcription factors (TFs) regulating the switch between self-renewal and differentiation in a multipotent Hematopoietic Progenitor Cell (HPC) line, EML (Erythroid, Myeloid, and Lymphoid) cells. Herein, we report binding maps for additional TFs (SOX4 and STAT3) by using chromatin immunoprecipitation (ChIP)-Sequencing, to address the underlying mechanisms regulating self-renewal properties of lineage-CD34+ subpopulation (Lin-CD34+ EML cells). Furthermore, we applied the Assay for Transposase Accessible Chromatin (ATAC)-Sequencing to globally identify the open chromatin regions associated with TF binding in the self-renewing Lin-CD34+ EML cells. Mass spectrometry (MS) was also used to quantify protein relative expression levels. Finally, by integrating the protein-protein interaction database, we built an expanded transcriptional regulatory and interaction network. We found that MAPK (Mitogen-activated protein kinase) pathway and TGF-β/SMAD signaling pathway components were highly enriched among the binding targets of these TFs in Lin-CD34+ EML cells. The present study integrates regulatory information at multiple levels to paint a more comprehensive picture of the HSPC self-renewal mechanisms.
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Affiliation(s)
- Yanan You
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain. Cell 2018; 174:350-362.e17. [PMID: 29887379 DOI: 10.1016/j.cell.2018.05.022] [Citation(s) in RCA: 408] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/23/2018] [Accepted: 05/10/2018] [Indexed: 01/23/2023]
Abstract
Noncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs-a long ncRNA, a circular RNA, and two microRNAs-using gene editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more effective than previously described examples of target-directed microRNA degradation, which come primarily from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7-targeted mRNAs and enables accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as in neurons, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network.
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Santos AK, Vieira MS, Vasconcellos R, Goulart VAM, Kihara AH, Resende RR. Decoding cell signalling and regulation of oligodendrocyte differentiation. Semin Cell Dev Biol 2018; 95:54-73. [PMID: 29782926 DOI: 10.1016/j.semcdb.2018.05.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
Oligodendrocytes are fundamental for the functioning of the nervous system; they participate in several cellular processes, including axonal myelination and metabolic maintenance for astrocytes and neurons. In the mammalian nervous system, they are produced through waves of proliferation and differentiation, which occur during embryogenesis. However, oligodendrocytes and their precursors continue to be generated during adulthood from specific niches of stem cells that were not recruited during development. Deficiencies in the formation and maturation of these cells can generate pathologies mainly related to myelination. Understanding the mechanisms involved in oligodendrocyte development, from the precursor to mature cell level, will allow inferring therapies and treatments for associated pathologies and disorders. Such mechanisms include cell signalling pathways that involve many growth factors, small metabolic molecules, non-coding RNAs, and transcription factors, as well as specific elements of the extracellular matrix, which act in a coordinated temporal and spatial manner according to a given stimulus. Deciphering those aspects will allow researchers to replicate them in vitro in a controlled environment and thus mimic oligodendrocyte maturation to understand the role of oligodendrocytes in myelination in pathologies and normal conditions. In this study, we review these aspects, based on the most recent in vivo and in vitro data on oligodendrocyte generation and differentiation.
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Affiliation(s)
- A K Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - M S Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil; Instituto Nanocell, Rua Santo Antônio, 420, 35500-041 Divinópolis, MG, Brazil
| | - R Vasconcellos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil; Instituto Nanocell, Rua Santo Antônio, 420, 35500-041 Divinópolis, MG, Brazil
| | - V A M Goulart
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil
| | - A H Kihara
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - R R Resende
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, 31270-901 Belo Horizonte, MG, Brazil; Instituto Nanocell, Rua Santo Antônio, 420, 35500-041 Divinópolis, MG, Brazil.
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Long Non-Coding RNAs in Neuronal Aging. Noncoding RNA 2018; 4:ncrna4020012. [PMID: 29670042 PMCID: PMC6027360 DOI: 10.3390/ncrna4020012] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
The expansion of long non-coding RNAs (lncRNAs) in organismal genomes has been associated with the emergence of sophisticated regulatory networks that may have contributed to more complex neuronal processes, such as higher-order cognition. In line with the important roles of lncRNAs in the normal functioning of the human brain, dysregulation of lncRNA expression has been implicated in aging and age-related neurodegenerative disorders. In this paper, we discuss the function and expression of known neuronal-associated lncRNAs, their impact on epigenetic changes, the contribution of transposable elements to lncRNA expression, and the implication of lncRNAs in maintaining the 3D nuclear architecture in neurons. Moreover, we discuss how the complex molecular processes that are orchestrated by lncRNAs in the aged brain may contribute to neuronal pathogenesis by promoting protein aggregation and neurodegeneration. Finally, this review explores the possibility that age-related disturbances of lncRNA expression change the genomic and epigenetic regulatory landscape of neurons, which may affect neuronal processes such as neurogenesis and synaptic plasticity.
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Dong X, Cuevas-Diaz Duran R, You Y, Wu JQ. Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. J Vis Exp 2018. [PMID: 29708547 DOI: 10.3791/57547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In mammalian cells, gene transcription is regulated in a cell type specific manner by the interactions of transcriptional factors with genomic DNA. Lineage-specific transcription factors are considered to play essential roles in cell specification and differentiation during development. ChIP coupled with high-throughput DNA sequencing (ChIP-seq) is widely used to analyze genome-wide binding sites of transcription factors (or its associated complex) to genomic DNA. However, a large number of cells are required for one standard ChIP reaction, which makes it difficult to study the limited number of isolated primary cells or rare cell populations. In order to understand the regulatory mechanism of oligodendrocyte lineage-specific transcription factor Olig2 in acutely purified mouse OPCs, a detailed method using ChIP-seq to identify the genome-wide binding sites of Olig2 (or Olig2 complex) is shown. First, the protocol explains how to purify the platelet-derived growth factor receptor alpha (PDGFRα) positive OPCs from mouse brains. Next, Olig2 antibody mediated ChIP and library construction are performed. The last part describes the bioinformatic software and procedures used for Olig2 ChIP-seq analysis. In summary, this paper reports a method to analyze the genome-wide bindings of transcriptional factor Olig2 in acutely purified brain OPCs.
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Affiliation(s)
- Xiaomin Dong
- The Vivian L. Smith Department of Neurosurgery, Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center
| | - Raquel Cuevas-Diaz Duran
- The Vivian L. Smith Department of Neurosurgery, Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center
| | - Yanan You
- The Vivian L. Smith Department of Neurosurgery, Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, Center for Stem Cell and Regenerative Medicine, University of Texas Health Science Center;
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Shi Z, Pan B, Feng S. The emerging role of long non-coding RNA in spinal cord injury. J Cell Mol Med 2018; 22:2055-2061. [PMID: 29392896 PMCID: PMC5867120 DOI: 10.1111/jcmm.13515] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
Spinal cord injury (SCI) is a significant health burden worldwide which causes permanent neurological deficits, and there are approximately 17,000 new cases each year. However, there are no effective and current treatments that lead to functional recovery because of the limited understanding of the pathogenic mechanism of SCI. In recent years, the biological roles of long non-coding RNAs (lncRNAs) in SCI have attracted great attention from the researchers all over the world, and an increasing number of studies have investigated the regulatory roles of lncRNAs in SCI. In this review, we summarized the biogenesis, classification and function of lncRNAs and focused on the investigations on the roles of lncRNAs involved in the pathogenic processes of SCI, including neuronal loss, astrocyte proliferation and activation, demyelination, microglia activation, inflammatory reaction and angiogenesis. This review will help understand the molecular mechanisms of SCI and facilitate the potential use of lncRNAs as diagnostic markers and therapeutic targets for SCI treatment.
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Affiliation(s)
- Zhongju Shi
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Pan
- Department of Orthopaedics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shiqing Feng
- Department of Orthopaedics, Tianjin Medical University General Hospital, Tianjin, China
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