201
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Wuebben EL, Rizzino A. The dark side of SOX2: cancer - a comprehensive overview. Oncotarget 2018; 8:44917-44943. [PMID: 28388544 PMCID: PMC5546531 DOI: 10.18632/oncotarget.16570] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/16/2017] [Indexed: 12/14/2022] Open
Abstract
The pluripotency-associated transcription factor SOX2 is essential during mammalian embryogenesis and later in life, but SOX2 expression can also be highly detrimental. Over the past 10 years, SOX2 has been shown to be expressed in at least 25 different cancers. This review provides a comprehensive overview of the roles of SOX2 in cancer and focuses on two broad topics. The first delves into the expression and function of SOX2 in cancer focusing on the connection between SOX2 levels and tumor grade as well as patient survival. As part of this discussion, we address the developing connection between SOX2 expression and tumor drug resistance. We also call attention to an under-appreciated property of SOX2, its levels in actively proliferating tumor cells appear to be optimized to maximize tumor growth - too little or too much SOX2 dramatically alters tumor growth. The second topic of this review focuses on the exquisite array of molecular mechanisms that control the expression and transcriptional activity of SOX2. In addition to its complex regulation at the transcriptional level, SOX2 expression and activity are controlled carefully by microRNAs, long non-coding RNAs, and post-translational modifications. In the Conclusion and Future Perspectives section, we point out that there are still important unanswered questions. Addressing these questions is expected to lead to new insights into the functions of SOX2 in cancer, which will help design novels strategies for more effectively treating some of the most deadly cancers.
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Affiliation(s)
- Erin L Wuebben
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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202
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Wang H, Wu J, Zhang X, Ding L, Zeng Q. Microarray analysis of the expression profile of lncRNAs reveals the key role of lncRNA BC088327 as an agonist to heregulin‑1β‑induced cell proliferation in peripheral nerve injury. Int J Mol Med 2018; 41:3477-3484. [PMID: 29568963 DOI: 10.3892/ijmm.2018.3571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/24/2017] [Indexed: 11/05/2022] Open
Abstract
Heregulin‑1β is capable of promoting the nerve regeneration of acellular nerve allografts with skin‑derived precursor differentiated Schwann cell (SC) therapy in peripheral nerve injury. Long non‑coding RNAs (lncRNAs) serve important roles in the regulation of gene transcription and trans-lation in multiple biological processes, but its association with the repair of peripheral nerve injury is unexplored. Therefore, in the present study, the aim was to identify novel indicators for peripheral nerve injury, and to detect whether there is an association between lncRNA expression and the treatment effect of heregulin‑1β on this disorder. The expression status of lncRNAs and mRNAs in a well‑built rat model with sciatic nerve injury was investigated using microarray assays. Based on the results of the microarray assays and quantitative polymerase chain reaction validation, it was inferred that lncRNA BC088327 was upregulated to the largest extent among all the lncRNAs. According to these findings, the role of BC088327 in peripheral nerve injury was further assessed by detecting the cell viability, cell cycle and apoptosis in a hypoxic SC cell model after suppressing the expression of BC088327 using specific small interfering RNA. Based on the results of the lncRNA microarray assay, 805 lncRNAs were significantly differentially expressed, among which, 323 lncRNAs were upregulated and 482 lncRNAs were downregulated. Based on the results of the mRNA microarray assay, 1,293 lncRNAs were significantly differentially expressed, including 603 upregulated and 690 downregulated lncRNAs. Moreover, knockdown of lncRNA BC088327 suppressed cell viability and induced cell apoptosis and S-phase cell cycle arrest in the SCs. In conclusion, expression profile changes of lncRNAs in peripheral nerve injuries were closely associated with treatment with heregulin‑1β. lncRNA BC088327 may play a synergistic role with heregulin‑1β in repairing peripheral injury, which has the potential be a biomarker for the detection of peripheral injury and a medical target for the development of therapeutic modalities.
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Affiliation(s)
- Houlei Wang
- Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
| | - Jingping Wu
- Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
| | - Xinchao Zhang
- Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
| | - Lei Ding
- Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
| | - Qingmin Zeng
- Department of Orthopedics, Jinshan Hospital of Fudan University, Shanghai 201508, P.R. China
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203
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Deng L, Wu H, Liu C, Zhan W, Zhang J. Probing the functions of long non-coding RNAs by exploiting the topology of global association and interaction network. Comput Biol Chem 2018; 74:360-367. [PMID: 29573966 DOI: 10.1016/j.compbiolchem.2018.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 02/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in many biological processes, such as immune response, development, differentiation and gene imprinting and are associated with diseases and cancers. But the functions of the vast majority of lncRNAs are still unknown. Predicting the biological functions of lncRNAs is one of the key challenges in the post-genomic era. In our work, We first build a global network including a lncRNA similarity network, a lncRNA-protein association network and a protein-protein interaction network according to the expressions and interactions, then extract the topological feature vectors of the global network. Using these features, we present an SVM-based machine learning approach, PLNRGO, to annotate human lncRNAs. In PLNRGO, we construct a training data set according to the proteins with GO annotations and train a binary classifier for each GO term. We assess the performance of PLNRGO on our manually annotated lncRNA benchmark and a protein-coding gene benchmark with known functional annotations. As a result, the performance of our method is significantly better than that of other state-of-the-art methods in terms of maximum F-measure and coverage.
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Affiliation(s)
- Lei Deng
- School of Software, Central South University, Changsha 410075, China
| | - Hongjie Wu
- School of Software, Central South University, Changsha 410075, China
| | - Chuyao Liu
- School of Software, Central South University, Changsha 410075, China
| | - Weihua Zhan
- School of Electronics and Computer Science, Zhejiang Wanli University, Ningbo 315100, China
| | - Jingpu Zhang
- School of Computer and Data Science, Henan University of Urban Construction, Pingdingshan 467000, China; School of Information Science and Engineering, Central South University, Changsha 410083, China.
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204
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Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease. Am J Hum Genet 2018; 102:427-446. [PMID: 29499164 DOI: 10.1016/j.ajhg.2018.02.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/01/2018] [Indexed: 12/22/2022] Open
Abstract
Genetic variation modulating risk of sporadic Parkinson disease (PD) has been primarily explored through genome-wide association studies (GWASs). However, like many other common genetic diseases, the impacted genes remain largely unknown. Here, we used single-cell RNA-seq to characterize dopaminergic (DA) neuron populations in the mouse brain at embryonic and early postnatal time points. These data facilitated unbiased identification of DA neuron subpopulations through their unique transcriptional profiles, including a postnatal neuroblast population and substantia nigra (SN) DA neurons. We use these population-specific data to develop a scoring system to prioritize candidate genes in all 49 GWAS intervals implicated in PD risk, including genes with known PD associations and many with extensive supporting literature. As proof of principle, we confirm that the nigrostriatal pathway is compromised in Cplx1-null mice. Ultimately, this systematic approach establishes biologically pertinent candidates and testable hypotheses for sporadic PD, informing a new era of PD genetic research.
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205
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Zhao Y, Cao F, Yu X, Chen C, Meng J, Zhong R, Zhang Y, Zhu D. Linc-RAM is required for FGF2 function in regulating myogenic cell differentiation. RNA Biol 2018; 15:404-412. [PMID: 29364044 DOI: 10.1080/15476286.2018.1431494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Myogenic differentiation of skeletal muscle stem cells, also known satellite cells, is tightly orchestrated by extrinsic and intrinsic regulators. Basic fibroblast growth factor (FGF2) is well documented to be implicated in satellite cell self-renewal and differentiation by repressing MyoD. We recently identified a MyoD-regulated and skeletal muscle-specifically expressed long non-coding RNA Linc-RAM which enhances myogenic differentiation by facilitating MyoD/Baf60c/Brg1 complex assembly. Herein, we investigated the transcriptional regulation and intracellular signaling pathway in mediating Linc-RAM gene expression during muscle cell differentiation. Firstly, we demonstrate Linc-RAM is negatively regulated by FGF2 via Ras/Raf/Mek/Erk signaling pathway in muscle cells. Overexpression of MyoD significantly attenuates repression of Linc-RAM promoter activities in C2C12 cells treated with FGF2. Knockout of MyoD abolishes FGF2-mediated repression of Linc-RAM gene transcription in satellite cells sorted from skeletal muscle of MyoD-/-;Pax7-nGFP mice, suggesting inhibition of MyoD is required for FGF2-mediated expression of Linc-RAM. For the functional significance, we show that overexpression of Linc-RAM rescues FGF2-induced inhibition of C2C12 cell differentiation, indicating inhibition of Linc-RAM is required for FGF2-mediated suppression of myogenic differentiation. Consistently, we are able to further corroborate the requirement of Linc-RAM inhibition for FGF2-modulated repression of myogenic differentiation by using an ex vivo cultured single fiber system and satellite cells sorted from Linc-RAM-/-;Pax7-nGFP knockout mice. Collectively, the present study not only reveals the intracellular signaling in FGF2-mediated Linc-RAM gene expression but also demonstrate the functional significance of Linc-RAM in FGF2-mediated muscle cell differentiation.
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Affiliation(s)
- Yixia Zhao
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Fengqi Cao
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Xiaohua Yu
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Chuyan Chen
- b Peking Union Medical College Hospital , Shuaifuyuan No.1, Beijing , China
| | - Jiao Meng
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Ran Zhong
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Yong Zhang
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
| | - Dahai Zhu
- a The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College , 5 Dong Dan San Tiao, Beijing , China
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206
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Banerjee P, Surendran H, Bharti K, Morishita K, Varshney A, Pal R. Long Noncoding RNA RP11-380D23.2 Drives Distal-Proximal Patterning of the Lung by Regulating PITX2 Expression. Stem Cells 2018; 36:218-229. [PMID: 29143419 DOI: 10.1002/stem.2740] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/18/2017] [Accepted: 10/23/2017] [Indexed: 02/01/2023]
Abstract
Early lung development is a tightly orchestrated process encompassing (a) formation of definitive endoderm, (b) anteriorization of definitive endoderm, followed by (c) specification and maturation of both proximal and distal lung precursors. Several reports detailing the interaction of genes and proteins during lung development are available; however, studies reporting the role(s) of long noncoding RNAs (lncRNA) in lung morphogenesis are limited. To investigate this, we tailored a protocol for differentiation of human-induced pluripotent stem cells into distal and proximal lung progenitors to mimic in vivo lung development. The authenticity of differentiated cells was confirmed by expression of key lung markers such as FoxA2, Sox-17, Nkx2.1, Pitx2, FoxJ1, CC10, SPC, and via scanning as well as transmission electron microscopy. We employed next generation sequencing to identify lncRNAs and categorized them based on their proximity to genes essential for lung morphogenesis. In-depth bioinformatical analysis of the sequencing data enabled identification of a novel lncRNA, RP11-380D23.2, which is located upstream of PITX2 and includes a binding site for PARP1. Chromatin immunoprecipitation and other relevant studies revealed that PARP1 is a repressor for PITX2. Whole genome microarray analysis of RP11-380D23.2/PITX2 knockdown populations of progenitors demonstrated enrichment in proximal progenitors and indicated altered distal-proximal patterning. Dysregulation of WNT effectors in both knockdowns highlighted direct modulation of PITX2 by RP11-380D23.2. Most of these results were validated in four independent hiPSC lines (including a patient-specific CFTR mutant line). Taken together, these findings offer a mechanistic explanation underpinning the role of RP11-380D23.2 during lung morphogenesis via WNT signaling. Stem Cells 2018;36:218-229.
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Affiliation(s)
- Poulomi Banerjee
- School of Regenerative Medicine, Manipal University, Bangalore, Karnataka, India
| | - Harshini Surendran
- School of Regenerative Medicine, Manipal University, Bangalore, Karnataka, India
| | - Kapil Bharti
- National Eye Institute, NIH, Bethesda, Maryland, USA
| | - Kaoru Morishita
- Departments of Pharmacology and Toxicology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India
| | - Anurag Varshney
- Departments of Pharmacology and Toxicology, Daiichi Sankyo India Pharma Private Limited, Gurgaon, Haryana, India
| | - Rajarshi Pal
- School of Regenerative Medicine, Manipal University, Bangalore, Karnataka, India
- Centre for Cellular and Molecular Platforms (C-CAMP), NCBS-TIFR Campus, Eyestem Research, Bangalore, Karnataka, India
- School of Life Sciences, TransDisciplinary University, Bangalore, Karnataka, India
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207
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Biscarini S, Capauto D, Peruzzi G, Lu L, Colantoni A, Santini T, Shneider NA, Caffarelli E, Laneve P, Bozzoni I. Characterization of the lncRNA transcriptome in mESC-derived motor neurons: Implications for FUS-ALS. Stem Cell Res 2018; 27:172-179. [PMID: 29449089 DOI: 10.1016/j.scr.2018.01.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/22/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are currently recognized as crucial players in nervous system development, function and pathology. In Amyotrophic Lateral Sclerosis (ALS), identification of causative mutations in FUS and TDP-43 or hexanucleotide repeat expansion in C9ORF72 point to the essential role of aberrant RNA metabolism in neurodegeneration. In this study, by taking advantage of an in vitro differentiation system generating mouse motor neurons (MNs) from embryonic stem cells, we identified and characterized the long non-coding transcriptome of MNs. Moreover, by using mutant mouse MNs carrying the equivalent of one of the most severe ALS-associated FUS alleles (P517L), we identified lncRNAs affected by this mutation. Comparative analysis with human MNs derived in vitro from induced pluripotent stem cells indicated that candidate lncRNAs are conserved between mouse and human. Our work provides a global view of the long non-coding transcriptome of MN, as a prerequisite toward the comprehension of the still poorly characterized non-coding side of MN physiopathology.
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Affiliation(s)
- Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Davide Capauto
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Lei Lu
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA.
| | - Alessio Colantoni
- Department of Biology and Biotechnology, Sapienza University of Rome, Italy.
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Neil A Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA.
| | - Elisa Caffarelli
- Institute of Molecular Biology and Pathology of CNR, Rome, Italy.
| | - Pietro Laneve
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy.
| | - Irene Bozzoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy; Department of Biology and Biotechnology, Sapienza University of Rome, Italy; Institute of Molecular Biology and Pathology of CNR, Rome, Italy; Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, Italy.
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208
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Panaliappan TK, Wittmann W, Jidigam VK, Mercurio S, Bertolini JA, Sghari S, Bose R, Patthey C, Nicolis SK, Gunhaga L. Sox2 is required for olfactory pit formation and olfactory neurogenesis through BMP restriction and Hes5 upregulation. Development 2018; 145:145/2/dev153791. [PMID: 29352015 PMCID: PMC5825848 DOI: 10.1242/dev.153791] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 12/11/2017] [Indexed: 12/26/2022]
Abstract
The transcription factor Sox2 is necessary to maintain pluripotency of embryonic stem cells, and to regulate neural development. Neurogenesis in the vertebrate olfactory epithelium persists from embryonic stages through adulthood. The role Sox2 plays for the development of the olfactory epithelium and neurogenesis within has, however, not been determined. Here, by analysing Sox2 conditional knockout mouse embryos and chick embryos deprived of Sox2 in the olfactory epithelium using CRISPR-Cas9, we show that Sox2 activity is crucial for the induction of the neural progenitor gene Hes5 and for subsequent differentiation of the neuronal lineage. Our results also suggest that Sox2 activity promotes the neurogenic domain in the nasal epithelium by restricting Bmp4 expression. The Sox2-deficient olfactory epithelium displays diminished cell cycle progression and proliferation, a dramatic increase in apoptosis and finally olfactory pit atrophy. Moreover, chromatin immunoprecipitation data show that Sox2 directly binds to the Hes5 promoter in both the PNS and CNS. Taken together, our results indicate that Sox2 is essential to establish, maintain and expand the neuronal progenitor pool by suppressing Bmp4 and upregulating Hes5 expression. Summary: Analysis of Sox2 mutant mouse and Sox2 CRISPR-targeted chick embryos reveals that Sox2 controls the establishment of sensory progenitors in the olfactory epithelium by suppressing Bmp4 and upregulating Hes5 expression.
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Affiliation(s)
| | - Walter Wittmann
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Vijay K Jidigam
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Sara Mercurio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Jessica A Bertolini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Soufien Sghari
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Raj Bose
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Cedric Patthey
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Silvia K Nicolis
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Lena Gunhaga
- Umeå Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
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209
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Clark BS, Blackshaw S. Understanding the Role of lncRNAs in Nervous System Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:253-282. [PMID: 28815543 DOI: 10.1007/978-981-10-5203-3_9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development. Additionally, we focus on recent endeavors that attempt to assign function to lncRNAs during nervous system development. We highlight discrepancies that have been observed between in vitro and in vivo studies of lncRNA function and the challenges facing researchers in conducting mechanistic analyses of lncRNAs in the developing nervous system. Altogether, this chapter highlights the emerging role of lncRNAs in the developing brain and sheds light on novel, RNA-mediated mechanisms by which nervous system development is controlled.
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Affiliation(s)
- Brian S Clark
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seth Blackshaw
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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210
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LncRNA-NEF antagonized epithelial to mesenchymal transition and cancer metastasis via cis-regulating FOXA2 and inactivating Wnt/β-catenin signaling. Oncogene 2018; 37:1445-1456. [DOI: 10.1038/s41388-017-0041-y] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 01/01/2023]
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211
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Wang L, Liu Y, Sun S, Lu M, Xia Y. Regulation of neuronal-glial fate specification by long non-coding RNAs. Rev Neurosci 2018; 27:491-9. [PMID: 26943605 DOI: 10.1515/revneuro-2015-0061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/06/2016] [Indexed: 12/20/2022]
Abstract
Neural stem cell transplantation is becoming a promising and attractive cell-based treatment modality for repairing the damaged central nervous system. One of the limitations of this approach is that the proportion of functional cells differentiated from stem cells still remains at a low level. In recent years, novel long non-coding RNAs (lncRNAs) are being discovered at a growing pace, suggesting that this class of molecules may act as novel regulators in neuronal-glial fate specification. In this review, we first describe the general features of lncRNAs that are more likely to be relevant to reveal their function. By this, we aim to point out the specific roles of a number of lncRNAs whose function has been described during neuronal and glial cell differentiation. There is no doubt that investigation of the lncRNAs will open a new window in studying neuronal-glial fate specification.
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212
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Long non-coding RNA RMST silencing protects against middle cerebral artery occlusion (MCAO)-induced ischemic stroke. Biochem Biophys Res Commun 2018; 495:2602-2608. [DOI: 10.1016/j.bbrc.2017.12.087] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/15/2017] [Indexed: 01/05/2023]
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213
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Yang D, Yang K, Yang M. Circular RNA in Aging and Age-Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1086:17-35. [DOI: 10.1007/978-981-13-1117-8_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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214
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Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI. Nonprotein-Coding RNAs as Regulators of Development in Tunicates. Results Probl Cell Differ 2018; 65:197-225. [PMID: 30083922 DOI: 10.1007/978-3-319-92486-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tunicates, or urochordates, are a group of small marine organisms that are found widely throughout the seas of the world. As most plausible sister group of the vertebrates, they are of utmost importance for a comprehensive understanding of chordate evolution; hence, they have served as model organisms for many aspects of the developmental biology. Current genomic analysis of tunicates indicates that their genomes evolved with a fast rate not only at the level of nucleotide substitutions but also in terms of genomic organization. The latter involves genome reduction, rearrangements, as well as the loss of some important coding and noncoding RNA (ncRNAs) elements and even entire genomic regions that are otherwise well conserved. These observations are largely based on evidence from comparative genomics resulting from the analysis of well-studied gene families such as the Hox genes and their noncoding elements. In this chapter, the focus lies on the ncRNA complement of tunicates, with a particular emphasis on microRNAs, which have already been studied extensively for other animal clades. MicroRNAs are known as important regulators of key genes in animal development, and they are intimately related to the increase morphological complexity in higher metazoans. Here we review the discovery, evolution, and genome organization of the miRNA repertoire, which has been drastically reduced and restructured in tunicates compared to the chordate ancestor. Known functions of microRNAs as regulators of development in tunicates are a central topic. For instance, we consider the role of miRNAs as regulators of the muscle development and their importance in the regulation of the differential expression during the oral siphon regeneration. Beyond microRNAs, we touch upon the functions of some other ncRNAs such as yellow crescent RNA, moRNAs, RMST lncRNAs, or spliced-leader (SL) RNAs, which have diverse functions associated with the embryonic development, neurogenesis, and mediation of mRNA stability in general.
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Affiliation(s)
- Cristian A Velandia-Huerto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.
- Biology Department, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - Adriaan Gittenberger
- Institute of Biology, Leiden University, Leiden, Netherlands
- GiMaRIS, BioScience Park Leiden, Leiden, Netherlands
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
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215
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Using Human iPSC-Derived Neurons to Uncover Activity-Dependent Non-Coding RNAs. Genes (Basel) 2017; 8:genes8120401. [PMID: 29261115 PMCID: PMC5748719 DOI: 10.3390/genes8120401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/05/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022] Open
Abstract
Humans are arguably the most complex organisms present on Earth with their ability to imagine, create, and problem solve. As underlying mechanisms enabling these capacities reside in the brain, it is not surprising that the brain has undergone an extraordinary increase in size and complexity within the last few million years. Human induced pluripotent stem cells (hiPSCs) can be differentiated into many cell types that were virtually inaccessible historically, such as neurons. Here, we used hiPSC-derived neurons to investigate the cellular response to activation at the transcript level. Neuronal activation was performed with potassium chloride (KCl) and its effects were assessed by RNA sequencing. Our results revealed the involvement of long non-coding RNAs and human-specific genetic variants in response to neuronal activation and help validate hiPSCs as a valuable resource for the study of human neuronal networks. In summary, we find that genes affected by KCl-triggered activation are implicated in pathways that drive cell proliferation, differentiation, and the emergence of specialized morphological features. Interestingly, non-coding RNAs of various classes are amongst the most highly expressed genes in activated hiPSC-derived neurons, thus suggesting these play crucial roles in neural pathways and may significantly contribute to the unique functioning of the human brain.
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216
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Review: adult neurogenesis contributes to hippocampal plasticity. Cell Tissue Res 2017; 373:693-709. [PMID: 29185071 DOI: 10.1007/s00441-017-2735-4] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/27/2017] [Indexed: 12/18/2022]
Abstract
Adult hippocampal neurogenesis is the process by which new functional neurons are added to the adult dentate gyrus of the hippocampus. Animal studies have shown that the degree of adult hippocampal neurogenesis is regulated by local environmental cues as well as neural network activities. Furthermore, accumulating evidence has suggested that adult hippocampal neurogenesis plays prominent roles in hippocampus-dependent brain functions. In this review, we summarize the mechanisms underlying the regulation of adult hippocampal neurogenesis at various developmental stages and propose how adult-born neurons contribute to structural and functional hippocampal plasticity.
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217
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Bielefeld P, Mooney C, Henshall DC, Fitzsimons CP. miRNA-Mediated Regulation of Adult Hippocampal Neurogenesis; Implications for Epilepsy. Brain Plast 2017; 3:43-59. [PMID: 29765859 PMCID: PMC5928558 DOI: 10.3233/bpl-160036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hippocampal neural stem/progenitor cells (NSPCs) proliferate and differentiate to generate new neurons across the life span of most mammals, including humans. This process takes place within a characteristic local microenvironment where NSPCs interact with a variety of other cell types and encounter systemic regulatory factors. Within this microenvironment, cell intrinsic gene expression programs are modulated by cell extrinsic signals through complex interactions, in many cases involving short non-coding RNA molecules, such as miRNAs. Here we review the regulation of gene expression in NSPCs by miRNAs and its possible implications for epilepsy, which has been linked to alterations in adult hippocampal neurogenesis.
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Affiliation(s)
- Pascal Bielefeld
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, The Netherlands
| | - Catherine Mooney
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - David C. Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Carlos P. Fitzsimons
- Neuroscience Program, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, The Netherlands
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218
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Xie L, Mao M, Xiong K, Jiang B. Circular RNAs: A Novel Player in Development and Disease of the Central Nervous System. Front Cell Neurosci 2017; 11:354. [PMID: 29167634 PMCID: PMC5682331 DOI: 10.3389/fncel.2017.00354] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023] Open
Abstract
Circular RNAs (circRNAs) own unique capabilities to communicate with nucleic acids and ribonucleoproteins and are emerging as indispensable compositions of the regulatory messages encoded in the genome. Due to lack of 3′ termini, circRNAs are more resistant to degradation by exonuclease RNase R and possess greater stability than linear RNAs. Moreover, circRNAs can act as microRNA (miRNA) sponge and affect messenger RNA (mRNA) splicing and transcription. By virtue of their great stability and elaborate regulatory mechanisms of gene expression, circRNAs play important roles in certain physiological activities. The development, homeostasis and stress response of the central nervous system (CNS) depend upon precise temporal and spatial regulation of gene networks. Moreover, emerging evidence has revealed that circRNAs are spatiotemporally regulated and dynamically expressed during brain development; therefore, they can exert significant influences on CNS development and diseases. In this review, we highlight the biogenesis of circRNAs and their central roles in regulation of CNS development and diseases.
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Affiliation(s)
- Lili Xie
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Mao Mao
- Departments of Ophthalmology and Anatomy, Institute for Human Genetics, UCSF School of Medicine, San Francisco, CA, United States
| | - Kun Xiong
- Department of Human Anatomy and Neurobiology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Bing Jiang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China
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219
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Abstract
A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.
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Affiliation(s)
- Francesco P Marchese
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain
| | - Ivan Raimondi
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain.,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain
| | - Maite Huarte
- University of Navarra, Center for Applied Medical Research (CIMA), Pamplona, 31008, Spain. .,Institute of Health Research of Navarra (IdiSNA), Pamplona, 31008, Spain.
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220
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Barter MJ, Gomez R, Hyatt S, Cheung K, Skelton AJ, Xu Y, Clark IM, Young DA. The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells. Development 2017; 144:4510-4521. [PMID: 29084806 PMCID: PMC5769619 DOI: 10.1242/dev.152504] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/25/2017] [Indexed: 12/31/2022]
Abstract
Long non-coding RNAs (lncRNAs) are expressed in a highly tissue-specific manner and function in various aspects of cell biology, often as key regulators of gene expression. In this study, we established a role for lncRNAs in chondrocyte differentiation. Using RNA sequencing we identified a human articular chondrocyte repertoire of lncRNAs from normal hip cartilage donated by neck of femur fracture patients. Of particular interest are lncRNAs upstream of the master chondrocyte transcription factor SOX9 locus. SOX9 is an HMG-box transcription factor that plays an essential role in chondrocyte development by directing the expression of chondrocyte-specific genes. Two of these lncRNAs are upregulated during chondrogenic differentiation of mesenchymal stem cells (MSCs). Depletion of one of these lncRNAs, LOC102723505, which we termed ROCR (regulator of chondrogenesis RNA), by RNA interference disrupted MSC chondrogenesis, concomitant with reduced cartilage-specific gene expression and incomplete matrix component production, indicating an important role in chondrocyte biology. Specifically, SOX9 induction was significantly ablated in the absence of ROCR, and overexpression of SOX9 rescued the differentiation of MSCs into chondrocytes. Our work sheds further light on chondrocyte-specific SOX9 expression and highlights a novel method of chondrocyte gene regulation involving a lncRNA. Summary: This study identified a chondrocyte repertoire of lncRNAs and discovered that ROCR (regulator of chondrogenesis RNA) is important for MSC chondrogenesis and cartilage gene expression by promoting the expression of SOX9.
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Affiliation(s)
- Matt J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rodolfo Gomez
- Musculoskeletal Pathology Group, Institute IDIS, Travesia choupana s/n, Hospital Clínico Universitario de Santiago, Santiago de Compostela, 15706, Spain
| | - Sam Hyatt
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Kat Cheung
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Andrew J Skelton
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Yaobo Xu
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ian M Clark
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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221
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Andersen RE, Lim DA. Forging our understanding of lncRNAs in the brain. Cell Tissue Res 2017; 371:55-71. [PMID: 29079882 DOI: 10.1007/s00441-017-2711-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
During both development and adulthood, the human brain expresses many thousands of long noncoding RNAs (lncRNAs), and aberrant lncRNA expression has been associated with a wide range of neurological diseases. Although the biological significance of most lncRNAs remains to be discovered, it is now clear that certain lncRNAs carry out important functions in neurodevelopment, neural cell function, and perhaps even diseases of the human brain. Given the relatively inclusive definition of lncRNAs-transcripts longer than 200 nucleotides with essentially no protein coding potential-this class of noncoding transcript is both large and very diverse. Furthermore, emerging data indicate that lncRNA genes can act via multiple, non-mutually exclusive molecular mechanisms, and specific functions are difficult to predict from lncRNA expression or sequence alone. Thus, the different experimental approaches used to explore the role of a lncRNA might each shed light upon distinct facets of its overall molecular mechanism, and combining multiple approaches may be necessary to fully illuminate the function of any particular lncRNA. To understand how lncRNAs affect brain development and neurological disease, in vivo studies of lncRNA function are required. Thus, in this review, we focus our discussion upon a small set of neural lncRNAs that have been experimentally manipulated in mice. Together, these examples illustrate how studies of individual lncRNAs using multiple experimental approaches can help reveal the richness and complexity of lncRNA function in both neurodevelopment and diseases of the brain.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.,Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, Ray and Dagmar Dolby Regeneration Medicine Building, 35 Medical Center Way, RMB 1037, San Francisco, CA, 94143, USA. .,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA. .,San Francisco Veterans Affairs Medical Center, San Francisco, CA, 94121, USA.
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222
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Wang A, Wang J, Liu Y, Zhou Y. Mechanisms of Long Non-Coding RNAs in the Assembly and Plasticity of Neural Circuitry. Front Neural Circuits 2017; 11:76. [PMID: 29109677 PMCID: PMC5660110 DOI: 10.3389/fncir.2017.00076] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/28/2017] [Indexed: 12/31/2022] Open
Abstract
The mechanisms underlying development processes and functional dynamics of neural circuits are far from understood. Long non-coding RNAs (lncRNAs) have emerged as essential players in defining identities of neural cells, and in modulating neural activities. In this review, we summarized latest advances concerning roles and mechanisms of lncRNAs in assembly, maintenance and plasticity of neural circuitry, as well as lncRNAs' implications in neurological disorders. We also discussed technical advances and challenges in studying functions and mechanisms of lncRNAs in neural circuitry. Finally, we proposed that lncRNA studies would advance our understanding on how neural circuits develop and function in physiology and disease conditions.
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Affiliation(s)
- Andi Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Junbao Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Liu
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Yan Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,Medical Research Institute, Wuhan University, Wuhan, China
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223
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Govindan S, Jabaudon D. Coupling progenitor and neuronal diversity in the developing neocortex. FEBS Lett 2017; 591:3960-3977. [PMID: 28895133 DOI: 10.1002/1873-3468.12846] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 12/16/2022]
Abstract
The adult neocortex is composed of several types of glutamatergic neurons, which are sequentially born from progenitors during development. The extent and nature of progenitor diversity, and how it relates to neuronal diversity, is still poorly understood. In this review, we discuss key features of neocortical progenitors across several species, including their morphological properties, cell cycling behaviour and molecular signatures, and how these features relate to the competence of these cells to generate distinct types of progenies.
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Affiliation(s)
| | - Denis Jabaudon
- Department of Basic Neuroscience, University of Geneva, Switzerland
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224
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Wang J, Jenjaroenpun P, Bhinge A, Angarica VE, Del Sol A, Nookaew I, Kuznetsov VA, Stanton LW. Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. Genome Res 2017; 27:1783-1794. [PMID: 29030469 PMCID: PMC5668937 DOI: 10.1101/gr.223313.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
Abstract
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators. Our data revealed the bifurcation and developmental tracks of the two NPC subpopulations, and we captured an early (24 h) transition phase that leads to alternative neuronal specifications. The consequent up-regulation and down-regulation of stage- and subpopulation-specific gene groups during the course of maturation revealed biological insights with regard to key regulatory transcription factors and lincRNAs that control cellular programs in the identified neuronal subpopulations.
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Affiliation(s)
- Jiaxu Wang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
| | - Piroon Jenjaroenpun
- Genome and Gene expression Data Analysis Division, Bioinformatics Institute, Singapore 138671
| | - Akshay Bhinge
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, Campus Belval, University of Luxembourg, L-4367 Luxembourg
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Vladimir A Kuznetsov
- Genome and Gene expression Data Analysis Division, Bioinformatics Institute, Singapore 138671
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore/A-STAR, Singapore 138672
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225
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Kong X, Liu W, Kong Y. Roles and expression profiles of long non-coding RNAs in triple-negative breast cancers. J Cell Mol Med 2017; 22:390-394. [PMID: 28941134 PMCID: PMC5742739 DOI: 10.1111/jcmm.13327] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/03/2017] [Indexed: 12/19/2022] Open
Abstract
Triple‐negative breast cancer (TNBC) refers to the breast cancers that express little human epidermal growth factor receptor 2 (HER2), progesterone receptor (PR) and oestrogen receptor (ER). When compared to other types of breast cancers, TNBC behaves more aggressively with relatively poorer prognosis. Moreover, except chemotherapy, no targeted treatments have been approved yet until now. Although the molecular‐biological mechanisms of the initiation and development of TNBC have been explored a lot, the exact details underlying its progressions are still not clear. Long non‐coding RNAs (lncRNAs), with the length greater than 200 nucleotides, are non‐protein coding transcripts. Previous researches have shown that lncRNAs are significantly involved in a variety of pathophysiological processes such as cell migration, invasion, proliferation, differentiation and development. lncRNAs’ dysregulated expressions have been observed in many types of tumours including TNBCs. This article will review the functional roles and dysregulations of lncRNAs in TNBCs. These lncRNAs are worthy of exploitation regarding their potential application values of TNBC's diagnosis and treatment.
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Affiliation(s)
- Xiangyi Kong
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Department of Breast Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenyue Liu
- Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Tissue Engineering and Wound Healing Laboratory, Department of Surgery, Division of Plastic Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yanguo Kong
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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226
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Wang Q, Wang N, Cai R, Zhao F, Xiong Y, Li X, Wang A, Lin P, Jin Y. Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window. Oncotarget 2017; 8:84360-84372. [PMID: 29137430 PMCID: PMC5663602 DOI: 10.18632/oncotarget.21031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/06/2017] [Indexed: 12/17/2022] Open
Abstract
Establishment of the receptive uterus is a crucial step for embryo implantation. In this study, the expression profiles and characterization of long non-coding RNAs (lncRNAs) in pregnant mouse uteri on day 4, day 5 at implantation sites and inter-implantation sites were conducted using RNA-seq. A total of 7,764 putative lncRNA transcripts were identified, including 6,179 known lncRNA transcripts and 1,585 novel lncRNA transcripts. Bioinformatics analysis of the cis and trans lncRNA targets showed that the differentially expressed lncRNAs were mainly involved in tissue remodelling, immune response and metabolism-related processes, indicating that lncRNAs could be involved in the regulation of embryo implantation. We also discovered that differentially expressed lncRNAs might regulate multiple signalling pathways that play an important role in the regulation of embryo implantation. In addition, nine known lncRNAs and four novel lncRNAs were randomly selected and validated by qRT-PCR. The expression of Tug1, Neat1, Gas5, Malat1, H19 and Rmst were significantly regulated in the mouse uterus during the implantation window. Our results are the first to systematically identify lncRNAs in the mouse uterus and provide a catalogue of lncRNAs for further understanding their functions in pregnant mouse uteri during the implantation window.
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Affiliation(s)
- Qi Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Nan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Rui Cai
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fan Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yongjie Xiong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Aihua Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Lin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yaping Jin
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
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227
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Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer MW, Gage FH. Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor Cells. Cell Stem Cell 2017; 21:618-634.e7. [PMID: 28919367 DOI: 10.1016/j.stem.2017.08.012] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/17/2017] [Accepted: 08/16/2017] [Indexed: 12/14/2022]
Abstract
Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that changes during differentiation. Nucleoporins are linked with cell-type-specific gene regulation, coupling physical changes in nuclear structure to transcriptional output; but, whether and how they coordinate with key fate-determining transcription factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2 in adult NeuPCs, where it is indispensable for their maintenance and controls neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional end sites correlates with increased or decreased gene expression, respectively, and inhibiting Nup153 expression alters open chromatin configurations at its target genes, disrupts genomic localization of Sox2, and promotes differentiation in vitro and a gliogenic fate switch in vivo. Together, these findings reveal that nuclear structural proteins may exert bimodal transcriptional effects to control cell fate.
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Affiliation(s)
- Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jonathan Y Hsu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lauren Hu
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Filipe V Jacinto
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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228
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Perry RBT, Ulitsky I. The functions of long noncoding RNAs in development and stem cells. Development 2017; 143:3882-3894. [PMID: 27803057 DOI: 10.1242/dev.140962] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, with tens of thousands of RNAs emanating from uni- and bi-directional promoters and from active enhancers. In vertebrates, thousands of loci in each species produce a class of transcripts called long noncoding RNAs (lncRNAs) that are typically expressed at low levels and do not appear to give rise to functional proteins. Substantial numbers of lncRNAs are expressed at specific stages of embryonic development, in many cases from regions flanking key developmental regulators. Here, we review the known biological functions of such lncRNAs and the emerging paradigms of their modes of action. We also provide an overview of the growing arsenal of methods for lncRNA identification, perturbation and functional characterization.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel
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229
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Long Y, Wang X, Youmans DT, Cech TR. How do lncRNAs regulate transcription? SCIENCE ADVANCES 2017; 3:eaao2110. [PMID: 28959731 PMCID: PMC5617379 DOI: 10.1126/sciadv.aao2110] [Citation(s) in RCA: 476] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/12/2017] [Indexed: 05/11/2023]
Abstract
It has recently become apparent that RNA, itself the product of transcription, is a major regulator of the transcriptional process. In particular, long noncoding RNAs (lncRNAs), which are so numerous in eukaryotes, function in many cases as transcriptional regulators. These RNAs function through binding to histone-modifying complexes, to DNA binding proteins (including transcription factors), and even to RNA polymerase II. In other cases, it is the act of lncRNA transcription rather than the lncRNA product that appears to be regulatory. We review recent progress in elucidating the molecular mechanisms by which lncRNAs modulate gene expression and future opportunities in this research field.
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Affiliation(s)
- Yicheng Long
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Daniel T. Youmans
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Anschutz Medical Campus, University of Colorado Denver, Aurora, CO 80045, USA
| | - Thomas R. Cech
- Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
- Corresponding author.
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230
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Human Long Noncoding RNA Regulation of Stem Cell Potency and Differentiation. Stem Cells Int 2017; 2017:6374504. [PMID: 28951743 PMCID: PMC5603141 DOI: 10.1155/2017/6374504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/12/2017] [Accepted: 08/02/2017] [Indexed: 12/15/2022] Open
Abstract
Because of their capability of differentiation into lineage-specific cells, stem cells are an attractive therapeutic modality in regenerative medicine. To develop an effective stem cell-based therapeutic strategy with predictable results, deeper understanding of the underlying molecular mechanisms of stem cell differentiation and/or pluripotency maintenance is required. Thus, reviewing the key factors involved in the transcriptional and epigenetic regulation of stem cell differentiation and maintenance is important. Accumulating data indicate that long noncoding RNAs (lncRNAs) mediate numerous biological processes, including stem cell differentiation and maintenance. Here, we review recent findings on the human lncRNA regulation of stem cell potency and differentiation. Although the clinical implication of these lncRNAs is only beginning to be elucidated, it is anticipated that lncRNAs will become important therapeutic targets in the near future.
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231
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Yan P, Luo S, Lu JY, Shen X. Cis- and trans-acting lncRNAs in pluripotency and reprogramming. Curr Opin Genet Dev 2017; 46:170-178. [PMID: 28843809 DOI: 10.1016/j.gde.2017.07.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Abstract
Pervasive transcription in mammalian genomes produces thousands of long noncoding RNA (lncRNA) transcripts. Although they have been implicated in diverse biological processes, the functional relevance of most lncRNAs remains unknown. Recent studies reveal the prevalence of lncRNA-mediated cis regulation on nearby transcription. In this review, we summarize cis- and trans-acting lncRNAs involved in stem cell pluripotency and reprogramming, highlighting the role of regulatory lncRNAs in providing an additional layer of complexity to the regulation of genes that govern cell fate during development.
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Affiliation(s)
- Pixi Yan
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sai Luo
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - J Yuyang Lu
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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232
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Alam T, Uludag M, Essack M, Salhi A, Ashoor H, Hanks JB, Kapfer C, Mineta K, Gojobori T, Bajic VB. FARNA: knowledgebase of inferred functions of non-coding RNA transcripts. Nucleic Acids Res 2017; 45:2838-2848. [PMID: 27924038 PMCID: PMC5389649 DOI: 10.1093/nar/gkw973] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/11/2016] [Indexed: 02/01/2023] Open
Abstract
Non-coding RNA (ncRNA) genes play a major role in control of heterogeneous cellular behavior. Yet, their functions are largely uncharacterized. Current available databases lack in-depth information of ncRNA functions across spectrum of various cells/tissues. Here, we present FARNA, a knowledgebase of inferred functions of 10,289 human ncRNA transcripts (2,734 microRNA and 7,555 long ncRNA) in 119 tissues and 177 primary cells of human. Since transcription factors (TFs) and TF co-factors (TcoFs) are crucial components of regulatory machinery for activation of gene transcription, cellular processes and diseases in which TFs and TcoFs are involved suggest functions of the transcripts they regulate. In FARNA, functions of a transcript are inferred from TFs and TcoFs whose genes co-express with the transcript controlled by these TFs and TcoFs in a considered cell/tissue. Transcripts were annotated using statistically enriched GO terms, pathways and diseases across cells/tissues based on guilt-by-association principle. Expression profiles across cells/tissues based on Cap Analysis of Gene Expression (CAGE) are provided. FARNA, having the most comprehensive function annotation of considered ncRNAs across widest spectrum of human cells/tissues, has a potential to greatly contribute to our understanding of ncRNA roles and their regulatory mechanisms in human. FARNA can be accessed at: http://cbrc.kaust.edu.sa/farna
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Affiliation(s)
- Tanvir Alam
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Mahmut Uludag
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Haitham Ashoor
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - John B Hanks
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Craig Kapfer
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
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233
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Sun W, Pei L, Liang Z. mRNA and Long Non-coding RNA Expression Profiles in Rats Reveal Inflammatory Features in Sepsis-Associated Encephalopathy. Neurochem Res 2017; 42:3199-3219. [DOI: 10.1007/s11064-017-2357-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 01/31/2023]
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234
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Tang J, Yu Y, Yang W. Long noncoding RNA and its contribution to autism spectrum disorders. CNS Neurosci Ther 2017; 23:645-656. [PMID: 28635106 PMCID: PMC6492731 DOI: 10.1111/cns.12710] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 12/13/2022] Open
Abstract
Recent studies have indicated that long noncoding RNAs (lncRNAs) play important roles in multiple processes, such as epigenetic regulation, gene expression regulation, development, nutrition-related and other diseases, toxic response, and response to drugs. Although the functional roles and mechanisms of several lncRNAs have been discovered, a better understanding of the vast majority of lncRNAs remains elusive. To understand the functional roles and mechanisms of lncRNAs is critical because these transcripts represent the majority of the transcriptional output of the mammalian genome. Recent studies have also suggested that lncRNAs are more abundant in the human brain and are involved in neurodevelopment and neurodevelopmental disorders, including autism spectrum disorders (ASDs). In this study, we review several known functions of lncRNAs and the potential contribution of lncRNAs to ASDs and to other genetic syndromes that have a similar clinical presentation to ASDs, such as fragile X syndrome and Rett syndrome.
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Affiliation(s)
- Jie Tang
- The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
- Department of Preventive MedicineSchool of Public HealthGuangzhou Medical UniversityXinzaoPanyu DistrictGuangzhouChina
| | - Yizhen Yu
- Department of Child and Women Health CareSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei Yang
- Department of Nutrition and Food HygieneHubei Key Laboratory of Food Nutrition and SafetyTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Nutrition and Food HygieneMOE Key Lab of Environment and HealthSchool of Public HealthTongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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235
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Delás MJ, Hannon GJ. lncRNAs in development and disease: from functions to mechanisms. Open Biol 2017; 7:170121. [PMID: 28747406 PMCID: PMC5541349 DOI: 10.1098/rsob.170121] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Differential expression of long non-coding RNAs (lncRNAs) during differentiation and their misregulation in cancer highlight their potential as cell fate regulators. While some example lncRNAs have been characterized in great detail, the functional in vivo relevance of others has been called into question. Finding functional lncRNAs will most probably require a combination of complementary approaches that will greatly vary depending on their mode of action. In this review, we discuss the different tools available to dissect genetically lncRNA requirements and how each is best suited to studies in particular contexts. Moreover, we review different strategies used to select candidate lncRNAs and give an overview of lncRNAs described to regulate development and cancer through different mechanisms.
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Affiliation(s)
- M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY 11724, USA
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY 11724, USA
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
- New York Genome Center, 101 6th Ave, New York, NY 10013, USA
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236
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Quan Z, Zheng D, Qing H. Regulatory Roles of Long Non-Coding RNAs in the Central Nervous System and Associated Neurodegenerative Diseases. Front Cell Neurosci 2017; 11:175. [PMID: 28713244 PMCID: PMC5491930 DOI: 10.3389/fncel.2017.00175] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes. Mounting evidence has indicated dysregulation or mutations in lncRNA gene loci are associated with a variety of CNS-associated neurodegenerative disorders, such as Alzheimer's, Parkinson's, Huntington's diseases, Amyotrophic Lateral Sclerosis and others. However, how lncRNAs contribute to these disorders remains to be further explored and studied. In this review article, we systematically and comprehensively summarize the current studies of lncRNAs, demonstrate the specificity of lncRNAs expressed in the brain, their functions during neural development and expression profiles in major cell types of the CNS, highlight the regulatory mechanisms of several studied lncRNAs that may play essential roles in the pathophysiology of neurodegenerative diseases, and discuss the current challenges and future perspectives of lncRNA studies involved in neurodegenerative and other diseases.
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Affiliation(s)
- Zhenzhen Quan
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Da Zheng
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Hong Qing
- School of Life Science, Beijing Institute of TechnologyBeijing, China
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237
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Long Noncoding RNAs in Pluripotency of Stem Cells and Cell Fate Specification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1008:223-252. [DOI: 10.1007/978-981-10-5203-3_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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238
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Wang P, Mokhtari R, Pedrosa E, Kirschenbaum M, Bayrak C, Zheng D, Lachman HM. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. Mol Autism 2017; 8:11. [PMID: 28321286 PMCID: PMC5357816 DOI: 10.1186/s13229-017-0124-1] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/15/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND CHD8 (chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous for CHD8 knockout (KO) alleles generated using CRISPR-Cas9 gene editing. A significant number of ASD and SZ candidate genes were among those that were differentially expressed in a comparison of heterozygous KO lines (CHD8+/-) vs isogenic controls (CHD8+/-), including the SZ and bipolar disorder (BD) candidate gene TCF4, which was markedly upregulated in CHD8+/- neuronal cells. METHODS In the current study, RNA-seq was carried out on CHD8+/- and isogenic control (CHD8+/+) cerebral organoids, which are 3-dimensional structures derived from iPS cells that model the developing human telencephalon. RESULTS TCF4 expression was, again, significantly upregulated. Pathway analysis carried out on differentially expressed genes (DEGs) revealed an enrichment of genes involved in neurogenesis, neuronal differentiation, forebrain development, Wnt/β-catenin signaling, and axonal guidance, similar to our previous study on NPCs and monolayer neurons. There was also significant overlap in our CHD8+/- DEGs with those found in a transcriptome analysis carried out by another group using cerebral organoids derived from a family with idiopathic ASD. Remarkably, the top DEG in our respective studies was the non-coding RNA DLX6-AS1, which was markedly upregulated in both studies; DLX6-AS1 regulates the expression of members of the DLX (distal-less homeobox) gene family. DLX1 was also upregulated in both studies. DLX genes code for transcription factors that play a key role in GABAergic interneuron differentiation. Significant overlap was also found in a transcriptome study carried out by another group using iPS cell-derived neurons from patients with BD, a condition characterized by dysregulated WNT/β-catenin signaling in a subgroup of affected individuals. CONCLUSIONS Overall, the findings show that distinct ASD, SZ, and BD candidate genes converge on common molecular targets-an important consideration for developing novel therapeutics in genetically heterogeneous complex traits.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Ryan Mokhtari
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Michael Kirschenbaum
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Can Bayrak
- Erciyes University School of Medicine, Kayseri, Turkey
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
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239
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Luginbühl J, Sivaraman DM, Shin JW. The essentiality of non-coding RNAs in cell reprogramming. Noncoding RNA Res 2017; 2:74-82. [PMID: 30159423 PMCID: PMC6096403 DOI: 10.1016/j.ncrna.2017.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/03/2017] [Accepted: 04/11/2017] [Indexed: 02/07/2023] Open
Abstract
In mammals, short (mi-) and long non-coding (lnc) RNAs are immensely abundant and they are proving to be more functional than ever before. Particularly in cell reprogramming, non-coding RNAs are essential to establish the pluripotent network and are indispensable to reprogram somatic cells to pluripotency. Through systematic screening and mechanistic studies, diverse functional features of both miRNA and lncRNAs have emerged as either scaffolds, inhibitors, or co-activators, necessary to orchestrate the intricacy of gene regulation. Furthermore, the collective characterizations of both miRNA and lncRNA reveal their interdependency (e.g. sequestering the function of the other) to modulate cell reprogramming. This review broadly explores the regulatory processes of cell reprogramming - with key functional examples in neuronal and cardiac differentiations - in the context of both short and long non-coding RNAs.
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Affiliation(s)
| | | | - Jay W. Shin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, 230-0045 Japan
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240
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Molecular basis for the genome engagement by Sox proteins. Semin Cell Dev Biol 2017; 63:2-12. [DOI: 10.1016/j.semcdb.2016.08.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 01/11/2023]
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241
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Reddy AS, O'Brien D, Pisat N, Weichselbaum CT, Sakers K, Lisci M, Dalal JS, Dougherty JD. A Comprehensive Analysis of Cell Type-Specific Nuclear RNA From Neurons and Glia of the Brain. Biol Psychiatry 2017; 81:252-264. [PMID: 27113499 PMCID: PMC4996761 DOI: 10.1016/j.biopsych.2016.02.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 02/05/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Studies in psychiatric genetics have identified >100 loci associated with disease risk, yet many of these loci are distant from protein coding genes. Recent characterization of the transcriptional landscape of cell lines and whole tissues has suggested widespread transcription in both coding and noncoding regions of the genome, including differential expression from loci that produce regulatory noncoding RNAs that function within the nucleus; however, the nuclear transcriptome of specific cell types in the brain has not been previously investigated. METHODS We defined the nuclear transcriptional landscape of the three major cellular divisions of the nervous system using flow sorting of genetically labeled nuclei from bacTRAP mouse lines. Next, we characterized the unique expression of coding, noncoding, and intergenic RNAs in the mature mouse brain with RNA-Seq and validation with independent methods. RESULTS We found diverse expression across the cell types of all classes of RNAs, including long noncoding RNAs, several of which were confirmed as highly enriched in the nuclei of specific cell types using anatomic methods. We also discovered several examples of cell type-specific expression of tandem gene fusions, and we report the first cell type-specific expression of circular RNAs-a neuron-specific and nuclear-enriched RNA arising from the gene Hnrnpu. CONCLUSIONS These data provide an important resource for studies evaluating the function of various noncoding RNAs in the brain, including noncoding RNAs that may play a role in psychiatric disease.
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Affiliation(s)
- Adarsh S Reddy
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri
| | - David O'Brien
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri.
| | - Nilambari Pisat
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Claire T Weichselbaum
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Kristina Sakers
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Miriam Lisci
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Jasbir S Dalal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
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242
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The Role of Noncoding RNAs in Neurodevelopmental Disorders: The Case of Rett Syndrome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:23-37. [DOI: 10.1007/978-3-319-53889-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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243
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Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression. Nat Rev Mol Cell Biol 2016; 17:756-770. [DOI: 10.1038/nrm.2016.126] [Citation(s) in RCA: 420] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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244
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Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI. Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. BMC Genomics 2016; 17:691. [PMID: 27576499 PMCID: PMC5006418 DOI: 10.1186/s12864-016-2934-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/12/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. RESULTS We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72 % of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. CONCLUSIONS The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.
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Affiliation(s)
- Cristian A. Velandia-Huerto
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia
| | - Adriaan A. Gittenberger
- Institute of Biology, Leiden University, Leiden, P.O. Box 9505, 2300 RA Netherlands
- GiMaRIS, BioScience Park Leiden, J.H. Oortweg 21, 2333 CH, Leiden, Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Federico D. Brown
- Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, Colombia
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo SP, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, Praia do Cabelo Gordo, São Sebastião, Brazil
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, D-04107 Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103 Germany
- Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103 Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090 Austria
- Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
| | - Clara I. Bermúdez-Santana
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia
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245
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Mouse models of Down syndrome: gene content and consequences. Mamm Genome 2016; 27:538-555. [PMID: 27538963 DOI: 10.1007/s00335-016-9661-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/27/2016] [Indexed: 12/25/2022]
Abstract
Down syndrome (DS), trisomy of human chromosome 21 (Hsa21), is challenging to model in mice. Not only is it a contiguous gene syndrome spanning 35 Mb of the long arm of Hsa21, but orthologs of Hsa21 genes map to segments of three mouse chromosomes, Mmu16, Mmu17, and Mmu10. The Ts65Dn was the first viable segmental trisomy mouse model for DS; it is a partial trisomy currently popular in preclinical evaluations of drugs for cognition in DS. Limitations of the Ts65Dn are as follows: (i) it is trisomic for 125 human protein-coding orthologs, but only 90 of these are Hsa21 orthologs and (ii) it lacks trisomy for ~75 Hsa21 orthologs. In recent years, several additional mouse models of DS have been generated, each trisomic for a different subset of Hsa21 genes or their orthologs. To best exploit these models and interpret the results obtained with them, prior to proposing clinical trials, an understanding of their trisomic gene content, relative to full trisomy 21, is necessary. Here we first review the functional information on Hsa21 protein-coding genes and the more recent annotation of a large number of functional RNA genes. We then discuss the conservation and genomic distribution of Hsa21 orthologs in the mouse genome and the distribution of mouse-specific genes. Lastly, we consider the strengths and weaknesses of mouse models of DS based on the number and nature of the Hsa21 orthologs that are, and are not, trisomic in each, and discuss their validity for use in preclinical evaluations of drug responses.
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The long non-coding RNA, SNHG6-003, functions as a competing endogenous RNA to promote the progression of hepatocellular carcinoma. Oncogene 2016; 36:1112-1122. [PMID: 27530352 DOI: 10.1038/onc.2016.278] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/25/2016] [Accepted: 07/01/2016] [Indexed: 01/17/2023]
Abstract
The expression of long non-coding RNAs (lncRNAs) is dysregulated in hepatocellular carcinoma (HCC). However, the functions and contributions of lncRNAs remain largely unknown. Here, we identified a critical role of SNHG6-003 in HCC. We found that five SNHG6 transcripts were differentially expressed in HCC tissues while only the SNHG6-003 had an oncogenic function. Ectopic expression of SNHG6-003 in HCC cells promoted cell proliferation and induced drug resistance, whereas SNHG6-003 knockdown promoted apoptosis. Moreover, SNHG6-003 functioned as a competitive endogenous RNA (ceRNA), effectively becoming sponge for miR-26a/b and thereby modulating the expression of transforming growth factor-β-activated kinase 1 (TAK1). Importantly, expression analysis revealed that both SNHG6-003 and TAK1 were upregulated in human cancers, exhibiting a co-expression pattern. In HCC patients, high expression of SNHG6-003 closely correlated with tumor progression and shorter survival. Thus, targeting the ceRNA network involving SNHG6-003 may be used as a treatment strategy against HCC.
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Nitsche A, Stadler PF. Evolutionary clues in lncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27436689 DOI: 10.1002/wrna.1376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/06/2016] [Accepted: 06/09/2016] [Indexed: 12/13/2022]
Abstract
The diversity of long non-coding RNAs (lncRNAs) in the human transcriptome is in stark contrast to the sparse exploration of their functions concomitant with their conservation and evolution. The pervasive transcription of the largely non-coding human genome makes the evolutionary age and conservation patterns of lncRNAs to a topic of interest. Yet it is a fairly unexplored field and not that easy to determine as for protein-coding genes. Although there are a few experimentally studied cases, which are conserved at the sequence level, most lncRNAs exhibit weak or untraceable primary sequence conservation. Recent studies shed light on the interspecies conservation of secondary structures among lncRNA homologs by using diverse computational methods. This highlights the importance of structure on functionality of lncRNAs as opposed to the poor impact of primary sequence changes. Further clues in the evolution of lncRNAs are given by selective constraints on non-coding gene structures (e.g., promoters or splice sites) as well as the conservation of prevalent spatio-temporal expression patterns. However, a rapid evolutionary turnover is observable throughout the heterogeneous group of lncRNAs. This still gives rise to questions about its functional meaning. WIREs RNA 2017, 8:e1376. doi: 10.1002/wrna.1376 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Anne Nitsche
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Institute de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Cedex, France
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany.,Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, Leipzig, Germany.,Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Santa Fe Institute, Santa Fe, NM, USA
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248
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Chen L, Feng P, Zhu X, He S, Duan J, Zhou D. Long non-coding RNA Malat1 promotes neurite outgrowth through activation of ERK/MAPK signalling pathway in N2a cells. J Cell Mol Med 2016; 20:2102-2110. [PMID: 27374227 PMCID: PMC5082393 DOI: 10.1111/jcmm.12904] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/09/2016] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) are playing critical roles in neurogenesis, yet the underlying molecular mechanisms remain largely elusive. Neurite outgrowth is an early step in neuronal differentiation and regeneration. Using in vitro differentiation of neuroblastoma-derived Neuro-2a (N2a) cell as a model, we performed expression profiling to identify lncRNAs putatively relevant for neurite outgrowth. We identified that Metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was one of the most significantly up-regulated lncRNAs during N2a cell differentiation. Malat1 knockdown resulted in defects in neurite outgrowth as well as enhanced cell death. To pinpoint signalling pathways perturbed by Malat1 depletion, we then performed a reporter-based screening to examine the activities of 50 signalling pathways in Malat1 knockdown cells. We found that Malat1 knockdown resulted in conspicuous inhibition of Mitogen-Activated Protein Kinase (MAPK) signaling pathway as well as abnormal activation of Peroxisome proliferator-activated receptor (PPAR) and P53 signalling pathway. Inhibition of ERK/MAPK pathway with PD98059 potently blocked N2a cell neurite outgrowth, whereas phorbol 12-myristate 13-acetate-induced ERK activation rescued defects in neurite outgrowth and cell death induced by Malat1 depletion. Together, our results established a critical role of Malat1 in the early step of neuronal differentiation through activating ERK/MAPK signalling pathway.
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Affiliation(s)
- Lei Chen
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China.
| | - Peimin Feng
- Department of Gastroenterology, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xi Zhu
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
| | - Shixu He
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
| | - Jialan Duan
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
| | - Dong Zhou
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, China
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Zhong J, Jiang L, Cheng C, Huang Z, Zhang H, Liu H, He J, Cao F, Peng J, Jiang Y, Sun X. Altered expression of long non-coding RNA and mRNA in mouse cortex after traumatic brain injury. Brain Res 2016; 1646:589-600. [PMID: 27380725 DOI: 10.1016/j.brainres.2016.07.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/27/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND OBJECTIVE The present study aims to detect the altered lncRNA expression in the mouse cortex after traumatic brain injury (TBI). We also simultaneously detected the altered mRNA profile to further analyze the possible function of lncRNA. METHOD C57BL/6 mice (n=18) were used to construct a controlled cortical impact model. At 24h post-TBI, the cortex around injury site was collected and the total RNA was extracted to construct the cDNA library. RNA sequencing (RNA-seq) was carried out followed by RT-PCR for confirmation. Bioinformatic analysis (including GO analysis, KEGG pathway and co-expression analysis) also were performed. RESULTS A total of 64,530 transcripts were detected in the current sequencing study, in which 27,457 transcripts were identified as mRNA and 37,073 transcripts as lncRNA. A total of 1580 mRNAs (1430 up-regulated and 150 down-regulated) and 823 lncRNAs (667 up-regulated and 156 down-regulated) were significantly changed according to the criteria ( (|)log2((fold change))|>1 and P<0.05). These altered mRNAs were mainly related to inflammatory and immunological activity, metabolism, neuronal and vascular network. The expression of single lncRNA may be related with several mRNAs, and so was the mRNA. Also, a total of 360 new mRNAs and 8041 new lncRNAs were identified. The good reproducibility and reliability of RNA-seq were confirmed by RT-PCR. CONCLUSION Numerous lncRNAs and mRNAs were significantly altered in mouse cortex around the injury site 24h after TBI. Our present data may provide a promising approach for further study about TBI.
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Affiliation(s)
- Jianjun Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Chongjie Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Zhijian Huang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hongrong Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Han Liu
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Junchi He
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Fang Cao
- Department of Cerebrovascular, the First Affiliated Hospital of Zunyi Medical College, Zunyi, Guizhou 653000, China
| | - Jianhua Peng
- Department of Neurosurgery, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichaun 646000, China
| | - Yong Jiang
- Department of Neurosurgery, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichaun 646000, China
| | - Xiaochuan Sun
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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Yang F, Liu YH, Dong SY, Yao ZH, Lv L, Ma RM, Dai XX, Wang J, Zhang XH, Wang OC. Co-expression networks revealed potential core lncRNAs in the triple-negative breast cancer. Gene 2016; 591:471-7. [PMID: 27380926 DOI: 10.1016/j.gene.2016.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/26/2016] [Accepted: 07/01/2016] [Indexed: 12/27/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer with unfavorable outcome. It is urgent to explore novel biomarkers and potential therapeutic targets in this malignancy. Increasing knowledge of long noncoding RNAs (lncRNAs) significantly deepens our understanding of cancer biology. Here, we sequenced eight paired TNBC tumor tissues and non-cancerous tissues, and validated significantly differentially expressed lncRNAs. Gene ontology (GO) and pathway analysis were used to investigate the function of differentially expressed mRNAs. Further, potential core lncRNAs in TNBC were identified by co-expression networks. Kaplan-Meier analysis also indicated that breast cancer patients with lower expression level of rhabdomyosarcoma 2 associated transcript (RMST), one of the potential core lncRNAs, had worse overall survival. To the best of our knowledge, it was the first report that RMST was involved in breast cancer. Our research provided a rich resource to the research community for further investigating lncRNAs functions and identifying lncRNAs with diagnostic and therapeutic potentials in TNBC.
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Affiliation(s)
- Fan Yang
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Ye-Huan Liu
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Si-Yang Dong
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Zhi-Han Yao
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Lin Lv
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Rui-Min Ma
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xuan-Xuan Dai
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Jiao Wang
- Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xiao-Hua Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China.
| | - Ou-Chen Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, PR China.
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