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Dayal S, Chaubey D, Joshi DC, Ranmale S, Pillai B. Noncoding RNAs: Emerging regulators of behavioral complexity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1847. [PMID: 38702948 DOI: 10.1002/wrna.1847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/06/2024]
Abstract
The mammalian genome encodes thousands of non-coding RNAs (ncRNAs), ranging in size from about 20 nucleotides (microRNAs or miRNAs) to kilobases (long non-coding RNAs or lncRNAs). ncRNAs contribute to a layer of gene regulation that could explain the evolution of massive phenotypic complexity even as the number of protein-coding genes remains unaltered. We propose that low conservation, poor expression, and highly restricted spatiotemporal expression patterns-conventionally considered ncRNAs may affect behavior through direct, rapid, and often sustained regulation of gene expression at the transcriptional, post-transcriptional, or translational levels. Besides these direct roles, their effect during neurodevelopment may manifest as behavioral changes later in the organism's life, especially when exposed to environmental cues like stress and seasonal changes. The lncRNAs affect behavior through diverse mechanisms like sponging of miRNAs, recruitment of chromatin modifiers, and regulation of alternative splicing. We highlight the need for synthesis between rigorously designed behavioral paradigms in model organisms and the wide diversity of behaviors documented by ethologists through field studies on organisms exquisitely adapted to their environmental niche. Comparative genomics and the latest advancements in transcriptomics provide an unprecedented scope for merging field and lab studies on model and non-model organisms to shed light on the role of ncRNAs in driving the behavioral responses of individuals and groups. We touch upon the technical challenges and contentious issues that must be resolved to fully understand the role of ncRNAs in regulating complex behavioral traits. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sanovar Dayal
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Divya Chaubey
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samruddhi Ranmale
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Beena Pillai
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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2
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Huang P, Wei S, Ren J, Tang Z, Guo M, Situ F, Zhang D, Zhu J, Xiao L, Xu J, Liu G. MicroRNA-124-3p alleviates cerebral ischaemia-induced neuroaxonal damage by enhancing Nrep expression. J Stroke Cerebrovasc Dis 2023; 32:106949. [PMID: 36535134 DOI: 10.1016/j.jstrokecerebrovasdis.2022.106949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Ischaemic stroke has a high death rate and frequently results in long-term and severe brain damage in survivors. miRNA-124-3p (miR-124-3p) treatment has been suggested to reduce ischaemia and play a vital function in avoiding neuron death. An investigation of the role of miR-124-3p, in the ischaemia damage repair or protection in the middle cerebral artery occlusion (MCAO) model and oxygen-glucose deprivation/reperfusion (OGD/R) model, was the purpose of this research. METHODS The expression of miRNA and mRNA in the MCAO model was predicted using bioinformatics analysis. The OGD/R neuronal model was developed. We examined the influence of a number of compounds on the OGD/R model in vitro using gain- and loss-of-function approaches. RESULTS For starters, miR-124-3p and Nrep level in the MCAO model were found to be lower in the model predicted by bioinformatics than in the sham-operated group. And then in the OGD/R model, miR-124-3p treatment reduced OGD/R neuronal damage, increased neuronal survival, and reduced apoptosis in cell lines. Moreover, we further looked at the impact of miR-124-3p on downstream Rnf38 and Nrep using the OGD/R model. Western blot analysis and dual-luciferase reporter assays indicated that miR-124-3p binds and inhibits Rnf38. Finally, although Nrep expression was reduced in the OGD/R model neuronal model, it was shown that miR-124-3p administration reduced apoptosis and increased neuronal activity, particularly with regard to axon regeneration-related proteins. CONCLUSION Our studies have shown that miR-124-3p may reduce neuronal injury by preventing Rnf38-mediated effects on the Nrep axis.
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Affiliation(s)
- Peng Huang
- Women and Children Medical Research Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China; Surgical Department, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Songren Wei
- Department of Neuropharmacology and Novel Drug Discovery, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jing Ren
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhuohong Tang
- Department of Pharmacy, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Mingjuan Guo
- Women and Children Medical Research Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Fen Situ
- Surgical Department, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Dan Zhang
- Surgical Department, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Jianghua Zhu
- Department of Pharmacy, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China
| | - Li Xiao
- Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China.
| | - Jiangping Xu
- Department of Neuropharmacology and Novel Drug Discovery, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Guoqing Liu
- Women and Children Medical Research Center, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China.
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3
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Pellegrini F, Padovano V, Biscarini S, Santini T, Setti A, Galfrè SG, Silenzi V, Vitiello E, Mariani D, Nicoletti C, Torromino G, De Leonibus E, Martone J, Bozzoni I. A KO mouse model for the lncRNA Lhx1os produces motor neuron alterations and locomotor impairment. iScience 2022; 26:105891. [PMID: 36647387 PMCID: PMC9840152 DOI: 10.1016/j.isci.2022.105891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Here, we describe a conserved motor neuron-specific long non-coding RNA, Lhx1os, whose knockout in mice produces motor impairment and postnatal reduction of mature motor neurons (MNs). The ER stress-response pathway result specifically altered with the downregulation of factors involved in the unfolded protein response (UPR). Lhx1os was found to bind the ER-associated PDIA3 disulfide isomerase and to affect the expression of the same set of genes controlled by this protein, indicating that the two factors act in conjunction to modulate the UPR. Altogether, the observed phenotype and function of Lhx1os indicate its important role in the control of MN homeostasis and function.
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Affiliation(s)
- Flaminia Pellegrini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy,Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Vittorio Padovano
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy,Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy,Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Silvia Giulia Galfrè
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Valentina Silenzi
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy,Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Erika Vitiello
- Center for Human Technologies (CHT) Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Davide Mariani
- Center for Human Technologies (CHT) Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Carmine Nicoletti
- DAHFMO - Section of Histology and Medical Embryology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Torromino
- Institute of Cellular Biology and Neurobiology "ABT", CNR, Monterotondo, 00015 Rome, Italy
| | - Elvira De Leonibus
- Institute of Cellular Biology and Neurobiology "ABT", CNR, Monterotondo, 00015 Rome, Italy,Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, 80078 Naples, Italy
| | - Julie Martone
- Institute of Molecular Biology and Pathology, CNR, 00185 Rome, Italy,Corresponding author
| | - Irene Bozzoni
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy,Center for Life Nano- & Neuro-Science@Sapienza of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy,Center for Human Technologies (CHT) Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy,Corresponding author
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4
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Carvelli A, Setti A, Desideri F, Galfrè SG, Biscarini S, Santini T, Colantoni A, Peruzzi G, Marzi MJ, Capauto D, Di Angelantonio S, Ballarino M, Nicassio F, Laneve P, Bozzoni I. A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. EMBO J 2022; 41:e108918. [PMID: 35698802 PMCID: PMC9251839 DOI: 10.15252/embj.2021108918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The transition from dividing progenitors to postmitotic motor neurons (MNs) is orchestrated by a series of events, which are mainly studied at the transcriptional level by analyzing the activity of specific programming transcription factors. Here, we identify a post‐transcriptional role of a MN‐specific transcriptional unit (MN2) harboring a lncRNA (lncMN2‐203) and two miRNAs (miR‐325‐3p and miR‐384‐5p) in this transition. Through the use of in vitro mESC differentiation and single‐cell sequencing of CRISPR/Cas9 mutants, we demonstrate that lncMN2‐203 affects MN differentiation by sponging miR‐466i‐5p and upregulating its targets, including several factors involved in neuronal differentiation and function. In parallel, miR‐325‐3p and miR‐384‐5p, co‐transcribed with lncMN2‐203, act by repressing proliferation‐related factors. These findings indicate the functional relevance of the MN2 locus and exemplify additional layers of specificity regulation in MN differentiation.
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Affiliation(s)
- Andrea Carvelli
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Silvia Giulia Galfrè
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Capauto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
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Zheng YQ, Suo GH, Liu D, Li HY, Wu YJ, Ni H. Nexmifa Regulates Axon Morphogenesis in Motor Neurons in Zebrafish. Front Mol Neurosci 2022; 15:848257. [PMID: 35431796 PMCID: PMC9009263 DOI: 10.3389/fnmol.2022.848257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Nexmif is mainly expressed in the central nervous system (CNS) and plays important roles in cell migration, cell to cell and cell-matrix adhesion, and maintains normal synaptic formation and function. Nevertheless, it is unclear how nexmif is linked to motor neuron morphogenesis. Here, we provided in situ hybridization evidence that nexmifa (zebrafish paralog) was localized to the brain and spinal cord and acted as a vital regulator of motor neuron morphogenesis. Nexmifa deficiency in zebrafish larvae generated abnormal primary motor neuron (PMN) development, including truncated Cap axons and decreased branches in Cap axons. Importantly, RNA-sequencing showed that nexmifa-depleted zebrafish embryos caused considerable CNS related gene expression alterations. Differentially expressed genes (DEGs) were mainly involved in axon guidance and several synaptic pathways, including glutamatergic, GABAergic, dopaminergic, cholinergic, and serotonergic synapse pathways, according to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. In particular, when compared with other pathways, DEGs were highest (84) in the axon guidance pathway, according to Organismal Systems. Efna5b, bmpr2b, and sema6ba were decreased markedly in nexmifa-depleted zebrafish embryos. Moreover, both overexpression of efna5b mRNA and sema6ba mRNA could partially rescued motor neurons morphogenesis. These observations supported nexmifa as regulating axon morphogenesis of motor neurons in zebrafish. Taken together, nexmifa elicited crucial roles during motor neuron development by regulating the morphology of neuronal axons.
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Affiliation(s)
- Yu-qin Zheng
- Division of Brain Science, Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, China
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Gui-hai Suo
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - Dong Liu
- School of Life Sciences, Nantong University, Nantong, China
| | - Hai-ying Li
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
| | - You-jia Wu
- Department of Pediatrics, Affiliated Hospital of Nantong University, Nantong, China
- You-jia Wu,
| | - Hong Ni
- Division of Brain Science, Institute of Pediatric Research, Children’s Hospital of Soochow University, Suzhou, China
- *Correspondence: Hong Ni,
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6
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The Effects of the Olig Family on the Regulation of Spinal Cord Development and Regeneration. Neurochem Res 2021; 46:2776-2782. [PMID: 34228233 DOI: 10.1007/s11064-021-03383-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/22/2022]
Abstract
Neurons and glial cells in the central nervous system (CNS) are generated from neuroepithelial cells in the ventricular zone that surrounds the embryonic neural tube. The proliferation and distinct differentiation of neural precursors occurs at certain stages and are regulated by a series of transcription factors leading to the generation of neuronal and glial cell subtypes. In this manuscript, we review the effects of the Olig family, namely, members Olig1, Olig2 and Olig3, on the distinct differentiation of glial and neuronal cells in the developing spinal cord and injured neural tissue.
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7
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Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S. Functional long non-coding and circular RNAs in zebrafish. Brief Funct Genomics 2021:elab014. [PMID: 33755040 DOI: 10.1093/bfgp/elab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023] Open
Abstract
The utility of model organisms to understand the function of a novel transcript/genes has allowed us to delineate their molecular mechanisms in maintaining cellular homeostasis. Organisms such as zebrafish have contributed a lot in the field of developmental and disease biology. Attributable to advancement and deep transcriptomics, many new transcript isoforms and non-coding RNAs such as long noncoding RNA (lncRNA) and circular RNAs (circRNAs) have been identified and cataloged in multiple databases and many more are yet to be identified. Various methods and tools have been utilized to identify lncRNAs/circRNAs in zebrafish using deep sequencing of transcriptomes as templates. Functional analysis of a few candidates such as tie1-AS, ECAL1 and CDR1as in zebrafish provides a prospective outline to approach other known or novel lncRNA/circRNA. New genetic alteration tools like TALENS and CRISPRs have helped in probing for the molecular function of lncRNA/circRNA in zebrafish. Further latest improvements in experimental and computational techniques offer the identification of lncRNA/circRNA counterparts in humans and zebrafish thereby allowing easy modeling and analysis of function at cellular level.
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8
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Vangoor VR, Gomes‐Duarte A, Pasterkamp RJ. Long non-coding RNAs in motor neuron development and disease. J Neurochem 2021; 156:777-801. [PMID: 32970857 PMCID: PMC8048821 DOI: 10.1111/jnc.15198] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
Abstract
Long non-coding RNAs (lncRNAs) are RNAs that exceed 200 nucleotides in length and that are not translated into proteins. Thousands of lncRNAs have been identified with functions in processes such as transcription and translation regulation, RNA processing, and RNA and protein sponging. LncRNAs show prominent expression in the nervous system and have been implicated in neural development, function and disease. Recent work has begun to report on the expression and roles of lncRNAs in motor neurons (MNs). The cell bodies of MNs are located in cortex, brainstem or spinal cord and their axons project into the brainstem, spinal cord or towards peripheral muscles, thereby controlling important functions such as movement, breathing and swallowing. Degeneration of MNs is a pathological hallmark of diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. LncRNAs influence several aspects of MN development and disruptions in these lncRNA-mediated effects are proposed to contribute to the pathogenic mechanisms underlying MN diseases (MNDs). Accumulating evidence suggests that lncRNAs may comprise valuable therapeutic targets for different MNDs. In this review, we discuss the role of lncRNAs (including circular RNAs [circRNAs]) in the development of MNs, discuss how lncRNAs may contribute to MNDs and provide directions for future research.
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Affiliation(s)
- Vamshidhar R. Vangoor
- Department of Translational NeuroscienceUniversity Medical Center Utrecht Brain CenterUtrecht UniversityUtrechtThe Netherlands
| | - Andreia Gomes‐Duarte
- Department of Translational NeuroscienceUniversity Medical Center Utrecht Brain CenterUtrecht UniversityUtrechtThe Netherlands
| | - R. Jeroen Pasterkamp
- Department of Translational NeuroscienceUniversity Medical Center Utrecht Brain CenterUtrecht UniversityUtrechtThe Netherlands
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9
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Tan L, Yu M, Li Y, Xue S, Chen J, Zhai Y, Fang X, Liu J, Liu J, Wu X, Xu H, Shen Q. Overexpression of Long Non-coding RNA 4933425B07 Rik Causes Urinary Malformations in Mice. Front Cell Dev Biol 2021; 9:594640. [PMID: 33681192 PMCID: PMC7933199 DOI: 10.3389/fcell.2021.594640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) is a common birth defect and is the leading cause of end-stage renal disease in children. The etiology of CAKUT is complex and includes mainly genetic and environmental factors. However, these factors cannot fully explain the etiological mechanism of CAKUT. Recently, participation of long non-coding RNAs (lncRNAs) in the development of the circulatory and nervous systems was demonstrated; however, the role of lncRNAs in the development of the kidney and urinary tract system is unclear. In this study, we used the piggyBac (PB) transposon-based mutagenesis to construct a mouse with lncRNA 4933425B07Rik (Rik) PB insertion (RikPB/PB) and detected overexpression of Rik and a variety of developmental abnormalities in the urinary system after PB insertion, mainly including renal hypo/dysplasia. The number of ureteric bud (UB) branches in the RikPB/PB embryonic kidney was significantly decreased in embryonic kidney culture. Only bone morphogenetic protein 4 (Bmp4), a key molecule regulating UB branching, is significantly downregulated in RikPB/PB embryonic kidney, while the expression levels of other molecules involved in the regulation of UB branching were not significantly different according to the RNA-sequencing (RNA-seq) data, and the results were verified by quantitative real-time polymerase chain reaction (RT-PCR) and immunofluorescence assays. Besides, the expression of pSmad1/5/8, a downstream molecule of BMP4 signaling, decreased by immunofluorescence. These findings suggest that abnormal expression of Rik may cause a reduction in the UB branches by reducing the expression levels of the UB branching-related molecule Bmp4, thus leading to the development of CAKUT.
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Affiliation(s)
- Lihong Tan
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Minghui Yu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yaxin Li
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Shanshan Xue
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Chen
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yihui Zhai
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaoyan Fang
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jialu Liu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jiaojiao Liu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaohui Wu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering and National Center for International Research of Development and Disease, Institute of Developmental Biology and Molecular Medicine, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Shanghai Kidney Development and Pediatric Kidney Disease Research Center, Children's Hospital of Fudan University, Shanghai, China
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Wang L, Song F, Zhu W, Fu J, Dong Z, Xu P. The stage-specific long non-coding RNAs and mRNAs identification and analysis during early development of common carp, Cyprinus carpio. Genomics 2020; 113:20-28. [PMID: 33271329 DOI: 10.1016/j.ygeno.2020.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/23/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Cyprinus carpio is considered an alternative vertebrate fish model to zebrafish. However, systemic times-series research on the lncRNAs and mRNAs during early development of C. carpio has not been reported yet. This study provides the first long non-coding RNA (lncRNA)-mRNA expression profiles during six main early development stages (2 h post-fertilization hpf, 6 hpf, 12 hpf, 20 hpf, 64 hpf and 1 day post-hatching). A total of 51,979 lncRNAs were identified. We screened the top 10 abundance lncRNAs and mRNAs and stage-specific lncRNAs and mRNAs (specificity measure SPM > 0.9). We identified significant differentially expressed lncRNAs and mRNAs (|log2 (fold change)| ≥ 1 and false discovery rate FDR of <0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified numerous signaling pathways. Additionally, the lncRNA-mRNA co-regulated network analysis of two lncRNAs (lncrps25 and malat1) and two mRNAs (mitf and troponin T) were investigated. Our results provide new insight into the role of lncRNAs and mRNAs, and would advance the understanding of lncRNA-mediated mechanisms in early development of fish.
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Affiliation(s)
- Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Feibiao Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Wenbin Zhu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Jianjun Fu
- Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
| | - Zaijie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China.
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Chen KW, Chen JA. Functional Roles of Long Non-coding RNAs in Motor Neuron Development and Disease. J Biomed Sci 2020; 27:38. [PMID: 32093746 PMCID: PMC7041250 DOI: 10.1186/s12929-020-00628-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have gained increasing attention as they exhibit highly tissue- and cell-type specific expression patterns. LncRNAs are highly expressed in the central nervous system and their roles in the brain have been studied intensively in recent years, but their roles in the spinal motor neurons (MNs) are largely unexplored. Spinal MN development is controlled by precise expression of a gene regulatory network mediated spatiotemporally by transcription factors, representing an elegant paradigm for deciphering the roles of lncRNAs during development. Moreover, many MN-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are associated with RNA metabolism, yet the link between MN-related diseases and lncRNAs remains obscure. In this review, we summarize lncRNAs known to be involved in MN development and disease, and discuss their potential future therapeutic applications.
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Affiliation(s)
- Kuan-Wei Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
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