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Branchi I. Uncovering the determinants of brain functioning, behavior and their interplay in the light of context. Eur J Neurosci 2024; 60:4687-4706. [PMID: 38558227 DOI: 10.1111/ejn.16331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Notwithstanding the huge progress in molecular and cellular neuroscience, our ability to understand the brain and develop effective treatments promoting mental health is still limited. This can be partially ascribed to the reductionist, deterministic and mechanistic approaches in neuroscience that struggle with the complexity of the central nervous system. Here, I introduce the Context theory of constrained systems proposing a novel role of contextual factors and genetic, molecular and neural substrates in determining brain functioning and behavior. This theory entails key conceptual implications. First, context is the main driver of behavior and mental states. Second, substrates, from genes to brain areas, have no direct causal link to complex behavioral responses as they can be combined in multiple ways to produce the same response and different responses can impinge on the same substrates. Third, context and biological substrates play distinct roles in determining behavior: context drives behavior, substrates constrain the behavioral repertoire that can be implemented. Fourth, since behavior is the interface between the central nervous system and the environment, it is a privileged level of control and orchestration of brain functioning. Such implications are illustrated through the Kitchen metaphor of the brain. This theoretical framework calls for the revision of key concepts in neuroscience and psychiatry, including causality, specificity and individuality. Moreover, at the clinical level, it proposes treatments inducing behavioral changes through contextual interventions as having the highest impact to reorganize the complexity of the human mind and to achieve a long-lasting improvement in mental health.
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Affiliation(s)
- Igor Branchi
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
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2
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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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3
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Lipp HP, Krackow S, Turkes E, Benner S, Endo T, Russig H. IntelliCage: the development and perspectives of a mouse- and user-friendly automated behavioral test system. Front Behav Neurosci 2024; 17:1270538. [PMID: 38235003 PMCID: PMC10793385 DOI: 10.3389/fnbeh.2023.1270538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/18/2023] [Indexed: 01/19/2024] Open
Abstract
IntelliCage for mice is a rodent home-cage equipped with four corner structures harboring symmetrical double panels for operant conditioning at each of the two sides, either by reward (access to water) or by aversion (non-painful stimuli: air-puffs, LED lights). Corner visits, nose-pokes and actual licks at bottle-nipples are recorded individually using subcutaneously implanted transponders for RFID identification of up to 16 adult mice housed in the same home-cage. This allows for recording individual in-cage activity of mice and applying reward/punishment operant conditioning schemes in corners using workflows designed on a versatile graphic user interface. IntelliCage development had four roots: (i) dissatisfaction with standard approaches for analyzing mouse behavior, including standardization and reproducibility issues, (ii) response to handling and housing animal welfare issues, (iii) the increasing number of mouse models had produced a high work burden on classic manual behavioral phenotyping of single mice. and (iv), studies of transponder-chipped mice in outdoor settings revealed clear genetic behavioral differences in mouse models corresponding to those observed by classic testing in the laboratory. The latter observations were important for the development of home-cage testing in social groups, because they contradicted the traditional belief that animals must be tested under social isolation to prevent disturbance by other group members. The use of IntelliCages reduced indeed the amount of classic testing remarkably, while its flexibility was proved in a wide range of applications worldwide including transcontinental parallel testing. Essentially, two lines of testing emerged: sophisticated analysis of spontaneous behavior in the IntelliCage for screening of new genetic models, and hypothesis testing in many fields of behavioral neuroscience. Upcoming developments of the IntelliCage aim at improved stimulus presentation in the learning corners and videotracking of social interactions within the IntelliCage. Its main advantages are (i) that mice live in social context and are not stressfully handled for experiments, (ii) that studies are not restricted in time and can run in absence of humans, (iii) that it increases reproducibility of behavioral phenotyping worldwide, and (iv) that the industrial standardization of the cage permits retrospective data analysis with new statistical tools even after many years.
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Affiliation(s)
- Hans-Peter Lipp
- Faculty of Medicine, Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Sven Krackow
- Institute of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Emir Turkes
- Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Seico Benner
- Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Ibaraki, Japan
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4
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 541] [Impact Index Per Article: 541.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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Filatova E. Transformer maze for the evaluation of the learning and memory in rodents. Heliyon 2022; 8:e11211. [PMID: 36325140 PMCID: PMC9619002 DOI: 10.1016/j.heliyon.2022.e11211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/25/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background Currently, different types of mazes are used to assess spatial learning and memory of rodents. The typical disadvantage is the inability to separate and exclude coincidences of the result of random choice with the correct one. The other problem is the impossibility of knowing whether the animal is guided by particular cues of the environment, or a map. New method Our novel transformer maze can be used to test learning and memory of rodents and their navigation. It is a multiple T-maze with passages in the interior walls. Its modular design allows to quickly change routes. The task can include external signals; for example, the colors of the interior walls, or it can be used without any cues. Results We compared Wistar and dopamine transporter heterozygous (DAT-HET) rats’ behavior in this novel paradigm using the black color of the wall as a cue. Entering a cul-de-sac compartment was considered an error. While Wistar rats learned the rule abruptly with the total number of errors rapidly decreasing, DAT-HET rats’ errors decreased gradually. We suppose that this reflects different strategies: insightful learning behavior is typical for Wistar rats, and trial-and-error learning is typical for DAT-HET rats. Comparison with existing methods The diversity of the chains of choices gives us confidence that trained animals do not make a choice randomly and are guided precisely by the cues. Moreover, we propose to use the same arena for a task with route-based navigation without any cues, and for a task with a visible and invisible feeder to study the path integration navigation within one box. Conclusions We suggest that the transformer maze could be a valuable tool for behavioral and pharmacological research to study learning, memory and navigation mechanisms.
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Identification of Hypothalamic Long Noncoding RNAs Associated with Hypertension and the Behavior/Neurological Phenotype of Hypertensive ISIAH Rats. Genes (Basel) 2022; 13:genes13091598. [PMID: 36140769 PMCID: PMC9498762 DOI: 10.3390/genes13091598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important role in the control of many physiological and pathophysiological processes, including the development of hypertension and other cardiovascular diseases. Nonetheless, the understanding of the regulatory function of many lncRNAs is still incomplete. This work is a continuation of our earlier study on the sequencing of hypothalamic transcriptomes of hypertensive ISIAH rats and control normotensive WAG rats. It aims to identify lncRNAs that may be involved in the formation of the hypertensive state and the associated behavioral features of ISIAH rats. Interstrain differences in the expression of seven lncRNAs were validated by quantitative PCR. Differential hypothalamic expression of lncRNAs LOC100910237 and RGD1562890 between hypertensive and normotensive rats was shown for the first time. Expression of four lncRNAs (Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1) correlated with transcription levels of many hypothalamic genes differentially expressed between ISIAH and WAG rats (DEGs), including genes associated with the behavior/neurological phenotype and hypertension. After functional annotation of these DEGs, it was concluded that lncRNAs Snhg4, LOC100910237, RGD1562890, and Tnxa-ps1 may be involved in the hypothalamic processes related to immune-system functioning and in the response to various exogenous and endogenous factors, including hormonal stimuli. Based on the functional enrichment analysis of the networks, an association of lncRNAs LOC100910237 and Tnxa-ps1 with retinol metabolism and an association of lncRNAs RGD1562890 and Tnxa-ps1 with type 1 diabetes mellitus are proposed for the first time. Based on a discussion, it is hypothesized that previously functionally uncharacterized lncRNA LOC100910237 is implicated in the regulation of hypothalamic processes associated with dopaminergic synaptic signaling, which may contribute to the formation of the behavioral/neurological phenotype and hypertensive state of ISIAH rats.
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Branchi I. Recentering neuroscience on behavior: The interface between brain and environment is a privileged level of control of neural activity. Neurosci Biobehav Rev 2022; 138:104678. [PMID: 35487322 DOI: 10.1016/j.neubiorev.2022.104678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 02/08/2023]
Abstract
Despite the huge and constant progress in the molecular and cellular neuroscience fields, our capability to understand brain alterations and treat mental illness is still limited. Therefore, a paradigm shift able to overcome such limitation is warranted. Behavior and the associated mental states are the interface between the central nervous system and the living environment. Since, in any system, the interface is a key regulator of system organization, behavior is proposed here as a unique and privileged level of control and orchestration of brain structure and activity. This view has relevant scientific and clinical implications. First, the study of behavior represents a singular starting point for the investigation of neural activity in an integrated and comprehensive fashion. Second, behavioral changes, accomplished through psychotherapy or environmental interventions, are expected to have the highest impact to specifically reorganize the complexity of the human mind and thus achieve a solid and long-lasting improvement in mental health.
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Affiliation(s)
- Igor Branchi
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
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Irwin AB, Bahabry R, Lubin FD. A putative role for lncRNAs in epigenetic regulation of memory. Neurochem Int 2021; 150:105184. [PMID: 34530054 PMCID: PMC8552959 DOI: 10.1016/j.neuint.2021.105184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
The central dogma of molecular genetics is defined as encoded genetic information within DNA, transcribed into messenger RNA, which contain the instructions for protein synthesis, thus imparting cellular functionality and ultimately life. This molecular genetic theory has given birth to the field of neuroepigenetics, and it is now well established that epigenetic regulation of gene transcription is critical to the learning and memory process. In this review, we address a potential role for a relatively new player in the field of epigenetic crosstalk - long non-coding RNAs (lncRNAs). First, we briefly summarize epigenetic mechanisms in memory formation and examine what little is known about the emerging role of lncRNAs during this process. We then focus discussions on how lncRNAs interact with epigenetic mechanisms to control transcriptional programs under various conditions in the brain, and how this may be applied to regulation of gene expression necessary for memory formation. Next, we explore how epigenetic crosstalk in turn serves to regulate expression of various individual lncRNAs themselves. To highlight the importance of further exploring the role of lncRNA in epigenetic regulation of gene expression, we consider the significant relationship between lncRNA dysregulation and declining memory reserve with aging, Alzheimer's disease, and epilepsy, as well as the promise of novel therapeutic interventions. Finally, we conclude with a discussion of the critical questions that remain to be answered regarding a role for lncRNA in memory.
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Affiliation(s)
- Ashleigh B Irwin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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Mieske P, Diederich K, Lewejohann L. Roaming in a Land of Milk and Honey: Life Trajectories and Metabolic Rate of Female Inbred Mice Living in a Semi Naturalistic Environment. Animals (Basel) 2021; 11:ani11103002. [PMID: 34680021 PMCID: PMC8532919 DOI: 10.3390/ani11103002] [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: 09/15/2021] [Revised: 10/12/2021] [Accepted: 10/16/2021] [Indexed: 12/17/2022] Open
Abstract
Despite tremendous efforts at standardization, the results of scientific studies can vary greatly, especially when considering animal research. It is important to emphasize that consistent different personality-like traits emerge and accumulate over time in laboratory mice despite genetic and environmental standardization. To understand to what extent variability can unfold over time, we conducted a long-term study using inbred mice living in an exceptionally complex environment comprising an area of 4.6 m2 spread over five levels. In this semi-naturalistic environment (SNE) the activity and spatial distribution of 20 female C57Bl/6J was recorded by radio-frequency identification (RFID). All individuals were monitored from an age of 11 months to 22 months and their individual pattern of spatial movement in time is described as roaming entropy. Overall, we detected an increase of diversification in roaming behavior over time with stabilizing activity patterns at the individual level. However, spontaneous behavior of the animals as well as physiological parameters did not correlate with cumulative roaming entropy. Moreover, the amount of variability did not exceed the literature data derived from mice living in restricted conventional laboratory conditions. We conclude that even taking quantum leaps towards improving animal welfare does not inevitably mean a setback in terms of data quality.
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Affiliation(s)
- Paul Mieske
- German Center for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (K.D.); (L.L.)
- Correspondence:
| | - Kai Diederich
- German Center for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (K.D.); (L.L.)
| | - Lars Lewejohann
- German Center for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (K.D.); (L.L.)
- Animal Behavior and Laboratory Animal Science, Institute of Animal Welfare, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany
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Liau WS, Samaddar S, Banerjee S, Bredy TW. On the functional relevance of spatiotemporally-specific patterns of experience-dependent long noncoding RNA expression in the brain. RNA Biol 2021; 18:1025-1036. [PMID: 33397182 DOI: 10.1080/15476286.2020.1868165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The majority of transcriptionally active RNA derived from the mammalian genome does not code for protein. Long noncoding RNA (lncRNA) is the most abundant form of noncoding RNA found in the brain and is involved in many aspects of cellular metabolism. Beyond their fundamental role in the nucleus as decoys for RNA-binding proteins associated with alternative splicing or as guides for the epigenetic regulation of protein-coding gene expression, recent findings indicate that activity-induced lncRNAs also regulate neural plasticity. In this review, we discuss how lncRNAs may exert molecular control over brain function beyond their known roles in the nucleus. We propose that subcellular localization is a critical feature of experience-dependent lncRNA activity in the brain, and that lncRNA-mediated control over RNA metabolism at the synapse serves to regulate local mRNA stability and translation, thereby influencing neuronal function, learning and memory.
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Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | | | | | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
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11
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Tian J, Yang L, Wang P, Yang L, Fan Z. Exogenous CGRP Regulates Apoptosis and Autophagy to Alleviate Traumatic Brain Injury Through Akt/mTOR Signalling Pathway. Neurochem Res 2020; 45:2926-2938. [PMID: 33063244 DOI: 10.1007/s11064-020-03141-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/11/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
With millions of traumatic brain injury (TBI) patients every year, TBI is regarded as one of the leading causes of human death and disability. Calcitonin gene-related peptide (CGRP) has been domenstrated to be a potential therapeutic target for TBI. However, the detailed effect and underlying mechanism of CGRP on the injured brain after TBI has hardly been investigated. In this work, we established TBI models of mice and injected CGRP before and after modelling to study its effects on the brain lesion, neurological functions and behaviours, neuron apoptosis and autophagy after TBI. Impacts of introduced CGRP on the activation of Akt/mTOR signalling in the cortical tissues surrounding injured areas after TBI were also evaluated. It was found that CGRP was reduced after TBI, and gradually restored over time. CGRP administration significantly restored the brain lesion induced by TBI. The permeability of blood-brain barrier and brain edema was increased dramatically after TBI, which was ameliorated by exogenous CGRP. Moreover, several neurological behaviour tests were performed, showing that CGRP introduction also relieved the cognitive abilities of mice which were impaired after TBI. Enhancing apoptosis and autophagy of neurons in the cortical tissues of injury sites following TBI were also alleviated by CGRP administration. Besides, CGRP-treated brain cortical tissues showed increased activation of Akt/mTOR signalling after TBI. Therefore, the results suggest that exogenous CGRP plays a neuroprotective role in the injuryed brain after TBI, to relieve cell apoptosis and autophagy, at least partially through Akt/mTOR signalling pathway. This finding also provides more evidence for the treatment of TBI through introducing exogenous CGRP or its related drugs.
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Affiliation(s)
- Jun Tian
- Department of Neurosurgery, Hebei Medical University, Shijiazhuang, Hebei Province, China
- Department of Neurosurgery, Shijiazhuang First Hospital, Shijiazhuang, Hebei Province, China
| | - Lei Yang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Hebei Key Laboratory of Environment and Human Health, Shijiazhuang, China
| | - Pengfei Wang
- Department of Neurosurgery, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Lijun Yang
- Department of Neurosurgery, Hebei Medical University, Shijiazhuang, Hebei Province, China.
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No.215, Heping Road, Shijiazhuang, 050000, Hebei Province, China.
| | - Zhenzeng Fan
- Department of Neurosurgery, Hebei Medical University, Shijiazhuang, Hebei Province, China.
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, No.215, Heping Road, Shijiazhuang, 050000, Hebei Province, China.
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12
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Oliveira NCM, Lins ÉM, Massirer KB, Bengtson MH. Translational Control during Mammalian Neocortex Development and Postembryonic Neuronal Function. Semin Cell Dev Biol 2020; 114:36-46. [PMID: 33020045 DOI: 10.1016/j.semcdb.2020.09.006] [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: 02/03/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022]
Abstract
The control of mRNA translation has key roles in the regulation of gene expression and biological processes such as mammalian cellular differentiation and identity. Methodological advances in the last decade have resulted in considerable progress towards understanding how translational control contributes to the regulation of diverse biological phenomena. In this review, we discuss recent findings in the involvement of translational control in the mammalian neocortex development and neuronal biology. We focus on regulatory mechanisms that modulate translational efficiency during neural stem cells self-renewal and differentiation, as well as in neuronal-related processes such as synapse, plasticity, and memory.
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Affiliation(s)
- Natássia Cristina Martins Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Érico Moreto Lins
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; PhD Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas, SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Mário Henrique Bengtson
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil.
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13
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Rusconi F, Battaglioli E, Venturin M. Psychiatric Disorders and lncRNAs: A Synaptic Match. Int J Mol Sci 2020; 21:ijms21093030. [PMID: 32344798 PMCID: PMC7246907 DOI: 10.3390/ijms21093030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Psychiatric disorders represent a heterogeneous class of multifactorial mental diseases whose origin entails a pathogenic integration of genetic and environmental influences. Incidence of these pathologies is dangerously high, as more than 20% of the Western population is affected. Despite the diverse origins of specific molecular dysfunctions, these pathologies entail disruption of fine synaptic regulation, which is fundamental to behavioral adaptation to the environment. The synapses, as functional units of cognition, represent major evolutionary targets. Consistently, fine synaptic tuning occurs at several levels, involving a novel class of molecular regulators known as long non-coding RNAs (lncRNAs). Non-coding RNAs operate mainly in mammals as epigenetic modifiers and enhancers of proteome diversity. The prominent evolutionary expansion of the gene number of lncRNAs in mammals, particularly in primates and humans, and their preferential neuronal expression does represent a driving force that enhanced the layering of synaptic control mechanisms. In the last few years, remarkable alterations of the expression of lncRNAs have been reported in psychiatric conditions such as schizophrenia, autism, and depression, suggesting unprecedented mechanistic insights into disruption of fine synaptic tuning underlying severe behavioral manifestations of psychosis. In this review, we integrate literature data from rodent pathological models and human evidence that proposes the biology of lncRNAs as a promising field of neuropsychiatric investigation.
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Affiliation(s)
- Francesco Rusconi
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
| | | | - Marco Venturin
- Correspondence: (F.R.); (M.V.); Tel.: +39-02-503-30445 (F.R.); +39-02-503-30443 (M.V.)
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14
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Abstract
Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized as biologically meaningful, the fraction of such transcripts out of the entire collection of lncRNAs remains a subject of vigorous debate. Here we review the evidence for and against biological functionalities of lncRNAs and attempt to arrive at potential modes of lncRNA functionality that would reconcile the contradictory conclusions. Finally, we discuss different strategies of phenotypic analyses that could be used to investigate such modes of lncRNA functionality.
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Affiliation(s)
- Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 201 Pan-Chinese S & T Building, 668 Jimei Road, Xiamen, 361021, China.
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15
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Brain Cytoplasmic RNAs in Neurons: From Biosynthesis to Function. Biomolecules 2020; 10:biom10020313. [PMID: 32079202 PMCID: PMC7072442 DOI: 10.3390/biom10020313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/13/2020] [Accepted: 02/13/2020] [Indexed: 01/10/2023] Open
Abstract
Flexibility in signal transmission is essential for high-level brain function. This flexibility is achieved through strict spatial and temporal control of gene expression in neurons. Given the key regulatory roles of a variety of noncoding RNAs (ncRNAs) in neurons, studying neuron-specific ncRNAs provides an important basis for understanding molecular principles of brain function. This approach will have wide use in understanding the pathogenesis of brain diseases and in the development of therapeutic agents in the future. Brain cytoplasmic RNAs (BC RNAs) are a leading paradigm for research on neuronal ncRNAs. Since the first confirmation of brain-specific expression of BC RNAs in 1982, their investigation has been an area of active research. In this review, we summarize key studies on the characteristics and functions of BC RNAs in neurons.
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16
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Lyu Y, Bai L, Qin C. Long noncoding RNAs in neurodevelopment and Parkinson's disease. Animal Model Exp Med 2019; 2:239-251. [PMID: 31942556 PMCID: PMC6930994 DOI: 10.1002/ame2.12093] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/12/2019] [Accepted: 11/20/2019] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules comprising more than 200 nucleotides, which are not translated into proteins. Many studies have shown that lncRNAs are involved in regulating a variety of biological processes, including immune, cancer, stress, development and differentiation at the transcriptional, epigenetic or post-transcriptional levels. Here, we review the role of lncRNAs in the process of neurodevelopment, neural differentiation, synaptic function, and pathogenesis of Parkinson's disease (PD). These pathomechanisms include protein misfolding and aggregation, disordered protein degradation, mitochondrial dysfunction, oxidative stress, autophagy, apoptosis, and neuroinflammation. This information will provide the basis of lncRNA-based disease diagnosis and drug treatment for PD.
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Affiliation(s)
- Ying Lyu
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
| | - Lin Bai
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
| | - Chuan Qin
- Institute of Medical Laboratory Animal ScienceChinese Academy of Medical Sciences & Comparative Medical CenterPeking Union Medical CollegeBeijingChina
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17
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The importance of long non-coding RNAs in neuropsychiatric disorders. Mol Aspects Med 2019; 70:127-140. [DOI: 10.1016/j.mam.2019.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 06/10/2019] [Accepted: 07/14/2019] [Indexed: 12/20/2022]
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18
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Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution. Cells 2019; 8:cells8111399. [PMID: 31698782 PMCID: PMC6912723 DOI: 10.3390/cells8111399] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 01/09/2023] Open
Abstract
Mammalian genomes encode tens of thousands of long-noncoding RNAs (lncRNAs), which are capable of interactions with DNA, RNA and protein molecules, thereby enabling a variety of transcriptional and post-transcriptional regulatory activities. Strikingly, about 40% of lncRNAs are expressed specifically in the brain with precisely regulated temporal and spatial expression patterns. In stark contrast to the highly conserved repertoire of protein-coding genes, thousands of lncRNAs have newly appeared during primate nervous system evolution with hundreds of human-specific lncRNAs. Their evolvable nature and the myriad of potential functions make lncRNAs ideal candidates for drivers of human brain evolution. The human brain displays the largest relative volume of any animal species and the most remarkable cognitive abilities. In addition to brain size, structural reorganization and adaptive changes represent crucial hallmarks of human brain evolution. lncRNAs are increasingly reported to be involved in neurodevelopmental processes suggested to underlie human brain evolution, including proliferation, neurite outgrowth and synaptogenesis, as well as in neuroplasticity. Hence, evolutionary human brain adaptations are proposed to be essentially driven by lncRNAs, which will be discussed in this review.
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19
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Wu W, Ji X, Zhao Y. Emerging Roles of Long Non-coding RNAs in Chronic Neuropathic Pain. Front Neurosci 2019; 13:1097. [PMID: 31680832 PMCID: PMC6813851 DOI: 10.3389/fnins.2019.01097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/30/2019] [Indexed: 02/06/2023] Open
Abstract
Chronic neuropathic pain, a type of chronic and potentially disabling pain caused by a disease or injury of the somatosensory nervous system, spinal cord injury, or various chronic conditions, such as viral infections (e.g., post-herpetic neuralgia), autoimmune diseases, cancers, and metabolic disorders (e.g., diabetes mellitus), is one of the most intense types of chronic pain, which incurs a major socio-economic burden and is a serious public health issue, with an estimated prevalence of 7–10% in adults throughout the world. Presently, the available drug treatments (e.g., anticonvulsants acting at calcium channels, serotonin-noradrenaline reuptake inhibitors, tricyclic antidepressants, opioids, topical lidocaine, etc.) for chronic neuropathic pain patients are still rare and have disappointing efficacy, which makes it difficult to relieve the patients’ painful symptoms, and, at best, they only try to reduce the patients’ ability to tolerate pain. Long non-coding RNAs (lncRNAs), a type of transcript of more than 200 nucleotides with no protein-coding or limited capacity, were identified to be abnormally expressed in the spinal cord, dorsal root ganglion, hippocampus, and prefrontal cortex under chronic neuropathic pain conditions. Moreover, a rapidly growing body of data has clearly pointed out that nearly 40% of lncRNAs exist specifically in the nervous system. Hence, it was speculated that these dysregulated lncRNAs might participate in the occurrence, development, and progression of chronic neuropathic pain. In other words, if we deeply delve into the potential roles of lncRNAs in the pathogenesis of chronic neuropathic pain, this may open up new strategies and directions for the development of novel targeted drugs to cure this refractory disorder. In this article, we primarily review the status of chronic neuropathic pain and provide a general overview of lncRNAs, the detailed roles of lncRNAs in the nervous system and its related diseases, and the abnormal expression of lncRNAs and their potential clinical applications in chronic neuropathic pain. We hope that through the above description, readers can gain a better understanding of the emerging roles of lncRNAs in chronic neuropathic pain.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Ji
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Zhao
- Department of Anesthesiology, Affiliated Hospital to Qingdao University, Qingdao, China
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20
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Grinman E, Espadas I, Puthanveettil SV. Emerging roles for long noncoding RNAs in learning, memory and associated disorders. Neurobiol Learn Mem 2019; 163:107034. [DOI: 10.1016/j.nlm.2019.107034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/03/2019] [Accepted: 06/05/2019] [Indexed: 12/13/2022]
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21
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Hoeppner MP, Denisenko E, Gardner PP, Schmeier S, Poole AM. An Evaluation of Function of Multicopy Noncoding RNAs in Mammals Using ENCODE/FANTOM Data and Comparative Genomics. Mol Biol Evol 2019; 35:1451-1462. [PMID: 29617896 PMCID: PMC5967550 DOI: 10.1093/molbev/msy046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mammalian diversification has coincided with a rapid proliferation of various types of noncoding RNAs, including members of both snRNAs and snoRNAs. The significance of this expansion however remains obscure. While some ncRNA copy-number expansions have been linked to functionally tractable effects, such events may equally likely be neutral, perhaps as a result of random retrotransposition. Hindering progress in our understanding of such observations is the difficulty in establishing function for the diverse features that have been identified in our own genome. Projects such as ENCODE and FANTOM have revealed a hidden world of genomic expression patterns, as well as a host of other potential indicators of biological function. However, such projects have been criticized, particularly from practitioners in the field of molecular evolution, where many suspect these data provide limited insight into biological function. The molecular evolution community has largely taken a skeptical view, thus it is important to establish tests of function. We use a range of data, including data drawn from ENCODE and FANTOM, to examine the case for function for the recent copy number expansion in mammals of six evolutionarily ancient RNA families involved in splicing and rRNA maturation. We use several criteria to assess evidence for function: conservation of sequence and structure, genomic synteny, evidence for transposition, and evidence for species-specific expression. Applying these criteria, we find that only a minority of loci show strong evidence for function and that, for the majority, we cannot reject the null hypothesis of no function.
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Affiliation(s)
- Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Elena Denisenko
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Paul P Gardner
- Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Anthony M Poole
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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22
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Cortini F, Roma F, Villa C. Emerging roles of long non-coding RNAs in the pathogenesis of Alzheimer's disease. Ageing Res Rev 2019; 50:19-26. [PMID: 30610928 DOI: 10.1016/j.arr.2019.01.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 01/01/2019] [Indexed: 01/02/2023]
Abstract
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disorder and represents the most common form of senile dementia. The pathogenesis of AD is not yet completely understood and no curative treatment is currently available. With the recent advancement in transcriptome-wide profiling approach, several non-coding RNAs (ncRNAs) have been identified. Among them, long non-coding RNAs (lncRNAs), which are long transcripts without apparent protein-coding capacity, have received increasing interest for their involvement in a wide range of biological processes as regulatory molecules. Recent studies have suggested that lncRNAs play a role in AD pathogenesis, although their specific influences in the disorder remain to be largely unknown. Herein, we will summarize the biology and mechanisms of action of the best characterized dysregulated lncRNAs in AD, focusing the attention on their potential role in the disease pathogenesis. A deeper understanding of the molecular mechanisms and the complex network of interactions in which they are implicated should open the doors to new research considering lncRNAs as novel therapeutic targets and prognostic/diagnostic biomarkers.
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Affiliation(s)
- Francesca Cortini
- Department of Clinical Sciences and Community Health, University of Milan, IRCCS Ca' Granda Foundation, Milan, Italy; UOC Occupational Medicine, Department of Medicine Preventive Services, IRCCS Ca Granda Foundation Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesca Roma
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.
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23
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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24
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He J, Tu C, Liu Y. Role of lncRNAs in aging and age-related diseases. Aging Med (Milton) 2018; 1:158-175. [PMID: 31942494 PMCID: PMC6880696 DOI: 10.1002/agm2.12030] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 01/10/2023] Open
Abstract
Aging is progressive physiological degeneration and consequently declined function, which is linked to senescence on both cellular and organ levels. Accumulating studies indicate that long noncoding RNAs (lncRNAs) play important roles in cellular senescence at all levels-transcriptional, post-transcriptional, translational, and post-translational. Understanding the molecular mechanism of lncRNAs underlying senescence could facilitate interpretation and intervention of aging and age-related diseases. In this review, we describe categories of known and novel lncRNAs that have been involved in the progression of senescence. We also identify the lncRNAs implicated in diseases arising from age-driven degeneration or dysfunction in some representative organs and systems (brains, liver, muscle, cardiovascular system, bone pancreatic islets, and immune system). Improved comprehension of lncRNAs in the aging process on all levels, from cell to organismal, may provide new insights into the amelioration of age-related pathologies and prolonged healthspan.
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Affiliation(s)
- Jieyu He
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Chao Tu
- Department of OrthopedicsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Youshuo Liu
- Department of GeriatricsThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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25
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The State of Long Non-Coding RNA Biology. Noncoding RNA 2018; 4:ncrna4030017. [PMID: 30103474 PMCID: PMC6162524 DOI: 10.3390/ncrna4030017] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022] Open
Abstract
Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure–function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.
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Handling FMRP and its molecular partners: Structural insights into Fragile X Syndrome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 141:3-14. [PMID: 30905341 DOI: 10.1016/j.pbiomolbio.2018.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/01/2018] [Indexed: 12/29/2022]
Abstract
Fragile X Mental Retardation Protein (FMRP) is a RNA-binding protein (RBP) known to control different steps of mRNA metabolism, even though its complete function is not fully understood yet. Lack or mutations of FMRP lead to Fragile X Syndrome (FXS), the most common form of inherited intellectual disability and a leading monogenic cause of autism spectrum disorder (ASD). It is well established that FMRP has a multi-domain architecture, a feature that allows this RBP to be engaged in a large interaction network with numerous proteins and mRNAs or non-coding RNAs. Insights into the three-dimensional (3D) structure of parts of its three domains (N-terminus, central domain and C-terminus) were obtained using Nuclear Magnetic Resonance and X-ray diffraction, but the complete 3D arrangement of each domain with respect to the others is still missing. Here, we review the structural features of FMRP and of the network of its protein and RNA interactions. Understanding these aspects is the first necessary step towards the design of novel compounds for new therapeutic interventions in FXS.
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Long Non-Coding RNAs in Neuronal Aging. Noncoding RNA 2018; 4:ncrna4020012. [PMID: 29670042 PMCID: PMC6027360 DOI: 10.3390/ncrna4020012] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 02/07/2023] Open
Abstract
The expansion of long non-coding RNAs (lncRNAs) in organismal genomes has been associated with the emergence of sophisticated regulatory networks that may have contributed to more complex neuronal processes, such as higher-order cognition. In line with the important roles of lncRNAs in the normal functioning of the human brain, dysregulation of lncRNA expression has been implicated in aging and age-related neurodegenerative disorders. In this paper, we discuss the function and expression of known neuronal-associated lncRNAs, their impact on epigenetic changes, the contribution of transposable elements to lncRNA expression, and the implication of lncRNAs in maintaining the 3D nuclear architecture in neurons. Moreover, we discuss how the complex molecular processes that are orchestrated by lncRNAs in the aged brain may contribute to neuronal pathogenesis by promoting protein aggregation and neurodegeneration. Finally, this review explores the possibility that age-related disturbances of lncRNA expression change the genomic and epigenetic regulatory landscape of neurons, which may affect neuronal processes such as neurogenesis and synaptic plasticity.
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28
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Marwari S, Dawe GS. (R)-fluoxetine enhances cognitive flexibility and hippocampal cell proliferation in mice. J Psychopharmacol 2018; 32:441-457. [PMID: 29458297 DOI: 10.1177/0269881118754733] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluoxetine is a clinically successful antidepressant. It is a racemic mixture of (R) and (S) stereoisomers. In preclinical studies, chronic treatment with fluoxetine (10 mg/kg) had antidepressant effects correlated with increased hippocampal cell proliferation in adult rodents. However, the contribution of the enantiomers of fluoxetine is largely unknown. We investigated the effects of treatment with (R)- and (S)-fluoxetine on cognitive behavioral paradigms and examined cell proliferation in the hippocampus of C57BL/6J female mice. In a behavioral sequencing task using the IntelliCage system in which discriminated spatial patterns of rewarded and never-rewarded corners were reversed serially, (R)-fluoxetine-treated mice showed rapid acquisition of behavioral sequencing (compared with S-fluoxetine) and cognitive flexibility in subsequent reversal stages in intra- and inter-session analysis. (R)-fluoxetine also increased cell proliferation in the hippocampus, in particular in the suprapyramidal blade of the dentate gyrus. (R)-fluoxetine had superior effects to (S)-fluoxetine in elevated plus maze, forced-swim and tail-suspension tests. These results suggest that (R)-fluoxetine, which has been reported to have a shorter half-life than (S)-fluoxetine, has superior antidepressant effects and more consistently improves spatial learning and memory. This profile offers advantages in depression treatment and may also aid management of the neurocognitive impairments associated with depression.
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Affiliation(s)
- Subhi Marwari
- 1 Department of Pharmacology, National University of Singapore, Singapore
| | - Gavin S Dawe
- 1 Department of Pharmacology, National University of Singapore, Singapore.,2 Neurobiology and Ageing Programme, Life Sciences Institute, University of Singapore, Singapore
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29
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Wang YC, Chuang YH, Shao Q, Chen JF, Chen SY. Brain cytoplasmic RNA 1 suppresses smooth muscle differentiation and vascular development in mice. J Biol Chem 2018; 293:5668-5678. [PMID: 29467228 DOI: 10.1074/jbc.ra117.001578] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/17/2018] [Indexed: 02/04/2023] Open
Abstract
The cardiovascular system develops during the early stages of embryogenesis, and differentiation of smooth muscle cells (SMCs) is essential for that process. SMC differentiation is critically regulated by transforming growth factor (TGF)-β/SMAD family member 3 (SMAD3) signaling, but other regulators may also play a role. For example, long noncoding RNAs (lncRNAs) regulate various cellular activities and events, such as proliferation, differentiation, and apoptosis. However, whether long noncoding RNAs also regulate SMC differentiation remains largely unknown. Here, using the murine cell line C3H10T1/2, we found that brain cytoplasmic RNA 1 (BC1) is an important regulator of SMC differentiation. BC1 overexpression suppressed, whereas BC1 knockdown promoted, TGF-β-induced SMC differentiation, as indicated by altered cell morphology and expression of multiple SMC markers, including smooth muscle α-actin (αSMA), calponin, and smooth muscle 22α (SM22α). BC1 appeared to block SMAD3 activity and inhibit SMC marker gene transcription. Mechanistically, BC1 bound to SMAD3 via RNA SMAD-binding elements (rSBEs) and thus impeded TGF-β-induced SMAD3 translocation to the nucleus. This prevented SMAD3 from binding to SBEs in SMC marker gene promoters, an essential event in SMC marker transcription. In vivo, BC1 overexpression in mouse embryos impaired vascular SMC differentiation, leading to structural defects in the artery wall, such as random breaks in the elastic lamina, abnormal collagen deposition on SM fibers, and disorganized extracellular matrix proteins in the media of the neonatal aorta. Our results suggest that BC1 is a suppressor of SMC differentiation during vascular development.
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Affiliation(s)
- Yung-Chun Wang
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602
| | - Ya-Hui Chuang
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602
| | - Qiang Shao
- the Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089
| | - Jian-Fu Chen
- the Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089
| | - Shi-You Chen
- From the Department of Physiology and Pharmacology, University of Georgia, Athens, Georgia 30602, .,the Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China, and
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Chung A, Dahan N, Alarcon JM, Fenton AA. Effects of regulatory BC1 RNA deletion on synaptic plasticity, learning, and memory. Learn Mem 2017; 24:646-649. [PMID: 29142061 PMCID: PMC5688958 DOI: 10.1101/lm.045617.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
Nonprotein coding dendritic BC1 RNA regulates translation of mRNAs in neurons. We examined two lines of BC1 knockout mice and report that loss of BC1 RNA exaggerates group I mGluR-stimulated LTD of the Schaffer collateral synapse, with one of the lines showing a much more enhanced DHPG-induced LTD than the other. When the animals were given the hippocampus-synaptic plasticity-dependent active place avoidance task, learning and memory were impaired in the BC1-KO line with the more severely altered DHPG-induced LTD. These findings indicate a role for BC1 RNA control of mGluR-dependent synaptic function in hippocampus and associated cognitive ability.
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Affiliation(s)
- Ain Chung
- Center for Neural Science, New York University, New York, New York 10003, USA
| | - Nessy Dahan
- Department of Pathology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Juan Marcos Alarcon
- The Robert F. Furchgott Center for Neural and Behavioral Science, Brooklyn, New York 11203, USA
- Department of Pathology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - André A Fenton
- Center for Neural Science, New York University, New York, New York 10003, USA
- The Robert F. Furchgott Center for Neural and Behavioral Science, Brooklyn, New York 11203, USA
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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31
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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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32
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The non-coding RNA BC1 regulates experience-dependent structural plasticity and learning. Nat Commun 2017; 8:293. [PMID: 28819097 PMCID: PMC5561022 DOI: 10.1038/s41467-017-00311-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 06/19/2017] [Indexed: 11/09/2022] Open
Abstract
The brain cytoplasmic (BC1) RNA is a non-coding RNA (ncRNA) involved in neuronal translational control. Absence of BC1 is associated with altered glutamatergic transmission and maladaptive behavior. Here, we show that pyramidal neurons in the barrel cortex of BC1 knock out (KO) mice display larger excitatory postsynaptic currents and increased spontaneous activity in vivo. Furthermore, BC1 KO mice have enlarged spine heads and postsynaptic densities and increased synaptic levels of glutamate receptors and PSD-95. Of note, BC1 KO mice show aberrant structural plasticity in response to whisker deprivation, impaired texture novel object recognition and altered social behavior. Thus, our study highlights a role for BC1 RNA in experience-dependent plasticity and learning in the mammalian adult neocortex, and provides insight into the function of brain ncRNAs regulating synaptic transmission, plasticity and behavior, with potential relevance in the context of intellectual disabilities and psychiatric disorders. Brain cytoplasmic (BC1) RNA is a non-coding RNA that has been implicated in translational regulation, seizure, and anxiety. Here, the authors show that in the cortex, BC1 RNA is required for sensory deprivation-induced structural plasticity of dendritic spines, as well as for correct sensory learning and social behaviors.
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33
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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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34
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Iacoangeli A, Dosunmu A, Eom T, Stefanov DG, Tiedge H. Regulatory BC1 RNA in cognitive control. ACTA ACUST UNITED AC 2017; 24:267-277. [PMID: 28620074 PMCID: PMC5473108 DOI: 10.1101/lm.045427.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/27/2022]
Abstract
Dendritic regulatory BC1 RNA is a non-protein-coding (npc) RNA that operates in the translational control of gene expression. The absence of BC1 RNA in BC1 knockout (KO) animals causes translational dysregulation that entails neuronal phenotypic alterations including prolonged epileptiform discharges, audiogenic seizure activity in vivo, and excessive cortical oscillations in the γ frequency band. Here we asked whether BC1 RNA control is also required for higher brain functions such as learning, memory, or cognition. To address this question, we used odor/object attentional set shifting tasks in which prefrontal cortical performance was assessed in a series of discrimination and conflict learning sessions. Results obtained in these behavioral trials indicate that BC1 KO animals were significantly impaired in their cognitive flexibility. When faced with conflicting information sources, BC1 KO animals committed regressive errors as they were compromised in their ability to disengage from recently acquired memories even though recall of such memories was in conflict with new situational context. The observed cognitive deficits are reminiscent of those previously described in subtypes of human autism spectrum disorders.
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Affiliation(s)
- Anna Iacoangeli
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Aderemi Dosunmu
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Taesun Eom
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Dimitre G Stefanov
- Statistical Design and Analysis, Research Division, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Henri Tiedge
- The Robert F. Furchgott Center for Neural and Behavioral Science, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA .,Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA.,Department of Neurology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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35
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Deveson IW, Hardwick SA, Mercer TR, Mattick JS. The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome. Trends Genet 2017; 33:464-478. [PMID: 28535931 DOI: 10.1016/j.tig.2017.04.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/24/2017] [Indexed: 01/02/2023]
Abstract
The combination of pervasive transcription and prolific alternative splicing produces a mammalian transcriptome of great breadth and diversity. The majority of transcribed genomic bases are intronic, antisense, or intergenic to protein-coding genes, yielding a plethora of short and long non-protein-coding regulatory RNAs. Long noncoding RNAs (lncRNAs) share most aspects of their biogenesis, processing, and regulation with mRNAs. However, lncRNAs are typically expressed in more restricted patterns, frequently from enhancers, and exhibit almost universal alternative splicing. These features are consistent with their role as modular epigenetic regulators. We describe here the key studies and technological advances that have shaped our understanding of the dimensions, dynamics, and biological relevance of the mammalian noncoding transcriptome.
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Affiliation(s)
- Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Simon A Hardwick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - John S Mattick
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW, Australia; St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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36
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Chen Y, Zhou J. LncRNAs: macromolecules with big roles in neurobiology and neurological diseases. Metab Brain Dis 2017; 32:281-291. [PMID: 28161776 DOI: 10.1007/s11011-017-9965-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/31/2017] [Indexed: 01/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are recently defined as thousands of RNA molecules longer than 200 nucleotides and lacking an appreciable open reading frame in mammals. Although lncRNAs lack protein-coding function, they play critical roles in the regulation of almost all the protein-coding genes in a cell at various stages including chromatin modification, transcription and post-transcriptional processing. It is thus not surprising that lncRNAs may be the crucial regulators in the normal development, physiology and pathology. LncRNAs in neuroscience is a novel research field. Interestingly, recent studies have demonstrated that many lncRNAs are highly expressed in brain and their dysregulations occur in neurological disorders. In this review, we describe the current understanding of lncRNAs in neurobiology and neurological diseases including cerebral injury. LncRNAs could be novel biomarkers and could be potential new targets for new drugs for many neurological diseases in the future, although the related studies are still at in the early stages.
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Affiliation(s)
- Ye Chen
- Department of Traditional Chinese Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, People's Republic of China
| | - Jun Zhou
- Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, No.25 Taiping Street, Luzhou, Sichuan Province, 646000, People's Republic of China.
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37
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Shi C, Zhang L, Qin C. Long non-coding RNAs in brain development, synaptic biology, and Alzheimer's disease. Brain Res Bull 2017; 132:160-169. [PMID: 28347717 DOI: 10.1016/j.brainresbull.2017.03.010] [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: 10/31/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022]
Abstract
Long non-coding RNAs (lncRNAs), which are long transcripts without apparent protein-coding roles, interfere with gene expression and signaling events at various stages. Increasing evidence has suggested that lncRNAs function in the regulation of tissue homeostasis and under pathophysiologic conditions. In the nervous system, the expression of lncRNAs has been detected and characterized under normal physiologic conditions and in disease states. Some lncRNAs regulate brain development and synaptic plasticity. In Alzheimer's disease (AD), several lncRNAs have been demonstrated to regulate β-amyloid production/generation, synaptic impairment, neurotrophin depletion, inflammation, mitochondrial dysfunction, and stress responses. This review summarizes data on lncRNA expression and focuses on neural lncRNAs that may function in AD. Although our understanding of lncRNAs remains in its infancy, this review provides insight into the contribution of lncRNAs to AD.
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Affiliation(s)
- Changhua Shi
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Ling Zhang
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Chuan Qin
- Comparative Medical Center, Peking Union Medical College (PUMC) and Institute of Laboratory Animal Science, Chinese Academy of Medical Science (CAMS), Beijing, China.
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38
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Puścian A, Łęski S, Kasprowicz G, Winiarski M, Borowska J, Nikolaev T, Boguszewski PM, Lipp HP, Knapska E. Eco-HAB as a fully automated and ecologically relevant assessment of social impairments in mouse models of autism. eLife 2016; 5. [PMID: 27731798 PMCID: PMC5092044 DOI: 10.7554/elife.19532] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/11/2016] [Indexed: 12/21/2022] Open
Abstract
Eco-HAB is an open source, RFID-based system for automated measurement and analysis of social preference and in-cohort sociability in mice. The system closely follows murine ethology. It requires no contact between a human experimenter and tested animals, overcoming the confounding factors that lead to irreproducible assessment of murine social behavior between laboratories. In Eco-HAB, group-housed animals live in a spacious, four-compartment apparatus with shadowed areas and narrow tunnels, resembling natural burrows. Eco-HAB allows for assessment of the tendency of mice to voluntarily spend time together in ethologically relevant mouse group sizes. Custom-made software for automated tracking, data extraction, and analysis enables quick evaluation of social impairments. The developed protocols and standardized behavioral measures demonstrate high replicability. Unlike classic three-chambered sociability tests, Eco-HAB provides measurements of spontaneous, ecologically relevant social behaviors in group-housed animals. Results are obtained faster, with less manpower, and without confounding factors. DOI:http://dx.doi.org/10.7554/eLife.19532.001
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Affiliation(s)
- Alicja Puścian
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Szymon Łęski
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Kasprowicz
- Center for Theoretical Physics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Electronic Systems, Warsaw University of Technology, Warsaw, Poland
| | - Maciej Winiarski
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Borowska
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz Nikolaev
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Paweł M Boguszewski
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Hans-Peter Lipp
- Institute of Anatomy, University of Zurich, Zurich, Switzerland.,School of Laboratory Medicine, Kwazulu-Natal University Durban, Durban, Republic of South Africa
| | - Ewelina Knapska
- Department of Neurophysiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
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39
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BC1 RNA motifs required for dendritic transport in vivo. Sci Rep 2016; 6:28300. [PMID: 27350115 PMCID: PMC4923876 DOI: 10.1038/srep28300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/20/2016] [Indexed: 12/26/2022] Open
Abstract
BC1 RNA is a small brain specific non-protein coding RNA. It is transported from the cell body into dendrites where it is involved in the fine-tuning translational control. Due to its compactness and established secondary structure, BC1 RNA is an ideal model for investigating the motifs necessary for dendritic localization. Previously, microinjection of in vitro transcribed BC1 RNA mutants into the soma of cultured primary neurons suggested the importance of RNA motifs for dendritic targeting. These ex vivo experiments identified a single bulged nucleotide (U22) and a putative K-turn (GA motif) structure required for dendritic localization or distal transport, respectively. We generated six transgenic mouse lines (three founders each) containing neuronally expressing BC1 RNA variants on a BC1 RNA knockout mouse background. In contrast to ex vivo data, we did not find indications of reduction or abolition of dendritic BC1 RNA localization in the mutants devoid of the GA motif or the bulged nucleotide. We confirmed the ex vivo data, which showed that the triloop terminal sequence had no consequence on dendritic transport. Interestingly, changing the triloop supporting structure completely abolished dendritic localization of BC1 RNA. We propose a novel RNA motif important for dendritic transport in vivo.
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40
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Li Z, Hao S, Yin H, Gao J, Yang Z. Autophagy ameliorates cognitive impairment through activation of PVT1 and apoptosis in diabetes mice. Behav Brain Res 2016; 305:265-77. [PMID: 26971628 DOI: 10.1016/j.bbr.2016.03.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 02/24/2016] [Accepted: 03/09/2016] [Indexed: 01/19/2023]
Abstract
The underlying mechanisms of cognitive impairment in diabetes remain incompletely characterized. Here we show that the autophagic inhibition by 3-methyladenine (3-MA) aggravates cognitive impairment in streptozotocin-induced diabetic mice, including exacerbation of anxiety-like behaviors and aggravation in spatial learning and memory, especially the spatial reversal memory. Further neuronal function identification confirmed that both long term potentiation (LTP) and depotentiation (DPT) were exacerbated by autophagic inhibition in diabetic mice, which indicating impairment of synaptic plasticity. However, no significant change of pair-pulse facilitation (PPF) was recorded in diabetic mice with autophagic suppression compared with the diabetic mice, which indicated that presynaptic function was not affected by autophagic inhibition in diabetes. Subsequent hippocampal neuronal cell death analysis showed that the apoptotic cell death, but not the regulated necrosis, significantly increased in autophagic suppression of diabetic mice. Finally, molecular mechanism that may lead to cell death was identified. The long non-coding RNA PVT1 (plasmacytoma variant translocation 1) expression was analyzed, and data revealed that PVT1 was decreased significantly by 3-MA in diabetes. These findings show that PVT1-mediated autophagy may protect hippocampal neurons from impairment of synaptic plasticity and apoptosis, and then ameliorates cognitive impairment in diabetes. These intriguing findings will help pave the way for exciting functional studies of autophagy in cognitive impairment and diabetes that may alter the existing paradigms.
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Affiliation(s)
- Zhigui Li
- College of Medicine, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Animal Models and Degenerative Neurological Diseases, Nankai University, Tianjin 300071, China
| | - Shuang Hao
- College of Medicine, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Animal Models and Degenerative Neurological Diseases, Nankai University, Tianjin 300071, China
| | - Hongqiang Yin
- College of Medicine, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Animal Models and Degenerative Neurological Diseases, Nankai University, Tianjin 300071, China
| | - Jing Gao
- College of Medicine, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Animal Models and Degenerative Neurological Diseases, Nankai University, Tianjin 300071, China
| | - Zhuo Yang
- College of Medicine, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Animal Models and Degenerative Neurological Diseases, Nankai University, Tianjin 300071, China.
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41
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Széll M, Danis J, Bata-Csörgő Z, Kemény L. PRINS, a primate-specific long non-coding RNA, plays a role in the keratinocyte stress response and psoriasis pathogenesis. Pflugers Arch 2016; 468:935-43. [PMID: 26935426 PMCID: PMC4893059 DOI: 10.1007/s00424-016-1803-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/23/2016] [Indexed: 12/30/2022]
Abstract
In the last few years with the recent emergence of high-throughput technologies, thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome. However, assigning functional annotation and determining cellular contexts for these RNAs are still in its infancy. As information gained about lncRNA structure, interacting partners, and roles in human diseases may be helpful in the characterization of novel lncRNAs, we review our knowledge on a selected group of lncRNAs that were identified serendipitously years ago by large-scale gene expression methods used to study human diseases. In particular, we focus on the Psoriasis-susceptibility-Related RNA Gene Induced by Stress (PRINS) lncRNA, first identified by our research group as a transcript highest expressed in psoriatic non-lesional epidermis. Results gathered for PRINS in the last 10 years indicate that it is conserved in primates and plays a role in keratinocyte stress response. Elevated levels of PRINS expression in psoriatic non-lesional keratinocytes alter the stress response of non-lesional epidermis and contribute to disease pathogenesis. Finally, we propose a categorization for the PRINS lncRNA based on a recently elaborated system for lncRNA classification.
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Affiliation(s)
- Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Somogyi B. u. 4, 6720, Hungary. .,MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.
| | - Judit Danis
- Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Zsuzsanna Bata-Csörgő
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
| | - Lajos Kemény
- MTA-SZTE Dermatological Research Group, Szeged, Korányi fasor 6, 6720, Hungary.,Department of Dermatology and Allergology, Faculty of Medicine, University of Szeged, Szeged, Korányi fasor 6, 6720, Hungary
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42
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The Ins and Outs of miRNA-Mediated Gene Silencing during Neuronal Synaptic Plasticity. Noncoding RNA 2016; 2:ncrna2010001. [PMID: 29657259 PMCID: PMC5831896 DOI: 10.3390/ncrna2010001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/18/2022] Open
Abstract
Neuronal connections through specialized junctions, known as synapses, create circuits that underlie brain function. Synaptic plasticity, i.e., structural and functional changes to synapses, occurs in response to neuronal activity and is a critical regulator of various nervous system functions, including long-term memory formation. The discovery of mRNAs, miRNAs, ncRNAs, ribosomes, translational repressors, and other RNA binding proteins in dendritic spines allows individual synapses to alter their synaptic strength rapidly through regulation of local protein synthesis in response to different physiological stimuli. In this review, we discuss our understanding of a number of miRNAs, ncRNAs, and RNA binding proteins that are emerging as important regulators of synaptic plasticity, which play a critical role in memory, learning, and diseases that arise when neuronal circuits are impaired.
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43
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Long Noncoding RNA-Directed Epigenetic Regulation of Gene Expression Is Associated With Anxiety-like Behavior in Mice. Biol Psychiatry 2015; 78:848-59. [PMID: 25792222 PMCID: PMC4532653 DOI: 10.1016/j.biopsych.2015.02.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND RNA-directed regulation of epigenetic processes has recently emerged as an important feature of mammalian differentiation and development. Perturbation of this regulatory system in the brain may contribute to the development of neuropsychiatric disorders. METHODS RNA sequencing was used to identify changes in the experience-dependent expression of long noncoding RNAs (lncRNAs) within the medial prefrontal cortex of adult mice. Transcripts were validated by real-time quantitative polymerase chain reaction and a candidate lncRNA, Gomafu, was selected for further investigation. The functional role of this schizophrenia-related lncRNA was explored in vivo by antisense oligonucleotide-mediated gene knockdown in the medial prefrontal cortex, followed by behavioral training and assessment of fear-related anxiety. Long noncoding RNA-directed epigenetic regulation of gene expression was investigated by chromatin and RNA immunoprecipitation assays. RESULTS RNA sequencing analysis revealed changes in the expression of a significant number of genes related to neural plasticity and stress, as well as the dynamic regulation of lncRNAs. In particular, we detected a significant downregulation of Gomafu lncRNA. Our results revealed that Gomafu plays a role in mediating anxiety-like behavior and suggest that this may occur through an interaction with a key member of the polycomb repressive complex 1, BMI1, which regulates the expression of the schizophrenia-related gene beta crystallin (Crybb1). We also demonstrated a novel role for Crybb1 in mediating fear-induced anxiety-like behavior. CONCLUSIONS Experience-dependent expression of lncRNAs plays an important role in the epigenetic regulation of adaptive behavior, and the perturbation of Gomafu may be related to anxiety and the development of neuropsychiatric disorders.
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44
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Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron 2015; 88:861-877. [DOI: 10.1016/j.neuron.2015.09.045] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Targeting the eIF4A RNA helicase as an anti-neoplastic approach. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:781-91. [DOI: 10.1016/j.bbagrm.2014.09.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 01/22/2023]
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46
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Raabe CA, Brosius J. Does every transcript originate from a gene? Ann N Y Acad Sci 2015; 1341:136-48. [PMID: 25847549 DOI: 10.1111/nyas.12741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 12/20/2022]
Abstract
Outdated gene definitions favored regions corresponding to mature messenger RNAs, in particular, the open reading frame. In eukaryotes, the intergenic space was widely regarded nonfunctional and devoid of RNA transcription. Original concepts were based on the assumption that RNA expression was restricted to known protein-coding genes and a few so-called structural RNA genes, such as ribosomal RNAs or transfer RNAs. With the discovery of introns and, more recently, sensitive techniques for monitoring genome-wide transcription, this view had to be substantially modified. Tiling microarrays and RNA deep sequencing revealed myriads of transcripts, which cover almost entire genomes. The tremendous complexity of non-protein-coding RNA transcription has to be integrated into novel gene definitions. Despite an ever-growing list of functional RNAs, questions concerning the mass of identified transcripts are under dispute. Here, we examined genome-wide transcription from various angles, including evolutionary considerations, and suggest, in analogy to novel alternative splice variants that do not persist, that the vast majority of transcripts represent raw material for potential, albeit rare, exaptation events.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
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Roberts TC, Morris KV, Wood MJA. The role of long non-coding RNAs in neurodevelopment, brain function and neurological disease. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0507. [PMID: 25135968 DOI: 10.1098/rstb.2013.0507] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts with low protein-coding potential that represent a large proportion of the transcriptional output of the cell. Many lncRNAs exhibit features indicative of functionality including tissue-restricted expression, localization to distinct subcellular structures, regulated expression and evolutionary conservation. Some lncRNAs have been shown to associate with chromatin-modifying activities and transcription factors, suggesting that a common mode of action may be to guide protein complexes to target genomic loci. However, the functions (if any) of the vast majority of lncRNA transcripts are currently unknown, and the subject of investigation. Here, we consider the putative role(s) of lncRNAs in neurodevelopment and brain function with an emphasis on the epigenetic regulation of gene expression. Associations of lncRNAs with neurodevelopmental/neuropsychiatric disorders, neurodegeneration and brain cancers are also discussed.
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Affiliation(s)
- Thomas C Roberts
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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Hillje AL, Beckmann E, Pavlou MAS, Jaeger C, Pacheco MP, Sauter T, Schwamborn JC, Lewejohann L. The neural stem cell fate determinant TRIM32 regulates complex behavioral traits. Front Cell Neurosci 2015; 9:75. [PMID: 25852471 PMCID: PMC4364253 DOI: 10.3389/fncel.2015.00075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 02/20/2015] [Indexed: 12/22/2022] Open
Abstract
In mammals, new neurons are generated throughout the entire lifespan in two restricted areas of the brain, the dentate gyrus (DG) of the hippocampus and the subventricular zone (SVZ)—olfactory bulb (OB) system. In both regions newborn neurons display unique properties that clearly distinguish them from mature neurons. Enhanced excitability and increased synaptic plasticity enables them to add specific properties to information processing by modulating the existing local circuitry of already established mature neurons. Hippocampal neurogenesis has been suggested to play a role in spatial-navigation learning, spatial memory, and spatial pattern separation. Cumulative evidences implicate that adult-born OB neurons contribute to learning processes and odor memory. We recently demonstrated that the cell fate determinant TRIM32 is upregulated in differentiating neuroblasts of the SVZ-OB system in the adult mouse brain. The absence of TRIM32 leads to increased progenitor cell proliferation and less cell death. Both effects accumulate in an overproduction of adult-generated OB neurons. Here, we present novel data from behavioral studies showing that such an enhancement of OB neurogenesis not necessarily leads to increased olfactory performance but in contrast even results in impaired olfactory capabilities. In addition, we show at the cellular level that TRIM32 protein levels increase during differentiation of neural stem cells (NSCs). At the molecular level, several metabolic intermediates that are connected to glycolysis, glycine, or cysteine metabolism are deregulated in TRIM32 knockout mice brain tissue. These metabolomics pathways are directly or indirectly linked to anxiety or depression like behavior. In summary, our study provides comprehensive data on how the impairment of neurogenesis caused by the loss of the cell fate determinant TRIM32 causes a decrease of olfactory performance as well as a deregulation of metabolomic pathways that are linked to mood disorders.
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Affiliation(s)
- Anna-Lena Hillje
- ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Westfälische Wilhelms-Universität Münster Münster, Germany ; Luxembourg Centre for Systems Biomedicine, University of Luxembourg Luxembourg, Luxembourg
| | - Elisabeth Beckmann
- Department of Behavioural Biology, Westfälische Wilhelms-Universität Münster Münster, Germany
| | - Maria A S Pavlou
- ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Westfälische Wilhelms-Universität Münster Münster, Germany ; Luxembourg Centre for Systems Biomedicine, University of Luxembourg Luxembourg, Luxembourg
| | - Christian Jaeger
- Life Sciences Research Unit, University of Luxembourg Luxembourg, Luxembourg
| | - Maria P Pacheco
- Life Sciences Research Unit, University of Luxembourg Luxembourg, Luxembourg
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg Luxembourg, Luxembourg
| | - Jens C Schwamborn
- ZMBE, Institute of Cell Biology, Stem Cell Biology and Regeneration Group, Westfälische Wilhelms-Universität Münster Münster, Germany ; Luxembourg Centre for Systems Biomedicine, University of Luxembourg Luxembourg, Luxembourg
| | - Lars Lewejohann
- Department of Behavioural Biology, Westfälische Wilhelms-Universität Münster Münster, Germany
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Kapusta A, Feschotte C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet 2014; 30:439-52. [PMID: 25218058 PMCID: PMC4464757 DOI: 10.1016/j.tig.2014.08.004] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 02/08/2023]
Abstract
Thousands of genes encoding long noncoding RNAs (lncRNAs) have been identified in all vertebrate genomes thus far examined. The list of lncRNAs partaking in arguably important biochemical, cellular, and developmental activities is steadily growing. However, it is increasingly clear that lncRNA repertoires are subject to weak functional constraint and rapid turnover during vertebrate evolution. We discuss here some of the factors that may explain this apparent paradox, including relaxed constraint on sequence to maintain lncRNA structure/function, extensive redundancy in the regulatory circuits in which lncRNAs act, as well as adaptive and non-adaptive forces such as genetic drift. We explore the molecular mechanisms promoting the birth and rapid evolution of lncRNA genes, with an emphasis on the influence of bidirectional transcription and transposable elements, two pervasive features of vertebrate genomes. Together these properties reveal a remarkably dynamic and malleable noncoding transcriptome which may represent an important source of robustness and evolvability.
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Affiliation(s)
- Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Mohanty V, Gökmen-Polar Y, Badve S, Janga SC. Role of lncRNAs in health and disease-size and shape matter. Brief Funct Genomics 2014; 14:115-29. [PMID: 25212482 DOI: 10.1093/bfgp/elu034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Most of the mammalian genome including a large fraction of the non-protein coding transcripts has been shown to be transcribed. Studies related to these non-coding RNA molecules have predominantly focused on smaller molecules like microRNAs. In contrast, long non-coding RNAs (lncRNAs) have long been considered to be transcriptional noise. Accumulating evidence suggests that lncRNAs are involved in key cellular and developmental processes. Several critical questions regarding functions and properties of lncRNAs and their circular forms remain to be answered. Increasing evidence from high-throughput sequencing screens also suggests the involvement of lncRNAs in diseases such as cancer, although the underlying mechanisms still need to be elucidated. Here, we discuss the current state of research in the field of lncRNAs, questions that need to be addressed in light of recent genome-wide studies documenting the landscape of lncRNAs, their functional roles and involvement in diseases. We posit that with the availability of high-throughput data sets it is not only possible to improve methods for predicting lncRNAs but will also facilitate our ability to elucidate their functions and phenotypes by using integrative approaches.
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