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Bliim N, Leshchyns'ka I, Keable R, Chen BJ, Curry-Hyde A, Gray L, Sytnyk V, Janitz M. Early transcriptome changes in response to chemical long-term potentiation induced via activation of synaptic NMDA receptors in mouse hippocampal neurons. Genomics 2018; 111:1676-1686. [PMID: 30465913 DOI: 10.1016/j.ygeno.2018.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 01/23/2023]
Abstract
Long term potentiation (LTP) is a form of synaptic plasticity. In the present study LTP was induced via activation of synaptic NMDA receptors in primary hippocampal neuron cultures from neonate mice and RNA was isolated for RNA sequencing at 20 min following LTP induction. RNA sequencing and differential expression testing was performed to determine the identity and abundance of protein-coding and non-coding RNAs in control and LTP induced neuron cultures. We show that expression levels of a small group of transcripts encoding proteins involved in negative regulation of gene expression (Adcyap1, Id3), protein translation (Rpl22L1), extracellular structure organization (Bgn), intracellular signalling (Ppm1H, Ntsr2, Cldn10) and protein citrullination (PAD2) are downregulated in the stimulated neurons. Our results suggest that the early stages of LTP are accompanied by the remodelling of the biosynthetic machinery, interactions with the extracellular matrix and intracellular signalling pathways at the transcriptional level.
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Affiliation(s)
- Nicola Bliim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Iryna Leshchyns'ka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ryan Keable
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ashton Curry-Hyde
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Lachlan Gray
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Vladimir Sytnyk
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany.
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52
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Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018; 8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.
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Affiliation(s)
- Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Raza-Ur Rahman
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Tonatiuh Pena Centeno
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Ramon O Vidal
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Hanna Wildhagen
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Burkhard Rammner
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Sarva Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Inga Urban
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37073, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Koray Kirli
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Eva Benito
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - André Fischer
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Roya Y Yousefi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
- Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Bonn
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany.
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
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53
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Long noncoding RNA GM12371 acts as a transcriptional regulator of synapse function. Proc Natl Acad Sci U S A 2018; 115:E10197-E10205. [PMID: 30297415 PMCID: PMC6205475 DOI: 10.1073/pnas.1722587115] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neuronal functions of long noncoding RNAs (lncRNAs) are poorly understood. Here we describe identification and function of lncRNA GM12371 in regulating synaptic transmission, synapse density, and dendritic arborization in primary hippocampal neurons. GM12371 expression is regulated by cAMP signaling and is critical for the activity regulated synaptic transmission. Importantly, GM12371 is associated with transcriptionally active chromatin and regulates expression of several genes involved in neuronal growth and development. Taken together, these results suggest that GM12371 acts as a transcriptional regulator of synapse function. Despite the growing evidence suggesting that long noncoding RNAs (lncRNAs) are critical regulators of several biological processes, their functions in the nervous system remain elusive. We have identified an lncRNA, GM12371, in hippocampal neurons that is enriched in the nucleus and necessary for synaptic communication, synapse density, synapse morphology, and dendritic tree complexity. Mechanistically, GM12371 regulates the expression of several genes involved in neuronal development and differentiation, as well as expression of specific lncRNAs and their cognate mRNA targets. Furthermore, we find that cAMP-PKA signaling up-regulates the expression of GM12371 and that its expression is essential for the activity-dependent changes in synaptic transmission in hippocampal neurons. Taken together, our data establish a key role for GM12371 in regulating synapse function.
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54
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Chen BJ, Yang B, Janitz M. Region-specific expression of circular RNAs in the mouse brain. Neurosci Lett 2017; 666:44-47. [PMID: 29253603 DOI: 10.1016/j.neulet.2017.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/04/2017] [Accepted: 12/10/2017] [Indexed: 10/24/2022]
Abstract
Circular RNAs (circRNAs) are abundant in mammalian brain and their expression is regulated in a tissue- and developmental stage-specific manner. Mammalian brain is the most transcriptionally complex organ. While many studies have extensively studied linear transcriptome and its biological functions in the brain, the circular transcriptome remains largely unexplored. This study focused on investigation of circRNA expression patterns in the mammalian brain regions critical for cognitive and memory functions and performed comparative analysis with the linear transcriptome. Altogether our study showed that circular and linear RNAs have independent expression patterns despite being derived from the same genomic locus, and that circular transcriptomes from different brain region have distinct characteristics in terms of transcript abundance and composition.
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Affiliation(s)
- Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Belinda Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia; Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany.
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55
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The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages. Sci Rep 2017; 7:10508. [PMID: 28874839 PMCID: PMC5585378 DOI: 10.1038/s41598-017-10853-6] [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: 06/09/2017] [Accepted: 08/15/2017] [Indexed: 01/06/2023] Open
Abstract
Next Generation Sequencing (NGS) strategies, like RNA-Seq, have revealed the transcription of a wide variety of long non-coding RNAs (lncRNAs) in the genomes of several organisms. In the present work we assessed the lncRNAs complement of Schistosoma mansoni, the blood fluke that causes schistosomiasis, ranked among the most prevalent parasitic diseases worldwide. We focused on the long intergenic/intervening ncRNAs (lincRNAs), hidden within the large amount of information obtained through RNA-Seq in S. mansoni (88 libraries). Our computational pipeline identified 7029 canonically-spliced putative lincRNA genes on 2596 genomic loci (at an average 2.7 isoforms per lincRNA locus), as well as 402 spliced lncRNAs that are antisense to protein-coding (PC) genes. Hundreds of lincRNAs showed traits for being functional, such as the presence of epigenetic marks at their transcription start sites, evolutionary conservation among other schistosome species and differential expression across five different life-cycle stages of the parasite. Real-time qPCR has confirmed the differential life-cycle stage expression of a set of selected lincRNAs. We have built PC gene and lincRNA co-expression networks, unraveling key biological processes where lincRNAs might be involved during parasite development. This is the first report of a large-scale identification and structural annotation of lncRNAs in the S. mansoni genome.
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56
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Abstract
The emerging complexity of the transcriptional landscape poses great challenges to our conventional preconceptions of how the genome regulates brain function and dysfunction. Non-protein-coding RNAs (ncRNAs) confer a high level of intricate and dynamic regulation of various molecular processes in the CNS and they have been implicated in neurodevelopment and brain ageing, as well as in synapse function and cognitive performance, in both health and disease. ncRNA-mediated processes may be involved in various aspects of the pathogenesis of neurodegenerative disorders. Understanding these events may help to develop novel diagnostic and therapeutic tools. Here, we provide an overview of the complex mechanisms that are affected by the diverse ncRNA classes that have been implicated in neurodegeneration.
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57
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Quan Z, Zheng D, Qing H. Regulatory Roles of Long Non-Coding RNAs in the Central Nervous System and Associated Neurodegenerative Diseases. Front Cell Neurosci 2017; 11:175. [PMID: 28713244 PMCID: PMC5491930 DOI: 10.3389/fncel.2017.00175] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Accumulating studies have revealed that the human genome encodes tens of thousands of long non-coding RNAs (lncRNAs), which participate in multiple biological networks modulating gene expression via transcriptional, post-transcriptional and epigenetic regulation. Strikingly, a large fraction of tissue-specific lncRNAs are expressed in the Central Nervous System (CNS) with precisely regulated temporal and spatial expression patterns. These brain-specific lncRNAs are also featured with the cell-type specificity, the highest signals of evolutionary conservation, and their preferential location adjacent to brain-expressed protein-coding genes. Mounting evidence has indicated dysregulation or mutations in lncRNA gene loci are associated with a variety of CNS-associated neurodegenerative disorders, such as Alzheimer's, Parkinson's, Huntington's diseases, Amyotrophic Lateral Sclerosis and others. However, how lncRNAs contribute to these disorders remains to be further explored and studied. In this review article, we systematically and comprehensively summarize the current studies of lncRNAs, demonstrate the specificity of lncRNAs expressed in the brain, their functions during neural development and expression profiles in major cell types of the CNS, highlight the regulatory mechanisms of several studied lncRNAs that may play essential roles in the pathophysiology of neurodegenerative diseases, and discuss the current challenges and future perspectives of lncRNA studies involved in neurodegenerative and other diseases.
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Affiliation(s)
- Zhenzhen Quan
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Da Zheng
- School of Life Science, Beijing Institute of TechnologyBeijing, China
| | - Hong Qing
- School of Life Science, Beijing Institute of TechnologyBeijing, China
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58
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Tripathi R, Chakraborty P, Varadwaj PK. Unraveling long non-coding RNAs through analysis of high-throughput RNA-sequencing data. Noncoding RNA Res 2017; 2:111-118. [PMID: 30159428 PMCID: PMC6096414 DOI: 10.1016/j.ncrna.2017.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/19/2017] [Accepted: 06/21/2017] [Indexed: 01/01/2023] Open
Abstract
Extensive genome-wide transcriptome study mediated by high throughput sequencing technique has revolutionized the study of genetics and epigenetic at unprecedented resolution. The research has revealed that besides protein-coding RNAs, large proportions of mammalian transcriptome includes a heap of regulatory non protein-coding RNAs, the number encoded within human genome is enigmatic. Many taboos developed in the past categorized these non-coding RNAs as ''dark matter" and "junks". Breaking the myth, RNA-seq-- a recently developed experimental technique is widely being used for studying non-coding RNAs which has acquired the limelight due to their physiological and pathological significance. The longest member of the ncRNA family-- long non-coding RNAs, acts as stable and functional part of a genome, guiding towards the important clues about the varied biological events like cellular-, structural- processes governing the complexity of an organism. Here, we review the most recent and influential computational approach developed to identify and quantify the long non-coding RNAs serving as an assistant for the users to choose appropriate tools for their specific research.
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Affiliation(s)
- Rashmi Tripathi
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, 211015, UP, India
| | - Pavan Chakraborty
- Department of Information Technology, Indian Institute of Information Technology Allahabad, Allahabad, 211015, UP, India
| | - Pritish Kumar Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology Allahabad, Allahabad, 211015, UP, India
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59
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An oscillopathic approach to developmental dyslexia: From genes to speech processing. Behav Brain Res 2017; 329:84-95. [DOI: 10.1016/j.bbr.2017.03.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/14/2017] [Accepted: 03/18/2017] [Indexed: 12/27/2022]
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60
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Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ. Improved definition of the mouse transcriptome via targeted RNA sequencing. Genome Res 2017; 26:705-16. [PMID: 27197243 PMCID: PMC4864457 DOI: 10.1101/gr.199760.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.
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Affiliation(s)
- Giovanni Bussotti
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
| | - Tommaso Leonardi
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lorenzo Malquori
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cedric Notredame
- Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St Vincent's Clinical School, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Anton J Enright
- EMBL, European Bioinformatics Institute, Cambridge, CB10 1SD, United Kingdom
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61
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Rizzo V, Touzani K, Raveendra BL, Swarnkar S, Lora J, Kadakkuzha BM, Liu XA, Zhang C, Betel D, Stackman RW, Puthanveettil SV. Encoding of contextual fear memory requires de novo proteins in the prelimbic cortex. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2017; 2:158-169. [PMID: 28503670 DOI: 10.1016/j.bpsc.2016.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Despite our understanding of the significance of the prefrontal cortex in the consolidation of long-term memories (LTM), its role in the encoding of LTM remains elusive. Here we investigated the role of new protein synthesis in the mouse medial prefrontal cortex (mPFC) in encoding contextual fear memory. METHODS Because a change in the association of mRNAs to polyribosomes is an indicator of new protein synthesis, we assessed the changes in polyribosome-associated mRNAs in the mPFC following contextual fear conditioning (CFC) in the mouse. Differential gene expression in mPFC was identified by polyribosome profiling (n = 18). The role of new protein synthesis in mPFC was determined by focal inhibition of protein synthesis (n = 131) and by intra-prelimbic cortex manipulation (n = 56) of Homer 3, a candidate identified from polyribosome profiling. RESULTS We identified several mRNAs that are differentially and temporally recruited to polyribosomes in the mPFC following CFC. Inhibition of protein synthesis in the prelimbic (PL), but not in the anterior cingulate cortex (ACC) region of the mPFC immediately after CFC disrupted encoding of contextual fear memory. Intriguingly, inhibition of new protein synthesis in the PL 6 hours after CFC did not impair encoding. Furthermore, expression of Homer 3, an mRNA enriched in polyribosomes following CFC, in the PL constrained encoding of contextual fear memory. CONCLUSIONS Our studies identify several molecular substrates of new protein synthesis in the mPFC and establish that encoding of contextual fear memories require new protein synthesis in PL subregion of mPFC.
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Affiliation(s)
- Valerio Rizzo
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Khalid Touzani
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Bindu L Raveendra
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Supriya Swarnkar
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Joan Lora
- Department of Psychology, Center for Complex Systems & Brain Sciences, College of Science, Florida Atlantic University, Jupiter, FL 33458
| | - Beena M Kadakkuzha
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida 130 Scripps Way, Jupiter, FL 33458
| | - Chao Zhang
- Department of Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College, New York. NY10065. USA
| | - Doron Betel
- Department of Medicine and Institute for Computational Biomedicine, Weill Cornell Medical College, New York. NY10065. USA
| | - Robert W Stackman
- Department of Psychology, Center for Complex Systems & Brain Sciences, College of Science, Florida Atlantic University, Jupiter, FL 33458
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62
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Huang X, Luo YL, Mao YS, Ji JL. The link between long noncoding RNAs and depression. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:73-78. [PMID: 27318257 DOI: 10.1016/j.pnpbp.2016.06.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 12/28/2022]
Abstract
The major depressive disorder (MDD) is a relatively common mental disorder from which that hundreds of million people have suffered, leading to displeasing life quality, which is characterized by health damage and even suicidal thoughts. The complicated development and functioning of MDD is still under exploration. Long noncoding RNA (lncRNAs) are highly expressed in the brain, could affect neural stem cell maintenance, neurogenesis and gliogenesis, brain patterning, synaptic and stress responses, and neural plasticity. The dysregulation of certain lncRNAs induces in neurodevelopmental, neurodegenerative and neuroimmunological disorders, primary brain tumors, and psychiatric diseases. Although advances have been made, no fully satisfactory treatments for major depression are available, further investigation is requested. And recently data showed that the expression level of the majority of lncRNAs demonstrated a clear tendency of upregulation, and the certain dysregulated miRNAs and lncRNAs in the MDD have been proved to have a co-synergism mechanism, that is why we speculate lncRNA might get the capability to regulate MDD. Few identified lncRNAs have been deeply studied in detailed experiments up until now, little predictions of their function have been raised, and further researches is calling for discover their signal pathway and related regulatory networks.
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Affiliation(s)
- Xiao Huang
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yan-Li Luo
- Department of Psychiatry, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Yue-Shi Mao
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian-Lin Ji
- Department of Psychological Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
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63
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Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA. lncRNA expression in the auditory forebrain during postnatal development. Gene 2016; 593:201-216. [PMID: 27544636 PMCID: PMC5034298 DOI: 10.1016/j.gene.2016.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/27/2016] [Accepted: 08/15/2016] [Indexed: 12/30/2022]
Abstract
The biological processes governing brain development and maturation depend on complex patterns of gene and protein expression, which can be influenced by many factors. One of the most overlooked is the long noncoding class of RNAs (lncRNAs), which are known to play important regulatory roles in an array of biological processes. Little is known about the distribution of lncRNAs in the sensory systems of the brain, and how lncRNAs interact with other mechanisms to guide the development of these systems. In this study, we profiled lncRNA expression in the mouse auditory forebrain during postnatal development at time points before and after the onset of hearing (P7, P14, P21, adult). First, we generated lncRNA profiles of the primary auditory cortex (A1) and medial geniculate body (MG) at each age. Then, we determined the differential patterns of expression by brain region and age. These analyses revealed that the lncRNA expression profile was distinct between both brain regions and between each postnatal age, indicating spatial and temporal specificity during maturation of the auditory forebrain. Next, we explored potential interactions between functionally-related lncRNAs, protein coding RNAs (pcRNAs), and associated proteins. The maturational trajectories (P7 to adult) of many lncRNA - pcRNA pairs were highly correlated, and predictive analyses revealed that lncRNA-protein interactions tended to be strong. A user-friendly database was constructed to facilitate inspection of the expression levels and maturational trajectories for any lncRNA or pcRNA in the database. Overall, this study provides an in-depth summary of lncRNA expression in the developing auditory forebrain and a broad-based foundation for future exploration of lncRNA function during brain development.
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Affiliation(s)
- Yan Guo
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Pan Zhang
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Quanhu Sheng
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Shilin Zhao
- Dept. of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Troy A Hackett
- Dept. of Hearing and Speech Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA.
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64
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Zimmermann-Peruzatto JM, Lazzari VM, Agnes G, Becker RO, de Moura AC, Guedes RP, Lucion AB, Almeida S, Giovenardi M. The Impact of Oxytocin Gene Knockout on Sexual Behavior and Gene Expression Related to Neuroendocrine Systems in the Brain of Female Mice. Cell Mol Neurobiol 2016; 37:803-815. [DOI: 10.1007/s10571-016-0419-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/17/2016] [Indexed: 01/13/2023]
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65
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Transcriptional regulation of long-term potentiation. Neurogenetics 2016; 17:201-210. [PMID: 27318935 DOI: 10.1007/s10048-016-0489-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
Abstract
Long-term potentiation (LTP), the persistent strengthening of synapses following high levels of stimulation, is a form of synaptic plasticity that has been studied extensively as a possible mechanism for learning and memory formation. The strengthening of the synapse that occurs during LTP requires cascades of complex molecular processes and the coordinated remodeling of pre-synaptic and post-synaptic neurons. Despite over four decades of research, our understanding of the transcriptional mechanisms and molecular processes underlying LTP remains incomplete. Identification of all the proteins and non-coding RNA transcripts expressed during LTP may provide greater insight into the molecular mechanisms involved in learning and memory formation.
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66
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Carletti F, Sardo P, Gambino G, Liu XA, Ferraro G, Rizzo V. Hippocampal Hyperexcitability is Modulated by Microtubule-Active Agent: Evidence from In Vivo and In Vitro Epilepsy Models in the Rat. Front Cell Neurosci 2016; 10:29. [PMID: 26903814 PMCID: PMC4746529 DOI: 10.3389/fncel.2016.00029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/29/2016] [Indexed: 11/13/2022] Open
Abstract
The involvement of microtubule dynamics on bioelectric activity of neurons and neurotransmission represents a fascinating target of research in the context of neural excitability. It has been reported that alteration of microtubule cytoskeleton can lead to profound modifications of neural functioning, with a putative impact on hyperexcitability phenomena. Altogether, in the present study we pointed at exploring the outcomes of modulating the degree of microtubule polymerization in two electrophysiological models of epileptiform activity in the rat hippocampus. To this aim, we used in vivo maximal dentate activation (MDA) and in vitro hippocampal epileptiform bursting activity (HEBA) paradigms to assess the effects of nocodazole (NOC) and paclitaxel (PAC), that respectively destabilize and stabilize microtubule structures. In particular, in the MDA paroxysmal discharge is electrically induced, whereas the HEBA is obtained by altering extracellular ionic concentrations. Our results provided evidence that NOC 10 μM was able to reduce the severity of MDA seizures, without inducing neurotoxicity as verified by the immunohistochemical assay. In some cases, paroxysmal discharge was completely blocked during the maximal effect of the drug. These data were also in agreement with the outcomes of in vitro HEBA, since NOC markedly decreased burst activity that was even silenced occasionally. In contrast, PAC at 10 μM did not exert a clear action in both paradigms. The present study, targeting cellular mechanisms not much considered so far, suggests the possibility that microtubule-active drugs could modulate brain hyperexcitability. This contributes to the hypothesis that cytoskeleton function may affect synaptic processes, relapsing on bioelectric aspects of epileptic activity.
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Affiliation(s)
- Fabio Carletti
- Department of "Experimental Biomedicine and Clinical Neuroscience" (Bio.Ne.C.), "Sezione di Fisiologia Umana G. Pagano", University of Palermo Palermo, Italy
| | - Pierangelo Sardo
- Department of "Experimental Biomedicine and Clinical Neuroscience" (Bio.Ne.C.), "Sezione di Fisiologia Umana G. Pagano", University of PalermoPalermo, Italy; Post-graduate School of Nutrition and Food Science, University of PalermoPalermo, Italy
| | - Giuditta Gambino
- Department of "Experimental Biomedicine and Clinical Neuroscience" (Bio.Ne.C.), "Sezione di Fisiologia Umana G. Pagano", University of Palermo Palermo, Italy
| | - Xin-An Liu
- Department of Neuroscience, The Scripps Research Institute Jupiter, FL, USA
| | - Giuseppe Ferraro
- Department of "Experimental Biomedicine and Clinical Neuroscience" (Bio.Ne.C.), "Sezione di Fisiologia Umana G. Pagano", University of PalermoPalermo, Italy; Post-graduate School of Nutrition and Food Science, University of PalermoPalermo, Italy
| | - Valerio Rizzo
- Department of "Experimental Biomedicine and Clinical Neuroscience" (Bio.Ne.C.), "Sezione di Fisiologia Umana G. Pagano", University of PalermoPalermo, Italy; Department of Neuroscience, The Scripps Research InstituteJupiter, FL, USA
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67
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Aprea J, Calegari F. Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain. EMBO J 2015; 34:2865-84. [PMID: 26516210 DOI: 10.15252/embj.201592655] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/05/2015] [Indexed: 01/17/2023] Open
Abstract
Evidence on the role of long non-coding (lnc) RNAs has been accumulating over decades, but it has been only recently that advances in sequencing technologies have allowed the field to fully appreciate their abundance and diversity. Despite this, only a handful of lncRNAs have been phenotypically or mechanistically studied. Moreover, novel lncRNAs and new classes of RNAs are being discovered at growing pace, suggesting that this class of molecules may have functions as diverse as protein-coding genes. Interestingly, the brain is the organ where lncRNAs have the most peculiar features including the highest number of lncRNAs that are expressed, proportion of tissue-specific lncRNAs and highest signals of evolutionary conservation. In this work, we critically review the current knowledge about the steps that have led to the identification of the non-coding transcriptome including the general features of lncRNAs in different contexts in terms of both their genomic organisation, evolutionary origin, patterns of expression, and function in the developing and adult mammalian brain.
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Affiliation(s)
- Julieta Aprea
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
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68
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Ward M, McEwan C, Mills JD, Janitz M. Conservation and tissue-specific transcription patterns of long noncoding RNAs. ACTA ACUST UNITED AC 2015; 1:2-9. [PMID: 27335896 PMCID: PMC4894084 DOI: 10.3109/23324015.2015.1077591] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/15/2015] [Indexed: 12/31/2022]
Abstract
Over the past decade, the focus of molecular biology has shifted from being predominately DNA and protein-centric to having a greater appreciation of RNA. It is now accepted that the genome is pervasively transcribed in tissue- and cell-specific manner, to produce not only protein-coding RNAs, but also an array of noncoding RNAs (ncRNAs). Many of these ncRNAs have been found to interact with DNA, protein and other RNA molecules where they exert regulatory functions. Long ncRNAs (lncRNAs) are a subclass of ncRNAs that are particularly interesting due to their cell-specific and species-specific expression patterns and unique conservation patterns. Currently, individual lncRNAs have been classified functionally; however, for the vast majority the functional relevance is unknown. To better categorize lncRNAs, an understanding of their specific expression patterns and evolutionary constraints are needed.
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Affiliation(s)
- Melanie Ward
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - Callum McEwan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - James D Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales , Sydney, NSW 2052, Australia
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