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Namjoshi SV, Raab-Graham KF. Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci 2017; 10:45. [PMID: 28286470 PMCID: PMC5323403 DOI: 10.3389/fnmol.2017.00045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
In the last decade, bioinformatic analyses of high-throughput proteomics and transcriptomics data have enabled researchers to gain insight into the molecular networks that may underlie lasting changes in synaptic efficacy. Development and utilization of these techniques have advanced the field of learning and memory significantly. It is now possible to move from the study of activity-dependent changes of a single protein to modeling entire network changes that require local protein synthesis. This data revolution has necessitated the development of alternative computational and statistical techniques to analyze and understand the patterns contained within. Thus, the focus of this review is to provide a synopsis of the journey and evolution toward big data techniques to address still unanswered questions regarding how synapses are modified to strengthen neuronal circuits. We first review the seminal studies that demonstrated the pivotal role played by local mRNA translation as the mechanism underlying the enhancement of enduring synaptic activity. In the interest of those who are new to the field, we provide a brief overview of molecular biology and biochemical techniques utilized for sample preparation to identify locally translated proteins using RNA sequencing and proteomics, as well as the computational approaches used to analyze these data. While many mRNAs have been identified, few have been shown to be locally synthesized. To this end, we review techniques currently being utilized to visualize new protein synthesis, a task that has proven to be the most difficult aspect of the field. Finally, we provide examples of future applications to test the physiological relevance of locally synthesized proteins identified by big data approaches.
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Affiliation(s)
- Sanjeev V Namjoshi
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA
| | - Kimberly F Raab-Graham
- Center for Learning and Memory, The University of Texas at Austin, AustinTX, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, AustinTX, USA; Department of Physiology and Pharmacology, Wake Forest Health Sciences, Medical Center Boulevard, Winston-SalemNC, USA
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Merlo L, Cimino F, Angileri FF, La Torre D, Conti A, Cardali SM, Saija A, Germanò A. Alteration in synaptic junction proteins following traumatic brain injury. J Neurotrauma 2015; 31:1375-85. [PMID: 24661152 DOI: 10.1089/neu.2014.3385] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Extensive research and scientific efforts have been focused on the elucidation of the pathobiology of cellular and axonal damage following traumatic brain injury (TBI). Conversely, few studies have specifically addressed the issue of synaptic dysfunction. Synaptic junction proteins may be involved in post-TBI alterations, leading to synaptic loss or disrupted plasticity. A Synapse Protein Database on synapse ontology identified 109 domains implicated in synaptic activities and over 5000 proteins, but few of these demonstrated to play a role in the synaptic dysfunction after TBI. These proteins are involved in neuroplasticity and neuromodulation and, most importantly, may be used as novel neuronal markers of TBI for specific intervention.
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Affiliation(s)
- Lucia Merlo
- 1 Department of Neurosciences, University of Messina , Messina, Italy
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Kang MG, Byun K, Kim JH, Park NH, Heinsen H, Ravid R, Steinbusch HW, Lee B, Park YM. Proteogenomics of the human hippocampus: The road ahead. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:788-97. [PMID: 25770686 DOI: 10.1016/j.bbapap.2015.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 12/26/2022]
Abstract
The hippocampus is one of the most essential components of the human brain and plays an important role in learning and memory. The hippocampus has drawn great attention from scientists and clinicians due to its clinical importance in diseases such as Alzheimer's disease (AD), non-AD dementia, and epilepsy. Understanding the function of the hippocampus and related disease mechanisms requires comprehensive knowledge of the orchestration of the genome, epigenome, transcriptome, proteome, and post-translational modifications (PTMs) of proteins. The past decade has seen remarkable advances in the high-throughput sequencing techniques that are collectively called next generation sequencing (NGS). NGS enables the precise analysis of gene expression profiles in cells and tissues, allowing powerful and more feasible integration of expression data from the gene level to the protein level, even allowing "-omic" level assessment of PTMs. In addition, improved bioinformatics algorithms coupled with NGS technology are finally opening a new era for scientists to discover previously unidentified and elusive proteins. In the present review, we will focus mainly on the proteomics of the human hippocampus with an emphasis on the integrated analysis of genomics, epigenomics, transcriptomics, and proteomics. Finally, we will discuss our perspectives on the potential and future of proteomics in the field of hippocampal biology. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Myoung-Goo Kang
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Kyunghee Byun
- Center for Genomics and Proteomics, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 406-840, Republic of Korea
| | - Jae Ho Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Nam Hyun Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Helmut Heinsen
- Morphological Brain Research Unit, Department of Psychiatry, Universität of Würzburg, Würzburg, Germany
| | - Rivka Ravid
- Brain Bank Consultant, Amsterdam, The Netherlands
| | - Harry W Steinbusch
- School for Mental Health and Neuroscience, Department of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Bonghee Lee
- Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea.
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea; Mass Spectrometry Research Center, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Republic of Korea.
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Rohoza LA, Dyubko TS, Galchenko SY, Sandomirsky BP. Peptide composition of extracts of cryopreserved pigs’ and piglets’ heart fragments. UKRAINIAN BIOCHEMICAL JOURNAL 2013. [DOI: 10.15407/ubj85.02.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Easley-Neal C, Fierro J, Buchanan J, Washbourne P. Late recruitment of synapsin to nascent synapses is regulated by Cdk5. Cell Rep 2013; 3:1199-212. [PMID: 23602570 DOI: 10.1016/j.celrep.2013.03.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 03/05/2013] [Accepted: 03/20/2013] [Indexed: 11/17/2022] Open
Abstract
Synapse formation is a complex process that involves the recruitment and assembly of a myriad of pre- and postsynaptic proteins. Despite being present at every synapse in the vertebrate CNS, little is known about the transport, recruitment, and stabilization of synapsin at nascent synapses during development. We examined the transport and recruitment of synapsin to nascent presynaptic terminals in vivo in the developing zebrafish spinal cord. Synapsin was transported in a transport packet independently of two other presynaptic organelles: synaptic vesicle (SV) protein transport vesicles (STVs) and Piccolo-containing active zone precursor transport vesicles (PTVs). During presynaptic assembly, recruitment of all three transport packets occurred in an ordered sequence: STVs preceded PTVs, which in turn preceded synapsin. Importantly, cyclin-dependent kinase 5 (Cdk5) specifically regulated the late recruitment of synapsin transport packets at synapses. These results point to additional layers of complexity in the established mechanisms of synaptogenesis.
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Valor LM, Barco A. Hippocampal gene profiling: toward a systems biology of the hippocampus. Hippocampus 2010; 22:929-41. [PMID: 21080408 DOI: 10.1002/hipo.20888] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2010] [Indexed: 01/17/2023]
Abstract
Transcriptomics and proteomics approaches give a unique perspective for understanding brain and hippocampal functions but also pose unique challenges because of the singular complexity of the nervous system. The proliferation of genome-wide expression studies during the last decade has provided important insight into the molecular underpinnings of brain anatomy, neural plasticity, and neurological diseases. Microarray technology has dominated transcriptomics research, but this situation is rapidly changing with the recent technological advances in high-throughput sequencing. The full potential of transcriptomics in the neurosciences will be achieved as a result of its integration with other "-omics" disciplines as well as the development of novel analytical bioinformatics and systems biology tools for meta-analysis. Here, we review some of the most relevant advances in the gene profiling of the hippocampus, its relationship with proteomics approaches, and the promising perspectives for the future.
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Affiliation(s)
- Luis M Valor
- Instituto de Neurociencias de Alicante, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Campus de Sant Joan, Apt. 18, Sant Joan d'Alacant, 03550, Alicante, Spain
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Du R, Long J, Yao J, Dong Y, Yang X, Tang S, Zuo S, He Y, Chen X. Subcellular Quantitative Proteomics Reveals Multiple Pathway Cross-Talk That Coordinates Specific Signaling and Transcriptional Regulation for the Early Host Response to LPS. J Proteome Res 2010; 9:1805-21. [DOI: 10.1021/pr900962c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ruyun Du
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Jing Long
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Jun Yao
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Yun Dong
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Xiaoli Yang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Siwei Tang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Shuai Zuo
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Yufei He
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
| | - Xian Chen
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, China, and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, North Carolina
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Díaz E. From microarrays to mechanisms of brain development and function. Biochem Biophys Res Commun 2009; 385:129-31. [DOI: 10.1016/j.bbrc.2009.05.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 05/14/2009] [Indexed: 12/29/2022]
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