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Tarannum R, Mun G, Quddos F, Swanger SA, Steward O, Farris S. Dendritically localized RNAs are packaged as diversely composed Ribonucleoprotein particles with heterogeneous copy number states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603387. [PMID: 39071419 PMCID: PMC11275876 DOI: 10.1101/2024.07.13.603387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Localization of mRNAs to dendrites is a fundamental mechanism by which neurons achieve spatiotemporal control of gene expression. Translationally repressed neuronal mRNA transport granules, also referred to as ribonuclear proteins (RNPs), have been shown to be trafficked as single or low copy number RNPs and as larger complexes with multiple copies and/or species of mRNAs. However, there is little evidence of either population in intact neuronal circuits. Using single molecule fluorescence in situ hybridization studies in the dendrites of adult rat and mouse hippocampus, we provide evidence that supports the existence of multi-transcript RNPs with the constituents varying in amounts for each RNA species. By competing-off fluorescently labeled probe with serial increases of unlabeled probe, we detected stepwise decreases in Arc RNP number and fluorescence intensity, suggesting Arc RNAs localize to dendrites in both low- and multiple-copy number RNPs. When probing for multiple mRNAs, we find that localized RNPs are heterogeneous in size and colocalization patterns that vary per RNA. Further, localized RNAs that are targeted by the same trans-acting element (FMRP) display greater levels of colocalization compared to an RNA not targeted by FMRP. Simultaneous visualization and assessment of colocalization using highly multiplexed imaging of a dozen mRNA species targeted by FMRP demonstrates that dendritic RNAs are mostly trafficked as heteromeric cargoes of multiple types of RNAs (at least one or more RNAs). Moreover, the composition of these RNA cargoes correlates with the abundance of the transcripts even after accounting for expression. Collectively, these results suggest that dendritic RNPs are packaged as heterogeneous co-assemblies of different mRNAs and that RNP contents may be driven, at least partially, by highly abundant dendritic RNAs; a model that favors efficiency over fine-tuned control for sustaining long-distance trafficking of thousands of messenger molecules.
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Affiliation(s)
- Renesa Tarannum
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Translational Biology, Medicine & Health Graduate Program, Virginia Tech, Blacksburg, Virginia
| | - Grace Mun
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
| | - Fatima Quddos
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Translational Biology, Medicine & Health Graduate Program, Virginia Tech, Blacksburg, Virginia
| | - Sharon A. Swanger
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
| | | | - Shannon Farris
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Center for Neurobiology Research, Roanoke, Virginia
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia
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2
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Patel RR, Gandhi P, Spencer K, Salem NA, Erikson CM, Borgonetti V, Vlkolinsky R, Rodriguez L, Nadav T, Bajo M, Roberts AJ, Dayne Mayfield R, Roberto M. Functional and morphological adaptation of medial prefrontal corticotropin releasing factor receptor 1-expressing neurons in male mice following chronic ethanol exposure. Neurobiol Stress 2024; 31:100657. [PMID: 38983690 PMCID: PMC11231756 DOI: 10.1016/j.ynstr.2024.100657] [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: 03/27/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/11/2024] Open
Abstract
Chronic ethanol dependence and withdrawal activate corticotropin releasing factor (CRF)-containing GABAergic neurons in the medial prefrontal cortex (mPFC), which tightly regulate glutamatergic pyramidal neurons. Using male CRF1:GFP reporter mice, we recently reported that CRF1-expressing (mPFCCRF1+) neurons predominantly comprise mPFC prelimbic layer 2/3 pyramidal neurons, undergo profound adaptations following chronic ethanol exposure, and regulate anxiety and conditioned rewarding effects of ethanol. To explore the effects of acute and chronic ethanol exposure on glutamate transmission, the impact of chronic alcohol on spine density and morphology, as well as persistent changes in dendritic-related gene expression, we employed whole-cell patch-clamp electrophysiology, diOlistic labeling for dendritic spine analysis, and dendritic gene expression analysis to further characterize mPFCCRF1+ and mPFCCRF1- prelimbic layer 2/3 pyramidal neurons. We found increased glutamate release in mPFCCRF1+ neurons with ethanol dependence, which recovered following withdrawal. In contrast, we did not observe significant changes in glutamate transmission in neighboring mPFCCRF1- neurons. Acute application of 44 mM ethanol significantly reduced glutamate release onto mPFCCRF1+ neurons, which was observed across all treatment groups. However, this sensitivity to acute ethanol was only evident in mPFCCRF1- neurons during withdrawal. In line with alterations in glutamate transmission, we observed a decrease in total spine density in mPFCCRF1+ neurons during dependence, which recovered following withdrawal, while again no changes were observed in mPFCCRF- neurons. Given the observed decreases in mPFCCRF1+ stubby spines during withdrawal, we then identified persistent changes at the dendritic gene expression level in mPFCCRF1+ neurons following withdrawal that may underlie these structural adaptations. Together, these findings highlight the varying responses of mPFCCRF1+ and mPFCCRF1- cell-types to acute and chronic ethanol exposure, as well as withdrawal, revealing specific functional, morphological, and molecular adaptations that may underlie vulnerability to ethanol and the lasting effects of ethanol dependence.
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Affiliation(s)
- Reesha R Patel
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Pauravi Gandhi
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Kathryn Spencer
- Core Microscopy Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Nihal A Salem
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Chloe M Erikson
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Vittoria Borgonetti
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Roman Vlkolinsky
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Larry Rodriguez
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Tali Nadav
- Animal Models Core Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Michal Bajo
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Amanda J Roberts
- Animal Models Core Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - R Dayne Mayfield
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Marisa Roberto
- Department of Molecular Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA, 92037, USA
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3
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Park I, Kim HJ, Shin J, Jung YJ, Lee D, Lim J, Park JM, Park JW, Kim J. AFM Imaging Reveals MicroRNA-132 to be a Positive Regulator of Synaptic Functions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306630. [PMID: 38493494 PMCID: PMC11077659 DOI: 10.1002/advs.202306630] [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: 09/13/2023] [Revised: 01/17/2024] [Indexed: 03/19/2024]
Abstract
The modification of synaptic and neural connections in adults, including the formation and removal of synapses, depends on activity-dependent synaptic and structural plasticity. MicroRNAs (miRNAs) play crucial roles in regulating these changes by targeting specific genes and regulating their expression. The fact that somatic and dendritic activity in neurons often occurs asynchronously highlights the need for spatial and dynamic regulation of protein synthesis in specific milieu and cellular loci. MicroRNAs, which can show distinct patterns of enrichment, help to establish the localized distribution of plasticity-related proteins. The recent study using atomic force microscopy (AFM)-based nanoscale imaging reveals that the abundance of miRNA(miR)-134 is inversely correlated with the functional activity of dendritic spine structures. However, the miRNAs that are selectively upregulated in potentiated synapses, and which can thereby support prospective changes in synaptic efficacy, remain largely unknown. Using AFM force imaging, significant increases in miR-132 in the dendritic regions abutting functionally-active spines is discovered. This study provides evidence for miR-132 as a novel positive miRNA regulator residing in dendritic shafts, and also suggests that activity-dependent miRNAs localized in distinct sub-compartments of neurons play bi-directional roles in controlling synaptic transmission and synaptic plasticity.
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Affiliation(s)
- Ikbum Park
- Technical Support Center for Chemical IndustryKorea Research Institute of Chemical Technology (KRICT)Ulsan44412Republic of Korea
| | - Hyun Jin Kim
- Department of Life SciencesPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
| | - Juyoung Shin
- Department of Life SciencesPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
| | - Yu Jin Jung
- Center for Specialty ChemicalsKorea Research Institute of Chemical Technology (KRICT)Ulsan44412Republic of Korea
| | - Donggyu Lee
- Division of Electronics and Information SystemDaegu Gyeongbuk Institute of Science and Technology (DGIST)Daegu42988Republic of Korea
| | - Ji‐seon Lim
- Department of ChemistryPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
| | - Jong Mok Park
- Technical Support Center for Chemical IndustryKorea Research Institute of Chemical Technology (KRICT)Ulsan44412Republic of Korea
| | - Joon Won Park
- Department of ChemistryPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
| | - Joung‐Hun Kim
- Department of Life SciencesPohang University of Science and Technology (POSTECH)Pohang37673Republic of Korea
- Institute of Convergence ScienceYonsei UniversitySeoul03722Republic of Korea
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Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB. Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. Nat Neurosci 2024; 27:822-835. [PMID: 38589584 PMCID: PMC11088998 DOI: 10.1038/s41593-024-01615-5] [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: 08/03/2023] [Accepted: 03/05/2024] [Indexed: 04/10/2024]
Abstract
Learning and memory require activity-induced changes in dendritic translation, but which mRNAs are involved and how they are regulated are unclear. In this study, to monitor how depolarization impacts local dendritic biology, we employed a dendritically targeted proximity labeling approach followed by crosslinking immunoprecipitation, ribosome profiling and mass spectrometry. Depolarization of primary cortical neurons with KCl or the glutamate agonist DHPG caused rapid reprogramming of dendritic protein expression, where changes in dendritic mRNAs and proteins are weakly correlated. For a subset of pre-localized messages, depolarization increased the translation of upstream open reading frames (uORFs) and their downstream coding sequences, enabling localized production of proteins involved in long-term potentiation, cell signaling and energy metabolism. This activity-dependent translation was accompanied by the phosphorylation and recruitment of the non-canonical translation initiation factor eIF4G2, and the translated uORFs were sufficient to confer depolarization-induced, eIF4G2-dependent translational control. These studies uncovered an unanticipated mechanism by which activity-dependent uORF translational control by eIF4G2 couples activity to local dendritic remodeling.
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Affiliation(s)
- Ezgi Hacisuleyman
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
| | - Caryn R Hale
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natalie Noble
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - John J Fak
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Misa Saito
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center, Dallas, TX, USA
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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5
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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6
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Cao J, Zheng Z, Sun D, Chen X, Cheng R, Lv T, An Y, Zheng J, Song J, Wu L, Yang C. Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing. Nat Biotechnol 2024:10.1038/s41587-023-02086-y. [PMID: 38228777 DOI: 10.1038/s41587-023-02086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Spatial transcriptomics technologies with high resolution often lack high sensitivity in mRNA detection. Here we report a dendrimeric DNA coordinate barcoding design for spatial RNA sequencing (Decoder-seq), which offers both high sensitivity and high resolution. Decoder-seq combines dendrimeric nanosubstrates with microfluidic coordinate barcoding to generate spatial arrays with a DNA density approximately ten times higher than previously reported methods while maintaining flexibility in resolution. We show that the high RNA capture efficiency of Decoder-seq improved the detection of lowly expressed olfactory receptor (Olfr) genes in mouse olfactory bulbs and contributed to the discovery of a unique layer enrichment pattern for two Olfr genes. The near-cellular resolution provided by Decoder-seq has enabled the construction of a spatial single-cell atlas of the mouse hippocampus, revealing dendrite-enriched mRNAs in neurons. When applying Decoder-seq to human renal cell carcinomas, we dissected the heterogeneous tumor microenvironment across different cancer subtypes and identified spatial gradient-expressed genes related to epithelial-mesenchymal transition with the potential to predict tumor prognosis and progression.
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Affiliation(s)
- Jiao Cao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhong Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Di Sun
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rui Cheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianpeng Lv
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu An
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junhua Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jia Song
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Department of Urology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, State Key Laboratory of Physical Chemical of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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7
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Ocharán-Mercado A, Loaeza-Loaeza J, Castro-Coronel Y, Acosta-Saavedra LC, Hernández-Kelly LC, Hernández-Sotelo D, Ortega A. RNA-Binding Proteins: A Role in Neurotoxicity? Neurotox Res 2023; 41:681-697. [PMID: 37776476 PMCID: PMC10682104 DOI: 10.1007/s12640-023-00669-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/15/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023]
Abstract
Despite sustained efforts to treat neurodegenerative diseases, little is known at the molecular level to understand and generate novel therapeutic approaches for these malignancies. Therefore, it is not surprising that neurogenerative diseases are among the leading causes of death in the aged population. Neurons require sophisticated cellular mechanisms to maintain proper protein homeostasis. These cells are generally sensitive to loss of gene expression control at the post-transcriptional level. Post-translational control responds to signals that can arise from intracellular processes or environmental factors that can be regulated through RNA-binding proteins. These proteins recognize RNA through one or more RNA-binding domains and form ribonucleoproteins that are critically involved in the regulation of post-transcriptional processes from splicing to the regulation of association of the translation machinery allowing a relatively rapid and precise modulation of the transcriptome. Neurotoxicity is the result of the biological, chemical, or physical interaction of agents with an adverse effect on the structure and function of the central nervous system. The disruption of the proper levels or function of RBPs in neurons and glial cells triggers neurotoxic events that are linked to neurodegenerative diseases such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), fragile X syndrome (FXS), and frontotemporal dementia (FTD) among many others. The connection between RBPs and neurodegenerative diseases opens a new landscape for potentially novel therapeutic targets for the intervention of these neurodegenerative pathologies. In this contribution, a summary of the recent findings of the molecular mechanisms involved in the plausible role of RBPs in RNA processing in neurodegenerative disease is discussed.
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Affiliation(s)
- Andrea Ocharán-Mercado
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Jaqueline Loaeza-Loaeza
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Yaneth Castro-Coronel
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Leonor C Acosta-Saavedra
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Luisa C Hernández-Kelly
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México
| | - Daniel Hernández-Sotelo
- Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas 88, Chilpancingo, Guerrero, 39086, México
| | - Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, San Pedro Zacatenco, 07300 CDMX, México.
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8
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Ament SA, Poulopoulos A. The brain's dark transcriptome: Sequencing RNA in distal compartments of neurons and glia. Curr Opin Neurobiol 2023; 81:102725. [PMID: 37196598 PMCID: PMC10524153 DOI: 10.1016/j.conb.2023.102725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/22/2023] [Accepted: 04/02/2023] [Indexed: 05/19/2023]
Abstract
Transcriptomic approaches are powerful strategies to map the molecular diversity of cells in the brain. Single-cell genomic atlases have now been compiled for entire mammalian brains. However, complementary techniques are only just beginning to map the subcellular transcriptomes from distal cellular compartments. We review single-cell datasets alongside subtranscriptome data from the mammalian brain to explore the development of cellular and subcellular diversity. We discuss how single-cell RNA-seq misses transcripts localized away from cell bodies, which form the 'dark transcriptome' of the brain: a collection of subtranscriptomes in dendrites, axons, growth cones, synapses, and endfeet with important roles in brain development and function. Recent advances in subcellular transcriptome sequencing are beginning to reveal these elusive pools of RNA. We outline the success stories to date in uncovering the constituent subtranscriptomes of neurons and glia, as well as present the emerging toolkit that is accelerating the pace of subtranscriptome discovery.
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Affiliation(s)
- Seth A Ament
- Department of Psychiatry, UM-MIND, and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexandros Poulopoulos
- Department of Pharmacology and UM-MIND, University of Maryland School of Medicine, Baltimore, MD, USA.
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9
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Fan Y, Andrusivová Ž, Wu Y, Chai C, Larsson L, He M, Luo L, Lundeberg J, Wang B. Expansion spatial transcriptomics. Nat Methods 2023; 20:1179-1182. [PMID: 37349575 PMCID: PMC11078125 DOI: 10.1038/s41592-023-01911-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
Capture array-based spatial transcriptomics methods have been widely used to resolve gene expression in tissues; however, their spatial resolution is limited by the density of the array. Here we present expansion spatial transcriptomics to overcome this limitation by clearing and expanding tissue prior to capturing the entire polyadenylated transcriptome with an enhanced protocol. This approach enables us to achieve higher spatial resolution while retaining high library quality, which we demonstrate using mouse brain samples.
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Affiliation(s)
- Yuhang Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Žaneta Andrusivová
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Yunming Wu
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ludvig Larsson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Mengxiao He
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Joakim Lundeberg
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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10
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Fang Z, Ford AJ, Hu T, Zhang N, Mantalaris A, Coskun AF. Subcellular spatially resolved gene neighborhood networks in single cells. CELL REPORTS METHODS 2023; 3:100476. [PMID: 37323566 PMCID: PMC10261906 DOI: 10.1016/j.crmeth.2023.100476] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 02/18/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Image-based spatial omics methods such as fluorescence in situ hybridization (FISH) generate molecular profiles of single cells at single-molecule resolution. Current spatial transcriptomics methods focus on the distribution of single genes. However, the spatial proximity of RNA transcripts can play an important role in cellular function. We demonstrate a spatially resolved gene neighborhood network (spaGNN) pipeline for the analysis of subcellular gene proximity relationships. In spaGNN, machine-learning-based clustering of subcellular spatial transcriptomics data yields subcellular density classes of multiplexed transcript features. The nearest-neighbor analysis produces heterogeneous gene proximity maps in distinct subcellular regions. We illustrate the cell-type-distinguishing capability of spaGNN using multiplexed error-robust FISH data of fibroblast and U2-OS cells and sequential FISH data of mesenchymal stem cells (MSCs), revealing tissue-source-specific MSC transcriptomics and spatial distribution characteristics. Overall, the spaGNN approach expands the spatial features that can be used for cell-type classification tasks.
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Affiliation(s)
- Zhou Fang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Machine Learning Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - Adam J. Ford
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Thomas Hu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Nicholas Zhang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
| | - Athanasios Mantalaris
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ahmet F. Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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11
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Wei A, Wang L. Prediction of Synaptically Localized RNAs in Human Neurons Using Developmental Brain Gene Expression Data. Genes (Basel) 2022; 13:1488. [PMID: 36011399 PMCID: PMC9408096 DOI: 10.3390/genes13081488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
In the nervous system, synapses are special and pervasive structures between axonal and dendritic terminals, which facilitate electrical and chemical communications among neurons. Extensive studies have been conducted in mice and rats to explore the RNA pool at synapses and investigate RNA transport, local protein synthesis, and synaptic plasticity. However, owing to the experimental difficulties of studying human synaptic transcriptomes, the full pool of human synaptic RNAs remains largely unclear. We developed a new machine learning method, called PredSynRNA, to predict the synaptic localization of human RNAs. Training instances of dendritically localized RNAs were compiled from previous rodent studies, overcoming the shortage of empirical instances of human synaptic RNAs. Using RNA sequence and gene expression data as features, various models with different learning algorithms were constructed and evaluated. Strikingly, the models using the developmental brain gene expression features achieved superior performance for predicting synaptically localized RNAs. We examined the relevant expression features learned by PredSynRNA and used an independent test dataset to further validate the model performance. PredSynRNA models were then applied to the prediction and prioritization of candidate RNAs localized to human synapses, providing valuable targets for experimental investigations into neuronal mechanisms and brain disorders.
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Affiliation(s)
- Anqi Wei
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
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12
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Wang Y, Song B, Wang S, Chen M, Xie Y, Xiao G, Wang L, Wang T. Sprod for de-noising spatially resolved transcriptomics data based on position and image information. Nat Methods 2022; 19:950-958. [PMID: 35927477 DOI: 10.1038/s41592-022-01560-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
Spatially resolved transcriptomics (SRT) provide gene expression close to, or even superior to, single-cell resolution while retaining the physical locations of sequencing and often also providing matched pathology images. However, SRT expression data suffer from high noise levels, due to the shallow coverage in each sequencing unit and the extra experimental steps required to preserve the locations of sequencing. Fortunately, such noise can be removed by leveraging information from the physical locations of sequencing, and the tissue organization reflected in corresponding pathology images. In this work, we developed Sprod, based on latent graph learning of matched location and imaging data, to impute accurate SRT gene expression. We validated Sprod comprehensively and demonstrated its advantages over previous methods for removing drop-outs in single-cell RNA-sequencing data. We showed that, after imputation by Sprod, differential expression analyses, pathway enrichment and cell-to-cell interaction inferences are more accurate. Overall, we envision de-noising by Sprod to become a key first step towards empowering SRT technologies for biomedical discoveries.
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Affiliation(s)
- Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bing Song
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mingyi Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Li Wang
- Department of Mathematics and Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX, USA.
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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13
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Hale CR, Sawicka K, Mora K, Fak JJ, Kang JJ, Cutrim P, Cialowicz K, Carroll TS, Darnell RB. FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons. eLife 2021; 10:e71892. [PMID: 34939924 PMCID: PMC8820740 DOI: 10.7554/elife.71892] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Neurons rely on translation of synaptic mRNAs in order to generate activity-dependent changes in plasticity. Here, we develop a strategy combining compartment-specific crosslinking immunoprecipitation (CLIP) and translating ribosome affinity purification (TRAP) in conditionally tagged mice to precisely define the ribosome-bound dendritic transcriptome of CA1 pyramidal neurons. We identify CA1 dendritic transcripts with differentially localized mRNA isoforms generated by alternative polyadenylation and alternative splicing, including many that have altered protein-coding capacity. Among dendritic mRNAs, FMRP targets were found to be overrepresented. Cell-type-specific FMRP-CLIP and TRAP in microdissected CA1 neuropil revealed 383 dendritic FMRP targets and suggests that FMRP differentially regulates functionally distinct modules in CA1 dendrites and cell bodies. FMRP regulates ~15-20% of mRNAs encoding synaptic functions and 10% of chromatin modulators, in the dendrite and cell body, respectively. In the absence of FMRP, dendritic FMRP targets had increased ribosome association, consistent with a function for FMRP in synaptic translational repression. Conversely, downregulation of FMRP targets involved in chromatin regulation in cell bodies suggests a role for FMRP in stabilizing mRNAs containing stalled ribosomes in this compartment. Together, the data support a model in which FMRP regulates the translation and expression of synaptic and nuclear proteins within different compartments of a single neuronal cell type.
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Affiliation(s)
- Caryn R Hale
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - Kirsty Sawicka
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - Kevin Mora
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - Jin Joo Kang
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - Paula Cutrim
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
| | - Katarzyna Cialowicz
- Bio-Imaging Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
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14
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Abstract
To form synaptic connections and store information, neurons continuously remodel their proteomes. The impressive length of dendrites and axons imposes logistical challenges to maintain synaptic proteins at locations remote from the transcription source (the nucleus). The discovery of thousands of messenger RNAs (mRNAs) near synapses suggested that neurons overcome distance and gain autonomy by producing proteins locally. It is not generally known, however, if, how, and when localized mRNAs are translated into protein. To investigate the translational landscape in neuronal subregions, we performed simultaneous RNA sequencing (RNA-seq) and ribosome sequencing (Ribo-seq) from microdissected rodent brain slices to identify and quantify the transcriptome and translatome in cell bodies (somata) as well as dendrites and axons (neuropil). Thousands of transcripts were differentially translated between somatic and synaptic regions, with many scaffold and signaling molecules displaying increased translation levels in the neuropil. Most translational changes between compartments could be accounted for by differences in RNA abundance. Pervasive translational regulation was observed in both somata and neuropil influenced by specific mRNA features (e.g., untranslated region [UTR] length, RNA-binding protein [RBP] motifs, and upstream open reading frames [uORFs]). For over 800 mRNAs, the dominant source of translation was the neuropil. We constructed a searchable and interactive database for exploring mRNA transcripts and their translation levels in the somata and neuropil [MPI Brain Research, The mRNA translation landscape in the synaptic neuropil. https://public.brain.mpg.de/dashapps/localseq/ Accessed 5 October 2021]. Overall, our findings emphasize the substantial contribution of local translation to maintaining synaptic protein levels and indicate that on-site translational control is an important mechanism to control synaptic strength.
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15
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Epple R, Krüger D, Berulava T, Brehm G, Ninov M, Islam R, Köster S, Fischer A. The Coding and Small Non-coding Hippocampal Synaptic RNAome. Mol Neurobiol 2021; 58:2940-2953. [PMID: 33569760 PMCID: PMC8128755 DOI: 10.1007/s12035-021-02296-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as microRNAs have also been described at synapses where they are believed to control mRNA availability for local translation. A combined dataset analyzing the synaptic coding and non-coding RNAome via next-generation sequencing approaches is, however, still lacking. Here, we isolate synaptosomes from the hippocampus of young wild-type mice and provide the coding and non-coding synaptic RNAome. These data are complemented by a novel approach for analyzing the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers. Our data show that synaptic microRNAs control almost the entire synaptic mRNAome, and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluidic chamber system, our findings also support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable for studying the dynamics of the synaptic RNAome in response to stimulation. In conclusion, our data provide a valuable resource and point to several important targets for further research.
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Affiliation(s)
- Robert Epple
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Dennis Krüger
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Tea Berulava
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Momchil Ninov
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rezaul Islam
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Andre Fischer
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany.
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany.
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16
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Pallos J, Jeng S, McWeeney S, Martin I. Dopamine neuron-specific LRRK2 G2019S effects on gene expression revealed by translatome profiling. Neurobiol Dis 2021; 155:105390. [PMID: 33984508 DOI: 10.1016/j.nbd.2021.105390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) mutations are the most common genetic cause of late-onset Parkinson's disease. The pathogenic G2019S mutation enhances LRRK2 kinase activity and induces neurodegeneration in C. elegans, Drosophila and rodent models through unclear mechanisms. Gene expression profiling has the potential to provide detailed insight into the biological pathways modulated by LRRK2 kinase activity. Prior in vivo studies have surveyed the effects of LRRK2 G2019S on genome-wide mRNA expression in complex brain tissues with high cellular heterogeneity, limiting their power to detect more restricted gene expression changes occurring in a cell type-specific manner. Here, we used translating ribosome affinity purification (TRAP) coupled to RNA-seq to profile dopamine neuron-specific gene expression changes caused by LRRK2 G2019S in the Drosophila CNS. A number of genes were differentially expressed in the presence of mutant LRRK2 that represent a broad range of molecular functions including DNA repair (RfC3), mRNA metabolism and translation (Ddx1 and lin-28), calcium homeostasis (MCU), and other categories (Ugt37c1, disp, l(1)G0196, CG6602, CG1126 and CG11068). Further analysis on a subset of these genes revealed that LRRK2 G2019S did not alter their expression across the whole brain, consistent with dopamine neuron-specific effects uncovered by the TRAP approach that may yield insight into the neurodegenerative process. To our knowledge, this is the first study to profile the effects of LRRK2 G2019S specifically on DA neuron gene expression in vivo. Beyond providing a set of differentially expressed gene candidates relevant to LRRK2, we demonstrate the effective use of TRAP to perform high-resolution assessment of dopamine neuron gene expression for the study of PD.
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Affiliation(s)
- Judit Pallos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Shannon McWeeney
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA.
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17
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Zolfaghari SI, Rabbani Khorasgani M, Noorbakhshnia M. The effects of lactobacilli (L. rhamnosus, L. reuteri, L. Plantarum) on LPS-induced memory impairment and changes in CaMKII-α and TNF-α genes expression in the hippocampus of rat. Physiol Behav 2021; 229:113224. [PMID: 33127463 DOI: 10.1016/j.physbeh.2020.113224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/15/2020] [Accepted: 10/24/2020] [Indexed: 12/20/2022]
Abstract
In recent years, some investigations have focused on the relationship between gut microbiota and brain function in healthy and disease conditions. Moreover, changes in the gut microbiome may affect memory, behavior, and cognition. This study aimed to evaluate the effect of lactobacilli on passive avoidance learning, hippocampal CaMKII-α, and TNF-α genes expression in one experimental model of neuroinflammtion. Male wistar rats (220-240 g) received daily oral gavage of different lactobacilli including L. rhamnosus, L. reuteri, and L. plantarum for 21 days. At the next step, behavioral test was performed and 4 hours after acute injection of LPS (1mg/kg, ip) retrieval was evaluated. Then the hippocampi were extracted and kept at _80°C. Finally CaMKII-α and TNF-α mRNA levels were evaluated by Real-time PCR. Our results showed that consumption of L. rhamnosus, L.reuteri, or L. plantarum significantly prevented LPS-induced enhancement of TNF-α mRNA and memory deterioration. Furthermore, L. rhamnosus significantly prevented changes induced by LPS on CaMKII-α mRNA levels. It seems the lactobacilli used in this study can affect brain function and memory performance by their immune-modulatory properties.
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Affiliation(s)
- Sayyed Iman Zolfaghari
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mohammad Rabbani Khorasgani
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Maryam Noorbakhshnia
- Department of Plant and Animal Biology, Faculty of Biological science and Technology, University of Isfahan, Iran.
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18
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Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
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Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
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19
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Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat Biotechnol 2020; 39:313-319. [PMID: 33288904 DOI: 10.1038/s41587-020-0739-1] [Citation(s) in RCA: 464] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023]
Abstract
Measurement of the location of molecules in tissues is essential for understanding tissue formation and function. Previously, we developed Slide-seq, a technology that enables transcriptome-wide detection of RNAs with a spatial resolution of 10 μm. Here we report Slide-seqV2, which combines improvements in library generation, bead synthesis and array indexing to reach an RNA capture efficiency ~50% that of single-cell RNA-seq data (~10-fold greater than Slide-seq), approaching the detection efficiency of droplet-based single-cell RNA-seq techniques. First, we leverage the detection efficiency of Slide-seqV2 to identify dendritically localized mRNAs in neurons of the mouse hippocampus. Second, we integrate the spatial information of Slide-seqV2 data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex, identifying underlying genetic programs that were poorly sampled with Slide-seq. The combination of near-cellular resolution and high transcript detection efficiency makes Slide-seqV2 useful across many experimental contexts.
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20
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Klein ME, Younts TJ, Cobo CF, Buxbaum AR, Aow J, Erdjument-Bromage H, Richard S, Malinow R, Neubert TA, Singer RH, Castillo PE, Jordan BA. Sam68 Enables Metabotropic Glutamate Receptor-Dependent LTD in Distal Dendritic Regions of CA1 Hippocampal Neurons. Cell Rep 2020; 29:1789-1799.e6. [PMID: 31722197 PMCID: PMC6871770 DOI: 10.1016/j.celrep.2019.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 08/15/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The transport and translation of dendritic mRNAs by RNA-binding proteins (RBPs) allows for spatially restricted gene expression in neuronal processes. Although local translation in neuronal dendrites is now well documented, there is little evidence for corresponding effects on local synaptic function. Here, we report that the RBP Sam68 promotes the localization and translation of Arc mRNA preferentially in distal dendrites of rodent hippocampal CA1 pyramidal neurons. Consistent with Arc function in translation-dependent synaptic plasticity, we find that Sam68 knockout (KO) mice display impaired metabotropic glutamate-receptor-dependent long-term depression (mGluR-LTD) and impaired structural plasticity exclusively at distal Schaffer-collateral synapses. Moreover, by using quantitative proteomics, we find that the Sam68 interactome contains numerous regulators of mRNA translation and synaptic function. This work identifies an important player in Arc expression, provides a general framework for Sam68 regulation of protein synthesis, and uncovers a mechanism that enables the precise spatiotemporal expression of long-term plasticity throughout neurons.
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Affiliation(s)
- Matthew E Klein
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Thomas J Younts
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Carmen Freire Cobo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Jonathan Aow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Departments of Oncology and Medicine, McGill University, Montréal, QC H3T 1E2, Canada
| | - Roberto Malinow
- Center for Neural Circuits and Behavior, Department of Neuroscience and Section for Neurobiology, Division of Biology, University of California at San Diego, San Diego, CA 92093, USA
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Robert H Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Janelia Research Campus of the Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Pablo E Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA.
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21
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Lottes EN, Cox DN. Homeostatic Roles of the Proteostasis Network in Dendrites. Front Cell Neurosci 2020; 14:264. [PMID: 33013325 PMCID: PMC7461941 DOI: 10.3389/fncel.2020.00264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular protein homeostasis, or proteostasis, is indispensable to the survival and function of all cells. Distinct from other cell types, neurons are long-lived, exhibiting architecturally complex and diverse multipolar projection morphologies that can span great distances. These properties present unique demands on proteostatic machinery to dynamically regulate the neuronal proteome in both space and time. Proteostasis is regulated by a distributed network of cellular processes, the proteostasis network (PN), which ensures precise control of protein synthesis, native conformational folding and maintenance, and protein turnover and degradation, collectively safeguarding proteome integrity both under homeostatic conditions and in the contexts of cellular stress, aging, and disease. Dendrites are equipped with distributed cellular machinery for protein synthesis and turnover, including dendritically trafficked ribosomes, chaperones, and autophagosomes. The PN can be subdivided into an adaptive network of three major functional pathways that synergistically govern protein quality control through the action of (1) protein synthesis machinery; (2) maintenance mechanisms including molecular chaperones involved in protein folding; and (3) degradative pathways (e.g., Ubiquitin-Proteasome System (UPS), endolysosomal pathway, and autophagy. Perturbations in any of the three arms of proteostasis can have dramatic effects on neurons, especially on their dendrites, which require tightly controlled homeostasis for proper development and maintenance. Moreover, the critical importance of the PN as a cell surveillance system against protein dyshomeostasis has been highlighted by extensive work demonstrating that the aggregation and/or failure to clear aggregated proteins figures centrally in many neurological disorders. While these studies demonstrate the relevance of derangements in proteostasis to human neurological disease, here we mainly review recent literature on homeostatic developmental roles the PN machinery plays in the establishment, maintenance, and plasticity of stable and dynamic dendritic arbors. Beyond basic housekeeping functions, we consider roles of PN machinery in protein quality control mechanisms linked to dendritic plasticity (e.g., dendritic spine remodeling during LTP); cell-type specificity; dendritic morphogenesis; and dendritic pruning.
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Affiliation(s)
- Erin N Lottes
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
| | - Daniel N Cox
- Neuroscience Institute, Georgia State University, Atlanta, GA, United States
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22
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Lo LHY, Lai KO. Dysregulation of protein synthesis and dendritic spine morphogenesis in ASD: studies in human pluripotent stem cells. Mol Autism 2020; 11:40. [PMID: 32460854 PMCID: PMC7251853 DOI: 10.1186/s13229-020-00349-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a brain disorder that involves changes in neuronal connections. Abnormal morphology of dendritic spines on postsynaptic neurons has been observed in ASD patients and transgenic mice that model different monogenetic causes of ASD. A number of ASD-associated genetic variants are known to disrupt dendritic local protein synthesis, which is essential for spine morphogenesis, synaptic transmission, and plasticity. Most of our understanding on the molecular mechanism underlying ASD depends on studies using rodents. However, recent advance in human pluripotent stem cells and their neural differentiation provides a powerful alternative tool to understand the cellular aspects of human neurological disorders. In this review, we summarize recent progress on studying mRNA targeting and local protein synthesis in stem cell-derived neurons, and discuss how perturbation of these processes may impact synapse development and functions that are relevant to cognitive deficits in ASD.
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Affiliation(s)
- Louisa Hoi-Ying Lo
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Kwok-On Lai
- School of Biomedical Sciences, Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China. .,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
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von Kügelgen N, Chekulaeva M. Conservation of a core neurite transcriptome across neuronal types and species. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1590. [PMID: 32059075 DOI: 10.1002/wrna.1590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 12/23/2022]
Abstract
The intracellular localization of mRNAs allows neurons to control gene expression in neurite extensions (axons and dendrites) and respond rapidly to local stimuli. This plays an important role in diverse processes including neuronal growth and synaptic plasticity, which in turn serves as a foundation for learning and memory. Recent high-throughput analyses have revealed that neurites contain hundreds to thousands of mRNAs, but an analysis comparing the transcriptomes derived from these studies has been lacking. Here we analyze 20 datasets pertaining to neuronal mRNA localization across species and neuronal types and identify a conserved set of mRNAs that had robustly localized to neurites in a high number of the studies. The set includes mRNAs encoding for ribosomal proteins and other components of the translation machinery, mitochondrial proteins, cytoskeletal components, and proteins associated with neurite formation. Our combinatorial analysis provides a unique resource for future hypothesis-driven research. This article is categorized under: RNA Export and Localization > RNA Localization RNA Evolution and Genomics > Computational Analyses of RNA RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Nicolai von Kügelgen
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marina Chekulaeva
- Non-coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
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Thelen MP, Kye MJ. The Role of RNA Binding Proteins for Local mRNA Translation: Implications in Neurological Disorders. Front Mol Biosci 2020; 6:161. [PMID: 32010708 PMCID: PMC6974540 DOI: 10.3389/fmolb.2019.00161] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
As neurons are one of the most highly polarized cells in our body, they require sophisticated cellular mechanisms to maintain protein homeostasis in their subcellular compartments such as axons and dendrites. When neuronal protein homeostasis is disturbed due to genetic mutations or deletions, this often results in degeneration of neurons leading to devastating outcome such as spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), and fragile X syndrome (FXS). Ribonucleoprotein (RNP) complexes are macromolecular complexes composed of RNA binding proteins (RBPs) and their target RNAs. RBPs contain RNA binding domains and bind to RNA molecules via specific sequence motifs. RNP complexes have various functions in gene expression including messenger RNA (mRNA) trafficking, RNA processing and silencing. In neurons, RBPs deliver specific sets of mRNAs to subcellular compartments such as axons and dendrites to be locally translated. Mutations or deletions in genes coding for RNPs have been reported as causes for neurological disorders such as SMA, ALS, and FXS. As RBPs determine axonal or dendritic mRNA repertoires as well as proteomes by trafficking selective mRNAs and regulating local protein synthesis, they play a crucial role for neuronal function. In this review, we summarize the role of well-known RBPs, SMN, TDP-43, FUS, and FMRP, and review their function for local protein synthesis in neurons. Furthermore, we discuss their pathological contribution to the neurological disorders.
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Affiliation(s)
| | - Min Jeong Kye
- Institute of Human Genetics, University of Cologne, Cologne, Germany
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26
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Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
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Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
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27
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Saini H, Bicknell AA, Eddy SR, Moore MJ. Free circular introns with an unusual branchpoint in neuronal projections. eLife 2019; 8:e47809. [PMID: 31697236 PMCID: PMC6879206 DOI: 10.7554/elife.47809] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.
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Affiliation(s)
- Harleen Saini
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
| | - Alicia A Bicknell
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Sean R Eddy
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Melissa J Moore
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
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28
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Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA. The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep. Science 2019; 366:366/6462/eaav2642. [DOI: 10.1126/science.aav2642] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 09/03/2019] [Indexed: 12/13/2022]
Abstract
Neurons have adapted mechanisms to traffic RNA and protein into distant dendritic and axonal arbors. Taking a biochemical approach, we reveal that forebrain synaptic transcript accumulation shows overwhelmingly daily rhythms, with two-thirds of synaptic transcripts showing time-of-day–dependent abundance independent of oscillations in the soma. These transcripts formed two sharp temporal and functional clusters, with transcripts preceding dawn related to metabolism and translation and those anticipating dusk related to synaptic transmission. Characterization of the synaptic proteome around the clock demonstrates the functional relevance of temporal gating for synaptic processes and energy homeostasis. Unexpectedly, sleep deprivation completely abolished proteome but not transcript oscillations. Altogether, the emerging picture is one of a circadian anticipation of messenger RNA needs in the synapse followed by translation as demanded by sleep-wake cycles.
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Affiliation(s)
- Sara B. Noya
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - David Colameo
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Franziska Brüning
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Spinnler
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Dennis Mircsof
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, University of Zurich–Eidgenosissche Technische Hochschule, Zurich, Switzerland
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Shiva K. Tyagarajan
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Maria S. Robles
- Institute of Medical Psychology, Medical Faculty, LMU Munich, Germany
| | - Steven A. Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
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29
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Farris S, Ward JM, Carstens KE, Samadi M, Wang Y, Dudek SM. Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2. Cell Rep 2019; 29:522-539.e6. [PMID: 31597108 PMCID: PMC6894405 DOI: 10.1016/j.celrep.2019.08.093] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/15/2019] [Accepted: 08/27/2019] [Indexed: 12/15/2022] Open
Abstract
RNA localization is one mechanism neurons use to spatially and temporally regulate gene expression at synapses. Here, we test the hypothesis that cells exhibiting distinct forms of synaptic plasticity will have differences in dendritically localized RNAs. Indeed, we discover that each major subregion of the adult mouse hippocampus expresses a unique complement of dendritic RNAs. Specifically, we describe more than 1,000 differentially expressed dendritic RNAs, suggesting that RNA localization and local translation are regulated in a cell type-specific manner. Furthermore, by focusing Gene Ontology analyses on the plasticity-resistant CA2, we identify an enrichment of mitochondria-associated pathways in CA2 cell bodies and dendrites, and we provide functional evidence that these pathways differentially influence plasticity and mitochondrial respiration in CA2. These data indicate that differences in dendritic transcriptomes may regulate cell type-specific properties important for learning and memory and may influence region-specific differences in disease pathology.
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Affiliation(s)
- Shannon Farris
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Kelly E Carstens
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Mahsa Samadi
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Yu Wang
- Cellular and Molecular Pathology, National Toxicology Program, NIH, Research Triangle Park, NC 27709, USA
| | - Serena M Dudek
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
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30
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Todorov G, Cunha C. Hypothesis: Regulation of neuroplasticity may involve I-motif and G-quadruplex DNA formation modulated by epigenetic mechanisms. Med Hypotheses 2019; 127:129-135. [PMID: 31088636 DOI: 10.1016/j.mehy.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 01/12/2023]
Abstract
Recent studies demonstrated the existence in vivo of various functional DNA structures that differ from the double helix. The G-quadruplex (G4) and intercalated motif (I-motif or IM) DNA structures are formed as knots where, correspondingly, guanines or cytosines on the same strand of DNA bind to each other. There are grounds to believe that G4 and IM sequences play a significant role in regulating gene expression considering their tendency to be found in or near regulatory sites (such as promoters, enhancers, and telomeres) as well as the correlation between the prevalence of G4 or IM conformations and specific phases of cell cycle. Notably, G4 and IM capable sequences tend to be found on the opposite strands of the same DNA site with at most one of the two structures formed at any given time. The recent evidence that K+, Mg2+ concentrations directly affect IM formation (and likely G4 formation indirectly) lead us to believe that these structures may play a major role in synaptic plasticity of neurons, and, therefore, in a variety of central nervous system (CNS) functions including memory, learning, habitual behaviors, pain perception and others. Furthermore, epigenetic mechanisms, which have an important role in synaptic plasticity and memory formation, were also shown to influence formation and stability of G4s and IMs. Our hypothesis is that non-canonical DNA and RNA structures could be an integral part of neuroplasticity control via gene expression regulation at the level of transcription, translation and splicing. We propose that the regulatory activity of DNA IM and G4 structures is modulated by DNA methylation/demethylation of the IM and/or G4 sequences, which facilitates the switch between canonical and non-canonical conformation. Other neuronal mechanisms interacting with the formation and regulatory activity of non-canonical DNA and RNA structures, particularly G4, IM and triplexes, may involve microRNAs as well as ion and proton fluxes. We are proposing experiments in acute brain slices and in vivo to test our hypothesis. The proposed studies would provide new insights into fundamental neuronal mechanisms in health and disease and potentially open new avenues for treating mental health disorders.
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Affiliation(s)
- German Todorov
- Emotional Brain Institute, Nathan Kline Institute, Orangeburg, NY, USA
| | - Catarina Cunha
- Emotional Brain Institute, Nathan Kline Institute, Orangeburg, NY, USA.
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31
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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32
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Middleton SA, Eberwine J, Kim J. Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. BMC Biol 2019; 17:5. [PMID: 30678683 PMCID: PMC6344992 DOI: 10.1186/s12915-019-0630-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/16/2019] [Indexed: 02/06/2023] Open
Abstract
Background RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different cell functions, e.g., in neuronal dendrites, localization is a critical step for long-lasting synaptic potentiation. However, there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. A comprehensive catalog of localized RNA can help dissect RBP/RNA interactions and localization motifs. Here, we utilize a single cell sub-cellular RNA sequencing approach to profile differentially localized RNAs from individual cells across multiple single cells to help identify a consistent set of localized RNA in mouse neurons. Results Using independent RNA sequencing from soma and dendrites of the same neuron, we deeply profiled the sub-cellular transcriptomes to assess the extent and variability of dendritic RNA localization in individual hippocampal neurons, including an assessment of differential localization of alternative 3′UTR isoforms. We identified 2225 dendritic RNAs, including 298 cases of 3′UTR isoform-specific localization. We extensively analyzed the localized RNAs for potential localization motifs, finding that B1 and B2 SINE elements are up to 5.7 times more abundant in localized RNA 3′UTRs than non-localized, and also functionally characterized the localized RNAs using protein structure analysis. Conclusion We integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource. This catalog of transcripts, including differentially localized isoforms and computationally hypothesized localization motifs, will help investigators further dissect the genome-scale mechanism of RNA localization. Electronic supplementary material The online version of this article (10.1186/s12915-019-0630-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah A Middleton
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd, Philadelphia, PA, 19104-6064, USA.,Present Address: Computational Biology, Target Sciences, GlaxoSmithKline R&D, 1250 S. Collegeville Road, Collegeville, PA, 19426, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 829 BRB II/III, 421 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd, Philadelphia, PA, 19104-6064, USA. .,Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA, 19104, USA.
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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34
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Gallagher C, Ramos A. Joining the dots - protein-RNA interactions mediating local mRNA translation in neurons. FEBS Lett 2018; 592:2932-2947. [PMID: 29856909 DOI: 10.1002/1873-3468.13121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining the complex network of connections required for neuronal communication requires the transport and in situ translation of large groups of mRNAs to create local proteomes. In this Review, we discuss the regulation of local mRNA translation in neurons and the RNA-binding proteins that recognise RNA zipcode elements and connect the mRNAs to the cellular transport networks, as well as regulate their translation control. However, mRNA recognition by the regulatory proteins is mediated by the combinatorial action of multiple RNA-binding domains. This increases the specificity and affinity of the interaction, while allowing the protein to recognise a diverse set of targets and mediate a range of mechanisms for translational regulation. The structural and molecular understanding of the interactions can be used together with novel microscopy and transcriptome-wide data to build a mechanistic framework for the regulation of local mRNA translation.
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Affiliation(s)
- Christopher Gallagher
- Institute of Structural and Molecular Biology, University College London, UK.,The Francis Crick Institute, London, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, UK
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35
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Translational profiling of stress-induced neuroplasticity in the CA3 pyramidal neurons of BDNF Val66Met mice. Mol Psychiatry 2018; 23:904-913. [PMID: 27956743 PMCID: PMC5468507 DOI: 10.1038/mp.2016.219] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/16/2016] [Accepted: 10/14/2016] [Indexed: 02/07/2023]
Abstract
Genetic susceptibility and environmental factors (such as stress) can interact to affect the likelihood of developing a mood disorder. Stress-induced changes in the hippocampus have been implicated in mood disorders, and mutations in several genes have now been associated with increased risk, such as brain-derived neurotrophic factor (BDNF). The hippocampus has important anatomical subdivisions, and pyramidal neurons of the vulnerable CA3 region show significant remodeling after chronic stress, but the mechanisms underlying their unique plasticity remain unknown. This study characterizes stress-induced changes in the in vivo translating mRNA of this cell population using a CA3-specific enhanced green fluorescent protein (EGFP) reporter fused to the L10a large ribosomal subunit (EGFPL10a). RNA-sequencing after isolation of polysome-bound mRNAs allows for cell-type-specific, genome-wide characterization of translational changes after stress. The data demonstrate that acute and chronic stress produce unique translational profiles and that the stress history of the animal can alter future reactivity of CA3 neurons. CA3-specific EGFPL10a mice were then crossed to the stress-susceptible BDNF Val66Met mouse line to characterize how a known genetic susceptibility alters both baseline translational profiles and the reactivity of CA3 neurons to stress. Not only do Met allele carriers exhibit distinct levels of baseline translation in genes implicated in ion channel function and cytoskeletal regulation, but they also activate a stress response profile that is highly dissimilar from wild-type mice. Closer examination of genes implicated in the mechanisms of neuroplasticity, such as the NMDA and AMPA subunits and the BDNF pathway, reveal how wild-type mice upregulate many of these genes in response to stress, but Met allele carriers fail to do so. These profiles provide a roadmap of stress-induced changes in a genetically homogenous population of hippocampal neurons and illustrate the profound effects of gene-environment interactions on the translational profile of these cells.
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36
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Tóth EN, Lohith A, Mondal M, Guo J, Fukamizu A, Pourmand N. Single-cell nanobiopsy reveals compartmentalization of mRNAs within neuronal cells. J Biol Chem 2018; 293:4940-4951. [PMID: 29378846 DOI: 10.1074/jbc.m117.800763] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 01/21/2018] [Indexed: 12/22/2022] Open
Abstract
In highly polarized cells such as neurons, compartmentalization of mRNA and of local protein synthesis enables remarkably fast, precise, and local responses to external stimuli. These responses are highly important for neuron growth cone guidance, synapse formation, and regeneration following injury. Because an altered spatial distribution of mRNA can result in mental retardation or neurodegenerative diseases, subcellular transcriptome analysis of neurons could be a useful tool for studying these conditions, but current techniques, such as in situ hybridization, bulk microarray, and RNA-Seq, impose tradeoffs between spatial resolution and multiplexing. To obtain a comprehensive analysis of the cell body versus neurite transcriptome from the same neuron, we have recently developed a label-free, single-cell nanobiopsy platform based on scanning ion conductance microscopy that uses electrowetting within a quartz nanopipette to extract cellular material from living cells with minimal disruption of the cellular membrane and milieu. In this study, we used this platform to collect samples from the cell bodies and neurites of human neurons and analyzed the mRNA pool with multiplex RNA sequencing. The minute volume of a nanobiopsy sample allowed us to extract samples from several locations in the same cell and to map the various mRNA species to specific subcellular locations. In addition to previously identified transcripts, we discovered new sets of mRNAs localizing to neurites, including nuclear genes such as Eomes and Hmgb3 In summary, our single-neuron nanobiopsy analysis provides opportunities to improve our understanding of intracellular mRNA transport and local protein composition in neuronal growth, connectivity, and function.
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Affiliation(s)
- Eszter N Tóth
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, Ibaraki 305-8577, Japan; Life Science Center, Tsukuba Advanced Research Alliance, Department of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan; Department of Biomolecular Engineering, Jack Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Akshar Lohith
- Department of Biomolecular Engineering, Jack Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Manas Mondal
- Department of Chemistry and Biochemistry & Biodesign Institute, Arizona State University, Tempe, Arizona 85287
| | - Jia Guo
- Department of Chemistry and Biochemistry & Biodesign Institute, Arizona State University, Tempe, Arizona 85287
| | - Akiyoshi Fukamizu
- Ph.D. Program in Human Biology, School of Integrative and Global Majors, Ibaraki 305-8577, Japan; Life Science Center, Tsukuba Advanced Research Alliance, Department of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan
| | - Nader Pourmand
- Department of Biomolecular Engineering, Jack Baskin School of Engineering, University of California at Santa Cruz, Santa Cruz, California 95064.
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37
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Van Driesche SJ, Martin KC. New frontiers in RNA transport and local translation in neurons. Dev Neurobiol 2018; 78:331-339. [DOI: 10.1002/dneu.22574] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Sarah J. Van Driesche
- Department of Biological Chemistry; University of California; Los Angeles California
| | - Kelsey C. Martin
- Department of Biological Chemistry; University of California; Los Angeles California
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38
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The Expanding Toolkit of Translating Ribosome Affinity Purification. J Neurosci 2018; 37:12079-12087. [PMID: 29237735 DOI: 10.1523/jneurosci.1929-17.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development.
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Nakayama K, Ohashi R, Shinoda Y, Yamazaki M, Abe M, Fujikawa A, Shigenobu S, Futatsugi A, Noda M, Mikoshiba K, Furuichi T, Sakimura K, Shiina N. RNG105/caprin1, an RNA granule protein for dendritic mRNA localization, is essential for long-term memory formation. eLife 2017; 6. [PMID: 29157358 PMCID: PMC5697933 DOI: 10.7554/elife.29677] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/22/2017] [Indexed: 12/18/2022] Open
Abstract
Local regulation of synaptic efficacy is thought to be important for proper networking of neurons and memory formation. Dysregulation of global translation influences long-term memory in mice, but the relevance of the regulation specific for local translation by RNA granules remains elusive. Here, we demonstrate roles of RNG105/caprin1 in long-term memory formation. RNG105 deletion in mice impaired synaptic strength and structural plasticity in hippocampal neurons. Furthermore, RNG105-deficient mice displayed unprecedentedly severe defects in long-term memory formation in spatial and contextual learning tasks. Genome-wide profiling of mRNA distribution in the hippocampus revealed an underlying mechanism: RNG105 deficiency impaired the asymmetric somato-dendritic localization of mRNAs. Particularly, RNG105 deficiency reduced the dendritic localization of mRNAs encoding regulators of AMPAR surface expression, which was consistent with attenuated homeostatic AMPAR scaling in dendrites and reduced synaptic strength. Thus, RNG105 has an essential role, as a key regulator of dendritic mRNA localization, in long-term memory formation. Messages pass from one nerve cell to the next across gaps called synapses. The first neuron releases chemical signals from the end of its long, thin nerve fiber. The second receives the message at receptors on branching structures known as dendrites. Each connection has a corresponding bump called a dendritic spine. As animals learn, these can grow larger, strengthening the connection. This is the basis of how memories form. To strengthen a synapse, the cell must transport the materials to the dendritic spine. The cell makes copies of the genetic instructions to strengthen the synapse in the form of messenger RNA (often shortened to mRNA). But, this happens in the body of the cell, a long way from the dendrites themselves. The mRNA travels from the cell body to the dendrites in collections of molecules referred to as ‘RNA granules’. One of the key components of the RNA granule system is a protein called RNG105/caprin1. Now, Nakayama, Ohashi et al. have engineered mice to delete the gene for RNG105/caprin1, revealing its effect on memory. Mice lacking RNG105/caprin1 struggled to make long-term memories. Unlike their normal counterparts, these mutant mice did not become accustomed to new environments or objects. They also found it more challenging to learn the position of a hidden platform in a water-based maze. Lastly, over time, the mutant mice forgot to be fearful of a dark chamber where they had received a small electric shock. Memories form in a part of the brain called the hippocampus and the dendritic spines in this region were smaller in mice lacking RNG105/caprin1. Furthermore, when the nerve cells from this part of the brain were grown in Petri dishes, they did not respond normally to stimulation. The dendritic spines of normal cells increased in size, but those on the cells lacking RNG105/caprin1 got smaller compared to normal cells. A closer look revealed that the distribution of mRNA in brain cells from mice lacking RNG105/caprin1 differed from that of normal mice. Some pieces of genetic information failed to make it from the cell body to the dendrites. This included mRNA involved in making regulators of a component of dendritic spines called the AMPA receptor. The AMPA receptor detects the chemical messenger, glutamate, and is crucial for memory formation. These findings further our understanding of long-term memory and open the way for future research into human disease. Mutations in RNA granule components, including RNG105/caprin1, have links to conditions such as amyotrophic lateral sclerosis (ALS) and autism spectrum disorder (ASD). Further investigation could reveal new targets for drug treatment.
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Affiliation(s)
- Kei Nakayama
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, SOKENDAI, Okazaki, Japan.,Okazaki Institute for Integrative Bioscience, Okazaki, Japan
| | - Rie Ohashi
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, SOKENDAI, Okazaki, Japan
| | - Yo Shinoda
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.,School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Maya Yamazaki
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akihiro Fujikawa
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Japan
| | - Shuji Shigenobu
- Department of Basic Biology, SOKENDAI, Okazaki, Japan.,Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - Akira Futatsugi
- Department of Basic Medical Science, Kobe City College of Nursing, Hyogo, Japan
| | - Masaharu Noda
- Department of Basic Biology, SOKENDAI, Okazaki, Japan.,Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki, Japan
| | - Katsuhiko Mikoshiba
- Laboratory for Developmental Neurobiology, Brain Science Institute, Wako, Japan
| | - Teiichi Furuichi
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan.,Department of Basic Biology, SOKENDAI, Okazaki, Japan.,Okazaki Institute for Integrative Bioscience, Okazaki, Japan
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40
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Transcriptomic Analysis of Ribosome-Bound mRNA in Cortical Neurites In Vivo. J Neurosci 2017; 37:8688-8705. [PMID: 28821669 DOI: 10.1523/jneurosci.3044-16.2017] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 06/29/2017] [Accepted: 07/21/2017] [Indexed: 01/19/2023] Open
Abstract
Localized translation in neurites helps regulate synaptic strength and development. Dysregulation of local translation is associated with many neurological disorders. However, due to technical limitations, study of this phenomenon has largely been limited to brain regions with laminar organization of dendrites such as the hippocampus or cerebellum. It has not been examined in the cortex, a region of importance for most neurological disorders, where dendrites of each neuronal population are densely intermingled with cell bodies of others. Therefore, we have developed a novel method, SynapTRAP, which combines synaptoneurosomal fractionation with translating ribosome affinity purification to identify ribosome-bound mRNA in processes of genetically defined cell types. We demonstrate SynapTRAP's efficacy and report local translation in the cortex of mice, where we identify a subset of mRNAs that are translated in dendrites by neuronal ribosomes. These mRNAs have disproportionately longer lengths, enrichment for FMRP binding and G-quartets, and their genes are under greater evolutionary constraint in humans. In addition, we show that alternative splicing likely regulates this phenomenon. Overall, SynapTRAP allows for rapid isolation of cell-type-specific localized translation and is applicable to classes of previously inaccessible neuronal and non-neuronal cells in vivoSIGNIFICANCE STATEMENT Instructions for making proteins are found in the genome, housed within the nucleus of each cell. These are then copied as RNA and exported to manufacture new proteins. However, in the brain, memory is thought to be encoded by strengthening individual connections (synapses) between neurons far from the nucleus. Thus, to efficiently make new proteins specifically where they are needed, neurons can transport RNAs to sites near synapses to locally produce proteins. Importantly, several mutations that cause autism disrupt this process. It has been assumed this process occurs in all brain regions, but has never been measured in the cortex. We applied a newly developed method measure to study, for the first time, local translation in cortical neurons.
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41
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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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42
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Chen PB, Kawaguchi R, Blum C, Achiro JM, Coppola G, O'Dell TJ, Martin KC. Mapping Gene Expression in Excitatory Neurons during Hippocampal Late-Phase Long-Term Potentiation. Front Mol Neurosci 2017; 10:39. [PMID: 28275336 PMCID: PMC5319997 DOI: 10.3389/fnmol.2017.00039] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
The persistence of long-lasting changes in synaptic connectivity that underlie long-term memory require new RNA and protein synthesis. To elucidate the temporal pattern of gene expression that gives rise to long-lasting neuronal plasticity, we analyzed differentially-expressed (DE) RNAs in mouse hippocampal slices following induction of late phase long-term potentiation (L-LTP) specifically within pyramidal excitatory neurons using Translating Ribosome Affinity Purification RNA sequencing (TRAP-seq). We detected time-dependent changes in up- and down-regulated ribosome-associated mRNAs over 2 h following L-LTP induction, with minimal overlap of DE transcripts between time points. TRAP-seq revealed greater numbers of DE transcripts and magnitudes of LTP-induced changes than RNA-seq of all cell types in the hippocampus. Neuron-enriched transcripts had greater changes at the ribosome-loading level than the total RNA level, while RNA-seq identified many non-neuronal DE mRNAs. Our results highlight the importance of considering both time course and cell-type specificity in activity-dependent gene expression during memory formation.
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Affiliation(s)
- Patrick B Chen
- Interdepartmental Program in Neurosciences, University of California, Los Angeles Los Angeles, CA, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles Los Angeles, CA, USA
| | - Charles Blum
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles Los Angeles, CA, USA
| | - Jennifer M Achiro
- Department of Biological Chemistry, University of California, Los Angeles Los Angeles, CA, USA
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles Los Angeles, CA, USA
| | - Thomas J O'Dell
- Department of Physiology, University of California, Los Angeles Los Angeles, CA, USA
| | - Kelsey C Martin
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los AngelesLos Angeles, CA, USA; Department of Biological Chemistry, University of California, Los AngelesLos Angeles, CA, USA
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43
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Bal NV, Susorov D, Chesnokova E, Kasianov A, Mikhailova T, Alkalaeva E, Balaban PM, Kolosov P. Upstream Open Reading Frames Located in the Leader of Protein Kinase Mζ mRNA Regulate Its Translation. Front Mol Neurosci 2016; 9:103. [PMID: 27790092 PMCID: PMC5061749 DOI: 10.3389/fnmol.2016.00103] [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: 07/14/2016] [Accepted: 09/30/2016] [Indexed: 12/17/2022] Open
Abstract
For protein synthesis that occurs locally in dendrites, the translational control mechanisms are much more important for neuronal functioning than the transcription levels. Here, we show that uORFs (upstream open reading frames) in the 5′ untranslated region (5′UTR) play a critical role in regulation of the translation of protein kinase Mζ (PKMζ). Elimination of these uORFs activates translation of the reporter protein in vitro and in primary cultures of rat hippocampal neurons. Using cell-free translation systems, we demonstrate that translational initiation complexes are formed only on uORFs. Further, we address the mechanism of translational repression of PKMζ translation, by uORFs. We observed an increase in translation of the reporter protein under the control of PKMζ leader in neuronal culture during non-specific activation by picrotoxin. We also show that such a mechanism is similar to the mechanism seen in cell stress, as application of sodium arsenite to neuron cultures induced translation of mRNA carrying PKMζ 5′UTR similarly to picrotoxin activation. Therefore, we suppose that phosphorylation of eIF2a, like in cell stress, is a main regulator of PKMζ translation. Altogether, our findings considerably extend our understanding of the role of uORF in regulation of PKMζ translation in activated neurons, important at early stages of LTP.
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Affiliation(s)
- Natalia V Bal
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Denis Susorov
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia; Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State UniversityMoscow, Russia
| | - Ekaterina Chesnokova
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Artem Kasianov
- Laboratory of System Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences Moscow, Russia
| | - Tatiana Mikhailova
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia
| | - Elena Alkalaeva
- Laboratory of Mechanisms and Control of Translation, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences Moscow, Russia
| | - Pavel M Balaban
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
| | - Peter Kolosov
- Cellular Neurobiology of Learning Laboratory, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
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44
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Mele M, Leal G, Duarte CB. Role of GABAAR trafficking in the plasticity of inhibitory synapses. J Neurochem 2016; 139:997-1018. [DOI: 10.1111/jnc.13742] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Miranda Mele
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Graciano Leal
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Carlos B. Duarte
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
- Department of Life Sciences; University of Coimbra; Coimbra Portugal
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45
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Cho JH, Huang BS, Gray JM. RNA sequencing from neural ensembles activated during fear conditioning in the mouse temporal association cortex. Sci Rep 2016; 6:31753. [PMID: 27557751 PMCID: PMC4997356 DOI: 10.1038/srep31753] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022] Open
Abstract
The stable formation of remote fear memories is thought to require neuronal gene induction in cortical ensembles that are activated during learning. However, the set of genes expressed specifically in these activated ensembles is not known; knowledge of such transcriptional profiles may offer insights into the molecular program underlying stable memory formation. Here we use RNA-Seq to identify genes whose expression is enriched in activated cortical ensembles labeled during associative fear learning. We first establish that mouse temporal association cortex (TeA) is required for remote recall of auditory fear memories. We then perform RNA-Seq in TeA neurons that are labeled by the activity reporter Arc-dVenus during learning. We identify 944 genes with enriched expression in Arc-dVenus+ neurons. These genes include markers of L2/3, L5b, and L6 excitatory neurons but not glial or inhibitory markers, confirming Arc-dVenus to be an excitatory neuron-specific but non-layer-specific activity reporter. Cross comparisons to other transcriptional profiles show that 125 of the enriched genes are also activity-regulated in vitro or induced by visual stimulus in the visual cortex, suggesting that they may be induced generally in the cortex in an experience-dependent fashion. Prominent among the enriched genes are those encoding potassium channels that down-regulate neuronal activity, suggesting the possibility that part of the molecular program induced by fear conditioning may initiate homeostatic plasticity.
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Affiliation(s)
- Jin-Hyung Cho
- Harvard Medical School, Genetics Department, 77 Ave Louis Pasteur NRB Room 356, Boston, Massachusetts 02115, USA
| | - Ben S Huang
- Harvard Medical School, Genetics Department, 77 Ave Louis Pasteur NRB Room 356, Boston, Massachusetts 02115, USA.,University of California at Los Angeles, David Geffen School of Medicine, Department of Neurology, 710 Westwood Plaza, Los Angeles, California 90095, USA
| | - Jesse M Gray
- Harvard Medical School, Genetics Department, 77 Ave Louis Pasteur NRB Room 356, Boston, Massachusetts 02115, USA
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46
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Perez JD, Rubinstein ND, Dulac C. New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain. Annu Rev Neurosci 2016; 39:347-84. [PMID: 27145912 DOI: 10.1146/annurev-neuro-061010-113708] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian evolution entailed multiple innovations in gene regulation, including the emergence of genomic imprinting, an epigenetic regulation leading to the preferential expression of a gene from its maternal or paternal allele. Genomic imprinting is highly prevalent in the brain, yet, until recently, its central roles in neural processes have not been fully appreciated. Here, we provide a comprehensive survey of adult and developmental brain functions influenced by imprinted genes, from neural development and wiring to synaptic function and plasticity, energy balance, social behaviors, emotions, and cognition. We further review the widespread identification of parental biases alongside monoallelic expression in brain tissues, discuss their potential roles in dosage regulation of key neural pathways, and suggest possible mechanisms underlying the dynamic regulation of imprinting in the brain. This review should help provide a better understanding of the significance of genomic imprinting in the normal and pathological brain of mammals including humans.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
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47
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Selvaraj S, Kitano H, Ohga H, Yamaguchi A, Matsuyama M. Expression changes of mRNAs encoding kisspeptins and their receptors and gonadotropin-releasing hormones during early development and gonadal sex differentiation periods in the brain of chub mackerel (Scomber japonicus). Gen Comp Endocrinol 2015; 222:20-32. [PMID: 25304825 DOI: 10.1016/j.ygcen.2014.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
In recent years, brain kisspeptin system has been shown to be involved in diverse reproductive function, including sexual differentiation in vertebrates. Our previous reports demonstrated that the chub mackerel (Scomber japonicus) brain expresses two kisspeptin (kiss1, kiss2), two kisspeptin receptor (kissr1, kissr2) and three gonadotropin-releasing hormone (gnrh1, gnrh2, gnrh3) genes. In the present study, using quantitative real-time PCR (qRT-PCR) assays, we analysed expression changes of these genes during early development (0-30dphs) and gonadal sex differentiation periods (37-60dphs). Absolute expression level of kiss-kissr-gnrh in the whole head was higher between 0 and 15dphs, in comparison to later developmental periods. Histological analyses revealed presence of sexually differentiated males and females with testicular and ovarian features at 37, 45, and 60dphs. In both males and females, kiss2, kissr1, and kissr2 levels were higher at 37dph, in comparison to 45 and 60dphs, with kiss1 showing no significant differences. Levels of all three gnrh mRNAs were higher at 45dph, in comparison to 60dph. Changes in the expression level of kiss-kissr-gnrh mRNAs in different brain regions of sexually differentiated males and females indicated differences in their regional distribution. These results suggest possible involvement of Kiss-KissR-GnRH systems during early development and gonadal sex differentiation in the chub mackerel.
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Affiliation(s)
- Sethu Selvaraj
- Laboratory of Marine Biology, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Hajime Kitano
- Fisheries Research Institute of Karatsu, Department of Joint Research, Faculty of Agriculture, Kyushu University, Saga 847-0132, Japan
| | - Hirofumi Ohga
- Laboratory of Marine Biology, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Akihiko Yamaguchi
- Laboratory of Marine Biology, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Michiya Matsuyama
- Laboratory of Marine Biology, Department of Bioresource Sciences, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan.
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48
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Niere F, Namjoshi S, Song E, Dilly GA, Schoenhard G, Zemelman BV, Mechref Y, Raab-Graham KF. Analysis of Proteins That Rapidly Change Upon Mechanistic/Mammalian Target of Rapamycin Complex 1 (mTORC1) Repression Identifies Parkinson Protein 7 (PARK7) as a Novel Protein Aberrantly Expressed in Tuberous Sclerosis Complex (TSC). Mol Cell Proteomics 2015; 15:426-44. [PMID: 26419955 DOI: 10.1074/mcp.m115.055079] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Indexed: 01/05/2023] Open
Abstract
Many biological processes involve the mechanistic/mammalian target of rapamycin complex 1 (mTORC1). Thus, the challenge of deciphering mTORC1-mediated functions during normal and pathological states in the central nervous system is challenging. Because mTORC1 is at the core of translation, we have investigated mTORC1 function in global and regional protein expression. Activation of mTORC1 has been generally regarded to promote translation. Few but recent works have shown that suppression of mTORC1 can also promote local protein synthesis. Moreover, excessive mTORC1 activation during diseased states represses basal and activity-induced protein synthesis. To determine the role of mTORC1 activation in protein expression, we have used an unbiased, large-scale proteomic approach. We provide evidence that a brief repression of mTORC1 activity in vivo by rapamycin has little effect globally, yet leads to a significant remodeling of synaptic proteins, in particular those proteins that reside in the postsynaptic density. We have also found that curtailing the activity of mTORC1 bidirectionally alters the expression of proteins associated with epilepsy, Alzheimer's disease, and autism spectrum disorder-neurological disorders that exhibit elevated mTORC1 activity. Through a protein-protein interaction network analysis, we have identified common proteins shared among these mTORC1-related diseases. One such protein is Parkinson protein 7, which has been implicated in Parkinson's disease, yet not associated with epilepsy, Alzheimers disease, or autism spectrum disorder. To verify our finding, we provide evidence that the protein expression of Parkinson protein 7, including new protein synthesis, is sensitive to mTORC1 inhibition. Using a mouse model of tuberous sclerosis complex, a disease that displays both epilepsy and autism spectrum disorder phenotypes and has overactive mTORC1 signaling, we show that Parkinson protein 7 protein is elevated in the dendrites and colocalizes with the postsynaptic marker postsynaptic density-95. Our work offers a comprehensive view of mTORC1 and its role in regulating regional protein expression in normal and diseased states.
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Affiliation(s)
- Farr Niere
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas; ‖Waggoner Center for Alcohol and Addiction Research, University of Texas, Austin, Texas
| | - Sanjeev Namjoshi
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas
| | - Ehwang Song
- **Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Geoffrey A Dilly
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas
| | - Grant Schoenhard
- ‡‡Pain Therapeutics, Inc., 7801 N Capital of Texas Hwy, #260, Austin, Texas 78731
| | - Boris V Zemelman
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas
| | - Yehia Mechref
- **Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409
| | - Kimberly F Raab-Graham
- From the ‡Center for Learning and Memory, University of Texas, Austin, 1 University Station C7000, Texas 78712; §Institute for Cell and Molecular Biology, University of Texas, Austin, Texas; ¶Institute for Neuroscience, University of Texas, Austin, Texas; ‖Waggoner Center for Alcohol and Addiction Research, University of Texas, Austin, Texas; ‡‡Pain Therapeutics, Inc., 7801 N Capital of Texas Hwy, #260, Austin, Texas 78731
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Cook-Snyder DR, Jones A, Reijmers LG. A retrograde adeno-associated virus for collecting ribosome-bound mRNA from anatomically defined projection neurons. Front Mol Neurosci 2015; 8:56. [PMID: 26557053 PMCID: PMC4617378 DOI: 10.3389/fnmol.2015.00056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/07/2015] [Indexed: 01/23/2023] Open
Abstract
The brain contains a large variety of projection neurons with different functional properties. The functional properties of projection neurons arise from their connectivity with other neurons and their molecular composition. We describe a novel tool for obtaining the gene expression profiles of projection neurons that are anatomically defined by the location of their soma and axon terminals. Our tool utilizes adeno-associated virus serotype 9 (AAV9), which we found to retrogradely transduce projection neurons after injection at the site of the axon terminals. We used AAV9 to express Enhanced Green Fluorescent Protein (EGFP)-tagged ribosomal protein L10a (EGFP-L10a), which enables the immunoprecipitation of EGFP-tagged ribosomes and associated mRNA with a method known as Translating Ribosome Affinity Purification (TRAP). To achieve high expression of the EGFP-L10a protein in projection neurons, we placed its expression under control of a 1.3 kb alpha-calcium/calmodulin-dependent protein kinase II (Camk2a) promoter. We injected the AAV9-Camk2a-TRAP virus in either the hippocampus or the bed nucleus of the stria terminalis (BNST) of the mouse brain. In both brain regions the 1.3 kb Camk2a promoter did not confer complete cell-type specificity around the site of injection, as EGFP-L10a expression was observed in Camk2a-expressing neurons as well as in neuronal and non-neuronal cells that did not express Camk2a. In contrast, cell-type specific expression was observed in Camk2a-positive projection neurons that were retrogradely transduced by AAV9-Camk2a-TRAP. Injection of AAV9-Camk2a-TRAP into the BNST enabled the use of TRAP to collect ribosome-bound mRNA from basal amygdala projection neurons that innervate the BNST. AAV9-Camk2a-TRAP provides a single-virus system that can be used for the molecular profiling of anatomically defined projection neurons in mice and other mammalian model organisms. In addition, AAV9-Camk2a-TRAP may enable the discovery of protein synthesis events that support information storage in projection neurons.
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Affiliation(s)
- Denise R Cook-Snyder
- Department of Neuroscience, School of Medicine, Tufts University Boston, MA, USA ; Department of Biology and Neuroscience Program, Carthage College Kenosha, WI, USA
| | - Alexander Jones
- Department of Neuroscience, School of Medicine, Tufts University Boston, MA, USA ; Graduate Program in Neuroscience, Sackler School of Graduate Biomedical Sciences, Tufts University Boston, MA, USA
| | - Leon G Reijmers
- Department of Neuroscience, School of Medicine, Tufts University Boston, MA, USA
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50
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Peixoto L, Risso D, Poplawski SG, Wimmer ME, Speed TP, Wood MA, Abel T. How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets. Nucleic Acids Res 2015. [PMID: 26202970 PMCID: PMC4652761 DOI: 10.1093/nar/gkv736] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or ‘batch effects’ can contribute unwanted variation to the data, commonly used RNA-seq normalization methods only correct for sequencing depth. The study of gene expression is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from experimental neuroscience, we show that batch effects can dominate the signal of interest; and that the choice of normalization method affects the power and reproducibility of the results. While commonly used global normalization methods are not able to adequately normalize the data, more recently developed RNA-seq normalization can. We focus on one particular method, RUVSeq and show that it is able to increase power and biological insight of the results. Finally, we provide a tutorial outlining the implementation of RUVSeq normalization that is applicable to a broad range of studies as well as meta-analysis of publicly available data.
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Affiliation(s)
- Lucia Peixoto
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Davide Risso
- Division of Biostatistics, School of Public Health, University of California, Berkeley, 344 Li Ka Shing Center, #3370, Berkeley, CA 94720-3370, USA
| | - Shane G Poplawski
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Mathieu E Wimmer
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
| | - Terence P Speed
- Department of Statistics, University of California, Berkeley, Department of Mathematics and Statistics, The University of Melbourne, Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Australia
| | - Marcelo A Wood
- University of California, Irvine, Department of Neurobiology and Behavior, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Smilow Center for Translational Research, Room 10-170, Building 421, 3400 Civic Center Boulevard, Philadelphia, PA 19104-6168, USA
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