1
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Kiebler MA, Bauer KE. RNA granules in flux: dynamics to balance physiology and pathology. Nat Rev Neurosci 2024:10.1038/s41583-024-00859-1. [PMID: 39367081 DOI: 10.1038/s41583-024-00859-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
The life cycle of an mRNA is a complex process that is tightly regulated by interactions between the mRNA and RNA-binding proteins, forming molecular machines known as RNA granules. Various types of these membrane-less organelles form inside cells, including neurons, and contribute critically to various physiological processes. RNA granules are constantly in flux, change dynamically and adapt to their local environment, depending on their intracellular localization. The discovery that RNA condensates can form by liquid-liquid phase separation expanded our understanding of how compartments may be generated in the cell. Since then, a plethora of new functions have been proposed for distinct condensates in cells that await their validation in vivo. The finding that dysregulation of RNA granules (for example, stress granules) is likely to affect neurodevelopmental and neurodegenerative diseases further boosted interest in this topic. RNA granules have various physiological functions in neurons and in the brain that we would like to focus on. We outline examples of state-of-the-art experiments including timelapse microscopy in neurons to unravel the precise functions of various types of RNA granule. Finally, we distinguish physiologically occurring RNA condensation from aberrant aggregation, induced by artificial RNA overexpression, and present visual examples to discriminate both forms in neurons.
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Affiliation(s)
- Michael A Kiebler
- Biomedical Center (BMC), Department of Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany.
| | - Karl E Bauer
- Biomedical Center (BMC), Department of Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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2
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Wang C, Jiang Y, Yang Z, Xu H, Khalid AK, Iftakhar T, Peng Y, Lu L, Zhang L, Bermudez L, Guo A, Chen Y. Host factor RBMX2 promotes epithelial cell apoptosis by downregulating APAF-1's Retention Intron after Mycobacterium bovis infection. Front Immunol 2024; 15:1431207. [PMID: 39308873 PMCID: PMC11412827 DOI: 10.3389/fimmu.2024.1431207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 08/15/2024] [Indexed: 09/25/2024] Open
Abstract
The Mycobacterium tuberculosis variant bovis (M. bovis) is a highly pathogenic environmental microorganism that causes bovine tuberculosis (bTB), a significant zoonotic disease. Currently, "test and culling" is the primary measure for controlling bTB, but it has been proven to be inadequate in animals due to their high susceptibility to the pathogen. Selective breeding for increased host resistance to bTB to reduce its prevalence is feasible. In this study, we found a vital host-dependent factor, RBMX2, that can potentially promote M. bovis infection. By knocking RBMX2 out, we investigated its function during M. bovis infection. Through transcriptome sequencing and alternative splicing transcriptome sequencing, we concluded that after M. bovis infection, embryo bovine lung (EBL) cells were significantly enriched in RNA splicing associated with apoptosis compared with wild-type EBL cells. Through protein/molecular docking, molecular dynamics simulations, and real-time quantitative PCR, we demonstrated that RBMX2 promotes the apoptosis of epithelial cells by upregulating and binding to apoptotic peptidase activating factor 1 (APAF-1), resulting in the alternative splicing of APAF-1 as a retention intron. To our knowledge, this is the first report of M. bovis affecting host epithelial cell apoptosis by hijacking RBMX2 to promote the intron splicing of downstream APAF-1. These findings may represent a significant contribution to the development of novel TB prevention and control strategies.
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Affiliation(s)
- Chao Wang
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Yanzhu Jiang
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Zhiming Yang
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Haojun Xu
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Abdul Karim Khalid
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tahira Iftakhar
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yongchong Peng
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Lu Lu
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Lei Zhang
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Luiz Bermudez
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Aizhen Guo
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yingyu Chen
- The National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
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3
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Shang X, Talross GJS, Carlson JR. Exitron splicing of odor receptor genes in Drosophila. Proc Natl Acad Sci U S A 2024; 121:e2320277121. [PMID: 38507450 PMCID: PMC10990081 DOI: 10.1073/pnas.2320277121] [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: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024] Open
Abstract
Proper expression of odor receptor genes is critical for the function of olfactory systems. In this study, we identified exitrons (exonic introns) in four of the 39 Odorant receptor (Or) genes expressed in the Drosophila antenna. Exitrons are sequences that can be spliced out from within a protein-coding exon, thereby altering the encoded protein. We focused on Or88a, which encodes a pheromone receptor, and found that exitron splicing of Or88a is conserved across five Drosophila species over 20 My of evolution. The exitron was spliced out in 15% of Or88a transcripts. Removal of this exitron creates a non-coding RNA rather than an RNA that encodes a stable protein. Our results suggest the hypothesis that in the case of Or88a, exitron splicing could act in neuronal modulation by decreasing the level of functional Or transcripts. Activation of Or88a-expressing olfactory receptor neurons via either optogenetics or pheromone stimulation increased the level of exitron-spliced transcripts, with optogenetic activation leading to a 14-fold increase. A fifth Or can also undergo an alternative splicing event that eliminates most of the canonical open reading frame. Besides these cases of alternative splicing, we found alternative polyadenylation of four Ors, and exposure of Or67c to its ligand ethyl lactate in the antenna downregulated all of its 3' isoforms. Our study reveals mechanisms by which neuronal activity could be modulated via regulation of the levels of Or isoforms.
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Affiliation(s)
- Xueying Shang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511
| | - Gaëlle J. S. Talross
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511
| | - John R. Carlson
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511
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4
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [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: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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5
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Di Liegro CM, Schiera G, Schirò G, Di Liegro I. Role of Post-Transcriptional Regulation in Learning and Memory in Mammals. Genes (Basel) 2024; 15:337. [PMID: 38540396 PMCID: PMC10970538 DOI: 10.3390/genes15030337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 06/14/2024] Open
Abstract
After many decades, during which most molecular studies on the regulation of gene expression focused on transcriptional events, it was realized that post-transcriptional control was equally important in order to determine where and when specific proteins were to be synthesized. Translational regulation is of the most importance in the brain, where all the steps of mRNA maturation, transport to different regions of the cells and actual expression, in response to specific signals, constitute the molecular basis for neuronal plasticity and, as a consequence, for structural stabilization/modification of synapses; notably, these latter events are fundamental for the highest brain functions, such as learning and memory, and are characterized by long-term potentiation (LTP) of specific synapses. Here, we will discuss the molecular bases of these fundamental events by considering both the role of RNA-binding proteins (RBPs) and the effects of non-coding RNAs involved in controlling splicing, editing, stability and translation of mRNAs. Importantly, it has also been found that dysregulation of mRNA metabolism/localization is involved in many pathological conditions, arising either during brain development or in the adult nervous system.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (C.M.D.L.); (G.S.)
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
- Neurology and Multiple Sclerosis Center, Unità Operativa Complessa (UOC), Foundation Institute “G. Giglio”, 90015 Cefalù, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy;
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6
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Gundermann DG, Lymer S, Blau J. A rapid and dynamic role for FMRP in the plasticity of adult neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555985. [PMID: 37693612 PMCID: PMC10491314 DOI: 10.1101/2023.09.01.555985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of Drosophila genetics to test if Fmr1 acutely affects adult neuronal plasticity in vivo, focusing on the s-LNv circadian pacemaker neurons that show 24 hour rhythms in structural plasticity. We found that over-expressing Fmr1 for only 4 hours blocks the activity-dependent expansion of s-LNv projections without altering the circadian clock or activity-regulated gene expression. Conversely, acutely reducing Fmr1 expression prevented s-LNv projections from retracting. One FMRP target that we identified in s-LNvs is sif, which encodes a Rac1 GEF. Our data indicate that FMRP normally reduces sif mRNA translation at dusk to reduce Rac1 activity. Overall, our data reveal a previously unappreciated rapid and direct role for FMRP in acutely regulating neuronal plasticity in adult neurons, and underscore the importance of RNA-binding proteins in this process.
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Affiliation(s)
- Daniel G Gundermann
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Seana Lymer
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
- Current address: Proteintech Genomics, 11588 Sorrento Valley Rd, San Diego, CA 92121
| | - Justin Blau
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
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7
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Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S. Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes. J Med Chem 2022; 65:13264-13287. [PMID: 36136092 DOI: 10.1021/acs.jmedchem.2c01106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LIMKs are important regulators of actin and microtubule dynamics, and they play essential roles in many cellular processes. Deregulation of LIMKs has been linked to the development of diverse diseases, including cancers and cognitive disabilities, but well-characterized inhibitors known as chemical probes are still lacking. Here, we report the characterization of three highly selective LIMK1/2 inhibitors covering all canonical binding modes (type I/II/III) and the structure-based design of the type II/III inhibitors. Characterization of these chemical probes revealed a low nanomolar affinity for LIMK1/2, and all inhibitors 1 (LIMKi3; type I), 48 (TH470; type II), and 15 (TH257; type III) showed excellent selectivity in a comprehensive scanMAX kinase selectivity panel. Phosphoproteomics revealed remarkable differences between type I and type II inhibitors compared with the allosteric inhibitor 15. In phenotypic assays such as neurite outgrowth models of fragile X-chromosome, 15 showed promising activity, suggesting the potential application of allosteric LIMK inhibitors treating this orphan disease.
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Affiliation(s)
- Thomas Hanke
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Risa Kashima
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, United States
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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8
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Bauer KE, Bargenda N, Schieweck R, Illig C, Segura I, Harner M, Kiebler MA. RNA supply drives physiological granule assembly in neurons. Nat Commun 2022; 13:2781. [PMID: 35589693 DOI: 10.1038/s41467-022-30067-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Membraneless cytoplasmic condensates of mRNAs and proteins, known as RNA granules, play pivotal roles in the regulation of mRNA fate. Their maintenance fine-tunes time and location of protein expression, affecting many cellular processes, which require complex protein distribution. Here, we report that RNA granules-monitored by DEAD-Box helicase 6 (DDX6)-disassemble during neuronal maturation both in cell culture and in vivo. This process requires neuronal function, as synaptic inhibition results in reversible granule assembly. Importantly, granule assembly is dependent on the RNA-binding protein Staufen2, known for its role in RNA localization. Altering the levels of free cytoplasmic mRNA reveals that RNA availability facilitates DDX6 granule formation. Specifically depleting RNA from DDX6 granules confirms RNA as an important driver of granule formation. Moreover, RNA is required for DDX6 granule assembly upon synaptic inhibition. Together, this data demonstrates how RNA supply favors RNA granule assembly, which not only impacts subcellular RNA localization but also translation-dependent synaptic plasticity, learning, and memory.
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Affiliation(s)
- Karl E Bauer
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Niklas Bargenda
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Rico Schieweck
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Christin Illig
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Inmaculada Segura
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.,Max Planck Institute for Biological Intelligence (in foundation), Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Max Harner
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
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9
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Ghiasi SM, Rutter GA. Consequences for Pancreatic β-Cell Identity and Function of Unregulated Transcript Processing. Front Endocrinol (Lausanne) 2021; 12:625235. [PMID: 33763030 PMCID: PMC7984428 DOI: 10.3389/fendo.2021.625235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence suggests a role for alternative splicing (AS) of transcripts in the normal physiology and pathophysiology of the pancreatic β-cell. In the apparent absence of RNA repair systems, RNA decay pathways are likely to play an important role in controlling the stability, distribution and diversity of transcript isoforms in these cells. Around 35% of alternatively spliced transcripts in human cells contain premature termination codons (PTCs) and are targeted for degradation via nonsense-mediated decay (NMD), a vital quality control process. Inflammatory cytokines, whose levels are increased in both type 1 (T1D) and type 2 (T2D) diabetes, stimulate alternative splicing events and the expression of NMD components, and may or may not be associated with the activation of the NMD pathway. It is, however, now possible to infer that NMD plays a crucial role in regulating transcript processing in normal and stress conditions in pancreatic β-cells. In this review, we describe the possible role of Regulated Unproductive Splicing and Translation (RUST), a molecular mechanism embracing NMD activity in relationship to AS and translation of damaged transcript isoforms in these cells. This process substantially reduces the abundance of non-functional transcript isoforms, and its dysregulation may be involved in pancreatic β-cell failure in diabetes.
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Affiliation(s)
- Seyed M. Ghiasi
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Park AJ, Shetty MS, Baraban JM, Abel T. Selective role of the translin/trax RNase complex in hippocampal synaptic plasticity. Mol Brain 2020; 13:145. [PMID: 33172471 PMCID: PMC7653721 DOI: 10.1186/s13041-020-00691-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/30/2020] [Indexed: 01/09/2023] Open
Abstract
Activity-dependent local protein synthesis is critical for synapse-specific, persistent plasticity. Abnormalities in local protein synthesis have been implicated in psychiatric disorders. We have recently identified the translin/trax microRNA-degrading enzyme as a novel mediator of protein synthesis at activated synapses. Additionally, translin knockout (KO) mice, which lack translin/trax, exhibit some of the behavioral abnormalities found in a mouse model of fragile X syndrome (fragile X mental retardation protein-FMRP-KO mice). Therefore, identifying signaling pathways interacting with translin/trax to support persistent synaptic plasticity is a translationally relevant goal. Here, as a first step to achieve this goal, we have assessed the requirement of translin/trax for multiple hippocampal synaptic plasticity paradigms that rely on distinct molecular mechanisms. We found that mice lacking translin/trax exhibited selective impairment in a form of persistent hippocampal plasticity, which requires postsynaptic protein kinase A (PKA) activity. In contrast, enduring forms of plasticity that are dependent on presynaptic PKA were unaffected. Furthermore, these mice did not display exaggerated metabotropic glutamate receptor-mediated long-term synaptic depression (mGluR-LTD), a hallmark of the FMRP KO mice. On the contrary, translin KO mice exhibited deficits in N-methyl-d-aspartate receptor (NMDAR) dependent LTD, a phenotype not observed in the FMRP knockouts. Taken together, these findings demonstrate that translin/trax mediates long-term synaptic plasticity that is dependent on postsynaptic PKA signaling and suggest that translin/trax and FMRP play distinct roles in hippocampal synaptic plasticity.
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Affiliation(s)
- Alan Jung Park
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Gogos Lab, Mortimer B. Zuckerman Mind Brain Behavior Institute, Jerome L. Greene Science Center, Columbia University, L5-053, 3227 Broadway, New York, NY, 10027, USA.
| | - Mahesh Shivarama Shetty
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-471 Bowen Science Building, 51 Newton Road, Iowa City, IA, 52242, USA.,Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 2312 Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, 52242, IA, USA
| | - Jay M Baraban
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ted Abel
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, 2-471 Bowen Science Building, 51 Newton Road, Iowa City, IA, 52242, USA. .,Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, 2312 Pappajohn Biomedical Discovery Building, 169 Newton Road, Iowa City, 52242, IA, USA.
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11
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van den Buuse M, Halley P, Hoyne GF. Behavioural phenotyping of thunder mice with a hypomorphic mutation of heterogeneous nuclear ribonuclear protein L-like (hnRNPLL) and reduced T cell function. Neurosci Lett 2020; 740:135469. [PMID: 33152455 DOI: 10.1016/j.neulet.2020.135469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/23/2020] [Accepted: 10/27/2020] [Indexed: 02/01/2023]
Abstract
Heterogeneous nuclear ribonuclear protein l-like (hnRNPLL) is an RNA binding protein that regulates alternative splicing of mRNA and is abundantly expressed in memory T lymphocytes of the immune system and in the brain. A hypomorphic allele of the gene encoding hnRNPLL (Hnrpllthunder) selectively reduces T cell accumulation in lymphoid tissues, but little is known about its effects in the brain. Therefore, we exposed Hnrpllthunder mice to a test battery with relevance for a range of psychiatric illnesses. Thunder mice showed enhanced immobility in the tail-suspension test for depression-related behaviours, impaired short-term spatial memory in the Y-maze and reduced avoidance learning in the active avoidance test. Thus, in addition to its reported effects on immune function, the hnRNPLL mutation in thunder mice selectively affected aspects of behaviour.
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Affiliation(s)
- Maarten van den Buuse
- Mental Health Research Institute of Victoria, Parkville, VIC, Australia; School of Psychology and Public Health, La Trobe University, Melbourne, VIC, Australia.
| | - Paul Halley
- Mental Health Research Institute of Victoria, Parkville, VIC, Australia
| | - Gerard F Hoyne
- Immunology Program, John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia; School of Health Sciences, University of Notre Dame Australia, Fremantle, WA, Australia
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12
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Koterniak B, Pilaka PP, Gracida X, Schneider LM, Pritišanac I, Zhang Y, Calarco JA. Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans. Genome Res 2020; 30:1766-1780. [PMID: 33127752 PMCID: PMC7706725 DOI: 10.1101/gr.267328.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Alternative splicing plays a major role in shaping tissue-specific transcriptomes. Among the broad tissue types present in metazoans, the central nervous system contains some of the highest levels of alternative splicing. Although many documented examples of splicing differences between broad tissue types exist, there remains much to be understood about the splicing factors and the cis sequence elements controlling tissue and neuron subtype-specific splicing patterns. By using translating ribosome affinity purification coupled with deep-sequencing (TRAP-seq) in Caenorhabditis elegans, we have obtained high coverage profiles of ribosome-associated mRNA for three broad tissue classes (nervous system, muscle, and intestine) and two neuronal subtypes (dopaminergic and serotonergic neurons). We have identified hundreds of splice junctions that exhibit distinct splicing patterns between tissue types or within the nervous system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified a likely mechanism of splicing repression by the RNA-binding protein UNC-75/CELF via interactions with cis elements that overlap a 5′ splice site. Alternatively spliced exons also overlap more frequently with intrinsically disordered peptide regions than constitutive exons. Moreover, regulated exons are often shorter than constitutive exons but are flanked by longer intron sequences. Among these tissue-regulated exons are several highly conserved microexons <27 nt in length. Collectively, our results indicate a rich layer of tissue-specific gene regulation at the level of alternative splicing in C. elegans that parallels the evolutionary forces and constraints observed across metazoa.
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Affiliation(s)
- Bina Koterniak
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Pallavi P Pilaka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Xicotencatl Gracida
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lisa-Marie Schneider
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Department of Chemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Iva Pritišanac
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.,Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Yun Zhang
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
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13
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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14
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Wu YF, Zhang YM, Ge HH, Ren CY, Zhang ZZ, Cao L, Wang F, Chen GH. Effects of Embryonic Inflammation and Adolescent Psychosocial Environment on Cognition and Hippocampal Staufen in Middle-Aged Mice. Front Aging Neurosci 2020; 12:578719. [PMID: 33024434 PMCID: PMC7516039 DOI: 10.3389/fnagi.2020.578719] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022] Open
Abstract
Accumulating evidence has indicated that embryonic inflammation could accelerate age-associated cognitive impairment, which can be attributed to dysregulation of synaptic plasticity-associated proteins, such as RNA-binding proteins (RBPs). Staufen is a double-stranded RBP that plays a critical role in the modulation of synaptic plasticity and memory. However, relatively few studies have investigated how embryonic inflammation affects cognition and neurobiology during aging, or how the adolescent psychosocial environment affects inflammation-induced remote cognitive impairment. Consequently, the aim of this study was to investigate whether these adverse factors can induce changes in Staufen expression, and whether these changes are correlated with cognitive impairment. In our study, CD-1 mice were administered lipopolysaccharides (LPS, 50 μg/kg) or an equal amount of saline (control) intraperitoneally during days 15–17 of gestation. At 2 months of age, male offspring were randomly exposed to stress (S), an enriched environment (E), or not treated (CON) and then assigned to five groups: LPS, LPS+S, LPS+E, CON, and CON+S. Mice were evaluated at 3-month-old (young) and 15-month-old (middle-aged). Cognitive function was assessed using the Morris water maze test, while Staufen expression was examined at both the protein and mRNA level using immunohistochemistry/western blotting and RNAscope technology, respectively. The results showed that the middle-aged mice had worse cognitive performance and higher Staufen expression than young mice. Embryonic inflammation induced cognitive impairment and increased Staufen expression in the middle-aged mice, whereas adolescent stress/an enriched environment would accelerated/mitigated these effects. Meanwhile, Staufen expression was closely correlated with cognitive performance. Our findings suggested embryonic inflammation can accelerate age-associated learning and memory impairments, and these effects may be related to the Staufen expression.
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Affiliation(s)
- Yong-Fang Wu
- Department of Neurology (Sleep Disorders), The Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Yue-Ming Zhang
- Department of Neurology (Sleep Disorders), The Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - He-Hua Ge
- Department of Neurology (Sleep Disorders), The Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Chong-Yang Ren
- Department of Neurology (Sleep Disorders), The Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Zhe-Zhe Zhang
- Department of Neurology and Critical Care, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Cao
- Department of Neurology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fang Wang
- Department of Neurology and Critical Care, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Gui-Hai Chen
- Department of Neurology (Sleep Disorders), The Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
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15
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Gumina V, Colombrita C, Fallini C, Bossolasco P, Maraschi AM, Landers JE, Silani V, Ratti A. TDP-43 and NOVA-1 RNA-binding proteins as competitive splicing regulators of the schizophrenia-associated TNIK gene. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194413. [PMID: 31382054 DOI: 10.1016/j.bbagrm.2019.194413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/31/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023]
Abstract
The RNA-binding protein TDP-43, associated to amyotrophic lateral sclerosis and frontotemporal dementia, regulates the alternative splicing of several genes, including the skipping of TNIK exon 15. TNIK, a genetic risk factor for schizophrenia and causative for intellectual disability, encodes for a Ser/Thr kinase regulating negatively F-actin dynamics. Here we show that in the human adult nervous system TNIK exon 15 is mostly included compared to the other tissues and that, during neuronal differentiation of human induced pluripotent stem cells and of human neuroblastoma cells, TNIK exon 15 inclusion increases independently of TDP-43 protein content. By studying the possible molecular interplay of TDP-43 with brain-specific splicing factors, we found that the neuronal NOVA-1 protein competitively inhibits both TDP-43 and hnRNPA2/B1 skipping activity on TNIK by means of a RNA-dependent interaction and that this competitive mechanism is common to other TDP-43 RNA targets. We also show that the TNIK protein isoforms including/excluding exon 15 differently regulate cell spreading in non-neuronal cells and neuritogenesis in primary cortical neurons. Our data suggest a complex regulation between the ubiquitous TDP-43 and the neuron-specific NOVA-1 splicing factors in the brain that may help better understand the pathobiology of both neurodegenerative diseases and schizophrenia.
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Affiliation(s)
- Valentina Gumina
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via F. Sforza 35, 20122 Milan, Italy
| | - Claudia Colombrita
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, ASC 6-1053, Worcester, MA 01605, USA.
| | - Patrizia Bossolasco
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy
| | - Anna Maria Maraschi
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy.
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, ASC 6-1053, Worcester, MA 01605, USA.
| | - Vincenzo Silani
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Via F. Sforza 35, 20122 Milan, Italy; "Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Via A. di Rudinì 8, 20142 Milan, Italy.
| | - Antonia Ratti
- Istituto Auxologico Italiano, IRCCS, Department of Neurology-Stroke Unit and Laboratory of Neuroscience, Via Zucchi 18, 20095, Cusano Milanino, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Fratelli Cervi 93, 20090, Segrate, Milan, Italy.
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16
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Roballo KCS, da Silveira JC, Bressan FF, de Souza AF, Pereira VM, Porras JEP, Rós FA, Pulz LH, Strefezzi RDF, Martins DDS, Meirelles FV, Ambrósio CE. Neurons-derived extracellular vesicles promote neural differentiation of ADSCs: a model to prevent peripheral nerve degeneration. Sci Rep 2019; 9:11213. [PMID: 31371742 PMCID: PMC6671995 DOI: 10.1038/s41598-019-47229-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
Potential mechanisms involved in neural differentiation of adipocyte derived stem cells (ADSCs) are still unclear. In the present study, extracellular vesicles (EVs) were tested as a potential mechanism involved in the neuronal differentiation of stem cells. In order to address this, ADSCs and neurons (BRC) were established in primary culture and co-culture at three timepoints. Furthermore, we evaluated protein and transcript levels of differentiated ADSCs from the same timepoints, to confirm phenotype change to neuronal linage. Importantly, neuron-derived EVs cargo and EVs originated from co-culture were analyzed and tested in terms of function, such as gene expression and microRNA levels related to the adult neurogenesis process. Ideal neuron-like cells were identified and, therefore, we speculated the in vivo function of these cells in acute sciatic nerve injury. Overall, our data demonstrated that ADSCs in indirect contact with neurons differentiated into neuron-like cells. Neuron-derived EVs appear to play an important role in this process carrying SNAP25, miR-132 and miR-9. Additionally, in vivo neuron-like cells helped in microenvironment modulation probably preventing peripheral nerve injury degeneration. Consequently, our findings provide new insight of future methods of ADSC induction into neuronal linage to be applied in peripheral nerve (PN) injury.
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Affiliation(s)
- Kelly Cristine Santos Roballo
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Juliano Coelho da Silveira
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil.
| | - Fabiana Fernandes Bressan
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Aline Fernanda de Souza
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Vitoria Mattos Pereira
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Jorge Eliecer Pinzon Porras
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil.,Faculty of Veterinary Medicine and Animal Science, Department of Posgraduation, University National of Columbia, Bogota, Colombia
| | - Felipe Augusto Rós
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Lidia Hildebrand Pulz
- Experimental and Comparative Pathology Department, Faculty of Veterinary Medicine and Animal Science, University of Sao Paulo, Av. Prof. Orlando Marques de Paiva, 87 - Butantã, 05508-010, São Paulo, SP, Brazil
| | - Ricardo de Francisco Strefezzi
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil.,Experimental and Comparative Pathology Department, Faculty of Veterinary Medicine and Animal Science, University of Sao Paulo, Av. Prof. Orlando Marques de Paiva, 87 - Butantã, 05508-010, São Paulo, SP, Brazil
| | - Daniele Dos Santos Martins
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Flavio Vieira Meirelles
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
| | - Carlos Eduardo Ambrósio
- Veterinary Medicine Department, Faculty of Animal Sciences and Food Engineering, University of Sao Paulo, Av. Duque de Caxias Norte 225, 13635-900, Pirassununga, SP, Brazil
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17
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Kim SH, Seo M, Hwang H, Moon DM, Son GH, Kim K, Rhim H. Physical and Functional Interaction between 5-HT 6 Receptor and Nova-1. Exp Neurobiol 2019; 28:17-29. [PMID: 30853821 PMCID: PMC6401546 DOI: 10.5607/en.2019.28.1.17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/17/2018] [Accepted: 01/04/2019] [Indexed: 01/22/2023] Open
Abstract
5-HT6 receptor (5-HT6R) is implicated in cognitive dysfunction, mood disorder, psychosis, and eating disorders. However, despite its significant role in regulating the brain functions, regulation of 5-HT6R at the molecular level is poorly understood. Here, using yeast two-hybrid assay, we found that human 5-HT6R directly binds to neuro-oncological ventral antigen 1 (Nova-1), a brain-enriched splicing regulator. The interaction between 5-HT6R and Nova-1 was confirmed using GST pull-down and co-immunoprecipitation assays in cell lines and rat brain. The splicing activity of Nova-1 was decreased upon overexpression of 5-HT6R, which was examined by detecting the spliced intermediates of gonadotropin-releasing hormone (GnRH), a known pre-mRNA target of Nova-1, using RT-PCR. In addition, overexpression of 5-HT6R induced the translocation of Nova-1 from the nucleus to cytoplasm, resulting in the reduced splicing activity of Nova-1. In contrast, overexpression of Nova-1 reduced the activity and the total protein levels of 5-HT6R. Taken together, these results indicate that when the expression levels of 5-HT6R or Nova-1 protein are not properly regulated, it may also deteriorate the function of the other.
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Affiliation(s)
- Soon-Hee Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Misun Seo
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Hongik Hwang
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Dong-Min Moon
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
| | - Gi Hoon Son
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Korea
| | - Kyungjin Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Korea
| | - Hyewhon Rhim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea.,Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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18
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Porter DF, Prasad A, Carrick BH, Kroll-Connor P, Wickens M, Kimble J. Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines. G3 (BETHESDA, MD.) 2019; 9:153-165. [PMID: 30459181 PMCID: PMC6325917 DOI: 10.1534/g3.118.200300] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022]
Abstract
Metazoan PUF (Pumilio and FBF) RNA-binding proteins regulate various biological processes, but a common theme across phylogeny is stem cell regulation. In Caenorhabditis elegans, FBF (fem-3 Binding Factor) maintains germline stem cells regardless of which gamete is made, but FBF also functions in the process of spermatogenesis. We have begun to "disentangle" these biological roles by asking which FBF targets are gamete-independent, as expected for stem cells, and which are gamete-specific. Specifically, we compared FBF iCLIP binding profiles in adults making sperm to those making oocytes. Normally, XX adults make oocytes. To generate XX adults making sperm, we used a fem-3(gf) mutant requiring growth at 25°; for comparison, wild-type oogenic hermaphrodites were also raised at 25°. Our FBF iCLIP data revealed FBF binding sites in 1522 RNAs from oogenic adults and 1704 RNAs from spermatogenic adults. More than half of these FBF targets were independent of germline gender. We next clustered RNAs by FBF-RNA complex frequencies and found four distinct blocks. Block I RNAs were enriched in spermatogenic germlines, and included validated target fog-3, while Block II and III RNAs were common to both genders, and Block IV RNAs were enriched in oogenic germlines. Block II (510 RNAs) included almost all validated FBF targets and was enriched for cell cycle regulators. Block III (21 RNAs) was enriched for RNA-binding proteins, including previously validated FBF targets gld-1 and htp-1 We suggest that Block I RNAs belong to the FBF network for spermatogenesis, and that Blocks II and III are associated with stem cell functions.
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Affiliation(s)
- Douglas F Porter
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Aman Prasad
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Peggy Kroll-Connor
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Wisconsin 53706
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19
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Kaitsuka T, Kiyonari H, Shiraishi A, Tomizawa K, Matsushita M. Deletion of Long Isoform of Eukaryotic Elongation Factor 1Bδ Leads to Audiogenic Seizures and Aversive Stimulus-Induced Long-Lasting Activity Suppression in Mice. Front Mol Neurosci 2018; 11:358. [PMID: 30333725 PMCID: PMC6176097 DOI: 10.3389/fnmol.2018.00358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/11/2018] [Indexed: 02/03/2023] Open
Abstract
Alternative splicing enables a gene to give rise to diverse protein products. The Eef1d gene produces two isoforms: a short isoform that encodes translation elongation factor 1Bδ (eEF1Bδ1), and a long isoform that encodes the heat shock-responsive transcription factor eEF1BδL. Previously, we found that eEF1BδL was a splice variant that was specific to the brain and testis, and the protein encoded is thought to have a function in the central nervous system. In this study, we generated knockout (KO) mice of C57BL/6J background that selectively lacked a specific exon in Eef1d for the long isoform. These KO mice lacked eEF1BδL, but not eEF1Bδ1, in the brain. Although the KO mice showed normal anxiety-related and learning behavior in behavioral tests, some showed severe seizures in response to loud sounds (90 dBA), an audiogenic seizures (AGS) response. Furthermore, after the KO mice had been subjected to the fear conditioning test, they showed remarkably decreased locomotor activity in their home cage and in the open-field and elevated plus-maze tests. After the fear conditioning test, a significant decrease in brain weight, atrophy of the hippocampus and midbrain, and reduced cortical layer thickness were observed in the KO mice. We also found a compensatory increase in the eEF1Bδ1 level and elevated protein synthesis with the induction of endoplasmic reticulum stress markers in these mice. Our results suggest that eEF1BδL has an important role in normal brain function especially when exposed to external stimuli.
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Affiliation(s)
- Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroshi Kiyonari
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, Kobe, Japan.,Genetic Engineering Team, RIKEN Center for Life Science Technologies, Kobe, Japan
| | - Aki Shiraishi
- Animal Resource Development Unit, RIKEN Center for Life Science Technologies, Kobe, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masayuki Matsushita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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20
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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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21
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Ortiz R, Georgieva MV, Gutiérrez S, Pedraza N, Fernández-Moya SM, Gallego C. Recruitment of Staufen2 Enhances Dendritic Localization of an Intron-Containing CaMKIIα mRNA. Cell Rep 2018; 20:13-20. [PMID: 28683307 DOI: 10.1016/j.celrep.2017.06.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/30/2017] [Accepted: 06/08/2017] [Indexed: 02/07/2023] Open
Abstract
Regulation of mRNA localization is a conserved cellular process observed in many types of cells and organisms. Asymmetrical mRNA distribution plays a particularly important role in the nervous system, where local translation of localized mRNA represents a key mechanism in synaptic plasticity. CaMKIIα is a very abundant mRNA detected in neurites, consistent with its crucial role at glutamatergic synapses. Here, we report the presence of CaMKIIα mRNA isoforms that contain intron i16 in dendrites, RNA granules, and synaptoneurosomes from primary neurons and brain. This subpopulation of unspliced mRNA preferentially localizes to distal dendrites in a synaptic-activity-dependent manner. Staufen2, a well-established marker of RNA transport in dendrites, interacts with intron i16 sequences and enhances its distal dendritic localization, pointing to the existence of intron-mediated mechanisms in the molecular pathways that modulate dendritic transport and localization of synaptic mRNAs.
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Affiliation(s)
- Raúl Ortiz
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Maya V Georgieva
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Sara Gutiérrez
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain
| | - Neus Pedraza
- Institut de Recerca Biomèdica de Lleida (IRBLleida), Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, 25198 Lleida, Catalonia, Spain
| | - Sandra M Fernández-Moya
- Biomedical Center, Division of Anatomy and Cell Biology, Ludwig Maximilians University, 82152 Planegg-Martinsried, Germany
| | - Carme Gallego
- Molecular Biology Institute of Barcelona (IBMB-CSIC), 08028 Barcelona, Catalonia, Spain.
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22
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Identification and characterization of new isoforms of human fas apoptotic inhibitory molecule (FAIM). PLoS One 2017; 12:e0185327. [PMID: 28981531 PMCID: PMC5628826 DOI: 10.1371/journal.pone.0185327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023] Open
Abstract
Fas Apoptosis Inhibitory Molecule (FAIM) is an evolutionarily highly conserved death receptor antagonist, widely expressed and known to participate in physiological and pathological processes. Two FAIM transcript variants have been characterized to date, namely FAIM short (FAIM-S) and FAIM long (FAIM-L). FAIM-S is ubiquitously expressed and serves as an anti-apoptotic protein in the immune system. Furthermore, in neurons, this isoform promotes NGF-induced neurite outgrowth through NF-кB and ERK signaling. In contrast FAIM-L is found only in neurons, where it exerts anti-apoptotic activity against several stimuli. In addition to these two variants, in silico studies point to the existence of two additional isoforms, neither of which have been characterized to date. In this regard, here we confirm the presence of these two additional FAIM isoforms in human fetal brain, fetal and adult testes, and placenta tissues. We named them FAIM-S_2a and FAIM-L_2a since they have the same sequence as FAIM-S and FAIM-L, but include exon 2a. PCR and western blot revealed that FAIM-S_2a shows ubiquitous expression in all the tissues and cellular models tested, while FAIM-L_2a is expressed exclusively in tissues of the nervous system. In addition, we found that, when overexpressed in non-neuronal cells, the splicing factor nSR100 induces the expression of the neuronal isoforms, thus identifying it as responsible for the generation of FAIM-L and FAIM-L_2a. Functionally, FAIM-S_2a and FAIM-L_2a increased neurite outgrowth in response to NGF stimulation in a neuronal model. This observation thus, supports the notion that these two isoforms are involved in neuronal differentiation. Furthermore, subcellular fractionation experiments revealed that, in contrast to FAIM-S and FAIM-L, FAIM-S_2a and FAIM-L_2a are able to localize to the nucleus, where they may have additional functions. In summary, here we report on two novel FAIM isoforms that may have relevant roles in the physiology and pathology of the nervous system.
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Controlling the Messenger: Regulated Translation of Maternal mRNAs in Xenopus laevis Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 953:49-82. [PMID: 27975270 DOI: 10.1007/978-3-319-46095-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The selective translation of maternal mRNAs encoding cell-fate determinants drives the earliest decisions of embryogenesis that establish the vertebrate body plan. This chapter will discuss studies in Xenopus laevis that provide insights into mechanisms underlying this translational control. Xenopus has been a powerful model organism for many discoveries relevant to the translational control of maternal mRNAs because of the large size of its oocytes and eggs that allow for microinjection of molecules and the relative ease of manipulating the oocyte to egg transition (maturation) and fertilization in culture. Consequently, many key studies have focused on the expression of maternal mRNAs during the oocyte to egg transition (the meiotic cell cycle) and the rapid cell divisions immediately following fertilization. This research has made seminal contributions to our understanding of translational regulatory mechanisms, but while some of the mRNAs under consideration at these stages encode cell-fate determinants, many encode cell cycle regulatory proteins that drive these early cell cycles. In contrast, while maternal mRNAs encoding key developmental (i.e., cell-fate) regulators that function after the first cleavage stages may exploit aspects of these foundational mechanisms, studies reveal that these mRNAs must also rely on distinct and, as of yet, incompletely understood mechanisms. These findings are logical because the functions of such developmental regulatory proteins have requirements distinct from cell cycle regulators, including becoming relevant only after fertilization and then only in specific cells of the embryo. Indeed, key maternal cell-fate determinants must be made available in exquisitely precise amounts (usually low), only at specific times and in specific cells during embryogenesis. To provide an appreciation for the regulation of maternal cell-fate determinant expression, an overview of the maternal phase of Xenopus embryogenesis will be presented. This section will be followed by a review of translational mechanisms operating in oocytes, eggs, and early cleavage-stage embryos and conclude with a discussion of how the regulation of key maternal cell-fate determinants at the level of translation functions in Xenopus embryogenesis. A key theme is that the molecular asymmetries critical for forming the body axes are established and further elaborated upon by the selective temporal and spatial regulation of maternal mRNA translation.
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24
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Regulated Intron Removal Integrates Motivational State and Experience. Cell 2017; 169:836-848.e15. [PMID: 28525754 DOI: 10.1016/j.cell.2017.05.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/23/2017] [Accepted: 05/01/2017] [Indexed: 11/23/2022]
Abstract
Myriad experiences produce transient memory, yet, contingent on the internal state of the organism and the saliency of the experience, only some memories persist over time. How experience and internal state influence the duration of memory at the molecular level remains unknown. A self-assembled aggregated state of Drosophila Orb2A protein is required specifically for long-lasting memory. We report that in the adult fly brain the mRNA encoding Orb2A protein exists in an unspliced non-protein-coding form. The convergence of experience and internal drive transiently increases the spliced protein-coding Orb2A mRNA. A screen identified pasilla, the fly ortholog of mammalian Nova-1/2, as a mediator of Orb2A mRNA processing. A single-nucleotide substitution in the intronic region that reduces Pasilla binding and intron removal selectively impairs long-term memory. We posit that pasilla-mediated processing of unspliced Orb2A mRNA integrates experience and internal state to control Orb2A protein abundance and long-term memory formation.
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Abstract
Neurons are amongst the most structurally complex cells and exhibit a high degree of spatial compartmentalization. Also, neurons exhibit rapid and dynamic signaling by processing information in a precise and, sometimes, spatially-restricted manner. The signaling that occurs in axons and dendrites necessitates the maintenance and modification of their local proteomes. Local translation of mRNAs into protein is one solution that neurons use to meet synaptic demand and activity. Here we review some of the key findings and recent discoveries that have shaped our understanding of local translation in neuronal function and highlight important new techniques that might pave the way for new insights.
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26
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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27
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Kopec AM, Rivera PD, Lacagnina MJ, Hanamsagar R, Bilbo SD. Optimized solubilization of TRIzol-precipitated protein permits Western blotting analysis to maximize data available from brain tissue. J Neurosci Methods 2017; 280:64-76. [PMID: 28192129 DOI: 10.1016/j.jneumeth.2017.02.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/24/2017] [Accepted: 02/06/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND Techniques simultaneously assessing multiple levels of molecular processing are appealing because molecular signaling underlying complex neural phenomena occurs at complementary levels. The TRIzol method isolates RNA and DNA, but protein retrieval is difficult due to inefficient solubilization of precipitated protein pellets. NEW METHOD We optimized a buffer for the efficient solubilization of protein from TRIzol-precipitated brain tissue for Western blotting analysis, which was also more effective at directly homogenizing brain tissue than RIPA buffer. RESULTS Protein yield during solubilization, in addition to protein yield via direct homogenization, is increased by optimizing concentrations of chemicals in a standard lysis buffer. Effective incubation parameters for both total protein yield and the analysis of post-translational modifications is remarkably flexible. Importantly, different neural cell types and protein classes are represented in solubilized protein samples. Moreover, we used dissociated mouse brain tissue to isolate microglia from other cell types and successfully resolved cell type-specific proteins from these small and difficult to attain samples. COMPARISON WITH EXISTING METHOD(S) Solubilization buffers to date have been comprised primarily of SDS or urea; the data herein demonstrate that components common to lysis buffers can also enhance protein solubilization both after direct homogenization and after precipitation. CONCLUSIONS This method is suitable for assessing gene and protein expression from a single brain sample, allowing for a more comprehensive evaluation of neural phenomena while minimizing the number of subjects.
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Affiliation(s)
- Ashley M Kopec
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Phillip D Rivera
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Richa Hanamsagar
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Staci D Bilbo
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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28
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Ustianenko D, Weyn-Vanhentenryck SM, Zhang C. Microexons: discovery, regulation, and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28188674 DOI: 10.1002/wrna.1418] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 12/16/2022]
Abstract
The importance of RNA splicing in numerous cellular processes is well established. However, an underappreciated aspect is the ability of the spliceosome to recognize a set of very small (3-30 nucleotide, 1-10 amino acid) exons named microexons. Despite their small size, microexons and their regulation through alternative splicing have now been shown to play critical roles in protein and system function. Here we review the discovery of microexons over time and the mechanisms by which their splicing is regulated, including recent progress made through deep RNA sequencing. We also discuss the functional role of microexons in biology and disease. WIREs RNA 2017, 8:e1418. doi: 10.1002/wrna.1418 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmytro Ustianenko
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | - Chaolin Zhang
- Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
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29
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The Cstf2t Polyadenylation Gene Plays a Sex-Specific Role in Learning Behaviors in Mice. PLoS One 2016; 11:e0165976. [PMID: 27812195 PMCID: PMC5094787 DOI: 10.1371/journal.pone.0165976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
Polyadenylation is an essential mechanism for the processing of mRNA 3′ ends. CstF-64 (the 64,000 Mr subunit of the cleavage stimulation factor; gene symbol Cstf2) is an RNA-binding protein that regulates mRNA polyadenylation site usage. We discovered a paralogous form of CstF-64 called τCstF-64 (Cstf2t). The Cstf2t gene is conserved in all eutherian mammals including mice and humans, but the τCstF-64 protein is expressed only in a subset of mammalian tissues, mostly testis and brain. Male mice that lack Cstf2t (Cstf2t-/- mice) experience disruption of spermatogenesis and are infertile, although female fertility is unaffected. However, a role for τCstF-64 in the brain has not yet been determined. Given the importance of RNA polyadenylation and splicing in neuronal gene expression, we chose to test the hypothesis that τCstF-64 is important for brain function. Male and female 185-day old wild type and Cstf2t-/- mice were examined for motor function, general activity, learning, and memory using rotarod, open field activity, 8-arm radial arm maze, and Morris water maze tasks. Male wild type and Cstf2t-/- mice did not show differences in learning and memory. However, female Cstf2t-/- mice showed significantly better retention of learned maze tasks than did female wild type mice. These results suggest that τCstf-64 is important in memory function in female mice. Interestingly, male Cstf2t-/- mice displayed less thigmotactic behavior than did wild type mice, suggesting that Cstf2t may play a role in anxiety in males. Taken together, our studies highlight the importance of mRNA processing in cognition and behavior as well as their established functions in reproduction.
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30
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Lipscombe D, Andrade A. Calcium Channel CaVα₁ Splice Isoforms - Tissue Specificity and Drug Action. Curr Mol Pharmacol 2016; 8:22-31. [PMID: 25966698 DOI: 10.2174/1874467208666150507103215] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 01/20/2015] [Accepted: 04/20/2015] [Indexed: 12/11/2022]
Abstract
Voltage-gated calcium ion channels are essential for numerous biological functions of excitable cells and there is wide spread appreciation of their importance as drug targets in the treatment of many disorders including those of cardiovascular and nervous systems. Each Cacna1 gene has the potential to generate a number of structurally, functionally, and in some cases pharmacologically unique CaVα1 subunits through alternative pre-mRNA splicing and the use of alternate promoters. Analyses of rapidly emerging deep sequencing data for a range of human tissue transcriptomes contain information to quantify tissue-specific and alternative exon usage patterns for Cacna1 genes. Cellspecific actions of nuclear DNA and RNA binding proteins control the use of alternate promoters and the selection of alternate exons during pre-mRNA splicing, and they determine the spectrum of protein isoforms expressed within different types of cells. Amino acid compositions within discrete protein domains can differ substantially among CaV isoforms expressed in different tissues, and such differences may be greater than those that exist across CaV channel homologs of closely related species. Here we highlight examples of CaV isoforms that have unique expression patterns and that exhibit different pharmacological sensitivities. Knowledge of expression patterns of CaV isoforms in different human tissues, cell populations, ages, and disease states should inform strategies aimed at developing the next generation of CaV channel inhibitors and agonists with improved tissue-specificity.
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Affiliation(s)
- Diane Lipscombe
- Department of Neuroscience, Brown University. Providence, RI, USA.
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31
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Fiszbein A, Kornblihtt AR. Histone methylation, alternative splicing and neuronal differentiation. NEUROGENESIS 2016; 3:e1204844. [PMID: 27606339 DOI: 10.1080/23262133.2016.1204844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/14/2016] [Accepted: 06/17/2016] [Indexed: 12/31/2022]
Abstract
Alternative splicing, as well as chromatin structure, greatly contributes to specific transcriptional programs that promote neuronal differentiation. The activity of G9a, the enzyme responsible for mono- and di-methylation of lysine 9 on histone H3 (H3K9me1 and H3K9me2) in mammalian euchromatin, has been widely implicated in the differentiation of a variety of cell types and tissues. In a recent work from our group (Fiszbein et al., 2016) we have shown that alternative splicing of G9a regulates its nuclear localization and, therefore, the efficiency of H3K9 methylation, which promotes neuronal differentiation. We discuss here our results in the light of a report from other group (Laurent et al. 2015) demonstrating a key role for the alternative splicing of the histone demethylase LSD1 in controlling specific gene expression in neurons. All together, these results illustrate the importance of alternative splicing in the generation of a proper equilibrium between methylation and demethylation of histones for the regulation of neuron-specific transcriptional programs.
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Affiliation(s)
- Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , Buenos Aires, Argentina
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32
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Guo C, Xue Y, Yang G, Yin S, Shi W, Cheng Y, Yan X, Fan S, Zhang H, Zeng F. Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells. Cell Biol Int 2016; 40:847-60. [PMID: 26289635 DOI: 10.1002/cbin.10539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/15/2015] [Indexed: 02/05/2023]
Abstract
Nanog is a well-known transcription factor that plays a fundamental role in stem cell self-renewal and the maintenance of their pluripotent cell identity. There remains a large data gap with respect to the spectrum of the key pluripotency transcription factors' interaction partners. Limited information is available concerning Nanog-associated RNA-binding proteins (RBPs), and the intrinsic protein-RNA interactions characteristic of the regulatory activities of Nanog. Herein, we used an improved affinity protocol to purify Nanog-interacting RBPs from mouse embryonic stem cells (ESCs), and 49 RBPs of Nanog were identified. Among them, the interaction of YBX1 and ILF3 with Nanog mRNA was further confirmed by in vitro assays, such as Western blot, RNA immunoprecipitation (RIP), and ex vivo methods, such as immunofluorescence staining and fluorescent in situ hybridization (FISH), MS2 in vivo biotin-tagged RNA affinity purification (MS2-BioTRAP). Interestingly, RNAi studies revealed that YBX1 and ILF3 positively affected the expression of Nanog and other pluripotency-related genes. Particularly, downregulation of YBX1 or ILF3 resulted in high expression of mesoderm markers. Thus, a reduction in the expression of YBX1 and ILF3 controls the expression of pluripotency-related genes in ESCs, suggesting their roles in further regulation of the pluripotent state of ESCs.
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Affiliation(s)
- Chuanliang Guo
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yan Xue
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Guanheng Yang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shang Yin
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wansheng Shi
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cheng
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoshuang Yan
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shuyue Fan
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huijun Zhang
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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33
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Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB. NOVA2-mediated RNA regulation is required for axonal pathfinding during development. eLife 2016; 5. [PMID: 27223325 PMCID: PMC4930328 DOI: 10.7554/elife.14371] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/23/2016] [Indexed: 01/13/2023] Open
Abstract
The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators. NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2. Transcriptome-wide searches for isoform-specific functions, using NOVA1 and NOVA2 specific HITS-CLIP and RNA-seq data from mouse cortex lacking either NOVA isoform, reveals that NOVA2 uniquely regulates alternative splicing events of a series of axon guidance related genes during cortical development. Corresponding axonal pathfinding defects were specific to NOVA2 deficiency: Nova2-/- but not Nova1-/- mice had agenesis of the corpus callosum, and axonal outgrowth defects specific to ventral motoneuron axons and efferent innervation of the cochlea. Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.
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Affiliation(s)
- Yuhki Saito
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Soledad Miranda-Rottmann
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Matteo Ruggiu
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | | | - John J Fak
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Ru Zhong
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Jeremy S Duncan
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, United States
| | - Brian A Fabella
- Laboratory of Sensory Neuroscience, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Harald J Junge
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, United States
| | - Zhe Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, United States
| | - Roberto Araya
- Department of Neurosciences, Faculty of Medicine, University of Montreal, Montreal, Canada
| | - Bernd Fritzsch
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, United States
| | - A J Hudspeth
- Laboratory of Sensory Neuroscience, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,New York Genome Center, New York, United States
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Wille M, Schümann A, Wree A, Kreutzer M, Glocker MO, Mutzbauer G, Schmitt O. The Proteome Profiles of the Cerebellum of Juvenile, Adult and Aged Rats--An Ontogenetic Study. Int J Mol Sci 2015; 16:21454-85. [PMID: 26370973 PMCID: PMC4613263 DOI: 10.3390/ijms160921454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/04/2015] [Accepted: 08/25/2015] [Indexed: 11/16/2022] Open
Abstract
In this study, we searched for proteins that change their expression in the cerebellum (Ce) of rats during ontogenesis. This study focuses on the question of whether specific proteins exist which are differentially expressed with regard to postnatal stages of development. A better characterization of the microenvironment and its development may result from these study findings. A differential two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of the samples revealed that the number of proteins of the functional classes differed depending on the developmental stages. Especially members of the functional classes of biosynthesis, regulatory proteins, chaperones and structural proteins show the highest differential expression within the analyzed stages of development. Therefore, members of these functional protein groups seem to be involved in the development and differentiation of the Ce within the analyzed development stages. In this study, changes in the expression of proteins in the Ce at different postnatal developmental stages (postnatal days (P) 7, 90, and 637) could be observed. At the same time, an identification of proteins which are involved in cell migration and differentiation was possible. Especially proteins involved in processes of the biosynthesis and regulation, the dynamic organization of the cytoskeleton as well as chaperones showed a high amount of differentially expressed proteins between the analyzed dates.
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Affiliation(s)
- Michael Wille
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Antje Schümann
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Andreas Wree
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
| | - Michael Kreutzer
- Proteome Center Rostock, Schillingallee 69, 18055 Rostock, Germany.
| | | | - Grit Mutzbauer
- Department of Pathology, Josef-Schneider-Str. 2, 97080 Würzburg, Germany.
| | - Oliver Schmitt
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany.
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Wang Z, Murigneux V, Le Hir H. Transcriptome-wide modulation of splicing by the exon junction complex. Genome Biol 2015; 15:551. [PMID: 25476502 PMCID: PMC4268817 DOI: 10.1186/s13059-014-0551-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/23/2022] Open
Abstract
Background The exon junction complex (EJC) is a dynamic multi-protein complex deposited onto nuclear spliced mRNAs upstream of exon-exon junctions. The four core proteins, eIF4A3, Magoh, Y14 and MLN51, are stably bound to mRNAs during their lifecycle, serving as a binding platform for other nuclear and cytoplasmic proteins. Recent evidence has shown that the EJC is involved in the splicing regulation of some specific events in both Drosophila and mammalian cells. Results Here, we show that knockdown of EJC core proteins causes widespread alternative splicing changes in mammalian cells. These splicing changes are specific to EJC core proteins, as knockdown of eIF4A3, Y14 and MLN51 shows similar splicing changes, and are different from knockdown of other splicing factors. The splicing changes can be rescued by a siRNA-resistant form of eIF4A3, indicating an involvement of EJC core proteins in regulating alternative splicing. Finally, we find that the splicing changes are linked with RNA polymerase II elongation rates. Conclusion Taken together, this study reveals that the coupling between EJC proteins and splicing is broader than previously suspected, and that a possible link exists between mRNP assembly and splice site recognition. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0551-7) contains supplementary material, which is available to authorized users.
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Fernández E, Li KW, Rajan N, De Rubeis S, Fiers M, Smit AB, Achsel T, Bagni C. FXR2P Exerts a Positive Translational Control and Is Required for the Activity-Dependent Increase of PSD95 Expression. J Neurosci 2015; 35:9402-8. [PMID: 26109663 PMCID: PMC6605191 DOI: 10.1523/jneurosci.4800-14.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 01/13/2023] Open
Abstract
In brain, specific RNA-binding proteins (RBPs) associate with localized mRNAs and function as regulators of protein synthesis at synapses exerting an indirect control on neuronal activity. Thus, the Fragile X Mental Retardation protein (FMRP) regulates expression of the scaffolding postsynaptic density protein PSD95, but the mode of control appears to be different from other FMRP target mRNAs. Here, we show that the fragile X mental retardation-related protein 2 (FXR2P) cooperates with FMRP in binding to the 3'-UTR of mouse PSD95/Dlg4 mRNA. Absence of FXR2P leads to decreased translation of PSD95/Dlg4 mRNA in the hippocampus, implying a role for FXR2P as translation activator. Remarkably, mGluR-dependent increase of PSD95 synthesis is abolished in neurons lacking Fxr2. Together, these findings show a coordinated regulation of PSD95/Dlg4 mRNA by FMRP and FXR2P that ultimately affects its fine-tuning during synaptic activity.
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Affiliation(s)
- Esperanza Fernández
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands, and
| | - Nicholas Rajan
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Silvia De Rubeis
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Mark Fiers
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands, and
| | - Tilmann Achsel
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium
| | - Claudia Bagni
- KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease, Leuven, Belgium, VIB Center for the Biology of Disease, 3000 Leuven, Belgium, University of Rome Tor Vergata, Department of Biomedicine and Prevention, 00133 Rome, Italy
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Quesnel-Vallières M, Irimia M, Cordes SP, Blencowe BJ. Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development. Genes Dev 2015; 29:746-59. [PMID: 25838543 PMCID: PMC4387716 DOI: 10.1101/gad.256115.114] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Quesnel-Vallières et al. show that loss of the vertebrate- and neural-specific Ser/Arg repeat-related protein of 100 kDa (nSR100/SRRM4) impairs development of the central and peripheral nervous systems. Accompanying these developmental defects are widespread changes in alternative splicing (AS) that primarily result in shifts to nonneural patterns for different classes of splicing events. The main component of the altered AS program comprises 3- to 27-nt neural microexons, and inclusion of a 6-nt nSR100-activated microexon in Unc13b transcripts is sufficient to rescue a neuritogenesis defect in nSR100 mutant primary neurons. Alternative splicing (AS) generates vast transcriptomic complexity in the vertebrate nervous system. However, the extent to which trans-acting splicing regulators and their target AS regulatory networks contribute to nervous system development is not well understood. To address these questions, we generated mice lacking the vertebrate- and neural-specific Ser/Arg repeat-related protein of 100 kDa (nSR100/SRRM4). Loss of nSR100 impairs development of the central and peripheral nervous systems in part by disrupting neurite outgrowth, cortical layering in the forebrain, and axon guidance in the corpus callosum. Accompanying these developmental defects are widespread changes in AS that primarily result in shifts to nonneural patterns for different classes of splicing events. The main component of the altered AS program comprises 3- to 27-nucleotide (nt) neural microexons, an emerging class of highly conserved AS events associated with the regulation of protein interaction networks in developing neurons and neurological disorders. Remarkably, inclusion of a 6-nt, nSR100-activated microexon in Unc13b transcripts is sufficient to rescue a neuritogenesis defect in nSR100 mutant primary neurons. These results thus reveal critical in vivo neurodevelopmental functions of nSR100 and further link these functions to a conserved program of neuronal microexon splicing.
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Affiliation(s)
- Mathieu Quesnel-Vallières
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Manuel Irimia
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Sabine P Cordes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada;
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Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A 2015; 112:3445-50. [PMID: 25737549 DOI: 10.1073/pnas.1502849112] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing (AS) dramatically expands the complexity of the mammalian brain transcriptome, but its atlas remains incomplete. Here we performed deep mRNA sequencing of mouse cortex to discover and characterize alternative exons with potential functional significance. Our analysis expands the list of AS events over 10-fold compared with previous annotations, demonstrating that 72% of multiexon genes express multiple splice variants in this single tissue. To evaluate functionality of the newly discovered AS events, we conducted comprehensive analyses on central nervous system (CNS) cell type-specific splicing, targets of tissue- or cell type-specific RNA binding proteins (RBPs), evolutionary selection pressure, and coupling of AS with nonsense-mediated decay (AS-NMD). We show that newly discovered events account for 23-42% of all cassette exons under tissue- or cell type-specific regulation. Furthermore, over 7,000 cassette exons are under evolutionary selection for regulated AS in mammals, 70% of which are new. Among these are 3,058 highly conserved cassette exons, including 1,014 NMD exons that may function directly to control gene expression levels. These NMD exons are particularly enriched in RBPs including splicing factors and interestingly also regulators for other steps of RNA metabolism. Unexpectedly, a second group of NMD exons reside in genes encoding chromatin regulators. Although the conservation of NMD exons in RBPs frequently extends into lower vertebrates, NMD exons in chromatin regulators are introduced later into the mammalian lineage, implying the emergence of a novel mechanism coupling AS and epigenetics. Our results highlight previously uncharacterized complexity and evolution in the mammalian brain transcriptome.
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39
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Wille M, Schümann A, Kreutzer M, Glocker MO, Wree A, Mutzbauer G, Schmitt O. The proteome profiles of the olfactory bulb of juvenile, adult and aged rats - an ontogenetic study. Proteome Sci 2015; 13:8. [PMID: 25709559 PMCID: PMC4337183 DOI: 10.1186/s12953-014-0058-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/19/2014] [Indexed: 12/30/2022] Open
Abstract
Background In this study, we searched for proteins that change their expression in the olfactory bulb (oB) of rats during ontogenesis. Up to now, protein expression differences in the developing animal are not fully understood. Our investigation focused on the question whether specific proteins exist which are only expressed during different development stages. This might lead to a better characterization of the microenvironment and to a better determination of factors and candidates that influence the differentiation of neuronal progenitor cells. Results After analyzing the samples by two-dimensional polyacrylamide gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), it could be shown that the number of expressed proteins differs depending on the developmental stages. Especially members of the functional classes, like proteins of biosynthesis, regulatory proteins and structural proteins, show the highest differential expression in the stages of development analyzed. Conclusion In this study, quantitative changes in the expression of proteins in the oB at different developmental stages (postnatal days (P) 7, 90 and 637) could be observed. Furthermore, the expression of many proteins was found at specific developmental stages. It was possible to identify these proteins which are involved in processes like support of cell migration and differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12953-014-0058-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Wille
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany
| | - Antje Schümann
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany
| | - Michael Kreutzer
- Proteome Center Rostock, Schillingallee 69, 18055 Rostock, Germany
| | | | - Andreas Wree
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany
| | - Grit Mutzbauer
- Department of Pathology, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
| | - Oliver Schmitt
- Department of Anatomy, Gertrudenstr. 9, 18055 Rostock, Germany
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40
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Kaitsuka T, Matsushita M. Regulation of translation factor EEF1D gene function by alternative splicing. Int J Mol Sci 2015; 16:3970-9. [PMID: 25686034 PMCID: PMC4346937 DOI: 10.3390/ijms16023970] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/04/2015] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing is an exquisite mechanism that allows one coding gene to have multiple functions. The alternative splicing machinery is necessary for proper development, differentiation and stress responses in a variety of organisms, and disruption of this machinery is often implicated in human diseases. Previously, we discovered a long form of eukaryotic elongation factor 1Bδ (eEF1Bδ; this long-form eEF1Bδ results from alternative splicing of EEF1D transcripts and regulates the cellular stress response by transcriptional activation, not translational enhancement, of heat-shock responsive genes. In this review, we discuss the molecular function of EEF1D alternative splicing products and the estimated implication of human diseases.
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Affiliation(s)
- Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
| | - Masayuki Matsushita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan.
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41
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Most D, Workman E, Harris RA. Synaptic adaptations by alcohol and drugs of abuse: changes in microRNA expression and mRNA regulation. Front Mol Neurosci 2014; 7:85. [PMID: 25565954 PMCID: PMC4267177 DOI: 10.3389/fnmol.2014.00085] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/22/2014] [Indexed: 12/18/2022] Open
Abstract
Local translation of mRNAs is a mechanism by which cells can rapidly remodel synaptic structure and function. There is ample evidence for a role of synaptic translation in the neuroadaptations resulting from chronic drug use and abuse. Persistent and coordinated changes of many mRNAs, globally and locally, may have a causal role in complex disorders such as addiction. In this review we examine the evidence that translational regulation by microRNAs drives synaptic remodeling and mRNA expression, which may regulate the transition from recreational to compulsive drug use. microRNAs are small, non-coding RNAs that control the translation of mRNAs in the cell and within spatially restricted sites such as the synapse. microRNAs typically repress the translation of mRNAs into protein by binding to the 3′UTR of their targets. As ‘master regulators’ of many mRNAs, changes in microRNAs could account for the systemic alterations in mRNA and protein expression observed with drug abuse and dependence. Recent studies indicate that manipulation of microRNAs affects addiction-related behaviors such as the rewarding properties of cocaine, cocaine-seeking behavior, and self-administration rates of alcohol. There is limited evidence, however, regarding how synaptic microRNAs control local mRNA translation during chronic drug exposure and how this contributes to the development of dependence. Here, we discuss research supporting microRNA regulation of local mRNA translation and how drugs of abuse may target this process. The ability of synaptic microRNAs to rapidly regulate mRNAs provides a discrete, localized system that could potentially be used as diagnostic and treatment tools for alcohol and other addiction disorders.
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Affiliation(s)
- Dana Most
- The Institute for Neuroscience, The University of Texas at Austin Austin, TX, USA ; Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
| | - Emily Workman
- The Institute for Neuroscience, The University of Texas at Austin Austin, TX, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin Austin, TX, USA
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42
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Villate O, Turatsinze JV, Mascali LG, Grieco FA, Nogueira TC, Cunha DA, Nardelli TR, Sammeth M, Salunkhe VA, Esguerra JLS, Eliasson L, Marselli L, Marchetti P, Eizirik DL. Nova1 is a master regulator of alternative splicing in pancreatic beta cells. Nucleic Acids Res 2014; 42:11818-30. [PMID: 25249621 PMCID: PMC4191425 DOI: 10.1093/nar/gku861] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) is a fundamental mechanism for the regulation of gene expression. It affects more than 90% of human genes but its role in the regulation of pancreatic beta cells, the producers of insulin, remains unknown. Our recently published data indicated that the ‘neuron-specific’ Nova1 splicing factor is expressed in pancreatic beta cells. We have presently coupled specific knockdown (KD) of Nova1 with RNA-sequencing to determine all splice variants and downstream pathways regulated by this protein in beta cells. Nova1 KD altered the splicing of nearly 5000 transcripts. Pathway analysis indicated that these genes are involved in exocytosis, apoptosis, insulin receptor signaling, splicing and transcription. In line with these findings, Nova1 silencing inhibited insulin secretion and induced apoptosis basally and after cytokine treatment in rodent and human beta cells. These observations identify a novel layer of regulation of beta cell function, namely AS controlled by key splicing regulators such as Nova1.
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Affiliation(s)
- Olatz Villate
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Jean-Valery Turatsinze
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Loriana G Mascali
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Fabio A Grieco
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Tatiane C Nogueira
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Daniel A Cunha
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Tarlliza R Nardelli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
| | - Michael Sammeth
- Laboratório Nacional de Computação Científica (LNCC), Petrópolis Rio de Janeiro, 25651-076, Brazil
| | - Vishal A Salunkhe
- Lund University Diabetes Centre, Unit of Islet cell Exocytosis, Department of Clinical Sciences Malmö, Lund University, CRC 91-11, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Jonathan L S Esguerra
- Lund University Diabetes Centre, Unit of Islet cell Exocytosis, Department of Clinical Sciences Malmö, Lund University, CRC 91-11, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Lena Eliasson
- Lund University Diabetes Centre, Unit of Islet cell Exocytosis, Department of Clinical Sciences Malmö, Lund University, CRC 91-11, Jan Waldenströms gata 35, 205 02 Malmö, Sweden
| | - Lorella Marselli
- Department of Clinical and Experimental Medicine, Pancreatic Islet Cell Laboratory, University of Pisa, Pisa, 56126, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, Pancreatic Islet Cell Laboratory, University of Pisa, Pisa, 56126, Italy
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels (ULB) B-1070, Belgium
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Rusconi F, Paganini L, Braida D, Ponzoni L, Toffolo E, Maroli A, Landsberger N, Bedogni F, Turco E, Pattini L, Altruda F, De Biasi S, Sala M, Battaglioli E. LSD1 Neurospecific Alternative Splicing Controls Neuronal Excitability in Mouse Models of Epilepsy. Cereb Cortex 2014; 25:2729-40. [PMID: 24735673 DOI: 10.1093/cercor/bhu070] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing in the brain is dynamic and instrumental to adaptive changes in response to stimuli. Lysine-specific demethylase 1 (LSD1/KDM1A) is a ubiquitously expressed histone H3Lys4 demethylase that acts as a transcriptional co-repressor in complex with its molecular partners CoREST and HDAC1/2. In mammalian brain, alternative splicing of LSD1 mini-exon E8a gives rise to neuroLSD1, a neurospecific isoform that, upon phosphorylation, acts as a dominant-negative causing disassembly of the co-repressor complex and de-repression of target genes. Here we show that the LSD1/neuroLSD1 ratio changes in response to neuronal activation and such effect is mediated by neurospecific splicing factors NOVA1 and nSR100/SRRM4 together with a novel cis-silencer. Indeed, we found that, in response to epileptogenic stimuli, downregulation of NOVA1 reduces exon E8a splicing and expression of neuroLSD1. Using behavioral and EEG analyses we observed that neuroLSD1-specific null mice are hypoexcitable and display decreased seizure susceptibility. Conversely, in a mouse model of Rett syndrome characterized by hyperexcitability, we measured higher levels of NOVA1 protein and upregulation of neuroLSD1. In conclusion, we propose that, in the brain, correct ratio between LSD1 and neuroLSD1 contributes to excitability and, when altered, could represent a pathogenic event associated with neurological disorders involving altered E/I.
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Affiliation(s)
| | - Leda Paganini
- Department of Medical Biotechnology and Translational Medicine
| | - Daniela Braida
- Department of Medical Biotechnology and Translational Medicine
| | - Luisa Ponzoni
- Department of Medical Biotechnology and Translational Medicine
| | | | - Annalisa Maroli
- Department of Medical Biotechnology and Translational Medicine
| | - Nicoletta Landsberger
- Theoretical and Applied Sciences, Division of Biomedical Research, University of Insubria, Busto Arsizio 21052, Italy San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Francesco Bedogni
- San Raffaele Rett Research Center, Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università Degli Studi di Torino, Turin 10126, Italy
| | - Linda Pattini
- Dipartimento di Elettronica, Informazione e Bioingegneria-Politecnico di Milano, Milan, Italy
| | - Fiorella Altruda
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, Università Degli Studi di Torino, Turin 10126, Italy
| | - Silvia De Biasi
- Department of Biosciences, Università Degli Studi di Milano, Milan 20122, Italy
| | - Mariaelvina Sala
- Department of Medical Biotechnology and Translational Medicine CNR, Institute of Neuroscience, Milan, Italy
| | - Elena Battaglioli
- Department of Medical Biotechnology and Translational Medicine CNR, Institute of Neuroscience, Milan, Italy
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Moore M, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc 2014; 9:263-93. [PMID: 24407355 PMCID: PMC4156013 DOI: 10.1038/nprot.2014.012] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The identification of sites where RNA-binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV cross-linking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high-throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide maps of RNA binding with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. The application of CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of cross-link-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes ∼8 d to prepare RNA for sequencing. Established pipelines for data analysis, including those for CIMS, take 3-4 d.
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Affiliation(s)
- Michael Moore
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
| | - Chaolin Zhang
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
| | - Emily Conn Gantman
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
| | - Aldo Mele
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
| | - Jennifer C. Darnell
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
| | - Robert B. Darnell
- Laboratory of Neuro-Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York 10065, USA
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45
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Di Liegro CM, Schiera G, Di Liegro I. Regulation of mRNA transport, localization and translation in the nervous system of mammals (Review). Int J Mol Med 2014; 33:747-62. [PMID: 24452120 PMCID: PMC3976132 DOI: 10.3892/ijmm.2014.1629] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 12/09/2013] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional control of mRNA trafficking and metabolism plays a critical role in the actualization and fine tuning of the genetic program of cells, both in development and in differentiated tissues. Cis-acting signals, responsible for post-transcriptional regulation, reside in the RNA message itself, usually in untranslated regions, 5′ or 3′ to the coding sequence, and are recognized by trans-acting factors: RNA-binding proteins (RBPs) and/or non-coding RNAs (ncRNAs). ncRNAs bind short mRNA sequences usually present in the 3′-untranslated (3′-UTR) region of their target messages. RBPs recognize specific nucleotide sequences and/or secondary/tertiary structures. Most RBPs assemble on mRNA at the moment of transcription and shepherd it to its destination, somehow determining its final fate. Regulation of mRNA localization and metabolism has a particularly important role in the nervous system where local translation of pre-localized mRNAs has been implicated in developing axon and dendrite pathfinding, and in synapse formation. Moreover, activity-dependent mRNA trafficking and local translation may underlie long-lasting changes in synaptic efficacy, responsible for learning and memory. This review focuses on the role of RBPs in neuronal development and plasticity, as well as possible connections between ncRNAs and RBPs.
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Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy
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Zhang Y, Cooke A, Park S, Dewey CN, Wickens M, Sheets MD. Bicaudal-C spatially controls translation of vertebrate maternal mRNAs. RNA (NEW YORK, N.Y.) 2013; 19:1575-82. [PMID: 24062572 PMCID: PMC3851724 DOI: 10.1261/rna.041665.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The Xenopus Cripto-1 protein is confined to the cells of the animal hemisphere during early embryogenesis where it regulates the formation of anterior structures. Cripto-1 protein accumulates only in animal cells because cripto-1 mRNA in cells of the vegetal hemisphere is translationally repressed. Here, we show that the RNA binding protein, Bicaudal-C (Bic-C), functioned directly in this vegetal cell-specific repression. While Bic-C protein is normally confined to vegetal cells, ectopic expression of Bic-C in animal cells repressed a cripto-1 mRNA reporter and associated with endogenous cripto-1 mRNA. Repression by Bic-C required its N-terminal domain, comprised of multiple KH motifs, for specific binding to relevant control elements within the cripto-1 mRNA and a functionally separable C-terminal translation repression domain. Bic-C-mediated repression required the 5' CAP and translation initiation factors, but not a poly(A) tail or the conserved SAM domain within Bic-C. Bic-C-directed immunoprecipitation followed by deep sequencing of associated mRNAs identified multiple Bic-C-regulated mRNA targets, including cripto-1 mRNA, providing new insights and tools for understanding the role of Bic-C in vertebrate development.
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Affiliation(s)
- Yan Zhang
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Amy Cooke
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Sookhee Park
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Colin N. Dewey
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Michael D. Sheets
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Corresponding authorE-mail
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Fernández E, Rajan N, Bagni C. The FMRP regulon: from targets to disease convergence. Front Neurosci 2013; 7:191. [PMID: 24167470 PMCID: PMC3807044 DOI: 10.3389/fnins.2013.00191] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/04/2013] [Indexed: 01/08/2023] Open
Abstract
The fragile X mental retardation protein (FMRP) is an RNA-binding protein that regulates mRNA metabolism. FMRP has been largely studied in the brain, where the absence of this protein leads to fragile X syndrome, the most frequent form of inherited intellectual disability. Since the identification of the FMRP gene in 1991, many studies have primarily focused on understanding the function/s of this protein. Hundreds of potential FMRP mRNA targets and several interacting proteins have been identified. Here, we report the identification of FMRP mRNA targets in the mammalian brain that support the key role of this protein during brain development and in regulating synaptic plasticity. We compared the genes from databases and genome-wide association studies with the brain FMRP transcriptome, and identified several FMRP mRNA targets associated with autism spectrum disorders, mood disorders and schizophrenia, showing a potential common pathway/s for these apparently different disorders.
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Affiliation(s)
- Esperanza Fernández
- Center for the Biology of Disease, Vlaams Institut voor Biotechnologie Leuven, Belgium ; Center for Human Genetics, Leuven Institute for Neuroscience and Disease, KU Leuven Leuven, Belgium
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Peng DX, Kelley RG, Quintin EM, Raman M, Thompson PM, Reiss AL. Cognitive and behavioral correlates of caudate subregion shape variation in fragile X syndrome. Hum Brain Mapp 2013; 35:2861-8. [PMID: 24038999 DOI: 10.1002/hbm.22376] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/16/2013] [Accepted: 07/10/2013] [Indexed: 11/10/2022] Open
Abstract
Individuals with fragile X syndrome (FXS) exhibit frontal lobe-associated cognitive and behavioral deficits, including impaired general cognitive abilities, perseverative behaviors, and social difficulties. Neural signals related to these functions are communicated through frontostriatal circuits, which connect with distinct regions of the caudate nucleus (CN). Enlargement of the CN is the most robust and reproduced neuroanatomical abnormality in FXS, but very little is known on how this affects behavioral/cognitive outcomes in this condition. Here, we investigated topography within focal regions of the CN associated with prefrontal circuitry and its link with aberrant behavior and intellect in FXS. Imaging data were acquired from 48 individuals with FXS, 28 IQ-matched controls without FXS (IQ-CTL), and 36 typically developing controls (TD-CTL). Of the total participant count, cognitive and behavioral assessment data were obtained from 44 individuals with FXS and 27 participants in the IQ-CTL group. CN volume and topography were compared between groups. Correlations were performed between CN topography and cognitive as well as behavioral measures within FXS and IQ-CTL groups. As expected, the FXS group had larger CN compared with both IQ-CTL and TD-CTL groups. Correlations between focal CN topography and frontal lobe-associated cognitive and behavioral deficits in the FXS group supported the hypothesis that CN enlargement is related to abnormal orbitofrontal-caudate and dorsolateral-caudate circuitry in FXS. These findings deepen our understanding of neuroanatomical mechanisms underlying cognitive-behavioral problems in FXS and hold promise for informing future behavioral and psychopharmacological interventions targeting specific neural pathways.
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Affiliation(s)
- Daniel X Peng
- Center for Interdisciplinary Brain Sciences Research (CIBSR), Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California
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Abstract
Neurons have their own systems for regulating RNA. Several multigene families encode RNA binding proteins (RNABPs) that are uniquely expressed in neurons, including the well-known neuron-specific markers ELAV and NeuN and the disease antigen NOVA. New technologies have emerged in recent years to assess the function of these proteins in vivo, and the answers are yielding insights into how and why neurons may regulate RNA in special ways-to increase cellular complexity, to localize messenger RNA (mRNA) spatially, and to regulate their expression in response to synaptic stimuli. The functions of such restricted neuronal proteins are likely to be complemented by more widely expressed RNABPs that may themselves have developed specialized functions in neurons, including Argonaute/microRNAs (miRNAs). Here we review what is known about such RNABPs and explore the potential biologic and neurologic significance of neuronal RNA regulatory systems.
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Affiliation(s)
- Robert B Darnell
- Department of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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Drosophila ORB protein in two mushroom body output neurons is necessary for long-term memory formation. Proc Natl Acad Sci U S A 2013; 110:7898-903. [PMID: 23610406 DOI: 10.1073/pnas.1216336110] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Memory is initially labile and gradually consolidated over time through new protein synthesis into a long-lasting stable form. Studies of odor-shock associative learning in Drosophila have established the mushroom body (MB) as a key brain structure involved in olfactory long-term memory (LTM) formation. Exactly how early neural activity encoded in thousands of MB neurons is consolidated into protein-synthesis-dependent LTM remains unclear. Here, several independent lines of evidence indicate that changes in two MB vertical lobe V3 (MB-V3) extrinsic neurons are required and contribute to an extended neural network involved in olfactory LTM: (i) inhibiting protein synthesis in MB-V3 neurons impairs LTM; (ii) MB-V3 neurons show enhanced neural activity after spaced but not massed training; (iii) MB-V3 dendrites, synapsing with hundreds of MB α/β neurons, exhibit dramatic structural plasticity after removal of olfactory inputs; (iv) neurotransmission from MB-V3 neurons is necessary for LTM retrieval; and (v) RNAi-mediated down-regulation of oo18 RNA-binding protein (involved in local regulation of protein translation) in MB-V3 neurons impairs LTM. Our results suggest a model of long-term memory formation that includes a systems-level consolidation process, wherein an early, labile olfactory memory represented by neural activity in a sparse subset of MB neurons is converted into a stable LTM through protein synthesis in dendrites of MB-V3 neurons synapsed onto MB α lobes.
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