1
|
Smukowski SN, Danyko C, Somberg J, Kaufman EJ, Course MM, Postupna N, Barker-Haliski M, Keene CD, Valdmanis PN. mRNA and circRNA mislocalization to synapses are key features of Alzheimer's disease. PLoS Genet 2024; 20:e1011359. [PMID: 39074152 PMCID: PMC11309398 DOI: 10.1371/journal.pgen.1011359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/08/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Proper transport of RNAs to synapses is essential for localized translation of proteins in response to synaptic signals and synaptic plasticity. Alzheimer's disease (AD) is a neurodegenerative disease characterized by accumulation of amyloid aggregates and hyperphosphorylated tau neurofibrillary tangles followed by widespread synapse loss. To understand whether RNA synaptic localization is impacted in AD, we performed RNA sequencing on synaptosomes and brain homogenates from AD patients and cognitively healthy controls. This resulted in the discovery of hundreds of mislocalized mRNAs in AD among frontal and temporal brain regions. Similar observations were found in an APPswe/PSEN1dE9 mouse model. Furthermore, major differences were observed among circular RNAs (circRNAs) localized to synapses in AD including two overlapping isoforms of circGSK3β, one upregulated, and one downregulated. Expression of these distinct isoforms affected tau phosphorylation in neuronal cells substantiating the importance of circRNAs in the brain and pointing to a new class of therapeutic targets.
Collapse
Affiliation(s)
- Samuel N. Smukowski
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Cassidy Danyko
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Fred Hutch Cancer Center, Basic Sciences Division, University of Washington, Seattle, Washington, United States of America
| | - Jenna Somberg
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Eli J. Kaufman
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Meredith M. Course
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Molecular Biology, Colorado College, Colorado Springs, Colorado, United States of America
| | - Nadia Postupna
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Melissa Barker-Haliski
- Department of Pharmacy, University of Washington School of Pharmacy, Seattle, Washington, United States of America
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Paul N. Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| |
Collapse
|
2
|
Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. Genes Dev 2024; 38:294-307. [PMID: 38688681 PMCID: PMC11146593 DOI: 10.1101/gad.351557.124] [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: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 using antisense oligonucleotides (ASOs) stimulates the expression of particular pre- and postsynaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized in puncta of both axons and dendrites that costain with Staufen1 protein, similar to neuronal RNA granules formed by locally translated mRNAs. Ribosome profiling of cultured mouse cortical neurons identified ribosome footprints within a 5' region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP-coding sequence in mouse embryonic stem cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wild-type neurons and showed that M1 expression was enhanced by synaptic stimulation with KCl. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
Collapse
Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA;
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| |
Collapse
|
3
|
Zhukova M, Schedl P, Shidlovskii YV. The role of secondary structures in the functioning of 3' untranslated regions of mRNA: A review of functions of 3' UTRs' secondary structures and hypothetical involvement of secondary structures in cytoplasmic polyadenylation in Drosophila. Bioessays 2024; 46:e2300099. [PMID: 38161240 PMCID: PMC11337203 DOI: 10.1002/bies.202300099] [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: 06/07/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
3' untranslated regions (3' UTRs) of mRNAs have many functions, including mRNA processing and transport, translational regulation, and mRNA degradation and stability. These different functions require cis-elements in 3' UTRs that can be either sequence motifs or RNA structures. Here we review the role of secondary structures in the functioning of 3' UTRs and discuss some of the trans-acting factors that interact with these secondary structures in eukaryotic organisms. We propose potential participation of 3'-UTR secondary structures in cytoplasmic polyadenylation in the model organism Drosophila melanogaster. Because the secondary structures of 3' UTRs are essential for post-transcriptional regulation of gene expression, their disruption leads to a wide range of disorders, including cancer and cardiovascular diseases. Trans-acting factors, such as STAU1 and nucleolin, which interact with 3'-UTR secondary structures of target transcripts, influence the pathogenesis of neurodegenerative diseases and tumor metastasis, suggesting that they are possible therapeutic targets.
Collapse
Affiliation(s)
- Mariya Zhukova
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Yulii V. Shidlovskii
- Laboratory of Gene Expression Regulation in Development, Russian Academy of Sciences, Institute of Gene Biology, Moscow, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| |
Collapse
|
4
|
Beletskiy A, Zolotar A, Fortygina P, Chesnokova E, Uroshlev L, Balaban P, Kolosov P. Downregulation of Ribosomal Protein Genes Is Revealed in a Model of Rat Hippocampal Neuronal Culture Activation with GABA(A)R/GlyRa2 Antagonist Picrotoxin. Cells 2024; 13:383. [PMID: 38474347 DOI: 10.3390/cells13050383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Long-read transcriptome sequencing provides us with a convenient tool for the thorough study of biological processes such as neuronal plasticity. Here, we aimed to perform transcriptional profiling of rat hippocampal primary neuron cultures after stimulation with picrotoxin (PTX) to further understand molecular mechanisms of neuronal activation. To overcome the limitations of short-read RNA-Seq approaches, we performed an Oxford Nanopore Technologies MinION-based long-read sequencing and transcriptome assembly of rat primary hippocampal culture mRNA at three time points after the PTX activation. We used a specific approach to exclude uncapped mRNAs during sample preparation. Overall, we found 23,652 novel transcripts in comparison to reference annotations, out of which ~6000 were entirely novel and mostly transposon-derived loci. Analysis of differentially expressed genes (DEG) showed that 3046 genes were differentially expressed, of which 2037 were upregulated and 1009 were downregulated at 30 min after the PTX application, with only 446 and 13 genes differentially expressed at 1 h and 5 h time points, respectively. Most notably, multiple genes encoding ribosomal proteins, with a high basal expression level, were downregulated after 30 min incubation with PTX; we suggest that this indicates redistribution of transcriptional resources towards activity-induced genes. Novel loci and isoforms observed in this study may help us further understand the functional mRNA repertoire in neuronal plasticity processes. Together with other NGS techniques, differential gene expression analysis of sequencing data obtained using MinION platform might provide a simple method to optimize further study of neuronal plasticity.
Collapse
Affiliation(s)
- Alexander Beletskiy
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Anastasia Zolotar
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Polina Fortygina
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Ekaterina Chesnokova
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Leonid Uroshlev
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Pavel Balaban
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
| | - Peter Kolosov
- Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia
- Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
5
|
Welle TM, Rajgor D, Garcia JD, Kareemo D, Zych SM, Gookin SE, Martinez TP, Dell’Acqua ML, Ford CP, Kennedy MJ, Smith KR. miRNA-mediated control of gephyrin synthesis drives sustained inhibitory synaptic plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.570420. [PMID: 38168421 PMCID: PMC10760056 DOI: 10.1101/2023.12.12.570420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Activity-dependent protein synthesis is crucial for many long-lasting forms of synaptic plasticity. However, our understanding of the translational mechanisms controlling inhibitory synapses is limited. One distinct form of inhibitory long-term potentiation (iLTP) enhances postsynaptic clusters of GABAARs and the primary inhibitory scaffold, gephyrin, to promote sustained synaptic strengthening. While we previously found that persistent iLTP requires mRNA translation, the precise mechanisms controlling gephyrin translation during this process remain unknown. Here, we identify miR153 as a novel regulator of Gphn mRNA translation which controls gephyrin protein levels and synaptic clustering, ultimately impacting GABAergic synaptic structure and function. We find that iLTP induction downregulates miR153, reversing its translational suppression of Gphn mRNA and allowing for increased de novo gephyrin protein synthesis and synaptic clustering during iLTP. Finally, we find that reduced miR153 expression during iLTP is driven by an excitation-transcription coupling pathway involving calcineurin, NFAT and HDACs, which also controls the miRNA-dependent upregulation of GABAARs. Overall, this work delineates a miRNA-dependent post-transcriptional mechanism that controls the expression of the key synaptic scaffold, gephyrin, and may converge with parallel miRNA pathways to coordinate gene upregulation to maintain inhibitory synaptic plasticity.
Collapse
Affiliation(s)
- Theresa M. Welle
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
- T.M.W and D.R. contributed equally to this work
| | - Dipen Rajgor
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
- T.M.W and D.R. contributed equally to this work
| | - Joshua D. Garcia
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Dean Kareemo
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Sarah M. Zych
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Sara E. Gookin
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Tyler P. Martinez
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Mark L. Dell’Acqua
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Christopher P. Ford
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Matthew J. Kennedy
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| | - Katharine R. Smith
- Department of Pharmacology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045
| |
Collapse
|
6
|
Liau WS, Zhao Q, Bademosi A, Gormal RS, Gong H, Marshall PR, Periyakaruppiah A, Madugalle SU, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove M, Davies J, Rauch S, He C, Dickinson BC, Li X, Wei W, Meunier FA, Fernández-Moya SM, Kiebler MA, Srinivasan B, Banerjee S, Clark M, Spitale RC, Bredy TW. Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nat Commun 2023; 14:7616. [PMID: 37993455 PMCID: PMC10665438 DOI: 10.1038/s41467-023-43535-1] [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: 02/24/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a specific set of lncRNAs that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these was a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single-molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.
Collapse
Affiliation(s)
- Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Adekunle Bademosi
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Rachel S Gormal
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Frédéric A Meunier
- Single Molecule Neuroscience Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Sandra M Fernández-Moya
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, 08908, Barcelona, Spain
| | - Michael A Kiebler
- Biomedical Centre, Ludwig Maximilian University of Munich, Munich, Germany
| | | | | | - Michael Clark
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, The University of California, Irvine, CA, USA
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
7
|
Larue GE, Roy SW. Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution. Nucleic Acids Res 2023; 51:10884-10908. [PMID: 37819006 PMCID: PMC10639083 DOI: 10.1093/nar/gkad797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Spliceosomal introns are gene segments removed from RNA transcripts by ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second 'minor' spliceosome is responsible for processing a tiny minority of introns. Despite its seemingly modest role, minor splicing has persisted for roughly 1.5 billion years of eukaryotic evolution. Identifying minor introns in over 3000 eukaryotic genomes, we report diverse evolutionary histories including surprisingly high numbers in some fungi and green algae, repeated loss, as well as general biases in their positional and genic distributions. We estimate that ancestral minor intron densities were comparable to those of vertebrates, suggesting a trend of long-term stasis. Finally, three findings suggest a major role for neutral processes in minor intron evolution. First, highly similar patterns of minor and major intron evolution contrast with both functionalist and deleterious model predictions. Second, observed functional biases among minor intron-containing genes are largely explained by these genes' greater ages. Third, no association of intron splicing with cell proliferation in a minor intron-rich fungus suggests that regulatory roles are lineage-specific and thus cannot offer a general explanation for minor splicing's persistence. These data constitute the most comprehensive view of minor introns and their evolutionary history to date, and provide a foundation for future studies of these remarkable genetic elements.
Collapse
Affiliation(s)
- Graham E Larue
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Scott W Roy
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA 95343, USA
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| |
Collapse
|
8
|
Madugalle SU, Liau WS, Zhao Q, Li X, Gong H, Marshall PR, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove MRB, Davies JWA, Kim G, Rauch S, He C, Dickinson BC, Fulopova B, Fletcher LN, Williams SR, Spitale RC, Bredy TW. Synapse-Enriched m 6A-Modified Malat1 Interacts with the Novel m 6A Reader, DPYSL2, and Is Required for Fear-Extinction Memory. J Neurosci 2023; 43:7084-7100. [PMID: 37669863 PMCID: PMC10601377 DOI: 10.1523/jneurosci.0943-23.2023] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
The RNA modification N6-methyladenosine (m6A) regulates the interaction between RNA and various RNA binding proteins within the nucleus and other subcellular compartments and has recently been shown to be involved in experience-dependent plasticity, learning, and memory. Using m6A RNA-sequencing, we have discovered a distinct population of learning-related m6A- modified RNAs at the synapse, which includes the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (Malat1). RNA immunoprecipitation and mass spectrometry revealed 12 new synapse-specific learning-induced m6A readers in the mPFC of male C57/BL6 mice, with m6A-modified Malat1 binding to a subset of these, including CYFIP2 and DPYSL2. In addition, a cell type- and synapse-specific, and state-dependent, reduction of m6A on Malat1 impairs fear-extinction memory; an effect that likely occurs through a disruption in the interaction between Malat1 and DPYSL2 and an associated decrease in dendritic spine formation. These findings highlight the critical role of m6A in regulating the functional state of RNA during the consolidation of fear-extinction memory, and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.SIGNIFICANCE STATEMENT We have discovered that learning-induced m6A-modified RNA (including the long noncoding RNA, Malat1) accumulates in the synaptic compartment. We have identified several new m6A readers that are associated with fear extinction learning and demonstrate a causal relationship between m6A-modified Malat1 and the formation of fear-extinction memory. These findings highlight the role of m6A in regulating the functional state of an RNA during memory formation and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.
Collapse
Affiliation(s)
| | - Wei-Siang Liau
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Qiongyi Zhao
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China 430071
- Medical Research Institute, Wuhan University, Wuhan, China 430014
| | - Hao Gong
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Paul R Marshall
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Ambika Periyakaruppiah
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Esmi L Zajaczkowski
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Laura J Leighton
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Haobin Ren
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Mason R B Musgrove
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Joshua W A Davies
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Gwangmin Kim
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Bryan C Dickinson
- Department of Chemistry, University of Chicago, Chicago, Illinois 60607
| | - Barbora Fulopova
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Lee N Fletcher
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Stephen R Williams
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia 4072
| |
Collapse
|
9
|
Borg R, Herrera P, Purkiss A, Cacciottolo R, Cauchi RJ. Reduced levels of ALS gene DCTN1 induce motor defects in Drosophila. Front Neurosci 2023; 17:1164251. [PMID: 37360176 PMCID: PMC10289029 DOI: 10.3389/fnins.2023.1164251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neuromuscular disease that has a strong genetic component. Deleterious variants in the DCTN1 gene are known to be a cause of ALS in diverse populations. DCTN1 encodes the p150 subunit of the molecular motor dynactin which is a key player in the bidirectional transport of cargos within cells. Whether DCTN1 mutations lead to the disease through either a gain or loss of function mechanism remains unresolved. Moreover, the contribution of non-neuronal cell types, especially muscle tissue, to ALS phenotypes in DCTN1 carriers is unknown. Here we show that gene silencing of Dctn1, the Drosophila main orthologue of DCTN1, either in neurons or muscles is sufficient to cause climbing and flight defects in adult flies. We also identify Dred, a protein with high homology to Drosophila Dctn1 and human DCTN1, that on loss of function also leads to motoric impairments. A global reduction of Dctn1 induced a significant reduction in the mobility of larvae and neuromuscular junction (NMJ) deficits prior to death at the pupal stage. RNA-seq and transcriptome profiling revealed splicing alterations in genes required for synapse organisation and function, which may explain the observed motor dysfunction and synaptic defects downstream of Dctn1 ablation. Our findings support the possibility that loss of DCTN1 function can lead to ALS and underscore an important requirement for DCTN1 in muscle in addition to neurons.
Collapse
Affiliation(s)
- Rebecca Borg
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Paul Herrera
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Angie Purkiss
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Rebecca Cacciottolo
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Ruben J. Cauchi
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, Msida, Malta
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| |
Collapse
|
10
|
Lau Zajaczkowski E, Zhao Q, Liau WS, Gong H, Umanda Madugalle S, Periyakaruppiah A, Jane Leighton L, Musgrove M, Ren H, Davies J, Robert Marshall P, William Bredy T. Localised Cdr1as activity is required for fear extinction memory. Neurobiol Learn Mem 2023:107777. [PMID: 37257557 DOI: 10.1016/j.nlm.2023.107777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Circular RNAs (circRNAs) comprise a novel class of regulatory RNAs that are abundant in the brain, particularly within synapses. They are highly stable, dynamically regulated, and display a range of functions, including serving as decoys for microRNAs and proteins and, in some cases, circRNAs also undergo translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, little is known about the link between circRNA function and memory. To address this, we examined circRNA in synaptosomes derived from the medial prefrontal cortex of fear extinction-trained male C57BL/6J mice and found 12837 circRNAs that were enriched at the synapse, including cerebellar degeneration-related protein 1 antisense RNA (Cdr1as). Targeted knockdown of Cdr1as in the neural processes of the infralimbic cortex led to impaired fear extinction memory. These findings highlight the involvement of localised circRNA activity at the synapse in memory formation.
Collapse
Affiliation(s)
- Esmi Lau Zajaczkowski
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Qiongyi Zhao
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Wei-Siang Liau
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Hao Gong
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Ambika Periyakaruppiah
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Laura Jane Leighton
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mason Musgrove
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Haobin Ren
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Joshua Davies
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul Robert Marshall
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia; Genome Sciences and Cancer Division & Eccles Institute of Neuroscience, Australian National University, Canberra, Australia.
| | - Timothy William Bredy
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.
| |
Collapse
|
11
|
Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
Collapse
Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
| |
Collapse
|
12
|
Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [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: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
Collapse
Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| |
Collapse
|
13
|
APC couples neuronal mRNAs to multiple kinesins, EB1, and shrinking microtubule ends for bidirectional mRNA motility. Proc Natl Acad Sci U S A 2022; 119:e2211536119. [PMID: 36469763 PMCID: PMC9897468 DOI: 10.1073/pnas.2211536119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding where in the cytoplasm mRNAs are translated is increasingly recognized as being as important as knowing the timing and level of protein expression. mRNAs are localized via active motor-driven transport along microtubules (MTs) but the underlying essential factors and dynamic interactions are largely unknown. Using biochemical in vitro reconstitutions with purified mammalian proteins, multicolor TIRF-microscopy, and interaction kinetics measurements, we show that adenomatous polyposis coli (APC) enables kinesin-1- and kinesin-2-based mRNA transport, and that APC is an ideal adaptor for long-range mRNA transport as it forms highly stable complexes with 3'UTR fragments of several neuronal mRNAs (APC-RNPs). The kinesin-1 KIF5A binds and transports several neuronal mRNP components such as FMRP, PURα and mRNA fragments weakly, whereas the transport frequency of the mRNA fragments is significantly increased by APC. APC-RNP-motor complexes can assemble on MTs, generating highly processive mRNA transport events. We further find that end-binding protein 1 (EB1) recruits APC-RNPs to dynamically growing MT ends and APC-RNPs track shrinking MTs, producing MT minus-end-directed RNA motility due to the high dwell times of APC on MTs. Our findings establish APC as a versatile mRNA-kinesin adaptor and a key factor for the assembly and bidirectional movement of neuronal transport mRNPs.
Collapse
|
14
|
Nikolaou N, Gordon PM, Hamid F, Taylor R, Lloyd-Jones J, Makeyev EV, Houart C. Cytoplasmic pool of U1 spliceosome protein SNRNP70 shapes the axonal transcriptome and regulates motor connectivity. Curr Biol 2022; 32:5099-5115.e8. [PMID: 36384140 DOI: 10.1016/j.cub.2022.10.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 09/09/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022]
Abstract
Regulation of pre-mRNA splicing and polyadenylation plays a profound role in neurons by diversifying the proteome and modulating gene expression in response to physiological cues. Although most of the pre-mRNA processing is thought to occur in the nucleus, numerous splicing regulators are also found in neurites. Here, we show that U1-70K/SNRNP70, a component of the major spliceosome, localizes in RNA-associated granules in zebrafish axons. We identify the extra-nuclear SNRNP70 as an important regulator of motor axonal growth, nerve-dependent acetylcholine receptor (AChR) clustering, and neuromuscular synaptogenesis. This cytoplasmic pool has a protective role for a limited number of transcripts regulating their abundance and trafficking inside axons. Moreover, non-nuclear SNRNP70 regulates splice variants of transcripts such as agrin, thereby controlling synapse formation. Our results point to an unexpected, yet essential, function of non-nuclear SNRNP70 in axonal development, indicating a role of spliceosome proteins in cytoplasmic RNA metabolism during neuronal connectivity.
Collapse
Affiliation(s)
- Nikolas Nikolaou
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK; Department of Life Sciences, University of Bath, Bath BA2 7AY, UK.
| | - Patricia M Gordon
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | | | - Eugene V Makeyev
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
| |
Collapse
|
15
|
Kiebler MA, Ninkovic J. RNA biology: Alternative splicing hits synaptic function and behavior. Curr Biol 2022; 32:R1314-R1316. [PMID: 36473442 DOI: 10.1016/j.cub.2022.10.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A new study finds the spliceosome protein SNRNP70 in cytoplasmic RNA granules in zebrafish motoneurons. Intriguingly, cytoplasmic SNRNP70 is essential for functional neuromuscular junctions, possibly due to a role in alternative splicing of z+agrin mRNA.
Collapse
Affiliation(s)
- Michael A Kiebler
- Department of Anatomy and Cell Biology, Biomedical Center Munich (BMC), Faculty of Medicine, LMU, Munich, Germany.
| | - Jovica Ninkovic
- Department of Anatomy and Cell Biology, Biomedical Center Munich (BMC), Faculty of Medicine, LMU, Munich, Germany; Institute of Stem Cell Research, Helmholtz Zentrum Munich, Munich, Germany
| |
Collapse
|
16
|
Di Liegro CM, Schiera G, Schirò G, Di Liegro I. RNA-Binding Proteins as Epigenetic Regulators of Brain Functions and Their Involvement in Neurodegeneration. Int J Mol Sci 2022; 23:ijms232314622. [PMID: 36498959 PMCID: PMC9739182 DOI: 10.3390/ijms232314622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
A central aspect of nervous system development and function is the post-transcriptional regulation of mRNA fate, which implies time- and site-dependent translation, in response to cues originating from cell-to-cell crosstalk. Such events are fundamental for the establishment of brain cell asymmetry, as well as of long-lasting modifications of synapses (long-term potentiation: LTP), responsible for learning, memory, and higher cognitive functions. Post-transcriptional regulation is in turn dependent on RNA-binding proteins that, by recognizing and binding brief RNA sequences, base modifications, or secondary/tertiary structures, are able to control maturation, localization, stability, and translation of the transcripts. Notably, most RBPs contain intrinsically disordered regions (IDRs) that are thought to be involved in the formation of membrane-less structures, probably due to liquid-liquid phase separation (LLPS). Such structures are evidenced as a variety of granules that contain proteins and different classes of RNAs. The other side of the peculiar properties of IDRs is, however, that, under altered cellular conditions, they are also prone to form aggregates, as observed in neurodegeneration. Interestingly, RBPs, as part of both normal and aggregated complexes, are also able to enter extracellular vesicles (EVs), and in doing so, they can also reach cells other than those that produced them.
Collapse
Affiliation(s)
- Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy
| | - Giuseppe Schirò
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica Avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
- Correspondence: ; Tel.: +39-091-238-97 (ext. 415/446)
| |
Collapse
|
17
|
Munk M, Villalobo E, Villalobo A, Berchtold MW. Differential expression of the three independent CaM genes coding for an identical protein: Potential relevance of distinct mRNA stability by different codon usage. Cell Calcium 2022; 107:102656. [DOI: 10.1016/j.ceca.2022.102656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/25/2022] [Indexed: 11/24/2022]
|
18
|
Petrić Howe M, Crerar H, Neeves J, Harley J, Tyzack GE, Klein P, Ramos A, Patani R, Luisier R. Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis. Genome Res 2022; 32:1808-1825. [PMID: 36180233 PMCID: PMC9712626 DOI: 10.1101/gr.276898.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/16/2022] [Indexed: 11/24/2022]
Abstract
Intron retention (IR) is now recognized as a dominant splicing event during motor neuron (MN) development; however, the role and regulation of intron-retaining transcripts (IRTs) localized to the cytoplasm remain particularly understudied. Here we show that IR is a physiological process that is spatiotemporally regulated during MN lineage restriction and that IRTs in the cytoplasm are detected in as many as 13% (n = 2297) of the genes expressed during this process. We identify a major class of cytoplasmic IRTs that are not associated with reduced expression of their own genes but instead show a high capacity for RNA-binding protein and miRNA occupancy. Finally, we show that ALS-causing VCP mutations lead to a selective increase in cytoplasmic abundance of this particular class of IRTs, which in turn temporally coincides with an increase in the nuclear expression level of predicted miRNA target genes. Altogether, our study identifies a previously unrecognized class of cytoplasmic intronic sequences with potential regulatory function beyond gene expression.
Collapse
Affiliation(s)
- Marija Petrić Howe
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Hamish Crerar
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Jacob Neeves
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Jasmine Harley
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Giulia E Tyzack
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Pierre Klein
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6XA, United Kingdom
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, London WC1E 6XA, United Kingdom
| | - Rickie Patani
- The Francis Crick Institute, London NW1 1AT, United Kingdom
- Department of Molecular Neuroscience, UCL Institute of Neurology, London WC1N 3AR, United Kingdom
| | - Raphaëlle Luisier
- Idiap Research Institute, Genomics and Health Informatics, CH-1920 Martigny, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| |
Collapse
|
19
|
Grzejda D, Mach J, Schweizer JA, Hummel B, Rezansoff AM, Eggenhofer F, Panhale A, Lalioti ME, Cabezas Wallscheid N, Backofen R, Felsenberg J, Hilgers V. The long noncoding RNA mimi scaffolds neuronal granules to maintain nervous system maturity. SCIENCE ADVANCES 2022; 8:eabo5578. [PMID: 36170367 PMCID: PMC9519039 DOI: 10.1126/sciadv.abo5578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/15/2022] [Indexed: 05/29/2023]
Abstract
RNA binding proteins and messenger RNAs (mRNAs) assemble into ribonucleoprotein granules that regulate mRNA trafficking, local translation, and turnover. The dysregulation of RNA-protein condensation disturbs synaptic plasticity and neuron survival and has been widely associated with human neurological disease. Neuronal granules are thought to condense around particular proteins that dictate the identity and composition of each granule type. Here, we show in Drosophila that a previously uncharacterized long noncoding RNA, mimi, is required to scaffold large neuronal granules in the adult nervous system. Neuronal ELAV-like proteins directly bind mimi and mediate granule assembly, while Staufen maintains condensate integrity. mimi granules contain mRNAs and proteins involved in synaptic processes; granule loss in mimi mutant flies impairs nervous system maturity and neuropeptide-mediated signaling and causes phenotypes of neurodegeneration. Our work reports an architectural RNA for a neuronal granule and provides a handle to interrogate functions of a condensate independently of those of its constituent proteins.
Collapse
Affiliation(s)
- Dominika Grzejda
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg 79104, Germany
- International Max Planck Research School for Molecular and Cellular Biology (IMPRS- MCB), Freiburg 79108, Germany
| | - Jana Mach
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Johanna Aurelia Schweizer
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel 4058, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Barbara Hummel
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Florian Eggenhofer
- Department of Computer Science, Albert Ludwig University of Freiburg, Freiburg 79110, Germany
| | - Amol Panhale
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Maria-Eleni Lalioti
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | - Rolf Backofen
- Department of Computer Science, Albert Ludwig University of Freiburg, Freiburg 79110, Germany
- BIOSS and CIBSS Centres for Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Johannes Felsenberg
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel 4058, Switzerland
| | - Valérie Hilgers
- Max-Planck-Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| |
Collapse
|
20
|
Mazille M, Buczak K, Scheiffele P, Mauger O. Stimulus-specific remodeling of the neuronal transcriptome through nuclear intron-retaining transcripts. EMBO J 2022; 41:e110192. [PMID: 36149731 DOI: 10.15252/embj.2021110192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 08/20/2022] [Accepted: 08/30/2022] [Indexed: 11/09/2022] Open
Abstract
The nuclear envelope has long been considered primarily a physical barrier separating nuclear and cytosolic contents. More recently, nuclear compartmentalization has been shown to have additional regulatory functions in controlling gene expression. A sizeable proportion of protein-coding mRNAs is more prevalent in the nucleus than in the cytosol, suggesting regulated mRNA trafficking to the cytosol, but the mechanisms underlying controlled nuclear mRNA retention remain unclear. Here, we provide a comprehensive map of the subcellular localization of mRNAs in mature mouse cortical neurons, and reveal that transcripts retained in the nucleus comprise the majority of stable intron-retaining mRNAs. Systematically probing the fate of nuclear transcripts upon neuronal stimulation, we found opposite effects on sub-populations of transcripts: while some are targeted for degradation, others complete splicing to generate fully mature mRNAs that are exported to the cytosol and mediate rapid increases in protein levels. Finally, different forms of stimulation mobilize distinct groups of intron-retaining transcripts, with this selectivity arising from the activation of specific signaling pathways. Overall, our findings uncover a cue-specific control of intron retention as a major regulator of acute remodeling of the neuronal transcriptome.
Collapse
Affiliation(s)
- Maxime Mazille
- Biozentrum of the University of Basel, Basel, Switzerland
| | | | | | - Oriane Mauger
- Biozentrum of the University of Basel, Basel, Switzerland
| |
Collapse
|
21
|
3’UTR-Seq analysis of chicken abdominal adipose tissue reveals widespread intron retention in 3’UTR and provides insight into molecular basis of feed efficiency. PLoS One 2022; 17:e0269534. [PMID: 35776773 PMCID: PMC9249230 DOI: 10.1371/journal.pone.0269534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Feed efficiency (FE) is an important trait in the broiler industry due to its direct correlation to efficient muscle growth instead of fat deposition. The present study characterized and compared gene expression profiles in abdominal fat from broiler chickens of different FE levels to enhance the understanding of FE biology. Specifically, traditional whole-transcript RNA-sequencing (RNA-seq) and 3’ UTR-sequencing (3’ UTR-seq) were applied to 22 and 61 samples, respectively. Overall, these two sequencing techniques shared a high correlation (0.76) between normalized counts, although 3’ UTR-seq showed a higher variance in sequencing and mapping performance statistics across samples and a lower rate of uniquely mapped reads. A higher percentage of 3’ UTR-seq reads mapped to introns suggested the frequent presence of cleavage sites in introns, thus warranting future research to study its regulatory function. Differential expression analysis identified 1198 differentially expressed genes (DEGs) between high FE (HFE) and intermediate FE (IFE) chickens with False Discovery Rate < 0.05 and fold change > 1.2. The processes that were significantly enriched by the DEGs included extracellular matrix remodeling and mechanisms impacting gene expression at the transcriptional and translational levels. Gene ontology enrichment analysis suggested that the divergence in fat deposition and FE in broiler chickens could be associated with peroxisome and lipid metabolism possibly regulated by G0/G1 switch gene 2 (G0S2).
Collapse
|
22
|
Ehses J, Schlegel M, Schröger L, Schieweck R, Derdak S, Bilban M, Bauer K, Harner M, Kiebler MA. The dsRBP Staufen2 governs RNP assembly of neuronal Argonaute proteins. Nucleic Acids Res 2022; 50:7034-7047. [PMID: 35687120 PMCID: PMC9262589 DOI: 10.1093/nar/gkac487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 05/10/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Mature microRNAs are bound by a member of the Argonaute (Ago1-4) protein family, forming the core of the RNA-induced silencing complex (RISC). Association of RISC with target mRNAs results in ribonucleoprotein (RNP) assembly involved in translational silencing or RNA degradation. Yet, the dynamics of RNP assembly and its underlying functional implications are unknown. Here, we have characterized the role of the RNA-binding protein Staufen2, a candidate Ago interactor, in RNP assembly. Staufen2 depletion resulted in the upregulation of Ago1/2 and the RISC effector proteins Ddx6 and Dcp1a. This upregulation was accompanied by the displacement of Ago1/2 from processing bodies, large RNPs implicated in RNA storage, and subsequent association of Ago2 with polysomes. In parallel, Staufen2 deficiency decreased global translation and increased dendritic branching. As the observed phenotypes can be rescued by Ago1/2 knockdown, we propose a working model in which both Staufen2 and Ago proteins depend on each other and contribute to neuronal homeostasis.
Collapse
Affiliation(s)
- Janina Ehses
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Melina Schlegel
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Luise Schröger
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Sophia Derdak
- Core Facilities, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University, of Vienna, 1090 Vienna, Austria
| | - Karl Bauer
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Max Harner
- Biomedical Center (BMC), Department for Cell Biology, Medical Faculty, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Michael A Kiebler
- To whom correspondence should be addressed. Tel: +49 89 2180 75884; Fax: +49 89 2180 75885;
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
RNA-binding protein dysfunction in neurodegeneration. Essays Biochem 2021; 65:975-986. [PMID: 34927200 DOI: 10.1042/ebc20210024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022]
Abstract
Protein homeostasis (proteostasis) is a prerequisite for cellular viability and plasticity. In particular, post-mitotic cells such as neurons rely on a tightly regulated safeguard system that allows for regulated protein expression. Previous investigations have identified RNA-binding proteins (RBPs) as crucial regulators of protein expression in nerve cells. However, during neurodegeneration, their ability to control the proteome is progressively disrupted. In this review, we examine the malfunction of key RBPs such as TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Staufen, Pumilio and fragile-X mental retardation protein (FMRP). Therefore, we focus on two key aspects of RBP dysfunctions in neurodegeneration: protein aggregation and dysregulation of their target RNAs. Moreover, we discuss how the chaperone system responds to changes in the RBP-controlled transcriptome. Based on recent findings, we propose a two-hit model in which both, harmful RBP deposits and target mRNA mistranslation contribute to neurodegeneration observed in RBPathologies.
Collapse
|
25
|
Landínez-Macías M, Urwyler O. The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System. Front Mol Neurosci 2021; 14:755686. [PMID: 34916907 PMCID: PMC8670310 DOI: 10.3389/fnmol.2021.755686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/18/2021] [Indexed: 01/25/2023] Open
Abstract
Neuronal morphogenesis, integration into circuits, and remodeling of synaptic connections occur in temporally and spatially defined steps. Accordingly, the expression of proteins and specific protein isoforms that contribute to these processes must be controlled quantitatively in time and space. A wide variety of post-transcriptional regulatory mechanisms, which act on pre-mRNA and mRNA molecules contribute to this control. They are thereby critically involved in physiological and pathophysiological nervous system development, function, and maintenance. Here, we review recent findings on how mRNA metabolism contributes to neuronal development, from neural stem cell maintenance to synapse specification, with a particular focus on axon growth, guidance, branching, and synapse formation. We emphasize the role of RNA-binding proteins, and highlight their emerging roles in the poorly understood molecular processes of RNA editing, alternative polyadenylation, and temporal control of splicing, while also discussing alternative splicing, RNA localization, and local translation. We illustrate with the example of the evolutionary conserved Musashi protein family how individual RNA-binding proteins are, on the one hand, acting in different processes of RNA metabolism, and, on the other hand, impacting multiple steps in neuronal development and circuit formation. Finally, we provide links to diseases that have been associated with the malfunction of RNA-binding proteins and disrupted post-transcriptional regulation.
Collapse
Affiliation(s)
- María Landínez-Macías
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Olivier Urwyler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| |
Collapse
|
26
|
RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons. Int J Mol Sci 2021; 22:ijms222313021. [PMID: 34884825 PMCID: PMC8657808 DOI: 10.3390/ijms222313021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/26/2022] Open
Abstract
RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3′-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.
Collapse
|
27
|
Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape. Biomedicines 2021; 9:biomedicines9111560. [PMID: 34829789 PMCID: PMC8615635 DOI: 10.3390/biomedicines9111560] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/10/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022] Open
Abstract
This paper concerns 3′-untranslated regions (3′UTRs) of mRNAs, which are non-coding regulatory platforms that control stability, fate and the correct spatiotemporal translation of mRNAs. Many mRNAs have polymorphic 3′UTR regions. Controlling 3′UTR length and sequence facilitates the regulation of the accessibility of functional effectors (RNA binding proteins, miRNAs or other ncRNAs) to 3′UTR functional boxes and motifs and the establishment of different regulatory landscapes for mRNA function. In this context, shortening of 3′UTRs would loosen miRNA or protein-based mechanisms of mRNA degradation, while 3′UTR lengthening would strengthen accessibility to these effectors. Alterations in the mechanisms regulating 3′UTR length would result in widespread deregulation of gene expression that could eventually lead to diseases likely linked to the loss (or acquisition) of specific miRNA binding sites. Here, we will review the mechanisms that control 3′UTR length dynamics and their alterations in human disorders. We will discuss, from a mechanistic point of view centered on the molecular machineries involved, the generation of 3′UTR variability by the use of alternative polyadenylation and cleavage sites, of mutually exclusive terminal alternative exons (exon skipping) as well as by the process of exonization of Alu cassettes to generate new 3′UTRs with differential functional features.
Collapse
|
28
|
Schieweck R, Schöneweiss EC, Harner M, Rieger D, Illig C, Saccà B, Popper B, Kiebler MA. Pumilio2 Promotes Growth of Mature Neurons. Int J Mol Sci 2021; 22:ijms22168998. [PMID: 34445704 PMCID: PMC8396670 DOI: 10.3390/ijms22168998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 01/05/2023] Open
Abstract
RNA-binding proteins (RBPs) are essential regulators controlling both the cellular transcriptome and translatome. These processes enable cellular plasticity, an important prerequisite for growth. Cellular growth is a complex, tightly controlled process. Using cancer cells as model, we looked for RBPs displaying strong expression in published transcriptome datasets. Interestingly, we found the Pumilio (Pum) protein family to be highly expressed in all these cells. Moreover, we observed that Pum2 is regulated by basic fibroblast growth factor (bFGF). bFGF selectively enhances protein levels of Pum2 and the eukaryotic initiation factor 4E (eIF4E). Exploiting atomic force microscopy and in vitro pulldown assays, we show that Pum2 selects for eIF4E mRNA binding. Loss of Pum2 reduces eIF4E translation. Accordingly, depletion of Pum2 led to decreased soma size and dendritic branching of mature neurons, which was accompanied by a reduction in essential growth factors. In conclusion, we identify Pum2 as an important growth factor for mature neurons. Consequently, it is tempting to speculate that Pum2 may promote cancer growth.
Collapse
Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
| | - Elisa-Charlott Schöneweiss
- Zentrum für Medizinische Biotechnologie (ZMB), University of Duisburg-Essen, 41541 Duisburg, Germany; (E.-C.S.); (B.S.)
| | - Max Harner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
| | - Daniela Rieger
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
| | - Christin Illig
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
| | - Barbara Saccà
- Zentrum für Medizinische Biotechnologie (ZMB), University of Duisburg-Essen, 41541 Duisburg, Germany; (E.-C.S.); (B.S.)
| | - Bastian Popper
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
- Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, 82152 München, Germany
- Correspondence: ; Tel.: +49-89-2180-71996
| | - Michael A. Kiebler
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 München, Germany; (R.S.); (M.H.); (D.R.); (C.I.); (M.A.K.)
| |
Collapse
|
29
|
Park J, Farris S. Spatiotemporal Regulation of Transcript Isoform Expression in the Hippocampus. Front Mol Neurosci 2021; 14:694234. [PMID: 34305526 PMCID: PMC8295539 DOI: 10.3389/fnmol.2021.694234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Proper development and plasticity of hippocampal neurons require specific RNA isoforms to be expressed in the right place at the right time. Precise spatiotemporal transcript regulation requires the incorporation of essential regulatory RNA sequences into expressed isoforms. In this review, we describe several RNA processing strategies utilized by hippocampal neurons to regulate the spatiotemporal expression of genes critical to development and plasticity. The works described here demonstrate how the hippocampus is an ideal investigative model for uncovering alternate isoform-specific mechanisms that restrict the expression of transcripts in space and time.
Collapse
Affiliation(s)
- Joun Park
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States
| | - Shannon Farris
- Fralin Biomedical Research Institute, Center for Neurobiology Research, Virginia Tech Carilion, Roanoke, VA, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| |
Collapse
|
30
|
Schieweck R, Riedemann T, Forné I, Harner M, Bauer KE, Rieger D, Ang FY, Hutten S, Demleitner AF, Popper B, Derdak S, Sutor B, Bilban M, Imhof A, Kiebler MA. Pumilio2 and Staufen2 selectively balance the synaptic proteome. Cell Rep 2021; 35:109279. [PMID: 34161769 DOI: 10.1016/j.celrep.2021.109279] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/05/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Neurons have the capacity to adapt to environmental stimuli, a phenomenon termed cellular plasticity. The underlying processes are controlled by a network of RNA-binding proteins (RBPs). Their precise impact, however, is largely unknown. To address this important question, we chose Pumilio2 (Pum2) and Staufen2 (Stau2), which both regulate synaptic transmission. Surprisingly, even though both RBPs dynamically interact with each other in neurons, their respective impact on the transcriptome and proteome is highly selective. Although Pum2 deficiency leads to reduced translation and protein expression, Stau2 depletion preferentially impacts RNA levels and increases protein abundance. Furthermore, we show that Pum2 activates expression of key GABAergic synaptic components, e.g., the GABAA receptor scaffold protein Gephyrin. Consequently, Pum2 depletion selectively reduced the amplitude of miniature inhibitory postsynaptic currents. Together, our data argue for an important role of RBPs to maintain proteostasis in order to control distinct aspects of synaptic transmission.
Collapse
Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Therese Riedemann
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center (BMC), Department for Molecular Biology (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Max Harner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Karl E Bauer
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Daniela Rieger
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Foong Yee Ang
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Saskia Hutten
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Antonia F Demleitner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Bastian Popper
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany; Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Sophia Derdak
- Medical University of Vienna, Core Facilities, Lazarettgasse 14, 1090 Vienna, Austria
| | - Bernd Sutor
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Martin Bilban
- Department of Laboratory Medicine and Core Facility Genomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Axel Imhof
- Biomedical Center (BMC), Department for Molecular Biology (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany.
| |
Collapse
|
31
|
Rodrigues EC, Grawenhoff J, Baumann SJ, Lorenzon N, Maurer SP. Mammalian Neuronal mRNA Transport Complexes: The Few Knowns and the Many Unknowns. Front Integr Neurosci 2021; 15:692948. [PMID: 34211375 PMCID: PMC8239176 DOI: 10.3389/fnint.2021.692948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized functions. According to current evidence, mRNAs are mostly transported in rather small packages of one to three copies, rarely containing different transcripts. This opens up fascinating logistic problems: how are hundreds of different mRNA cargoes sorted into distinct packages and how are they coupled to and released from motor proteins to produce the observed mRNA distributions? Are all mRNAs transported by the same transport machinery, or are there different adaptors or motors for different transcripts or classes of mRNAs? A variety of often indirect evidence exists for the involvement of proteins in mRNA localization, but relatively little is known about the essential activities required for the actual transport process. Here, we summarize the different types of available evidence for interactions that connect mammalian mRNAs to motor proteins to highlight at which point further research is needed to uncover critical missing links. We further argue that a combination of discovery approaches reporting direct interactions, in vitro reconstitution, and fast perturbations in cells is an ideal future strategy to unravel essential interactions and specific functions of proteins in mRNA transport processes.
Collapse
Affiliation(s)
- Elsa C. Rodrigues
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Julia Grawenhoff
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian J. Baumann
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Nicola Lorenzon
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Sebastian P. Maurer
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| |
Collapse
|
32
|
Díaz M, Mesa-Herrera F, Marín R. DHA and Its Elaborated Modulation of Antioxidant Defenses of the Brain: Implications in Aging and AD Neurodegeneration. Antioxidants (Basel) 2021; 10:antiox10060907. [PMID: 34205196 PMCID: PMC8228037 DOI: 10.3390/antiox10060907] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
DHA (docosahexaenoic acid) is perhaps the most pleiotropic molecule in nerve cell biology. This long-chain highly unsaturated fatty acid has evolved to accomplish essential functions ranging from structural components allowing fast events in nerve cell membrane physiology to regulation of neurogenesis and synaptic function. Strikingly, the plethora of DHA effects has to take place within the hostile pro-oxidant environment of the brain parenchyma, which might suggest a molecular suicide. In order to circumvent this paradox, different molecular strategies have evolved during the evolution of brain cells to preserve DHA and to minimize the deleterious effects of its oxidation. In this context, DHA has emerged as a member of the “indirect antioxidants” family, the redox effects of which are not due to direct redox interactions with reactive species, but to modulation of gene expression within thioredoxin and glutathione antioxidant systems and related pathways. Weakening or deregulation of these self-protecting defenses orchestrated by DHA is associated with normal aging but also, more worryingly, with the development of neurodegenerative diseases. In the present review, we elaborate on the essential functions of DHA in the brain, including its role as indirect antioxidant, the selenium connection for proper antioxidant function and their changes during normal aging and in Alzheimer’s disease.
Collapse
Affiliation(s)
- Mario Díaz
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, School of Biology, Universidad de La Laguna, 38206 Tenerife, Spain;
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSP), Universidad de La Laguna, 38206 Tenerife, Spain
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38206 Tenerife, Spain;
- Correspondence:
| | - Fátima Mesa-Herrera
- Laboratory of Membrane Physiology and Biophysics, Department of Animal Biology, School of Biology, Universidad de La Laguna, 38206 Tenerife, Spain;
| | - Raquel Marín
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38206 Tenerife, Spain;
- Laboratory of Cellular Neurobiology, Department of Basic Medical Sciences, School of Medicine, Universidad de La Laguna, 38206 Tenerife, Spain
| |
Collapse
|
33
|
Tyzack GE, Neeves J, Crerar H, Klein P, Ziff O, Taha DM, Luisier R, Luscombe NM, Patani R. Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. Brain 2021; 144:1985-1993. [PMID: 33693641 PMCID: PMC8370440 DOI: 10.1093/brain/awab078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/22/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
We recently described aberrantly increased cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as new hallmarks of amyotrophic lateral sclerosis (ALS). However, the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep sequencing of nuclear and cytoplasmic fractions of human induced pluripotent stem cells undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins. Remarkably, TDP-43, SFPQ and FUS—RNA binding proteins known for nuclear-to-cytoplasmic mislocalization in ALS—abundantly and specifically bind to this aberrant cytoplasmic pool of IRTs. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.
Collapse
Affiliation(s)
- Giulia E Tyzack
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jacob Neeves
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Hamish Crerar
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Pierre Klein
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Oliver Ziff
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Doaa M Taha
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.,Zoology Department, Faculty of Science, Alexandria University, Alexandria 21511, Egypt
| | - Raphaëlle Luisier
- Genomics and Health Informatics Group, Idiap Research Institute, CH - 1920 Martigny, Switzerland
| | - Nicholas M Luscombe
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Rickie Patani
- Human Stem Cells and Neurodegeneration Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| |
Collapse
|
34
|
Abouward R, Schiavo G. Walking the line: mechanisms underlying directional mRNA transport and localisation in neurons and beyond. Cell Mol Life Sci 2021; 78:2665-2681. [PMID: 33341920 PMCID: PMC8004493 DOI: 10.1007/s00018-020-03724-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/02/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022]
Abstract
Messenger RNA (mRNA) localisation enables a high degree of spatiotemporal control on protein synthesis, which contributes to establishing the asymmetric protein distribution required to set up and maintain cellular polarity. As such, a tight control of mRNA localisation is essential for many biological processes during development and in adulthood, such as body axes determination in Drosophila melanogaster and synaptic plasticity in neurons. The mechanisms controlling how mRNAs are localised, including diffusion and entrapment, local degradation and directed active transport, are largely conserved across evolution and have been under investigation for decades in different biological models. In this review, we will discuss the standing of the field regarding directional mRNA transport in light of the recent discovery that RNA can hitchhike on cytoplasmic organelles, such as endolysosomes, and the impact of these transport modalities on our understanding of neuronal function during development, adulthood and in neurodegeneration.
Collapse
Affiliation(s)
- Reem Abouward
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
35
|
Oliveira NCM, Lins ÉM, Massirer KB, Bengtson MH. Translational Control during Mammalian Neocortex Development and Postembryonic Neuronal Function. Semin Cell Dev Biol 2020; 114:36-46. [PMID: 33020045 DOI: 10.1016/j.semcdb.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022]
Abstract
The control of mRNA translation has key roles in the regulation of gene expression and biological processes such as mammalian cellular differentiation and identity. Methodological advances in the last decade have resulted in considerable progress towards understanding how translational control contributes to the regulation of diverse biological phenomena. In this review, we discuss recent findings in the involvement of translational control in the mammalian neocortex development and neuronal biology. We focus on regulatory mechanisms that modulate translational efficiency during neural stem cells self-renewal and differentiation, as well as in neuronal-related processes such as synapse, plasticity, and memory.
Collapse
Affiliation(s)
- Natássia Cristina Martins Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Érico Moreto Lins
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; PhD Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas, SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering - CBMEG, University of Campinas - UNICAMP, 13083-875, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil
| | - Mário Henrique Bengtson
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas - UNICAMP, 13083-862, Campinas, SP, Brazil; Center of Medicinal Chemistry - CQMED, Structural Genomics Consortium - SGC, University of Campinas - UNICAMP, 13083-886, Campinas, SP, Brazil.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Ehses J, Fernández-Moya SM, Schröger L, Kiebler MA. Synergistic regulation of Rgs4 mRNA by HuR and miR-26/RISC in neurons. RNA Biol 2020; 18:988-998. [PMID: 32779957 PMCID: PMC8216180 DOI: 10.1080/15476286.2020.1795409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The negative regulator of G-protein signalling 4 (Rgs4) is linked to several neurologic diseases, e.g. schizophrenia, addiction, seizure and pain perception. Consequently, Rgs4 expression is tightly regulated, resulting in high mRNA and protein turnover. The post-transcriptional control of gene expression is mediated via RNA-binding proteins (RBPs) that interact with mRNAs in a combinatorial fashion. Here, we show that in neurons the RBP HuR reduces endogenous Rgs4 expression by destabilizing Rgs4 mRNA. Interestingly, in smooth muscle cells, Rgs4 is stabilized by HuR, indicating tissue-dependent differences in HuR function. Using in vitro RNA-based pulldown experiments, we identify the functional AU-rich element (ARE) within the Rgs4 3ʹ-UTR that is recognized and bound by HuR. Bioinformatic analysis uncovered that this ARE lies within a highly conserved area next to a miR-26 binding site. We find that the neuronal-enriched miR-26 negatively influences Rgs4 expression in neurons. Further, HuR and miR-26 act synergistically in fluorescent reporter assays. Together, our data suggest a regulatory mechanism, in which an RBP selectively destabilizes a target mRNA in cooperation with a miRNA and the RISC machinery.
Collapse
Affiliation(s)
- Janina Ehses
- BioMedical Center, Medical Faculty, Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Sandra M Fernández-Moya
- BioMedical Center, Medical Faculty, Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Luise Schröger
- BioMedical Center, Medical Faculty, Ludwig Maximilians University of Munich, Martinsried, Germany
| | - Michael A Kiebler
- BioMedical Center, Medical Faculty, Ludwig Maximilians University of Munich, Martinsried, Germany
| |
Collapse
|
38
|
Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules. Biomolecules 2020; 10:biom10020167. [PMID: 31978946 PMCID: PMC7072219 DOI: 10.3390/biom10020167] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.
Collapse
|
39
|
Roy R, Shiina N, Wang DO. More dynamic, more quantitative, unexpectedly intricate: Advanced understanding on synaptic RNA localization in learning and memory. Neurobiol Learn Mem 2019; 168:107149. [PMID: 31881355 DOI: 10.1016/j.nlm.2019.107149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/25/2019] [Accepted: 12/23/2019] [Indexed: 01/13/2023]
Abstract
Synaptic signaling exhibits great diversity, complexity, and plasticity which necessitates maintenance and rapid modification of a local proteome. One solution neurons actively exploit to meet such demands is the strategic deposition of mRNAs encoding proteins for both basal and experience-driven activities into ribonucleoprotein complexes at the synapse. Transcripts localized in this manner can be rapidly accessed for translation in response to a diverse range of stimuli in a temporal- and spatially-restricted manner. Here we review recent findings on localized RNAs and RNA binding proteins in the context of learning and memory, as revealed by cutting-edge in-vitro and in-vivo technologies capable of yielding quantitative and dynamic information. The new technologies include proteomic and transcriptomic analyses, high-resolution multiplexed RNA imaging, single-molecule RNA tracking in living neurons, animal models and human neuron cell models. Among many recent advances in the field, RNA chemical modification has emerged as one of the new regulatory layers of gene expression at synapse that is complex and yet largely unexplored. These exciting new discoveries have enhanced our understanding of the modulation mechanisms of synaptic gene expression and their roles in cognition.
Collapse
Affiliation(s)
- Rohini Roy
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobuyuki Shiina
- Laboratory of Neuronal Cell Biology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, SOKENDAI, Okazaki, Japan; Exploratory Research Center on Life and Living Systems, Okazaki, Japan.
| | - Dan Ohtan Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Liaoning, China; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; The Keihanshin Consortium for Fostering the Next Generation of Global Leaders in Research (K-CONNEX), Kyoto University, Kyoto, Japan.
| |
Collapse
|
40
|
Saini H, Bicknell AA, Eddy SR, Moore MJ. Free circular introns with an unusual branchpoint in neuronal projections. eLife 2019; 8:e47809. [PMID: 31697236 PMCID: PMC6879206 DOI: 10.7554/elife.47809] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.
Collapse
Affiliation(s)
- Harleen Saini
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
| | - Alicia A Bicknell
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Sean R Eddy
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Melissa J Moore
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| |
Collapse
|
41
|
Wang X, You X, Langer JD, Hou J, Rupprecht F, Vlatkovic I, Quedenau C, Tushev G, Epstein I, Schaefke B, Sun W, Fang L, Li G, Hu Y, Schuman EM, Chen W. Full-length transcriptome reconstruction reveals a large diversity of RNA and protein isoforms in rat hippocampus. Nat Commun 2019; 10:5009. [PMID: 31676752 PMCID: PMC6825209 DOI: 10.1038/s41467-019-13037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022] Open
Abstract
Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies.
Collapse
Affiliation(s)
- Xi Wang
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany.
- German Cancer Research Center, 69120, Heidelberg, Germany.
| | - Xintian You
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Jingyi Hou
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Fiona Rupprecht
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Irena Vlatkovic
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Claudia Quedenau
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Irina Epstein
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Guipeng Li
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438, Frankfurt, Germany
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
- Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
| |
Collapse
|
42
|
Bauer KE, Segura I, Gaspar I, Scheuss V, Illig C, Ammer G, Hutten S, Basyuk E, Fernández-Moya SM, Ehses J, Bertrand E, Kiebler MA. Live cell imaging reveals 3'-UTR dependent mRNA sorting to synapses. Nat Commun 2019; 10:3178. [PMID: 31320644 PMCID: PMC6639396 DOI: 10.1038/s41467-019-11123-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 06/25/2019] [Indexed: 12/20/2022] Open
Abstract
mRNA transport restricts translation to specific subcellular locations, which is the basis for many cellular functions. However, the precise process of mRNA sorting to synapses in neurons remains elusive. Here we use Rgs4 mRNA to investigate 3′-UTR-dependent transport by MS2 live-cell imaging. The majority of observed RNA granules display 3′-UTR independent bidirectional transport in dendrites. Importantly, the Rgs4 3′-UTR causes an anterograde transport bias, which requires the Staufen2 protein. Moreover, the 3′-UTR mediates dynamic, sustained mRNA recruitment to synapses. Visualization at high temporal resolution enables us to show mRNA patrolling dendrites, allowing transient interaction with multiple synapses, in agreement with the sushi-belt model. Modulation of neuronal activity by either chemical silencing or local glutamate uncaging regulates both the 3′-UTR-dependent transport bias and synaptic recruitment. This dynamic and reversible mRNA recruitment to active synapses would allow translation and synaptic remodeling in a spatially and temporally adaptive manner. Asymmetric subcellular mRNA distribution is important for local translation of neuronal mRNAs. Here the authors employed MS2 live-cell imaging and showed that the reporter mRNA containing the 3’ UTR of Rgs4 shows an anterograde transport bias, dependent on neuronal activity and the protein Staufen2, and mediates sustained mRNA recruitment to synapses.
Collapse
Affiliation(s)
- Karl E Bauer
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Inmaculada Segura
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Imre Gaspar
- EMBL, Meyerhofstraße 1, 69117, Heidelberg, Germany.,Institute of Molecular Biotechnology, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Volker Scheuss
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Christin Illig
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Georg Ammer
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.,MPI of Neurobiology, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Saskia Hutten
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Eugénia Basyuk
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France.,Institut de Génétique Humaine de Montpellier, CNRS UMR9002, Université de Montpellier, 141 rue de la Cardonille, 34396, Montpellier, France
| | - Sandra M Fernández-Moya
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Janina Ehses
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Université de Montpellier, 1919 route de Mende, 34293, Montpellier, France
| | - Michael A Kiebler
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
| |
Collapse
|
43
|
Schieweck R, Kiebler MA. Posttranscriptional Gene Regulation of the GABA Receptor to Control Neuronal Inhibition. Front Mol Neurosci 2019; 12:152. [PMID: 31316346 PMCID: PMC6611381 DOI: 10.3389/fnmol.2019.00152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
Behavior and higher cognition rely on the transfer of information between neurons through specialized contact sites termed synapses. Plasticity of neuronal circuits, a prerequisite to respond to environmental changes, is intrinsically coupled with the nerve cell’s ability to form, structurally modulate or remove synapses. Consequently, the synaptic proteome undergoes dynamic alteration on demand in a spatiotemporally restricted manner. Therefore, proper protein localization at synapses is essential for synaptic function. This process is regulated by: (i) protein transport and recruitment; (ii) local protein synthesis; and (iii) synaptic protein degradation. These processes shape the transmission efficiency of excitatory synapses. Whether and how these processes influence synaptic inhibition is, however, widely unknown. Here, we summarize findings on fundamental regulatory processes that can be extrapolated to inhibitory synapses. In particular, we focus on known aspects of posttranscriptional regulation and protein dynamics of the GABA receptor (GABAR). Finally, we propose that local (co)-translational control mechanism might control transmission of inhibitory synapses.
Collapse
Affiliation(s)
- Rico Schieweck
- Department of Cell Biology and Anatomy, Medical Faculty, Biomedical Center (BMC), Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Michael A Kiebler
- Department of Cell Biology and Anatomy, Medical Faculty, Biomedical Center (BMC), Ludwig-Maximilians-University of Munich, Munich, Germany
| |
Collapse
|
44
|
Altered Glutamate Receptor Ionotropic Delta Subunit 2 Expression in Stau2-Deficient Cerebellar Purkinje Cells in the Adult Brain. Int J Mol Sci 2019; 20:ijms20071797. [PMID: 30979012 PMCID: PMC6480955 DOI: 10.3390/ijms20071797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 01/13/2023] Open
Abstract
Staufen2 (Stau2) is an RNA-binding protein that is involved in dendritic spine morphogenesis and function. Several studies have recently investigated the role of Stau2 in the regulation of its neuronal target mRNAs, with particular focus on the hippocampus. Here, we provide evidence for Stau2 expression and function in cerebellar Purkinje cells. We show that Stau2 downregulation (Stau2GT) led to an increase of glutamate receptor ionotropic delta subunit 2 (GluD2) in Purkinje cells when animals performed physical activity by voluntary wheel running compared with the age-matched wildtype (WT) mice (C57Bl/6J). Furthermore, Stau2GT mice showed lower performance in motor coordination assays but enhanced motor learning abilities than did WT mice, concomitantly with an increase in dendritic GluD2 expression. Together, our results suggest the novel role of Stau2 in Purkinje cell synaptogenesis in the mouse cerebellum.
Collapse
|
45
|
Andreassi C, Crerar H, Riccio A. Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity. Front Mol Neurosci 2018; 11:304. [PMID: 30210293 PMCID: PMC6121099 DOI: 10.3389/fnmol.2018.00304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their extraordinary cytoarchitecture. This formidable task is achieved, at least in part, by targeting mRNA to subcellular compartments where they are rapidly translated. mRNA transcripts are the conveyor of genetic information from DNA to the translational machinery, however, they are also endowed with additional functions linked to both the coding sequence (open reading frame, or ORF) and the flanking 5′ and 3′ untranslated regions (UTRs), that may harbor coding-independent functions. In this review, we will highlight recent evidences supporting new coding-dependent and -independent functions of mRNA and discuss how nuclear and cytoplasmic post-transcriptional modifications of mRNA contribute to localization and translation in mammalian cells with specific emphasis on neurons. We also describe recently developed techniques that can be employed to study RNA dynamics at subcellular level in eukaryotic cells in developing and regenerating neurons.
Collapse
Affiliation(s)
- Catia Andreassi
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Hamish Crerar
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Antonella Riccio
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| |
Collapse
|
46
|
Gallagher C, Ramos A. Joining the dots - protein-RNA interactions mediating local mRNA translation in neurons. FEBS Lett 2018; 592:2932-2947. [PMID: 29856909 DOI: 10.1002/1873-3468.13121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining the complex network of connections required for neuronal communication requires the transport and in situ translation of large groups of mRNAs to create local proteomes. In this Review, we discuss the regulation of local mRNA translation in neurons and the RNA-binding proteins that recognise RNA zipcode elements and connect the mRNAs to the cellular transport networks, as well as regulate their translation control. However, mRNA recognition by the regulatory proteins is mediated by the combinatorial action of multiple RNA-binding domains. This increases the specificity and affinity of the interaction, while allowing the protein to recognise a diverse set of targets and mediate a range of mechanisms for translational regulation. The structural and molecular understanding of the interactions can be used together with novel microscopy and transcriptome-wide data to build a mechanistic framework for the regulation of local mRNA translation.
Collapse
Affiliation(s)
- Christopher Gallagher
- Institute of Structural and Molecular Biology, University College London, UK.,The Francis Crick Institute, London, UK
| | - Andres Ramos
- Institute of Structural and Molecular Biology, University College London, UK
| |
Collapse
|
47
|
Popper B, Demleitner A, Bolivar VJ, Kusek G, Snyder-Keller A, Schieweck R, Temple S, Kiebler MA. Staufen2 deficiency leads to impaired response to novelty in mice. Neurobiol Learn Mem 2018; 150:107-115. [PMID: 29496644 DOI: 10.1016/j.nlm.2018.02.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/25/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
Staufen2 (Stau2) is a double-stranded RNA-binding protein (RBP) involved in posttranscriptional gene expression control in neurons. In flies, staufen contributes to learning and long-term memory formation. To study the impact of mammalian Stau2 on behavior, we generated a novel gene-trap mouse model that yields significant constitutive downregulation of Stau2 (Stau2GT). In order to investigate the effect of Stau2 downregulation on hippocampus-dependent behavior, we performed a battery of behavioral assays, i.e. open field, novel object recognition/location (NOR/L) and Barnes maze. Stau2GT mice displayed reduced locomotor activity in the open field and altered novelty preference in the NOR and NOL paradigms. Adult Stau2GT male mice failed to discriminate between familiar and newly introduced objects but showed enhanced spatial novelty detection. Additionally, we observed deficits in discriminating different spatial contexts in a Barnes maze assay. Together, our data suggest that Stau2 contributes to novelty preference and explorative behavior that is a driver for proper spatial learning in mice.
Collapse
Affiliation(s)
- Bastian Popper
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany; Biomedical Center (BMC), Core Facility Animal Models, Ludwig-Maximilians-University, Munich, Germany
| | - Antonia Demleitner
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany
| | - Valerie J Bolivar
- Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Sciences, University at Albany School of Public Health, State University of New York, Albany, NY, USA
| | - Gretchen Kusek
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY, USA
| | - Abigail Snyder-Keller
- Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Sciences, University at Albany School of Public Health, State University of New York, Albany, NY, USA
| | - Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany.
| | - Sally Temple
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY, USA
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology & Anatomy, Medical Faculty, Ludwig-Maximilians-University, Munich, Germany.
| |
Collapse
|
48
|
Jorquera R, González C, Clausen P, Petersen B, Holmes DS. Improved ontology for eukaryotic single-exon coding sequences in biological databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-6. [PMID: 30239665 PMCID: PMC6146118 DOI: 10.1093/database/bay089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022]
Abstract
Efficient extraction of knowledge from biological data requires the development of structured vocabularies to unambiguously define biological terms. This paper proposes descriptions and definitions to disambiguate the term 'single-exon gene'. Eukaryotic Single-Exon Genes (SEGs) have been defined as genes that do not have introns in their protein coding sequences. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancer and neurological/developmental disorders and many exhibit tissue-specific transcription. Unfortunately, the term 'SEGs' is rife with ambiguity, leading to biological misinterpretations. In the classic definition, no distinction is made between SEGs that harbor introns in their untranslated regions (UTRs) versus those without. This distinction is important to make because the presence of introns in UTRs affects transcriptional regulation and post-transcriptional processing of the mRNA. In addition, recent whole-transcriptome shotgun sequencing has led to the discovery of many examples of single-exon mRNAs that arise from alternative splicing of multi-exon genes, these single-exon isoforms are being confused with SEGs despite their clearly different origin. The increasing expansion of RNA-seq datasets makes it imperative to distinguish the different SEG types before annotation errors become indelibly propagated in biological databases. This paper develops a structured vocabulary for their disambiguation, allowing a major reassessment of their evolutionary trajectories, regulation, RNA processing and transport, and provides the opportunity to improve the detection of gene associations with disorders including cancers, neurological and developmental diseases.
Collapse
Affiliation(s)
- Roddy Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Carolina González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile
| | - Philip Clausen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Bent Petersen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - David S Holmes
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Avenida Zañartu 1482, Ñuñoa, Santiago, Chile.,Centro de Genómica y Bioinformática Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| |
Collapse
|
49
|
Berger SM, Fernández-Lamo I, Schönig K, Fernández Moya SM, Ehses J, Schieweck R, Clementi S, Enkel T, Grothe S, von Bohlen Und Halbach O, Segura I, Delgado-García JM, Gruart A, Kiebler MA, Bartsch D. Forebrain-specific, conditional silencing of Staufen2 alters synaptic plasticity, learning, and memory in rats. Genome Biol 2017; 18:222. [PMID: 29149906 PMCID: PMC5693596 DOI: 10.1186/s13059-017-1350-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/26/2017] [Indexed: 12/16/2022] Open
Abstract
Background Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution of RNA-binding proteins (RBPs) to these processes in vivo. Results To delineate the role of the double-stranded RBP Staufen2 (Stau2), we generate a transgenic rat model, in which Stau2 expression is conditionally silenced by Cre-inducible expression of a microRNA (miRNA) targeting Stau2 mRNA in adult forebrain neurons. Known physiological mRNA targets for Stau2, such as RhoA, Complexin 1, and Rgs4 mRNAs, are found to be dysregulated in brains of Stau2-deficient rats. In vivo electrophysiological recordings reveal synaptic strengthening upon stimulation, showing a shift in the frequency-response function of hippocampal synaptic plasticity to favor long-term potentiation and impair long-term depression in Stau2-deficient rats. These observations are accompanied by deficits in hippocampal spatial working memory, spatial novelty detection, and in tasks investigating associative learning and memory. Conclusions Together, these experiments reveal a critical contribution of Stau2 to various forms of synaptic plasticity including spatial working memory and cognitive management of new environmental information. These findings might contribute to the development of treatments for conditions associated with learning and memory deficits. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1350-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Stefan M Berger
- Department of Molecular Biology, CIMH and Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Iván Fernández-Lamo
- Division of Neurosciences, Pablo de Olavide University, 41013, Seville, Spain.,Present Address: Institute Cajal (CSIC), 28002, Madrid, Spain
| | - Kai Schönig
- Department of Molecular Biology, CIMH and Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Sandra M Fernández Moya
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, 82152, Planegg-Martinsried, Germany
| | - Janina Ehses
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, 82152, Planegg-Martinsried, Germany
| | - Rico Schieweck
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, 82152, Planegg-Martinsried, Germany
| | - Stefano Clementi
- Department of Molecular Biology, CIMH and Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Thomas Enkel
- Department of Molecular Biology, CIMH and Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Sascha Grothe
- Institute for Anatomy and Cell Biology, University Medicine Greifswald, 17487, Greifswald, Germany
| | | | - Inmaculada Segura
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, 82152, Planegg-Martinsried, Germany.
| | | | - Agnès Gruart
- Division of Neurosciences, Pablo de Olavide University, 41013, Seville, Spain
| | - Michael A Kiebler
- BioMedical Center, Medical Faculty, Ludwig Maximilians University, 82152, Planegg-Martinsried, Germany.
| | - Dusan Bartsch
- Department of Molecular Biology, CIMH and Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
| |
Collapse
|
50
|
Terenzio M, Schiavo G, Fainzilber M. Compartmentalized Signaling in Neurons: From Cell Biology to Neuroscience. Neuron 2017; 96:667-679. [PMID: 29096079 DOI: 10.1016/j.neuron.2017.10.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 09/27/2017] [Accepted: 10/09/2017] [Indexed: 12/18/2022]
Abstract
Neurons are the largest known cells, with complex and highly polarized morphologies. As such, neuronal signaling is highly compartmentalized, requiring sophisticated transfer mechanisms to convey and integrate information within and between sub-neuronal compartments. Here, we survey different modes of compartmentalized signaling in neurons, highlighting examples wherein the fundamental cell biological processes of protein synthesis and degradation, membrane trafficking, and organelle transport are employed to enable the encoding and integration of information, locally and globally within a neuron. Comparisons to other cell types indicate that neurons accentuate widely shared mechanisms, providing invaluable models for the compartmentalization and transfer mechanisms required and used by most eukaryotic cells.
Collapse
Affiliation(s)
- Marco Terenzio
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Giampietro Schiavo
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London WC1N 3BG, UK; Discoveries Centre for Regenerative and Precision Medicine at UCL, London WC1N 3BG, UK; UK Dementia Research Institute at UCL, London WC1E 6BT, UK
| | - Mike Fainzilber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|