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Elhajjajy SI, Weng Z. A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.20.631609. [PMID: 39896518 PMCID: PMC11785142 DOI: 10.1101/2025.01.20.631609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions of most RBPs are not well-characterized. Previous studies have shown that motif context is an important contributor to RBP binding specificity, but its precise role remains unclear. Despite recent computational advances to predict RBP binding, existing methods are challenging to interpret and largely lack a categorical focus on RBP motif contexts and RBP-RBP interactions. There remains a need for interpretable predictive models to disambiguate the contextual determinants of RBP binding specificity in vivo . Here, we present a novel and comprehensive pipeline to address these knowledge gaps. We devise a Natural Language Processing-based decomposition method to deconstruct sequences into entities consisting of a central target k -mer and its flanking regions, then use this representation to formulate the RBP binding prediction task as a weakly supervised Multiple Instance Learning problem. To interpret our predictions, we introduce a deterministic motif discovery algorithm designed to handle our data structure, recapitulating the established motifs of numerous RBPs as validation. Importantly, we characterize the binding motifs and binding contexts for 71 RBPs, with many of them being novel. Finally, through feature integration, transitive inference, and a new cross-prediction approach, we propose novel cooperative and competitive RBP-RBP interaction partners and hypothesize their potential regulatory functions. In summary, we present a complete computational strategy for investigating the contextual determinants of specific RBP binding, and we demonstrate the significance of our findings in delineating RBP binding patterns, interactions, and functions.
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Xiao J, Wang WX. Patterns and Crucial Regulation of Alternative Splicing During Early Development in Zebrafish. J Mol Biol 2022; 434:167821. [PMID: 36087778 DOI: 10.1016/j.jmb.2022.167821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 10/31/2022]
Abstract
Many vertebrate genes generate multiple transcript variants that may encode functionally distinct protein isoforms, but the transcriptomes of various developmental stages are poorly defined. Identifying the transcriptome and its regulation during the normal developmental process is the key to deciphering the developmental stage-specific functions of genes. Here we presented a systematic assessment of the temporal alternative splicing (AS) events during the critical development stages to capture the dynamic gene expression changes and AS in zebrafish. An unexpected transcriptome complexity generated by AS was observed during zebrafish development. The patterns of AS events varied substantially among developmental stages despite the similarities in the total proportion of AS genes. We further found that AS afforded substantial functional diversification of genes through the generation of stage-specific AS events from broadly protein-coding genes as an essential developmental regulatory mechanism. Skipped exon (SE) showed the strongest signals among developmental AS (devAS), suggesting that devAS events generated by SE may be necessary for the normal development of zebrafish. Most developmental genes regulated by AS mechanisms were not modulated in terms of their overall expression levels, indicating that AS shaped the transcriptome independently from transcriptional regulation during development. 128-cell stage was a critical stage for gene transcription during embryonic development. Splicing factors as an essential developmental regulator underwent AS in the potential autoregulatory feedback loop and expressed multiple isoforms. Thus, zebrafish development was shaped by an interplay of programs controlling gene expression levels and AS. Overall, we provided a global view of developmental patterns of AS during zebrafish development and revealed that AS transitions were the crucial regulatory component of zebrafish embryonic development.
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Affiliation(s)
- Jie Xiao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
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3
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Fisher E, Feng J. RNA splicing regulators play critical roles in neurogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1728. [PMID: 35388651 DOI: 10.1002/wrna.1728] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Alternative RNA splicing increases transcript diversity in different cell types and under varying conditions. It is executed with the help of RNA splicing regulators (RSRs), which are operationally defined as RNA-binding proteins (RBPs) that regulate alternative splicing, but not directly catalyzing the chemical reactions of splicing. By systematically searching for RBPs and manually identifying those that regulate splicing, we curated 305 RSRs in the human genome. Surprisingly, most of the RSRs are involved in neurogenesis. Among these RSRs, we focus on nine families (PTBP, NOVA, RBFOX, ELAVL, CELF, DBHS, MSI, PCBP, and MBNL) that play essential roles in the neurogenic pathway. A better understanding of their functions will provide novel insights into the role of splicing in brain development, health, and disease. This comprehensive review serves as a stepping-stone to explore the diverse and complex set of RSRs as fundamental regulators of neural development. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
| | - Jian Feng
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York, USA
- Veterans Affairs Western New York Healthcare System, Buffalo, New York, USA
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A Monoclonal Anti-HMGB1 Antibody Attenuates Neurodegeneration in an Experimental Animal Model of Glaucoma. Int J Mol Sci 2022; 23:ijms23084107. [PMID: 35456925 PMCID: PMC9028318 DOI: 10.3390/ijms23084107] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
Neuroinflammation is a crucial process for the loss of retinal ganglion cells (RGC), a major characteristic of glaucoma. High expression of high-mobility group box protein 1 (HMGB1) plays a detrimental role in inflammatory processes and is elevated in the retinas of glaucoma patients. Therefore, this study aimed to investigate the effects of the intravitreal injection of an anti-HMGB1 monoclonal antibody (anti-HMGB1 Ab) in an experimental animal model of glaucoma. Two groups of Spraque Dawley rats received episcleral vein occlusion to chronically elevate intraocular pressure (IOP): (1) the IgG group, intravitreal injection of an unspecific IgG as a control, n = 5, and (2) the HMGB1 group, intravitreal injection of an anti-HMGB1 Ab, n = 6. IOP, retinal nerve fiber layer thickness (RNFLT), and the retinal flash response were monitored longitudinally. Post-mortem examinations included immunohistochemistry, microarray, and mass spectrometric analysis. RNFLT was significantly increased in the HMGB1 group compared with the IgG group (p < 0.001). RGC density showed improved neuronal cell survival in the retina in HMGB1 compared with the IgG group (p < 0.01). Mass spectrometric proteomic analysis of retinal tissue showed an increased abundance of RNA metabolism-associated heterogeneous nuclear ribonucleoproteins (hnRNPs), such as hnRNP U, D, and H2, in animals injected with the anti-HMGB1 Ab, indicating that the application of the antibody may cause increased gene expression. Microarray analysis showed a significantly decreased expression of C-X-C motif chemokine ligand 8 (CXCL8, p < 0.05) and connective tissue growth factor (CTGF, p < 0.01) in the HMGB1 group. Thus, these data suggest that intravitreal injection of anti-HMGB1 Ab reduced HMGB1-dependent inflammatory signaling and mediated RGC neuroprotection.
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Gagné M, Deshaies JE, Sidibé H, Benchaar Y, Arbour D, Dubinski A, Litt G, Peyrard S, Robitaille R, Sephton CF, Vande Velde C. hnRNP A1B, a Splice Variant of HNRNPA1, Is Spatially and Temporally Regulated. Front Neurosci 2021; 15:724307. [PMID: 34630013 PMCID: PMC8498194 DOI: 10.3389/fnins.2021.724307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022] Open
Abstract
RNA binding proteins (RBPs) play a key role in cellular growth, homoeostasis and survival and are tightly regulated. A deep understanding of their spatiotemporal regulation is needed to understand their contribution to physiology and pathology. Here, we have characterized the spatiotemporal expression pattern of hnRNP A1 and its splice variant hnRNP A1B in mice. We have found that hnRNP A1B expression is more restricted to the CNS compared to hnRNP A1, and that it can form an SDS-resistant dimer in the CNS. Also, hnRNP A1B expression becomes progressively restricted to motor neurons in the ventral horn of the spinal cord, compared to hnRNP A1 which is more broadly expressed. We also demonstrate that hnRNP A1B is present in neuronal processes, while hnRNP A1 is absent. This finding supports a hypothesis that hnRNP A1B may have a cytosolic function in neurons that is not shared with hnRNP A1. Our results demonstrate that both isoforms are differentially expressed across tissues and have distinct localization profiles, suggesting that the two isoforms may have specific subcellular functions that can uniquely contribute to disease progression.
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Affiliation(s)
- Myriam Gagné
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Jade-Emmanuelle Deshaies
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Hadjara Sidibé
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Yousri Benchaar
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Danielle Arbour
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Alicia Dubinski
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Gurleen Litt
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Sarah Peyrard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada
| | - Richard Robitaille
- Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
| | - Chantelle F Sephton
- Department of Psychiatry and Neuroscience, CERVO Brain Research Centre, Laval University, Quebec City, QC, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Department of Neurosciences, Université de Montréal, Montréal, QC, Canada
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Robinson H, Ruelcke JE, Lewis A, Bond CS, Fox AH, Bharti V, Wani S, Cloonan N, Lai A, Margolin D, Li L, Salomon C, Richards RS, Farrell A, Gardiner RA, Parton RG, Cristino AS, Hill MM. Caveolin-1-driven membrane remodelling regulates hnRNPK-mediated exosomal microRNA sorting in cancer. Clin Transl Med 2021; 11:e381. [PMID: 33931969 PMCID: PMC8031663 DOI: 10.1002/ctm2.381] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Caveolae proteins play diverse roles in cancer development and progression. In prostate cancer, non-caveolar caveolin-1 (CAV1) promotes metastasis, while CAVIN1 attenuates CAV1-induced metastasis. Here, we unveil a novel mechanism linking CAV1 to selective loading of exosomes with metastasis-promoting microRNAs. RESULTS We identify hnRNPK as a CAV1-regulated microRNA binding protein. In the absence of CAVIN1, non-caveolar CAV1 drives localisation of hnRPNK to multi-vesicular bodies (MVBs), recruiting AsUGnA motif-containing miRNAs and causing their release within exosomes. This process is dependent on the lipid environment of membranes as shown by cholesterol depletion using methyl-β-cyclodextrin or by treatment with n-3 polyunsaturated fatty acids. Consistent with a role in bone metastasis, knockdown of hnRNPK in prostate cancer PC3 cells abolished the ability of PC3 extracellular vesicles (EV) to induce osteoclastogenesis, and biofluid EV hnRNPK is elevated in metastatic prostate and colorectal cancer. CONCLUSIONS Taken together, these results support a novel pan-cancer mechanism for CAV1-driven exosomal release of hnRNPK and associated miRNA in metastasis, which is modulated by the membrane lipid environment.
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Affiliation(s)
- Harley Robinson
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Jayde E. Ruelcke
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
| | - Amanda Lewis
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Charles S. Bond
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Archa H. Fox
- School of Molecular SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Human SciencesThe University of Western AustraliaCrawleyWAAustralia
- The Harry Perkins Institute of Medical ResearchQEII Medical CentreNedlandsWAAustralia
| | - Vandhana Bharti
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Shivangi Wani
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Nicole Cloonan
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Andrew Lai
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - David Margolin
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Li Li
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
| | - Carlos Salomon
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
- Maternal‐Fetal Medicine, Department of Obstetrics and GynecologyOchsner Clinic FoundationNew OrleansUSA
- Department of Clinical Biochemistry and Immunology, Faculty of PharmacyUniversity of ConcepciónConcepciónChile
| | - Renée S. Richards
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Aine Farrell
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert A. Gardiner
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women's HospitalThe University of QueenslandBrisbaneQueenslandAustralia
| | - Robert G. Parton
- Institute for Molecular BioscienceThe University of QueenslandSt LuciaQueenslandAustralia
- Centre for Microscopy and MicroanalysisThe University of QueenslandSt LuciaQueenslandAustralia
| | - Alexandre S. Cristino
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- Griffith Institute for Drug DiscoveryGriffith UniversityBrisbaneQueenslandAustralia
| | - Michelle M. Hill
- The University of Queensland Diamantina InstituteThe University of QueenslandWoolloongabbaQueenslandAustralia
- QIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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7
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Sha N, Wang HW, Sun B, Gong M, Miao P, Jiang XL, Yang XF, Li M, Xu LX, Feng CX, Yang YY, Zhang J, Zhu WJ, Gao YY, Feng X, Ding X. The role of pineal microRNA-325 in regulating circadian rhythms after neonatal hypoxic-ischemic brain damage. Neural Regen Res 2021; 16:2071-2077. [PMID: 33642396 PMCID: PMC8343300 DOI: 10.4103/1673-5374.308101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Circadian rhythm disorder is a common, but often neglected, consequence of neonatal hypoxic-ischemic brain damage (HIBD). However, the underlying molecular mechanisms remain largely unknown. We previously showed that, in a rat model of HIBD, up-regulation of microRNA-325 (miR-325) in the pineal gland is responsible for the suppression of Aanat, a key enzyme involved in melatonin synthesis and circadian rhythm regulation. To better understand the mechanism by which miR-325 affects circadian rhythms in neonates with HIBD, we compared clinical samples from neonates with HIBD and samples from healthy neonates recruited from the First Affiliated Hospital of Soochow University (Dushuhu Branch) in 2019. We found that circulating miR-325 levels correlated positively with the severity of sleep and circadian rhythm disorders in neonates with HIBD. Furthermore, a luciferase reporter gene assay revealed that LIM homeobox 3 (LHX3) is a novel downstream target of miR-325. In addition, in miR-325 knock-down mice, the transcription factor LHX3 exhibited an miR-325-dependent circadian pattern of expression in the pineal gland. We established a neonatal mouse model of HIBD by performing double-layer ligation of the left common carotid artery and exposing the pups to a low-oxygen environment for 2 hours. Lhx3 mRNA expression was significantly down-regulated in these mice and partially rescued in miR-325 knockout mice subjected to the same conditions. Finally, we showed that improvement in circadian rhythm-related behaviors in animals with HIBD was dependent on both miR-325 and LHX3. Taken together, our findings suggest that the miR-325-LHX3 axis is responsible for regulating circadian rhythms and provide novel insights into the identification of potential therapeutic targets for circadian rhythm disorders in patients with neonatal HIBD. The clinical trial was approved by Institutional Review Board of Children's Hospital of Soochow University (approval No. 2015028) on July 20, 2015. Animal experiments were approved by Animal Care and Use Committee, School of Medicine, Soochow University, China (approval No. XD-2016-1) on January 15, 2016.
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Affiliation(s)
- Ning Sha
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou; Department of Pediatrics, Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu Province, China
| | - Hua-Wei Wang
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Bin Sun
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Min Gong
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Po Miao
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xiao-Lu Jiang
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xiao-Feng Yang
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Mei Li
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Li-Xiao Xu
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Chen-Xi Feng
- Pediatrics Research Institute, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Yuan-Yuan Yang
- Department of Pediatrics, The First Affiliated Hospital of Soochow University (Dushuhu Branch), Suzhou, Jiangsu Province, China
| | - Jie Zhang
- Cambridge-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Wen-Jing Zhu
- Cambridge-SU Genomic Resource Center, Soochow University, Suzhou, Jiangsu Province, China
| | - Yuan-Yuan Gao
- Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xing Feng
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Ding
- Soochow Key Laboratory of Prevention and Treatment of Child Brain injury, Children's Hospital of Soochow University, Suzhou, Jiangsu Province, China
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Weghorst F, Mirzakhanyan Y, Samimi K, Dhillon M, Barzik M, Cunningham LL, Gershon PD, Cramer KS. Caspase-3 Cleaves Extracellular Vesicle Proteins During Auditory Brainstem Development. Front Cell Neurosci 2020; 14:573345. [PMID: 33281555 PMCID: PMC7689216 DOI: 10.3389/fncel.2020.573345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/26/2022] Open
Abstract
Sound localization requires extremely precise development of auditory brainstem circuits, the molecular mechanisms of which are largely unknown. We previously demonstrated a novel requirement for non-apoptotic activity of the protease caspase-3 in chick auditory brainstem development. Here, we used mass spectrometry to identify proteolytic substrates of caspase-3 during chick auditory brainstem development. These auditory brainstem caspase-3 substrates were enriched for proteins previously shown to be cleaved by caspase-3, especially in non-apoptotic contexts. Functional annotation analysis revealed that our caspase-3 substrates were also enriched for proteins associated with several protein categories, including proteins found in extracellular vesicles (EVs), membrane-bound nanoparticles that function in intercellular communication. The proteome of EVs isolated from the auditory brainstem was highly enriched for our caspase-3 substrates. Additionally, we identified two caspase-3 substrates with known functions in axon guidance, namely Neural Cell Adhesion Molecule (NCAM) and Neuronal-glial Cell Adhesion Molecule (Ng-CAM), that were found in auditory brainstem EVs and expressed in the auditory pathway alongside cleaved caspase-3. Taken together, these data suggest a novel developmental mechanism whereby caspase-3 influences auditory brainstem circuit formation through the proteolytic cleavage of extracellular vesicle (EV) proteins.
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Affiliation(s)
- Forrest Weghorst
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Yeva Mirzakhanyan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Kian Samimi
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Mehron Dhillon
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
| | - Melanie Barzik
- Section on Sensory Cell Biology, NIDCD, NIH, Bethesda, MD, United States
| | - Lisa L. Cunningham
- Section on Sensory Cell Biology, NIDCD, NIH, Bethesda, MD, United States
| | - Paul D. Gershon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Karina S. Cramer
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, United States
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9
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Walsh MB, Janzen E, Wingrove E, Hosseinibarkooie S, Muela NR, Davidow L, Dimitriadi M, Norabuena EM, Rubin LL, Wirth B, Hart AC. Genetic modifiers ameliorate endocytic and neuromuscular defects in a model of spinal muscular atrophy. BMC Biol 2020; 18:127. [PMID: 32938453 PMCID: PMC7495824 DOI: 10.1186/s12915-020-00845-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022] Open
Abstract
Background Understanding the genetic modifiers of neurodegenerative diseases can provide insight into the mechanisms underlying these disorders. Here, we examine the relationship between the motor neuron disease spinal muscular atrophy (SMA), which is caused by reduced levels of the survival of motor neuron (SMN) protein, and the actin-bundling protein Plastin 3 (PLS3). Increased PLS3 levels suppress symptoms in a subset of SMA patients and ameliorate defects in SMA disease models, but the functional connection between PLS3 and SMN is poorly understood. Results We provide immunohistochemical and biochemical evidence for large protein complexes localized in vertebrate motor neuron processes that contain PLS3, SMN, and members of the hnRNP F/H family of proteins. Using a Caenorhabditis elegans (C. elegans) SMA model, we determine that overexpression of PLS3 or loss of the C. elegans hnRNP F/H ortholog SYM-2 enhances endocytic function and ameliorates neuromuscular defects caused by decreased SMN-1 levels. Furthermore, either increasing PLS3 or decreasing SYM-2 levels suppresses defects in a C. elegans ALS model. Conclusions We propose that hnRNP F/H act in the same protein complex as PLS3 and SMN and that the function of this complex is critical for endocytic pathways, suggesting that hnRNP F/H proteins could be potential targets for therapy development.
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Affiliation(s)
- Melissa B Walsh
- Department of Neuroscience, Brown University, 185 Meeting Street, Mailbox GL-N, Providence, RI, 02912, USA
| | - Eva Janzen
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Emily Wingrove
- Department of Neuroscience, Brown University, 185 Meeting Street, Mailbox GL-N, Providence, RI, 02912, USA
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Natalia Rodriguez Muela
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lance Davidow
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Maria Dimitriadi
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hertfordshire, UK
| | - Erika M Norabuena
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lee L Rubin
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Anne C Hart
- Department of Neuroscience, Brown University, 185 Meeting Street, Mailbox GL-N, Providence, RI, 02912, USA.
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10
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Schiapparelli LM, Shah SH, Ma Y, McClatchy DB, Sharma P, Li J, Yates JR, Goldberg JL, Cline HT. The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo. Cell Rep 2020; 28:1935-1947.e5. [PMID: 31412257 PMCID: PMC6707540 DOI: 10.1016/j.celrep.2019.07.037] [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: 03/20/2019] [Revised: 06/03/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022] Open
Abstract
The brain processes information and generates cognitive and motor outputs through functions of spatially organized proteins in different types of neurons. More complete knowledge of proteins and their distributions within neuronal compartments in intact circuits would help in the understanding of brain function. We used unbiased in vivo protein labeling with intravitreal NHS-biotin for discovery and analysis of endogenous axonally transported proteins in the visual system using tandem mass spectrometric proteomics, biochemistry, and both light and electron microscopy. Purification and proteomic analysis of biotinylated peptides identified ~1,000 proteins transported from retinal ganglion cells into the optic nerve and ~575 biotinylated proteins recovered from presynaptic compartments of lateral geniculate nucleus and superior colliculus. Approximately 360 biotinylated proteins were differentially detected in the two retinal targets. This study characterizes axonally transported proteins in the healthy adult visual system by analyzing proteomes from multiple compartments of retinal ganglion cell projections in the intact brain. Axonal protein transport is essential for circuit function. Schiapparelli et al. use unbiased in vivo protein labeling and mass spectrometry to identify ~1,000 proteins in the “RGC axonal transportome.” About 350 retinal proteins are differentially transported to the lateral geniculate nucleus or the superior colliculus, indicating target-specific diversity in presynaptic protein content.
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Affiliation(s)
- Lucio M Schiapparelli
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sahil H Shah
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA; Neuroscience Graduate Program and Medical Scientist Training Program, University of California, San Diego, La Jolla, CA 92093, USA; Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel B McClatchy
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pranav Sharma
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jianli Li
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey L Goldberg
- Byers Eye Institute and Spencer Center for Vision Research, Stanford University, Palo Alto, CA 94303, USA
| | - Hollis T Cline
- Department of Neuroscience and the Dorris Neuroscience Center, Scripps Research Institute, La Jolla, CA 92037, USA.
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11
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Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. miR-7 Knockdown by Peptide Nucleic Acids in the Ascidian Ciona intestinalis. Int J Mol Sci 2019; 20:ijms20205127. [PMID: 31623150 PMCID: PMC6829576 DOI: 10.3390/ijms20205127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) are synthetic mimics of natural oligonucleotides, which bind complementary DNA/RNA strands with high sequence specificity. They display numerous advantages, but in vivo applications are still rare. One of the main drawbacks of PNAs application is the poor cellular uptake that could be overcome by using experimental models, in which microinjection techniques allow direct delivery of molecules into eggs. Thus, in this communication, we investigated PNAs efficiency in miR-7 downregulation and compared its effects with those obtained with the commercially available antisense molecule, Antagomir (Dharmacon) in the ascidian Ciona intestinalis. Ascidians are marine invertebrates closely related to vertebrates, in which PNA techniques have not been applied yet. Our results suggested that anti-miR-7 PNAs were able to reach their specific targets in the developing ascidian embryos with high efficiency, as the same effects were obtained with both PNA and Antagomir. To the best of our knowledge, this is the first evidence that unmodified PNAs can be applied in in vivo knockdown strategies when directly injected into eggs.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16126 Genova, Italy.
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
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12
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Wang Z, Qiu H, He J, Liu L, Xue W, Fox A, Tickner J, Xu J. The emerging roles of hnRNPK. J Cell Physiol 2019; 235:1995-2008. [PMID: 31538344 DOI: 10.1002/jcp.29186] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) is an DNA/RNA-binding protein and regulates a wide range of biological processes and disease pathogenesis. It contains 3 K-homologous (KH) domains, which are conserved in other RNA-binding proteins, mediate nucleic acid binding activity, and function as an enhancer or repressor of gene transcription. Phosphorylation of the protein alters its regulatory function, which also enables the protein to serve as a docking platform for the signal transduction proteins. In terms of the function of hnRNPK, it is central to many cellular events, including long noncoding RNA (lncRNA) regulation, cancer development and bone homoeostasis. Many studies have identified hnRNPK as an oncogene, where it is overexpressed in cancer tissues compared with the nonneoplastic tissues and its expression level is related to the prognosis of different types of host malignancies. However, hnRNPK has also been identified as a tumour suppressor, as it is important for the activation of the p53/p21 pathway. Recently, the protein is also found to be exclusively related to the regulation of paraspeckles and lncRNAs such as Neat1, Lncenc1 and Xist. Interestingly, hnRNPK has been found to associate with the Kabuki-like syndrome and Au-Kline syndrome with prominent skeletal abnormalities. In vitro study revealed that the hnRNPK protein is essential for the formation of osteoclast, in line with its importance in the skeletal system.
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Affiliation(s)
- Ziyi Wang
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Heng Qiu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jianbo He
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia.,Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Langxia Liu
- Key laboratory of functional protein research of Guangdong higher education institutes, Institute of life and health engineering, Jinan University, Guangzhou, China
| | - Wei Xue
- Department of Biomedical Engineering, Jinan University, Guangzhou, China
| | - Archa Fox
- School of Human Sciences and Molecular Sciences, The University of Western Australia and Harry Perkins Institute of Medical Research, Centre for Medical Research, The University of Western Australia, Perth, Western Australia, Australia
| | - Jennifer Tickner
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Jiake Xu
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
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13
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Xu Y, Li R, Zhang K, Wu W, Wang S, Zhang P, Xu H. The multifunctional RNA-binding protein hnRNPK is critical for the proliferation and differentiation of myoblasts. BMB Rep 2018; 51:350-355. [PMID: 29898807 PMCID: PMC6089871 DOI: 10.5483/bmbrep.2018.51.7.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 11/20/2022] Open
Abstract
HnRNPK is a multifunctional protein that participates in chromatin remodeling, transcription, RNA splicing, mRNA stability and translation. Here, we uncovered the function of hnRNPK in regulating the proliferation and differentiation of myoblasts. hnRNPK was mutated in the C2C12 myoblast cell line using the CRISPR/Cas9 system. A decreased proliferation rate was observed in hnRNPK-mutated cells, suggesting an impaired proliferation phenotype. Furthermore, increased G2/M phase, decreased S phase and increased sub-G1 phase cells were detected in the hnRNPK-mutated cell lines. The expression analysis of key cell cycle regulators indicated mRNA of Cyclin A2 was significantly increased in the mutant myoblasts compared to the control cells, while Cyclin B1, Cdc25b and Cdc25c were decreased sharply. In addition to the myoblast proliferation defect, the mutant cells exhibited defect in myotube formation. The myotube formation marker, myosin heavy chain (MHC), was decreased sharply in hnRNPK-mutated cells compared to control myoblasts during differentiation. The deficiency in hnRNPK also resulted in the repression of Myog expression, a key myogenic regulator during differentiation. Together, our data demonstrate that hnRNPK is required for myoblast proliferation and differentiation and may be an essential regulator of myoblast function.
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Affiliation(s)
- Yongjie Xu
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Rui Li
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Kaili Zhang
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Wei Wu
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Suying Wang
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Pengpeng Zhang
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Haixia Xu
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
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14
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Lee SJ, Oses-Prieto JA, Kawaguchi R, Sahoo PK, Kar AN, Rozenbaum M, Oliver D, Chand S, Ji H, Shtutman M, Miller-Randolph S, Taylor RJ, Fainzilber M, Coppola G, Burlingame AL, Twiss JL. hnRNPs Interacting with mRNA Localization Motifs Define Axonal RNA Regulons. Mol Cell Proteomics 2018; 17:2091-2106. [PMID: 30038033 DOI: 10.1074/mcp.ra118.000603] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 07/05/2018] [Indexed: 12/30/2022] Open
Abstract
mRNA translation in axons enables neurons to introduce new proteins at sites distant from their cell body. mRNA-protein interactions drive this post-transcriptional regulation, yet knowledge of RNA binding proteins (RBP) in axons is limited. Here we used proteomics to identify RBPs interacting with the axonal localizing motifs of Nrn1, Hmgb1, Actb, and Gap43 mRNAs, revealing many novel RBPs in axons. Interestingly, no RBP is shared between all four RNA motifs, suggesting graded and overlapping specificities of RBP-mRNA pairings. A systematic assessment of axonal mRNAs interacting with hnRNP H1, hnRNP F, and hnRNP K, proteins that bound with high specificity to Nrn1 and Hmgb1, revealed that axonal mRNAs segregate into axon growth-associated RNA regulons based on hnRNP interactions. Axotomy increases axonal transport of hnRNPs H1, F, and K, depletion of these hnRNPs decreases axon growth and reduces axonal mRNA levels and axonal protein synthesis. Thus, subcellular hnRNP-interacting RNA regulons support neuronal growth and regeneration.
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Affiliation(s)
- Seung Joon Lee
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Juan A Oses-Prieto
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Riki Kawaguchi
- ¶Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095
| | - Pabitra K Sahoo
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Amar N Kar
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Meir Rozenbaum
- ‖Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - David Oliver
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | - Shreya Chand
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Hao Ji
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | - Michael Shtutman
- **Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208
| | | | - Ross J Taylor
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208
| | - Mike Fainzilber
- ‖Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Giovanni Coppola
- ¶Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095.,‡‡Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095
| | - Alma L Burlingame
- §Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158
| | - Jeffery L Twiss
- From the ‡Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208;
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15
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Gallardo M, Hornbaker MJ, Zhang X, Hu P, Bueso-Ramos C, Post SM. Aberrant hnRNP K expression: All roads lead to cancer. Cell Cycle 2017; 15:1552-7. [PMID: 27049467 DOI: 10.1080/15384101.2016.1164372] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The classification of a gene as an oncogene or a tumor suppressor has been a staple of cancer biology for decades. However, as we delve deeper into the biology of these genes, this simple classification has become increasingly difficult for some. In the case of heterogeneous nuclear ribonuclear protein K (hnRNP K), its role as a tumor suppressor has recently been described in acute myeloid leukemia and demonstrated in a haploinsufficient mouse model. In contrast, data from other clinical correlation studies suggest that hnRNP K may be more fittingly described as an oncogene, due to its increased levels in a variety of malignancies. hnRNP K is a multifunctional protein that can regulate both oncogenic and tumor suppressive pathways through a bevy of chromatin-, DNA-, RNA-, and protein-mediated activates, suggesting its aberrant expression may have broad-reaching cellular impacts. In this review, we highlight our current understanding of hnRNP K, with particular emphasis on its apparently dichotomous roles in tumorigenesis.
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Affiliation(s)
- Miguel Gallardo
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Marisa J Hornbaker
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA.,b The University of Texas Graduate School of Biomedical Sciences at Houston , Houston , TX , USA
| | - Xiaorui Zhang
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Peter Hu
- c School of Health Professions, The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Carlos Bueso-Ramos
- d Department of Hematopathology , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
| | - Sean M Post
- a Department of Leukemia , The University of Texas, MD Anderson Cancer Center , Houston , TX , USA
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16
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Zhou JY, Chen M, Ma L, Wang X, Chen YG, Liu SL. Role of CD44(high)/CD133(high) HCT-116 cells in the tumorigenesis of colon cancer. Oncotarget 2016; 7:7657-66. [PMID: 26840024 PMCID: PMC4884945 DOI: 10.18632/oncotarget.7084] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/13/2016] [Indexed: 12/21/2022] Open
Abstract
This study aimed to explore cell surface biomarkers related to cancer stem cells (CSCs) and their role in the tumorigenesis of colon cancer. Various colon cancer cell lines were screened for CD133 and CD44 expression. CD44high/CD133high and CD44low/CD133low cells were separately isolated by Fluorescence-Activated Cell Sorting (FACS). The cell proliferation, colony formation, cell cycle characteristics, and tumorigenic properties in CD44high/CD133high and CD44low/CD133low cells were investigated through in vitro experiments and in vivo tumor xenograft models. The expression profiles of stem cell-related genes were examined by RT-PCR. With HCT-116 cells, flow cytometry analysis revealed that CD44high/CD133high cells had higher proliferation potency than CD44low/CD133low cells. Compared to CD44low/CD133low cells, CD44high/CD133high cells had more stem cell-related genes, and displayed increased tumorigenic ability. In summary, CD44high/CD133high cells isolated from HCT-116 cells harbor CSC properties that may be related to the tumor growth of colon cancer. These results suggest that CD44 and CD133 could be strong markers of colorectal cancer stem cells.
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Affiliation(s)
- Jin-Yong Zhou
- Central Laboratory, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Min Chen
- Department of Internal Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Long Ma
- Department of Urology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Xiaoxiao Wang
- Department of Medical Science Research, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Yu-Gen Chen
- Department of Colorectal Surgery, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Shen-Lin Liu
- Department of Oncology, The Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
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17
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Bryant CD, Yazdani N. RNA-binding proteins, neural development and the addictions. GENES BRAIN AND BEHAVIOR 2016; 15:169-86. [PMID: 26643147 DOI: 10.1111/gbb.12273] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 12/25/2022]
Abstract
Transcriptional and post-transcriptional regulation of gene expression defines the neurobiological mechanisms that bridge genetic and environmental risk factors with neurobehavioral dysfunction underlying the addictions. More than 1000 genes in the eukaryotic genome code for multifunctional RNA-binding proteins (RBPs) that can regulate all levels of RNA biogenesis. More than 50% of these RBPs are expressed in the brain where they regulate alternative splicing, transport, localization, stability and translation of RNAs during development and adulthood. Dysfunction of RBPs can exert global effects on their targetomes that underlie neurodegenerative disorders such as Alzheimer's and Parkinson's diseases as well as neurodevelopmental disorders, including autism and schizophrenia. Here, we consider the evidence that RBPs influence key molecular targets, neurodevelopment, synaptic plasticity and neurobehavioral dysfunction underlying the addictions. Increasingly well-powered genome-wide association studies in humans and mammalian model organisms combined with ever more precise transcriptomic and proteomic approaches will continue to uncover novel and possibly selective roles for RBPs in the addictions. Key challenges include identifying the biological functions of the dynamic RBP targetomes from specific cell types throughout subcellular space (e.g. the nuclear spliceome vs. the synaptic translatome) and time and manipulating RBP programs through post-transcriptional modifications to prevent or reverse aberrant neurodevelopment and plasticity underlying the addictions.
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Affiliation(s)
- C D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - N Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
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18
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Hutchins EJ, Belrose JL, Szaro BG. A novel role for the nuclear localization signal in regulating hnRNP K protein stability in vivo. Biochem Biophys Res Commun 2016; 478:772-6. [DOI: 10.1016/j.bbrc.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/04/2016] [Indexed: 01/12/2023]
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19
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Geuens T, Bouhy D, Timmerman V. The hnRNP family: insights into their role in health and disease. Hum Genet 2016; 135:851-67. [PMID: 27215579 PMCID: PMC4947485 DOI: 10.1007/s00439-016-1683-5] [Citation(s) in RCA: 740] [Impact Index Per Article: 82.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that contribute to multiple aspects of nucleic acid metabolism including alternative splicing, mRNA stabilization, and transcriptional and translational regulation. Many hnRNPs share general features, but differ in domain composition and functional properties. This review will discuss the current knowledge about the different hnRNP family members, focusing on their structural and functional divergence. Additionally, we will highlight their involvement in neurodegenerative diseases and cancer, and the potential to develop RNA-based therapies.
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Affiliation(s)
- Thomas Geuens
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Delphine Bouhy
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Group, VIB Molecular Genetics Department, University of Antwerp-CDE, Parking P4, Building V, Room 1.30, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Neurogenetics Laboratory, Institute Born Bunge, University of Antwerp, Antwerp, Belgium.
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20
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Dash S, Siddam AD, Barnum CE, Janga SC, Lachke SA. RNA-binding proteins in eye development and disease: implication of conserved RNA granule components. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:527-57. [PMID: 27133484 DOI: 10.1002/wrna.1355] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
Abstract
The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, the orthologs or family members of several conserved transcription and signaling regulators such as Pax6, Six3, Prox1, and Bmp4 are commonly required for their development. In contrast, our understanding of posttranscriptional regulation in eye development and disease, particularly regarding the function of RNA-binding proteins (RBPs), is limited. We examine the present knowledge of RBPs in eye development in the insect model Drosophila as well as several vertebrate models such as fish, frog, chicken, and mouse. Interestingly, of the 42 RBPs that have been investigated for their expression or function in vertebrate eye development, 24 (~60%) are recognized in eukaryotic cells as components of RNA granules such as processing bodies, stress granules, or other specialized ribonucleoprotein (RNP) complexes. We discuss the distinct developmental and cellular events that may necessitate potential RBP/RNA granule-associated RNA regulon models to facilitate posttranscriptional control of gene expression in eye morphogenesis. In support of these hypotheses, three RBPs and RNP/RNA granule components Tdrd7, Caprin2, and Stau2 are linked to ocular developmental defects such as congenital cataract, Peters anomaly, and microphthalmia in human patients or animal models. We conclude by discussing the utility of interdisciplinary approaches such as the bioinformatics tool iSyTE (integrated Systems Tool for Eye gene discovery) to prioritize RBPs for deriving posttranscriptional regulatory networks in eye development and disease. WIREs RNA 2016, 7:527-557. doi: 10.1002/wrna.1355 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Soma Dash
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Carrie E Barnum
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University & Purdue University Indianapolis, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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21
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Wang C, Szaro BG. Post-transcriptional regulation mediated by specific neurofilament introns in vivo. J Cell Sci 2016; 129:1500-11. [PMID: 26906423 DOI: 10.1242/jcs.185199] [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: 12/18/2015] [Accepted: 02/17/2016] [Indexed: 11/20/2022] Open
Abstract
Neurons regulate genes post-transcriptionally to coordinate the supply of cytoskeletal proteins, such as the medium neurofilament (NEFM), with demand for structural materials in response to extracellular cues encountered by developing axons. By using a method for evaluating functionality of cis-regulatory gene elements in vivo through plasmid injection into Xenopus embryos, we discovered that splicing of a specific nefm intron was required for robust transgene expression, regardless of promoter or cell type. Transgenes utilizing the nefm 3'-UTR but substituting other nefm introns expressed little or no protein owing to defects in handling of the messenger (m)RNA as opposed to transcription or splicing. Post-transcriptional events at multiple steps, but mainly during nucleocytoplasmic export, contributed to these varied levels of protein expression. An intron of the β-globin gene was also able to promote expression in a manner identical to that of the nefm intron, implying a more general preference for certain introns in controlling nefm expression. These results expand our knowledge of intron-mediated gene expression to encompass neurofilaments, indicating an additional layer of complexity in the control of a cytoskeletal gene needed for developing and maintaining healthy axons.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Ben G Szaro
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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22
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Zhang P, Wang N, Lin X, Jin L, Xu H, Li R, Huang H. Expression and localization of heterogeneous nuclear ribonucleoprotein K in mouse ovaries and preimplantation embryos. Biochem Biophys Res Commun 2016; 471:260-5. [PMID: 26850853 DOI: 10.1016/j.bbrc.2016.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 01/08/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNP K), an evolutionarily conserved protein, is involved in several important cellular processes that are relevant to cell proliferation, differentiation, apoptosis, and cancer development. However, details of hnRNP K expression during mammalian oogenesis and preimplantation embryo development are lacking. The present study investigates the expression and cellular localization of K protein in the mouse ovaries and preimplantation embryos using immunostaining. We demonstrate, for the first time, that hnRNP K is abundantly expressed in the nuclei of mouse oocytes in primordial, primary and secondary follicles. In germ vesicle (GV)-stage oocytes, hnRNP K accumulates in the germinal vesicle in a spot distribution manner. After germinal vesicle breakdown, speckled hnRNP K is diffusely distributed in the cytoplasm. However, after fertilization, the K protein relocates into the female and male pronucleus and persists in the blastomere nuclei. Localization of K protein in the human ovary and ovarian granulosa cell tumor (GCT) was also investigated. Overall, this study provides important morphological evidence to better understand the possible roles of hnRNP K in mammalian oogenesis and early embryo development.
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Affiliation(s)
- Ping Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ningling Wang
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xianhua Lin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Jin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Xu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Rong Li
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hefeng Huang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Mardakheh FK, Paul A, Kümper S, Sadok A, Paterson H, Mccarthy A, Yuan Y, Marshall CJ. Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions. Dev Cell 2015; 35:344-57. [PMID: 26555054 PMCID: PMC4643311 DOI: 10.1016/j.devcel.2015.10.005] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 08/23/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
Abstract
Polarization of cells into a protrusive front and a retracting cell body is the hallmark of mesenchymal-like cell migration. Many mRNAs are localized to protrusions, but it is unclear to what degree mRNA localization contributes toward protrusion formation. We performed global quantitative analysis of the distributions of mRNAs, proteins, and translation rates between protrusions and the cell body by RNA sequencing (RNA-seq) and quantitative proteomics. Our results reveal local translation as a key determinant of protein localization to protrusions. Accordingly, inhibition of local translation destabilizes protrusions and inhibits mesenchymal-like morphology. Interestingly, many mRNAs localized to protrusions are translationally repressed. Specific cis-regulatory elements within mRNA UTRs define whether mRNAs are locally translated or repressed. Finally, RNAi screening of RNA-binding proteins (RBPs) enriched in protrusions revealed trans-regulators of localized translation that are functionally important for protrusions. We propose that by deciphering the localized mRNA UTR code, these proteins regulate protrusion stability and mesenchymal-like morphology.
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Affiliation(s)
- Faraz K Mardakheh
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
| | - Angela Paul
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Sandra Kümper
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Amine Sadok
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Hugh Paterson
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Afshan Mccarthy
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Yinyin Yuan
- Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Christopher J Marshall
- Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
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24
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Ebrahimie E, Nurollah Z, Ebrahimi M, Hemmatzadeh F, Ignjatovic J. Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders. Mol Biol Rep 2015; 42:1377-90. [PMID: 26246405 DOI: 10.1007/s11033-015-3916-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 07/22/2015] [Indexed: 01/01/2023]
Abstract
Pandemic influenza remains as a substantial threat to humans with a widespread panic worldwide. In contrast, seasonal (non-pandemic) has a mild non-lethal infection each year. The underlying mechanisms governing the detrimental effects of pandemic influenza are yet to be known. Transcriptomic-based network discovery and gene ontology (GO) analysis of host response to pandemic influenza, compared to seasonal influenza, can shed light on the differential mechanisms which pandemic influenza is employed during evolution. Here, using microarray data of infected ferrets with pandemic and seasonal influenza (as a model), we evaluated the possible link between altered genes after pandemic infection with activation of neuronal disorders. To this end, we utilized novel computational biology techniques including differential transcriptome analysis, network construction, GO enrichment, and GO network to investigate the underlying mechanisms of pandemic influenza infection and host interaction. In comparison to seasonal influenza, pandemic influenza differentially altered the expression of 31 genes with direct involvement in activity of central nervous system (CNS). Network topology highlighted the high interactions of IRF1, NKX2-1 and NR5A1 as well as MIR27A, MIR19A, and MIR17. TGFB2, NCOA3 and SP1 were the central transcription factors in the networks. Pandemic influenza remarkably downregulated GPM6A and GTPase. GO network demonstrated the key roles of GPM6A and GTPase in regulation of important functions such as synapse assembly and neuron projection. For the first time, we showed that besides interference with cytokine/chemokine storm and neuraminidase enzyme, H1N1 pandemic influenza is able to directly affect neuronal gene networks. The possibility of application of some key regulators such as GPM6A protein, MIR128, and MIR367 as candidate therapeutic agents is discussed. The presented approach established a new way to unravel unknown pathways in virus-associated CNS dysfunction by utilizing global transcriptomic data, network and GO analysis.
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Affiliation(s)
- Esmaeil Ebrahimie
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia,
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25
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Wang J, Hu B, Cao F, Sun S, Zhang Y, Zhu Q. Down regulation of lncSCIR1 after spinal cord contusion injury in rat. Brain Res 2015; 1624:314-320. [PMID: 26254726 DOI: 10.1016/j.brainres.2015.07.052] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 12/19/2022]
Abstract
Extensive changes occur at transcriptional level after traumatic spinal cord injury (SCI). In this study, we performed a large scale screening of expression changes of long (>200 nt) RNA transcripts including both coding and non-coding RNA species in a rat contusion SCI model. We validated significant down-regulation of one long non-coding RNA (lncSCIR1) at 1, 4, and 7 days postinjury. lncSCIR1 knockdown promoted astrocyte proliferation and migration in vitro. We further validated the strong association between lncSCIR1 knock down and the expression changes of four mRNAs after injury. Our data indicated that lncSCIR1 down-regulation might play a detrimental role in the pathophysiology of traumatic SCI and thereby provided new insights into the studies of potential therapeutic targets for traumatic central nervous system (CNS) injuries.
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Affiliation(s)
- Jing Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China
| | - Bo Hu
- Deparment of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China
| | - Fei Cao
- Deparment of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China
| | - Shenggang Sun
- Deparment of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China
| | - Yunjian Zhang
- Deparment of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China
| | - Qing Zhu
- Deparment of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 JieFang Avenue, Wuhan 430022, China.
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26
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Wang H, Wu M, Zhan C, Ma E, Yang M, Yang X, Li Y. Neurofilament proteins in axonal regeneration and neurodegenerative diseases. Neural Regen Res 2015; 7:620-6. [PMID: 25745454 PMCID: PMC4346988 DOI: 10.3969/j.issn.1673-5374.2012.08.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 02/05/2012] [Indexed: 12/21/2022] Open
Abstract
Neurofilament protein is a component of the mature neuronal cytoskeleton, and it interacts with the zygosome, which is mediated by neurofilament-related proteins. Neurofilament protein regulates enzyme function and the structure of linker proteins. In addition, neurofilament gene expression plays an important role in nervous system development. Previous studies have shown that neurofilament gene transcriptional regulation is crucial for neurofilament protein expression, especially in axonal regeneration and degenerative diseases. Post-transcriptional regulation increased neurofilament protein gene transcription during axonal regeneration, ultimately resulting in a pattern of neurofilament protein expression. An expression imbalance of post-transcriptional regulatory proteins and other disorders could lead to amyotrophic lateral sclerosis or other neurodegenerative diseases. These findings indicated that after transcription, neurofilament protein regulated expression of related proteins and promoted regeneration of damaged axons, suggesting that regulation disorders could lead to neurodegenerative diseases.
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Affiliation(s)
- Haitao Wang
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
| | - Minfei Wu
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
| | - Chuanjun Zhan
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
| | - Enyuan Ma
- Department of Orthopedic Surgery, Beihua University Affiliated Hospital, Jilin 132000, Jilin Province, China
| | - Maoguang Yang
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
| | - Xiaoyu Yang
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
| | - Yingpu Li
- Department of Spine Surgery, China-Japan Union Hospital, Jilin University, Changchun 130033, Jilin Province, China
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27
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Ding X, Sun B, Huang J, Xu L, Pan J, Fang C, Tao Y, Hu S, Li R, Han X, Miao P, Wang Y, Yu J, Feng X. The role of miR-182 in regulating pineal CLOCK expression after hypoxia-ischemia brain injury in neonatal rats. Neurosci Lett 2015; 591:75-80. [PMID: 25684245 DOI: 10.1016/j.neulet.2015.02.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/14/2015] [Accepted: 02/11/2015] [Indexed: 11/18/2022]
Abstract
Circadian rhythm disorder is a common neurological deficit caused by neonatal hypoxic-ischemic brain damage (HIBD). However, little is known about its underlying mechanisms. Our previous studies revealed a significant elevation of clock genes at the protein, but not mRNA, levels in the pineal gland after neonatal HIBD. To investigate the mechanisms of post-transcriptional regulation on clock genes, we screened changes of miRNA levels in the pineal gland after neonatal HIBD using high-throughput arrays. Within the miRNAs whose expression was significantly down-regulated, we identified one miRNA (miR182) that targeted the 3'-untranslated region (3'-UTR) of Clock, a key component of clock genes, and played a crucial role in regulating CLOCK expression after oxygen-glucose deprivation in primarily cultured pinealocytes. Our findings therefore provide new insight on studies of therapeutic targets for circadian rhythm disturbance after neonatal HIBD.
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Affiliation(s)
- Xin Ding
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Bin Sun
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Jian Huang
- Center for Circadian Clocks, Medical College, Soochow University, Suzhou 215003, PR China
| | - Lixiao Xu
- Department of Hematology and Oncology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Jian Pan
- Department of Hematology and Oncology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Chen Fang
- Department of Endocrinology, The Second Affiliated Hospital of Soochow University, Suzhou 225003, PR China
| | - Yanfang Tao
- Department of Hematology and Oncology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Shukun Hu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200040, PR China
| | - Ronghu Li
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Xing Han
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Po Miao
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Ying Wang
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Jian Yu
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China
| | - Xing Feng
- Division of Neonatology, Affiliated Children's Hospital of Soochow University, Suzhou 215003, PR China.
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28
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Liu Y, Wang C, Destin G, Szaro BG. Microtubule-associated protein tau promotes neuronal class II β-tubulin microtubule formation and axon elongation in embryonic Xenopus laevis. Eur J Neurosci 2015; 41:1263-75. [PMID: 25656701 DOI: 10.1111/ejn.12848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/13/2014] [Accepted: 01/07/2015] [Indexed: 01/06/2023]
Abstract
Compared with its roles in neurodegeneration, much less is known about microtubule-associated protein tau's normal functions in vivo, especially during development. The external development and ease of manipulating gene expression of Xenopus laevis embryos make them especially useful for studying gene function during early development. To study tau's functions in axon outgrowth, we characterized the most prominent tau isoforms of Xenopus embryos and manipulated their expression. None of these four isoforms were strictly analogous to those commonly studied in mammals, as all constitutively contained exon 10, which is preferentially removed from mammalian fetal tau isoforms, as well as exon 8, which in mammals is rare. Nonetheless, like mammalian tau, Xenopus tau exhibited alternative splicing of exon 4a, which in mammals distinguishes 'big' tau of peripheral neurons, and exon 6. Strongly suppressing tau expression with antisense morpholino oligonucleotides only modestly compromised peripheral nerve outgrowth of intact tadpoles, but severely disrupted neuronal microtubules containing class II β-tubulins while leaving other microtubules largely unperturbed. Thus, the relatively mild dependence of axon development on tau likely resulted from having only a single class of microtubules disrupted by its loss. Also, consistent with its greater expression in long peripheral axons, boosting expression of 'big' tau increased neurite outgrowth significantly and enhanced tubulin acetylation more so than did the smaller isoform. These data demonstrate the utility of Xenopus as a tool to gain new insights into tau's functions in vivo.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Chen Wang
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Giovanny Destin
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ben G Szaro
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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29
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He L, Xue X, Wang Z, Hou E, Liu Y, Liang M, Zhang Y, Tian Z. Transcriptional regulation of heterogeneous nuclear ribonucleoprotein K gene expression. Biochimie 2014; 109:27-35. [PMID: 25497182 DOI: 10.1016/j.biochi.2014.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/03/2014] [Indexed: 01/05/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is importantly involved in the regulation of development, DNA damage response, and several human diseases. The molecular mechanisms that control the expression of hnRNP K are largely unknown. In the present study, we investigated the detailed mechanism of the transcriptional regulation of human hnRNP K gene. Two activating and one repressive elements located in the proximal segment of the transcriptional initiation site were identified in hnRNP K gene. A 19 bp-region was responsible for the inhibitory activities of the repressor element. Twenty proteins were identified by DNA-affinity purification and mass spectrometry analyses as binding partners of the primary activating element in the hnRNP K promoter. Chromatin immunoprecipitation and EMSA analysis confirmed the binding of Sp1 with hnRNP K promoter. Sp1 enhanced the promoter activity, increased the expression of hnRNP K, and reduced the mRNA level of angiotensinogen, a gene known to be negatively regulated by hnRNP K. In summary, the current study characterized the promoter elements that regulate the transcription of human hnRNP K gene, identified 20 proteins that bind to the primary activating element of hnRNP K promoter, and demonstrated a functional effect of Sp1 on hnRNP K transcription.
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Affiliation(s)
- Liqing He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China; State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China
| | - Xiaochang Xue
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China
| | - Zhengjun Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Entai Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yong Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyu Liang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yingqi Zhang
- State Key Laboratory of Cancer Biology, Department of Biopharmaceutics, School of Pharmacy, The Fourth Military Medical University, Xi'an 710032, China.
| | - Zhongmin Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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30
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Wang C, Szaro BG. A method for using direct injection of plasmid DNA to study cis-regulatory element activity in F0 Xenopus embryos and tadpoles. Dev Biol 2014; 398:11-23. [PMID: 25448690 DOI: 10.1016/j.ydbio.2014.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 10/31/2014] [Accepted: 11/11/2014] [Indexed: 11/17/2022]
Abstract
The ability to express exogenous reporter genes in intact, externally developing embryos, such as Xenopus, is a powerful tool for characterizing the activity of cis-regulatory gene elements during development. Although methods exist for generating transgenic Xenopus lines, more simplified methods for use with F0 animals would significantly speed the characterization of these elements. We discovered that injecting 2-cell stage embryos with a plasmid bearing a ϕC31 integrase-targeted attB element and two dual β-globin HS4 insulators flanking a reporter transgene in opposite orientations relative to each other yielded persistent expression with sufficiently high penetrance for characterizing the activity of the promoter without having to coinject integrase RNA. Expression began appropriately during development and persisted into swimming tadpole stages without perturbing the expression of the cognate endogenous gene. Coinjected plasmids having the same elements but expressing different reporter proteins were reliably coexpressed within the same cells, providing a useful control for variations in injections between animals. To overcome the high propensity of these plasmids to undergo recombination, we developed a method for generating them using conventional cloning methods and DH5α cells for propagation. We conclude that this method offers a convenient and reliable way to evaluate the activity of cis-regulatory gene elements in the intact F0 embryo.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.
| | - Ben G Szaro
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.
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31
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Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is an RNA-binding protein implicated in RNA metabolism. Here, we investigated the role of hnRNP K in synapse function. We demonstrated that hnRNP K regulates dendritic spine density and long-term potentiation (LTP) in cultured hippocampal neurons from embryonic rats. LTP requires the extracellular signal-regulated kinase (ERK)1/2-mediated phosphorylation and cytoplasmic accumulation of hnRNP K. Moreover, hnRNP K knockdown prevents ERK cascade activation and GluA1-S845 phosphorylation and surface delivery, which are essential steps for LTP. These findings establish hnRNP K as a new critical regulator of synaptic transmission and plasticity in hippocampal neurons.
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c-Jun N-terminal kinase phosphorylation of heterogeneous nuclear ribonucleoprotein K regulates vertebrate axon outgrowth via a posttranscriptional mechanism. J Neurosci 2013; 33:14666-80. [PMID: 24027268 DOI: 10.1523/jneurosci.4821-12.2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
c-Jun N-terminal kinase (JNK) mediates cell signaling essential for axon outgrowth, but the associated substrates and underlying mechanisms are poorly understood. We identified in Xenopus laevis embryos a novel posttranscriptional mechanism whereby JNK regulates axonogenesis by phosphorylating a specific site on heterogeneous nuclear ribonucleoprotein K (hnRNP K). Both JNK inhibition and hnRNP K knockdown inhibited axon outgrowth and translation of hnRNP K-regulated cytoskeletal RNAs (tau and neurofilament medium), effects that were alleviated by expressing phosphomimetic, but not phosphodeficient, forms of hnRNP K. Immunohistochemical and biochemical analyses indicated that JNK phosphorylation of hnRNP K occurred within the cytoplasm and was necessary for the translational initiation of hnRNP K-targeted RNAs but not for hnRNP K intracellular localization or RNA binding. Thus, in addition to its known roles in transcription and cytoskeletal organization, JNK acts posttranscriptionally through hnRNP K to regulate translation of proteins crucial for axonogenesis.
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Cao W, Razanau A, Feng D, Lobo VG, Xie J. Control of alternative splicing by forskolin through hnRNP K during neuronal differentiation. Nucleic Acids Res 2012; 40:8059-71. [PMID: 22684629 PMCID: PMC3439897 DOI: 10.1093/nar/gks504] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The molecular basis of cell signal-regulated alternative splicing at the 3′ splice site remains largely unknown. We isolated a protein kinase A-responsive ribonucleic acid (RNA) element from a 3′ splice site of the synaptosomal-associated protein 25 (Snap25) gene for forskolin-inhibited splicing during neuronal differentiation of rat pheochromocytoma PC12 cells. The element binds specifically to heterogeneous nuclear ribonucleo protein (hnRNP) K in a phosphatase-sensitive way, which directly competes with the U2 auxiliary factor U2AF65, an essential component of early spliceosomes. Transcripts with similarly localized hnRNP K target motifs upstream of alternative exons are enriched in genes often associated with neurological diseases. We show that such motifs upstream of the Runx1 exon 6 also bind hnRNP K, and importantly, hnRNP K is required for forskolin-induced repression of the exon. Interestingly, this exon encodes the peptide domain that determines the switch of the transcriptional repressor/activator activity of Runx1, a change known to be critical in specifying neuron lineages. Consistent with an important role of the target genes in neurons, knocking down hnRNP K severely disrupts forskolin-induced neurite growth. Thus, through hnRNP K, the neuronal differentiation stimulus forskolin targets a critical 3′ splice site component of the splicing machinery to control alternative splicing of crucial genes. This also provides a regulated direct competitor of U2AF65 for cell signal control of 3′ splice site usage.
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Affiliation(s)
- Wenguang Cao
- Department of Physiology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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34
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Heterogeneous nuclear ribonucleoprotein K, an RNA-binding protein, is required for optic axon regeneration in Xenopus laevis. J Neurosci 2012; 32:3563-74. [PMID: 22399778 DOI: 10.1523/jneurosci.5197-11.2012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Axotomized optic axons of Xenopus laevis, in contrast to those of mammals, retain their ability to regenerate throughout life. To better understand the molecular basis for this successful regeneration, we focused on the role of an RNA-binding protein, heterogeneous nuclear ribonucleoprotein (hnRNP) K, because it is required for axonogenesis during development and because several of its RNA targets are under strong post-transcriptional control during regeneration. At 11 d after optic nerve crush, hnRNP K underwent significant translocation into the nucleus of retinal ganglion cells (RGCs), indicating that the protein became activated during regeneration. To suppress its expression, we intravitreously injected an antisense Vivo-Morpholino oligonucleotide targeting hnRNP K. In uninjured eyes, it efficiently knocked down hnRNP K expression in only the RGCs, without inducing either an axotomy response or axon degeneration. After optic nerve crush, staining for multiple markers of regenerating axons showed no regrowth of axons beyond the lesion site with hnRNP K knockdown. RGCs nonetheless responded to the injury by increasing expression of multiple growth-associated RNAs and experienced no additional neurodegeneration above that normally seen with optic nerve injury. At the molecular level, hnRNP K knockdown during regeneration inhibited protein, but not mRNA, expression of several known hnRNP K RNA targets (NF-M, GAP-43) by compromising their efficient nuclear transport and disrupting their loading onto polysomes for translation. Our study therefore provides evidence of a novel post-transcriptional regulatory pathway orchestrated by hnRNP K that is essential for successful CNS axon regeneration.
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35
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Wang J, Sun S, Cao X, Deng X, Zhang Y, Zhu Q. Retracted: Overexpression of αCP2, a translational repressor of GAP-43, inhibited axon outgrowth during development in Xenopus laevis. Biochem Biophys Res Commun 2012; 419:262-7. [PMID: 22342981 DOI: 10.1016/j.bbrc.2012.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
Abstract
The 3'-untranslated regions (3'-UTRs) of growth-associated protein 43 (GAP-43), which is crucial for neural development and axonal regeneration, are highly conserved among vertebrates. Previous studies in mammals have identified one U-rich cis element within GAP-43 3'-UTR and several trans factors that regulate its mRNA stability. However, much less is known in lower vertebrates. The Xenopus GAP-43 3'-UTR, despite its high similarity with those in higher vertebrates, contains unique CU-rich sequences, suggesting the existence of novel cis elements and trans factors. In current study, we isolated four proteins bound to GAP-43 3'-UTR from juvenile frog brain using affinity purification. Mass spectrometry identified Hu antigen D (HuD) and poly(C) binding protein 2 (αCP2) as the proteins forming 48- and 44-kDa ribonucleoprotein complexes, respectively. We validated the association between αCP2 and GAP-43 3'-UTR in vivo. After confirming the post-transcriptional effects of αCP2 on GAP-43 expression, we demonstrated that αCP2 directly inhibited the translation of GAP-43 gene, without affecting its mRNA stability. αCP2 overexpression led to decreased level of GAP-43 protein and significantly inhibited axonal outgrowth in primarily cultured neurons. Our study therefore provided insights on novel functions of αCP2 in vertebrate nervous system during development and new mechanisms of post-transcriptional regulation for GAP-43 gene.
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Affiliation(s)
- Jing Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
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Proepper C, Steinestel K, Schmeisser MJ, Heinrich J, Steinestel J, Bockmann J, Liebau S, Boeckers TM. Heterogeneous nuclear ribonucleoprotein k interacts with Abi-1 at postsynaptic sites and modulates dendritic spine morphology. PLoS One 2011; 6:e27045. [PMID: 22102872 PMCID: PMC3216941 DOI: 10.1371/journal.pone.0027045] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 10/09/2011] [Indexed: 12/31/2022] Open
Abstract
Background Abelson-interacting protein 1 (Abi-1) plays an important role for dendritic branching and synapse formation in the central nervous system. It is localized at the postsynaptic density (PSD) and rapidly translocates to the nucleus upon synaptic stimulation. At PSDs Abi-1 is in a complex with several other proteins including WASP/WAVE or cortactin thereby regulating the actin cytoskeleton via the Arp 2/3 complex. Principal Findings We identified heterogeneous nuclear ribonucleoprotein K (hnRNPK), a 65 kDa ssDNA/RNA-binding-protein that is involved in multiple intracellular signaling cascades, as a binding partner of Abi-1 at postsynaptic sites. The interaction with the Abi-1 SH3 domain is mediated by the hnRNPK-interaction (KI) domain. We further show that during brain development, hnRNPK expression becomes more and more restricted to granule cells of the cerebellum and hippocampal neurons where it localizes in the cell nucleus as well as in the spine/dendritic compartment. The downregulation of hnRNPK in cultured hippocampal neurons by RNAi results in an enlarged dendritic tree and a significant increase in filopodia formation. This is accompanied by a decrease in the number of mature synapses. Both effects therefore mimic the neuronal morphology after downregulation of Abi-1 mRNA in neurons. Conclusions Our findings demonstrate a novel interplay between hnRNPK and Abi-1 in the nucleus and at synaptic sites and show obvious similarities regarding both protein knockdown phenotypes. This indicates that hnRNPK and Abi-1 act synergistic in a multiprotein complex that regulates the crucial balance between filopodia formation and synaptic maturation in neurons.
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Affiliation(s)
| | - Konrad Steinestel
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- Department of Pathology, BWK Hospital Ulm, Ulm, Germany
| | | | - Jutta Heinrich
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Julie Steinestel
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Juergen Bockmann
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Stefan Liebau
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- * E-mail: (TMB); (SL)
| | - Tobias M. Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- * E-mail: (TMB); (SL)
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Liu Y, Szaro BG. hnRNP K post-transcriptionally co-regulates multiple cytoskeletal genes needed for axonogenesis. Development 2011; 138:3079-90. [PMID: 21693523 DOI: 10.1242/dev.066993] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The RNA-binding protein, hnRNP K, is essential for axonogenesis. Suppressing its expression in Xenopus embryos yields terminally specified neurons with severely disorganized microtubules, microfilaments and neurofilaments, raising the hypothesis that hnRNP K post-transcriptionally regulates multiple transcripts of proteins that organize the axonal cytoskeleton. To identify downstream candidates for this regulation, RNAs that co-immunoprecipitated from juvenile brain with hnRNP K were identified on microarrays. A substantial number of these transcripts were linked to the cytoskeleton and to intracellular localization, trafficking and transport. Injection into embryos of a non-coding RNA bearing multiple copies of an hnRNP K RNA-binding consensus sequence found within these transcripts largely phenocopied hnRNP K knockdown, further supporting the idea that it regulates axonogenesis through its binding to downstream target RNAs. For further study of regulation by hnRNP K of the cytoskeleton during axon outgrowth, we focused on three validated RNAs representing elements associated with all three polymers - Arp2, tau and an α-internexin-like neurofilament. All three were co-regulated post-transcriptionally by hnRNP K, as hnRNP K knockdown yielded comparable defects in their nuclear export and translation but not transcription. Directly knocking down expression of all three together, but not each one individually, substantially reproduced the axonless phenotype, providing further evidence that regulation of axonogenesis by hnRNP K occurs largely through pleiotropic effects on cytoskeletal-associated targets. These experiments provide evidence that hnRNP K is the nexus of a novel post-transcriptional regulatory module controlling the synthesis of proteins that integrate all three cytoskeletal polymers to form the axon.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY 12222, USA
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Laursen LS, Chan CW, Ffrench-Constant C. Translation of myelin basic protein mRNA in oligodendrocytes is regulated by integrin activation and hnRNP-K. ACTA ACUST UNITED AC 2011; 192:797-811. [PMID: 21357748 PMCID: PMC3051817 DOI: 10.1083/jcb.201007014] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
α6β1-integrin interacts with hnRNP-K, an mRNA-binding protein, during oligodendrocyte differentiation to promote translation of MBP mRNA and myelin synthesis. Myelination in the central nervous system provides a unique example of how cells establish asymmetry. The myelinating cell, the oligodendrocyte, extends processes to and wraps multiple axons of different diameter, keeping the number of wraps proportional to the axon diameter. Local regulation of protein synthesis represents one mechanism used to control the different requirements for myelin sheath at each axo–glia interaction. Prior work has established that β1-integrins are involved in the axoglial interactions that initiate myelination. Here, we show that integrin activation regulates translation of a key sheath protein, myelin basic protein (MBP), by reversing the inhibitory effect of the mRNA 3′UTR. During oligodendrocyte differentiation and myelination α6β1-integrin interacts with hnRNP-K, an mRNA-binding protein, which binds to MBP mRNA and translocates from the nucleus to the myelin sheath. Furthermore, knockdown of hnRNP-K inhibits MBP protein synthesis during myelination. Together, these results identify a novel pathway by which axoglial adhesion molecules coordinate MBP synthesis with myelin sheath formation.
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Affiliation(s)
- Lisbeth S Laursen
- MRC Centre for Regenerative Medicine and MS Society Translational Research Centre, Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, Scotland, UK.
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Szaro BG, Strong MJ. Regulation of Cytoskeletal Composition in Neurons: Transcriptional and Post-transcriptional Control in Development, Regeneration, and Disease. ADVANCES IN NEUROBIOLOGY 2011. [DOI: 10.1007/978-1-4419-6787-9_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Wang Y, Fang H, Cao Y, Liu LS, Jiang M. Jintang Black Goat (Capra hircas) hnRNP K: Molecular Cloning, Sequence Analysis and Expression Detection. JOURNAL OF APPLIED ANIMAL RESEARCH 2010. [DOI: 10.1080/09712119.2010.10539503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Szaro BG, Strong MJ. Post-transcriptional control of neurofilaments: New roles in development, regeneration and neurodegenerative disease. Trends Neurosci 2010; 33:27-37. [DOI: 10.1016/j.tins.2009.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2009] [Revised: 09/21/2009] [Accepted: 10/06/2009] [Indexed: 12/17/2022]
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Ripoll JJ, Rodríguez-Cazorla E, González-Reig S, Andújar A, Alonso-Cantabrana H, Perez-Amador MA, Carbonell J, Martínez-Laborda A, Vera A. Antagonistic interactions between Arabidopsis K-homology domain genes uncover PEPPER as a positive regulator of the central floral repressor FLOWERING LOCUS C. Dev Biol 2009; 333:251-62. [DOI: 10.1016/j.ydbio.2009.06.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2009] [Revised: 06/25/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022]
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Lin AC, Tan CL, Lin CL, Strochlic L, Huang YS, Richter JD, Holt CE. Cytoplasmic polyadenylation and cytoplasmic polyadenylation element-dependent mRNA regulation are involved in Xenopus retinal axon development. Neural Dev 2009; 4:8. [PMID: 19254368 PMCID: PMC2661069 DOI: 10.1186/1749-8104-4-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 03/02/2009] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Translation in axons is required for growth cone chemotropic responses to many guidance cues. Although locally synthesized proteins are beginning to be identified, how specific mRNAs are selected for translation remains unclear. Control of poly(A) tail length by cytoplasmic polyadenylation element (CPE) binding protein 1 (CPEB1) is a conserved mechanism for mRNA-specific translational regulation that could be involved in regulating translation in axons. RESULTS We show that cytoplasmic polyadenylation is required in Xenopus retinal ganglion cell (RGC) growth cones for translation-dependent, but not translation-independent, chemotropic responses in vitro, and that inhibition of CPE binding through dominant-negative interference severely reduces axon outgrowth in vivo. CPEB1 mRNA transcripts are present at low levels in RGCs but, surprisingly, CPEB1 protein was not detected in eye or brain tissue, and CPEB1 loss-of-function does not affect chemotropic responses or pathfinding in vivo. UV cross-linking experiments suggest that CPE-binding proteins other than CPEB1 in the retina regulate retinal axon development. CONCLUSION These results indicate that cytoplasmic polyadenylation and CPE-mediated translational regulation are involved in retinal axon development, but that CPEB1 may not be the key regulator of polyadenylation in the developing retina.
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Affiliation(s)
- Andrew C Lin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| | - Chin Lik Tan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
- Cambridge Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Robinson Way, Cambridge, CB2 2PY, UK
| | - Chien-Ling Lin
- Program in Molecular Medicine, University of Massachusetts Medical School, Plantation St, Worcester, MA 01605, USA
| | - Laure Strochlic
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
- Institut National de la Santé et de la Recherche Médicale, Biologie des Jonctions Neuromusculaires, Université Paris V, Paris, France
| | - Yi-Shuian Huang
- Program in Molecular Medicine, University of Massachusetts Medical School, Plantation St, Worcester, MA 01605, USA
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2 Academia Road, Taipei 11529, Taiwan
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Plantation St, Worcester, MA 01605, USA
| | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3DY, UK
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Ananthakrishnan L, Szaro BG. Transcriptional and translational dynamics of light neurofilament subunit RNAs during Xenopus laevis optic nerve regeneration. Brain Res 2008; 1250:27-40. [PMID: 19027722 DOI: 10.1016/j.brainres.2008.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 10/24/2008] [Accepted: 11/01/2008] [Indexed: 12/01/2022]
Abstract
Neurofilaments (NFs), which comprise one of three cytoskeletal polymers of vertebrate axons, are heteropolymers of multiple NF subunit proteins. During Xenopus laevis optic nerve regeneration, NF subunit composition undergoes progressive changes that correlate with regenerative success. Understanding the relative contributions of transcriptional and post-transcriptional gene regulatory mechanisms to these changes should therefore provide insights into the control of the axonal growth program. Previously, we examined this issue with respect to the medium neurofilament protein (NF-M). Because the integrity of NF heteropolymers depends upon maintaining properly balanced expression among multiple subunits, we have now extended this analysis to include the four light NF subunits - peripherin, the light NF triplet protein (NF-L), and two additional alpha-internexin-like proteins. Within 3 days after an optic nerve crush injury to one eye, primary transcript levels of NF subunits increased in both eyes. Levels of mRNA, however, increased in only the operated eye and did so later than did increases in primary transcript, indicating that mRNA levels are under significant post-transcriptional regulation. As measured by polysome profiling, the translational efficiencies of individual NF subunit mRNAs also shifted throughout regeneration, with operated eye mRNAs being generally more translationally active than those of unoperated eyes. Also, in operated eyes, the precise mix of efficiently and poorly translated messages throughout regeneration varied independently for each subunit, indicating that their translations are fine-tuned separately. These results suggest a model whereby traumatic disruption of visual circuitry leads to increased expression of NF primary transcripts in both eyes. These increases are subsequently modulated post-transcriptionally to accommodate shifting demands at each phase of regeneration for NF heteropolymers of differing composition in regrowing axons.
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