1
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Hayden AN, Brandel KL, Merlau PR, Vijayakumar P, Leptich EJ, Pietryk EW, Gaytan ES, Ni CW, Chao HT, Rosenfeld JA, Arey RN. Behavioral screening of conserved RNA-binding proteins reveals CEY-1/YBX RNA-binding protein dysfunction leads to impairments in memory and cognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574402. [PMID: 38260399 PMCID: PMC10802296 DOI: 10.1101/2024.01.05.574402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
RNA-binding proteins (RBPs) regulate translation and plasticity which are required for memory. RBP dysfunction has been linked to a range of neurological disorders where cognitive impairments are a key symptom. However, of the 2,000 RBPs in the human genome, many are uncharacterized with regards to neurological phenotypes. To address this, we used the model organism C. elegans to assess the role of 20 conserved RBPs in memory. We identified eight previously uncharacterized memory regulators, three of which are in the C. elegans Y-Box (CEY) RBP family. Of these, we determined that cey-1 is the closest ortholog to the mammalian Y-Box (YBX) RBPs. We found that CEY-1 is both necessary in the nervous system for memory ability and sufficient to increase memory. Leveraging human datasets, we found both copy number variation losses and single nucleotide variants in YBX1 and YBX3 in individuals with neurological symptoms. We identified one predicted deleterious YBX3 variant of unknown significance, p.Asn127Tyr, in two individuals with neurological symptoms. Introducing this variant into endogenous cey-1 locus caused memory deficits in the worm. We further generated two humanized worm lines expressing human YBX3 or YBX1 at the cey-1 locus to test evolutionary conservation of YBXs in memory and the potential functional significance of the p.Asn127Tyr variant. Both YBX1/3 can functionally replace cey-1, and introduction of p.Asn127Tyr into the humanized YBX3 locus caused memory deficits. Our study highlights the worm as a model to reveal memory regulators and identifies YBX dysfunction as a potential new source of rare neurological disease.
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Affiliation(s)
- Ashley N Hayden
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Katie L Brandel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Paul R Merlau
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | | | - Emily J Leptich
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
| | - Edward W Pietryk
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
| | - Elizabeth S Gaytan
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Postbaccalaureate Research Education Program, Baylor College of Medicine, Houston, TX, 77030
| | - Connie W Ni
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Neuroscience, Rice University, Houston, TX 77005
| | - Hsiao-Tuan Chao
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030
- Baylor Genetics Laboratories, Houston, TX 77021
| | - Rachel N Arey
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030
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2
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Volpe S, Listro R, Ambrosio FA, Garbagnoli M, Linciano P, Rossi D, Costa G, Alcaro S, Vasile F, Hirsch AKH, Collina S. Identification of HuR-RNA Interfering Compounds by Dynamic Combinatorial Chemistry and Fluorescence Polarization. ACS Med Chem Lett 2023; 14:1509-1516. [PMID: 37970588 PMCID: PMC10641899 DOI: 10.1021/acsmedchemlett.3c00303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023] Open
Abstract
The RNA binding protein HuR regulates the post-transcriptional process of different oncogenes and tumor suppressor genes, and its dysregulation is linked with cancer. Thus, modulating the complex HuR-RNA represents a promising anticancer strategy. To search for novel HuR ligands able to interfere with the HuR-RNA complex, the protein-templated dynamic combinatorial chemistry (pt-DCC) method was utilized. The recombinant RRM1+2 protein construct, which contains essential domains for ligand-HuR binding and exhibits enhanced solubility and stability compared to the native protein, was used for pt-DCC. Seven acylhydrazones with over 80% amplification were identified. The binding of the fragments to HuR extracted from DCC was validated using STD-NMR, and molecular modeling studies revealed the ability of the compounds to bind HuR at the mRNA binding pocket. Notably, three compounds effectively interfered with HuR-RNA binding in fluorescence polarization studies, suggesting their potential as foundational compounds for developing anticancer HuR-RNA interfering agents.
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Affiliation(s)
- Serena
Della Volpe
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz
Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Roberta Listro
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Francesca Alessandra Ambrosio
- Department
of Experimental and Clinical Medicine, University
“Magna Græcia” of Catanzaro, Campus “S. Venuta”,
Viale Europa, 88100 Catanzaro, Italy
| | - Martina Garbagnoli
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Pasquale Linciano
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giosuè Costa
- Department
of Health Sciences, University “Magna
Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science
Academic Spin-Off, University “Magna
Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Department
of Health Sciences, University “Magna
Græcia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
- Net4Science
Academic Spin-Off, University “Magna
Græcia” of Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Vasile
- Department
of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Anna K. H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz
Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Simona Collina
- Department
of Drug Sciences, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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3
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Kattan FG, Koukouraki P, Anagnostopoulos AK, Tsangaris GT, Doxakis E. RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of SNCA transcripts. Open Biol 2023; 13:230158. [PMID: 37989221 PMCID: PMC10688287 DOI: 10.1098/rsob.230158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023] Open
Abstract
Alpha-synuclein (SNCA) accumulation plays a central role in the pathogenesis of Parkinson's disease. Determining and interfering with the mechanisms that control SNCA expression is one approach to limiting disease progression. Currently, most of our understanding of SNCA regulation is protein-based. Post-transcriptional mechanisms directly regulating SNCA mRNA expression via its 3' untranslated region (3'UTR) were investigated here. Mass spectrometry of proteins pulled down from murine brain lysates using a biotinylated SNCA 3'UTR revealed multiple RNA-binding proteins, of which HNRNPD/AUF1 was chosen for further analysis. AUF1 bound both proximal and distal regions of the SNCA 3'UTR, but not the 5'UTR or CDS. In the nucleus, AUF1 attenuated SNCA pre-mRNA maturation and was indispensable for the export of SNCA transcripts. AUF1 destabilized SNCA transcripts in the cytosol, primarily those with shorter 3'UTRs, independently of microRNAs by recruiting the CNOT1-CNOT7 deadenylase complex to trim the polyA tail. Furthermore, AUF1 inhibited SNCA mRNA binding to ribosomes. These data identify AUF1 as a multi-tasking protein regulating maturation, nucleocytoplasmic shuttling, stability and translation of SNCA transcripts.
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Affiliation(s)
- Fedon-Giasin Kattan
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
- Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Pelagia Koukouraki
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Athanasios K. Anagnostopoulos
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - George T. Tsangaris
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA), Soranou Efesiou 4, Athens 11527, Greece
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4
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Marchesi N, Linciano P, Campagnoli LIM, Fahmideh F, Rossi D, Costa G, Ambrosio FA, Barbieri A, Collina S, Pascale A. Short- and Long-Term Regulation of HuD: A Molecular Switch Mediated by Folic Acid? Int J Mol Sci 2023; 24:12201. [PMID: 37569576 PMCID: PMC10418318 DOI: 10.3390/ijms241512201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The RNA-binding protein HuD has been shown to play a crucial role in gene regulation in the nervous system and is involved in various neurological and psychiatric diseases. In this study, through the creation of an interaction network on HuD and its potential targets, we identified a strong association between HuD and several diseases of the nervous system. Specifically, we focused on the relationship between HuD and the brain-derived neurotrophic factor (BDNF), whose protein is implicated in several neuronal diseases and is involved in the regulation of neuronal development, survival, and function. To better investigate this relationship and given that we previously demonstrated that folic acid (FA) is able to directly bind HuD itself, we performed in vitro experiments in neuron-like human SH-SY5Y cells in the presence of FA, also known to be a pivotal environmental factor influencing the nervous system development. Our findings show that FA exposure results in a significant increase in both HuD and BDNF transcripts and proteins after 2 and 4 h of treatment, respectively. Similar data were obtained after 2 h of FA incubation followed by 2 h of washout. This increase was no longer detected upon 24 h of FA exposure, probably due to a signaling shutdown mechanism. Indeed, we observed that following 24 h of FA exposure HuD is methylated. These findings indicate that FA regulates BDNF expression via HuD and suggest that FA can behave as an epigenetic modulator of HuD in the nervous system acting via short- and long-term mechanisms. Finally, the present results also highlight the potential of BDNF as a therapeutic target for specific neurological and psychiatric diseases.
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Affiliation(s)
- Nicoletta Marchesi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Pasquale Linciano
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | | | - Foroogh Fahmideh
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | - Giosuè Costa
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (G.C.); (F.A.A.)
- Net4Science Academic Spin-Off, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy
- Associazione CRISEA-Centro di Ricerca e Servizi Avanzati per l’Innovazione Rurale, 88055 Catanzaro, Italy
| | - Francesca Alessandra Ambrosio
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy; (G.C.); (F.A.A.)
| | - Annalisa Barbieri
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry Section, University of Pavia, 27100 Pavia, Italy; (P.L.); (D.R.); (S.C.)
| | - Alessia Pascale
- Department of Drug Sciences, Pharmacology Section, University of Pavia, 27100 Pavia, Italy; (L.I.M.C.); (F.F.); (A.B.)
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5
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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6
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Titus MB, Chang AW, Olesnicky EC. Exploring the Diverse Functional and Regulatory Consequences of Alternative Splicing in Development and Disease. Front Genet 2021; 12:775395. [PMID: 34899861 PMCID: PMC8652244 DOI: 10.3389/fgene.2021.775395] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a fundamental mechanism of eukaryotic RNA regulation that increases the transcriptomic and proteomic complexity within an organism. Moreover, alternative splicing provides a framework for generating unique yet complex tissue- and cell type-specific gene expression profiles, despite using a limited number of genes. Recent efforts to understand the negative consequences of aberrant splicing have increased our understanding of developmental and neurodegenerative diseases such as spinal muscular atrophy, frontotemporal dementia and Parkinsonism linked to chromosome 17, myotonic dystrophy, and amyotrophic lateral sclerosis. Moreover, these studies have led to the development of innovative therapeutic treatments for diseases caused by aberrant splicing, also known as spliceopathies. Despite this, a paucity of information exists on the physiological roles and specific functions of distinct transcript spliceforms for a given gene. Here, we will highlight work that has specifically explored the distinct functions of protein-coding spliceforms during development. Moreover, we will discuss the use of alternative splicing of noncoding exons to regulate the stability and localization of RNA transcripts.
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Affiliation(s)
- M Brandon Titus
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W Chang
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C Olesnicky
- University of Colorado Colorado Springs, Colorado Springs, CO, United States
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7
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Guo H, Jiang Y, Gu Z, Ren L, Zhu C, Yu S, Wei R. ZFP36 protects against oxygen-glucose deprivation/reoxygenation-induced mitochondrial fragmentation and neuronal apoptosis through inhibiting NOX4-DRP1 pathway. Brain Res Bull 2021; 179:57-67. [PMID: 34896479 DOI: 10.1016/j.brainresbull.2021.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/20/2021] [Accepted: 12/06/2021] [Indexed: 01/23/2023]
Abstract
The imbalance of mitochondrial dynamics plays an important role in the pathogenesis of cerebral ischemia/reperfusion (I/R) injury. Zinc-finger protein 36 (ZFP36) has been documented to have neuroprotective effects, however, whether ZFP36 is involved in the regulation of neuronal survival during cerebral I/R injury remains unknown. In this study, we found that the transcriptional and translational levels of ZFP36 were increased in immortalized hippocampal HT22 neuronal cells after oxygen-glucose deprivation/reoxygenation (OGD/R) treatment. ZFP36 gene silencing exacerbated OGD/R-induced dynamin-related protein 1 (DRP1) activity, mitochondrial fragmentation, oxidative stress and neuronal apoptosis, whereas ZFP36 overexpression exhibited the opposite effects. Besides, we found that NADPH oxidase 4 (NOX4) was upregulated by OGD/R, and NOX4 inhibition remarkably attenuated OGD/R-instigated DRP1 activity, mitochondrial fragmentation and neuronal apoptosis. Further study demonstrated that ZFP36 targeted NOX4 mRNA directly by binding to the AU-rich elements (AREs) in the NOX4 3'-untranslated regions (3'-UTR) and inhibited NOX4 expression. Taken together, our data indicate that ZFP36 protects against OGD/R-induced neuronal injury by inhibiting NOX4-mediated DRP1 activation and excessive mitochondrial fission. Pharmacological targeting of ZFP36 to suppress excessive mitochondrial fission may provide new therapeutic strategies in the treatment of cerebral I/R injury.
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Affiliation(s)
- Hengjiang Guo
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yan Jiang
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhiqing Gu
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Lulu Ren
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Change Zhu
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Shenghua Yu
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Rong Wei
- Department of Anesthesiology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China.
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8
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Chandra PK, Cikic S, Baddoo MC, Rutkai I, Guidry JJ, Flemington EK, Katakam PV, Busija DW. Transcriptome analysis reveals sexual disparities in gene expression in rat brain microvessels. J Cereb Blood Flow Metab 2021; 41:2311-2328. [PMID: 33715494 PMCID: PMC8392780 DOI: 10.1177/0271678x21999553] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sex is an important determinant of brain microvessels (MVs) function and susceptibility to cerebrovascular and neurological diseases, but underlying mechanisms are unclear. Using high throughput RNA sequencing analysis, we examined differentially expressed (DE) genes in brain MVs from young, male, and female rats. Bioinformatics analysis of the 23,786 identified genes indicates that 298 (1.2%) genes were DE using False Discovery Rate criteria (FDR; p < 0.05), of which 119 (40%) and 179 (60%) genes were abundantly expressed in male and female MVs, respectively. Nucleic acid binding, enzyme modulator, and transcription factor were the top three DE genes, which were more highly expressed in male than female MVs. Synthesis of glycosylphosphatidylinositol (GPI), biosynthesis of GPI-anchored proteins, steroid and cholesterol synthesis, were the top three significantly enriched canonical pathways in male MVs. In contrast, respiratory chain, ribosome, and 3 ́-UTR-mediated translational regulation were the top three enriched canonical pathways in female MVs. Different gene functions of MVs were validated by proteomic analysis and western blotting. Our novel findings reveal major sex disparities in gene expression and canonical pathways of MVs and these differences provide a foundation to study the underlying mechanisms and consequences of sex-dependent differences in cerebrovascular and other neurological diseases.
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Affiliation(s)
- Partha K Chandra
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sinisa Cikic
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Melody C Baddoo
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ibolya Rutkai
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jessie J Guidry
- Tulane Brain Institute, Tulane University, New Orleans, LA, USA
| | - Erik K Flemington
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Prasad Vg Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
| | - David W Busija
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA.,Department of Pathology, Tulane University School of Medicine, New Orleans, LA, USA
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9
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Titus MB, Wright EG, Bono JM, Poliakon AK, Goldstein BR, Super MK, Young LA, Manaj M, Litchford M, Reist NE, Killian DJ, Olesnicky EC. The conserved alternative splicing factor caper regulates neuromuscular phenotypes during development and aging. Dev Biol 2021; 473:15-32. [PMID: 33508255 PMCID: PMC7987824 DOI: 10.1016/j.ydbio.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/17/2022]
Abstract
RNA-binding proteins play an important role in the regulation of post-transcriptional gene expression throughout the nervous system. This is underscored by the prevalence of mutations in genes encoding RNA splicing factors and other RNA-binding proteins in a number of neurodegenerative and neurodevelopmental disorders. The highly conserved alternative splicing factor Caper is widely expressed throughout the developing embryo and functions in the development of various sensory neural subtypes in the Drosophila peripheral nervous system. Here we find that caper dysfunction leads to aberrant neuromuscular junction morphogenesis, as well as aberrant locomotor behavior during larval and adult stages. Despite its widespread expression, our results indicate that caper function is required to a greater extent within the nervous system, as opposed to muscle, for neuromuscular junction development and for the regulation of adult locomotor behavior. Moreover, we find that Caper interacts with the RNA-binding protein Fmrp to regulate adult locomotor behavior. Finally, we show that caper dysfunction leads to various phenotypes that have both a sex and age bias, both of which are commonly seen in neurodegenerative disorders in humans.
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Affiliation(s)
- M Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Andrea K Poliakon
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Brandon R Goldstein
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Meg K Super
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Lauren A Young
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Melpomeni Manaj
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Morgan Litchford
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Noreen E Reist
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Darrell J Killian
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
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10
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Ravanidis S, Bougea A, Karampatsi D, Papagiannakis N, Maniati M, Stefanis L, Doxakis E. Differentially Expressed Circular RNAs in Peripheral Blood Mononuclear Cells of Patients with Parkinson's Disease. Mov Disord 2021; 36:1170-1179. [PMID: 33433033 PMCID: PMC8248110 DOI: 10.1002/mds.28467] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/18/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background New noninvasive and affordable molecular approaches that will complement current practices and increase the accuracy of Parkinson's disease (PD) diagnosis are urgently needed. Circular RNAs (circRNAs) are stable noncoding RNAs that accumulate with aging in neurons and are increasingly shown to regulate all aspects of neuronal development and function. Objectives Τhe aims of this study were to identify differentially expressed circRNAs in blood mononuclear cells of patients with idiopathic PD and explore the competing endogenous RNA networks affected. Methods Eighty‐seven circRNAs were initially selected based on relatively high gene expression in the human brain. More than half of these were readily detectable in blood mononuclear cells using real‐time reverse transcription‐polymerase chain reaction. Comparative expression analysis was then performed in blood mononuclear cells from 60 control subjects and 60 idiopathic subjects with PD. Results Six circRNAs were significantly down‐regulated in patients with PD. The classifier that best distinguished PD consisted of four circRNAs with an area under the curve of 0.84. Cross‐linking immunoprecipitation‐sequencing data revealed that the RNA‐binding proteins bound by most of the deregulated circRNAs include the neurodegeneration‐associated FUS, TDP43, FMR1, and ATXN2. MicroRNAs predicted to be sequestered by most deregulated circRNAs have the Gene Ontology categories “protein modification” and “transcription factor activity” mostly enriched. Conclusions This is the first study that identifies specific circRNAs that may serve as diagnostic biomarkers for PD. Because they are highly expressed in the brain and are derived from genes with essential brain functions, they may also hint on the PD pathways affected. © 2021 Biomedical Research Foundation, Academy of Athens. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Anastasia Bougea
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Dimitra Karampatsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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11
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Alqawlaq S, Livne-Bar I, Williams D, D'Ercole J, Leung SW, Chan D, Tuccitto A, Datti A, Wrana JL, Corbett AH, Schmitt-Ulms G, Sivak JM. An endogenous PI3K interactome promoting astrocyte-mediated neuroprotection identifies a novel association with RNA-binding protein ZC3H14. J Biol Chem 2021; 296:100118. [PMID: 33234594 PMCID: PMC7948738 DOI: 10.1074/jbc.ra120.015389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 11/06/2022] Open
Abstract
Astrocytes can support neuronal survival through a range of secreted signals that protect against neurotoxicity, oxidative stress, and apoptotic cascades. Thus, analyzing the effects of the astrocyte secretome may provide valuable insight into these neuroprotective mechanisms. Previously, we characterized a potent neuroprotective activity mediated by retinal astrocyte conditioned media (ACM) on retinal and cortical neurons in metabolic stress models. However, the molecular mechanism underlying this complex activity in neuronal cells has remained unclear. Here, a chemical genetics screen of kinase inhibitors revealed phosphoinositide 3-kinase (PI3K) as a central player transducing ACM-mediated neuroprotection. To identify additional proteins contributing to the protective cascade, endogenous PI3K was immunoprecipitated from neuronal cells exposed to ACM or control media, followed by MS/MS proteomic analyses. These data pointed toward a relatively small number of proteins that coimmunoprecipitated with PI3K, and surprisingly only five were regulated by the ACM signal. These hits included expected PI3K interactors, such as the platelet-derived growth factor receptor A (PDGFRA), as well as novel RNA-binding protein interactors ZC3H14 (zinc finger CCCH-type containing 14) and THOC1 (THO complex protein 1). In particular, ZC3H14 has recently emerged as an important RNA-binding protein with multiple roles in posttranscriptional regulation. In validation studies, we show that PI3K recruitment of ZC3H14 is necessary for PDGF-induced neuroprotection and that this interaction is present in primary retinal ganglion cells. Thus, we identified a novel non-cell autonomous neuroprotective signaling cascade mediated through PI3K that requires recruitment of ZC3H14 and may present a promising strategy to promote astrocyte-secreted prosurvival signals.
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Affiliation(s)
- Samih Alqawlaq
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Izhar Livne-Bar
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Declan Williams
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Joseph D'Ercole
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Darren Chan
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandra Tuccitto
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada
| | - Alessandro Datti
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jeffrey L Wrana
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Gerold Schmitt-Ulms
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Ontario, Canada
| | - Jeremy M Sivak
- Department of Vision Science, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Ophthalmology and Vision Science, University of Toronto School of Medicine, Toronto, Ontario, Canada.
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12
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El Azzouzi H, Vilaça AP, Feyen DAM, Gommans WM, de Weger RA, Doevendans PAF, Sluijter JPG. Cardiomyocyte Specific Deletion of ADAR1 Causes Severe Cardiac Dysfunction and Increased Lethality. Front Cardiovasc Med 2020; 7:30. [PMID: 32258062 PMCID: PMC7093378 DOI: 10.3389/fcvm.2020.00030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/21/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Adenosine deaminase acting on RNA 1 (ADAR1) is a double-stranded RNA-editing enzyme that is involved in several functions including the deamination of adenosine to inosine, RNA interference (RNAi) mechanisms and microRNA (miRNA) processing, rendering ADAR1 essential for life. Methods and Results: To investigate whether maintenance of ADAR1 expression is required for normal myocardial homeostasis, we bypassed the early embryonic lethality of ADAR1-null mice through the use of a tamoxifen-inducible Cre recombinase under the control of the cardiac-specific α-myosin heavy chain promoter (αMHC). Targeted ADAR1 deletion in adult mice caused a significant increase in lethality accompanied by severe ventricular remodeling and quick and spontaneous cardiac dysfunction, induction of stress markers and overall reduced expression of miRNAs. Administration of a selective inhibitor of the unfolded protein response (UPR) stress significantly blunted the deleterious effects and improved cardiac function thereby prolonging animal survival. In vitro restoring miR-199a-5p levels in cardiomyocytes lacking ADAR1 diminished UPR activation and concomitant apoptosis. Conclusions: Our findings demonstrate an essential role for ADAR1 in cardiomyocyte survival and maintenance of cardiac function through a mechanism that integrates ADAR1 dependent miRNA processing and the suppression of UPR stress.
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Affiliation(s)
- Hamid El Azzouzi
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Andreia P Vilaça
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Dries A M Feyen
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Willemijn M Gommans
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, United States
| | - Roel A de Weger
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Pieter A F Doevendans
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Interuniversity Cardiology Institute Netherlands, Royal Netherlands Academy of Sciences, Utrecht, Netherlands.,Utrecht University, Utrecht, Netherlands
| | - Joost P G Sluijter
- Laboratory of Experimental Cardiology, Circulatory Health Laboratory, Department of Cardiology, Regenerative Medicine Center, University Medical Center Utrecht, Utrecht, Netherlands.,Interuniversity Cardiology Institute Netherlands, Royal Netherlands Academy of Sciences, Utrecht, Netherlands.,Utrecht University, Utrecht, Netherlands
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13
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Zhao YF, He XX, Song ZF, Guo Y, Zhang YN, Yu HL, He ZX, Xiong WC, Guo W, Zhu XJ. Human antigen R-regulated mRNA metabolism promotes the cell motility of migrating mouse neurons. Development 2020; 147:dev.183509. [PMID: 32098764 PMCID: PMC7097226 DOI: 10.1242/dev.183509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/13/2020] [Indexed: 01/02/2023]
Abstract
Neocortex development during embryonic stages requires the precise control of mRNA metabolism. Human antigen R (HuR) is a well-studied mRNA-binding protein that regulates mRNA metabolism, and it is highly expressed in the neocortex during developmental stages. Deletion of HuR does not impair neural progenitor cell proliferation or differentiation, but it disturbs the laminar structure of the neocortex. We report that HuR is expressed in postmitotic projection neurons during mouse brain development. Specifically, depletion of HuR in these neurons led to a mislocalization of CDP+ neurons in deeper layers of the cortex. Time-lapse microscopy showed that HuR was required for the promotion of cell motility in migrating neurons. PCR array identified profilin 1 (Pfn1) mRNA as a major binding partner of HuR in neurons. HuR positively mediated the stability of Pfn1 mRNA and influenced actin polymerization. Overexpression of Pfn1 successfully rescued the migration defects of HuR-deleted neurons. Our data reveal a post-transcriptional mechanism that maintains actin dynamics during neuronal migration. Summary: Maintaining actin dynamics is crucial for cell motility. Post-transcriptional regulation plays a pivotal role in supporting actin dynamics during neuronal migration.
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Affiliation(s)
- Yi-Fei Zhao
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Xiao-Xiao He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Zi-Fei Song
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Ye Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan-Ning Zhang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Hua-Li Yu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Zi-Xuan He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Wen-Cheng Xiong
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Weixiang Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China .,Graduate School, University of Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Juan Zhu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
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14
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Musashi‐2 and related stem cell proteins in the mouse suprachiasmatic nucleus and their potential role in circadian rhythms. Int J Dev Neurosci 2019; 75:44-58. [DOI: 10.1016/j.ijdevneu.2019.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/17/2019] [Accepted: 04/30/2019] [Indexed: 01/14/2023] Open
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15
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Della Volpe S, Nasti R, Queirolo M, Unver MY, Jumde VK, Dömling A, Vasile F, Potenza D, Ambrosio FA, Costa G, Alcaro S, Zucal C, Provenzani A, Di Giacomo M, Rossi D, Hirsch AKH, Collina S. Novel Compounds Targeting the RNA-Binding Protein HuR. Structure-Based Design, Synthesis, and Interaction Studies. ACS Med Chem Lett 2019; 10:615-620. [PMID: 30996806 DOI: 10.1021/acsmedchemlett.8b00600] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/21/2019] [Indexed: 12/14/2022] Open
Abstract
The key role of RNA-binding proteins (RBPs) in regulating post-transcriptional processes and their involvement in several pathologies (i.e., cancer and neurodegeneration) have highlighted their potential as therapeutic targets. In this scenario, Embryonic Lethal Abnormal Vision (ELAV) or Hu proteins and their complexes with target mRNAs have been gaining growing attention. Compounds able to modulate the complex stability could constitute an innovative pharmacological strategy for the treatment of numerous diseases. Nevertheless, medicinal-chemistry efforts aimed at developing such compounds are still at an early stage. As part of our ongoing research in this field, we hereby present the rational design and synthesis of structurally novel HuR ligands, potentially acting as HuR-RNA interferers. The following assessment of the structural features of their interaction with HuR, combining saturation-transfer difference NMR and in silico studies, provides a guide for further research on the development of new effective interfering compounds of the HuR-RNA complex.
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Affiliation(s)
- Serena Della Volpe
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Rita Nasti
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Michele Queirolo
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Varsha K. Jumde
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Francesca Vasile
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | - Donatella Potenza
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy
| | | | - Giosué Costa
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Chiara Zucal
- Department of CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, TN, Italy
| | | | - Marcello Di Giacomo
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Anna K. H. Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization and Department of Pharmacy, Saarland University, Campus Building E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747 AG, Groningen, The Netherlands
| | - Simona Collina
- Department of Drug Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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16
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Mao S, Zhang S, Zhou Z, Shi X, Huang T, Feng W, Yao C, Gu X, Yu B. Alternative RNA splicing associated with axon regeneration after rat peripheral nerve injury. Exp Neurol 2018; 308:80-89. [DOI: 10.1016/j.expneurol.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/11/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
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17
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Exploration of ligand binding modes towards the identification of compounds targeting HuR: a combined STD-NMR and Molecular Modelling approach. Sci Rep 2018; 8:13780. [PMID: 30214075 PMCID: PMC6137155 DOI: 10.1038/s41598-018-32084-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/29/2018] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional processes have been recognised as pivotal in the control of gene expression, and impairments in RNA processing are reported in several pathologies (i.e., cancer and neurodegeneration). Focusing on RNA-binding proteins (RBPs), the involvement of Embryonic Lethal Abnormal Vision (ELAV) or Hu proteins and their complexes with target mRNAs in the aetiology of various dysfunctions, has suggested the great potential of compounds able to interfere with the complex stability as an innovative pharmacological strategy for the treatment of numerous diseases. Here, we present a rational follow-up investigation of the interaction between ELAV isoform HuR and structurally-related compounds (i.e., flavonoids and coumarins), naturally decorated with different functional groups, by means of STD-NMR and Molecular Modelling. Our results represent the foundation for the development of potent and selective ligands able to interfere with ELAV–RNA complexes.
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18
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Olesnicky EC, Wright EG. Drosophila as a Model for Assessing the Function of RNA-Binding Proteins during Neurogenesis and Neurological Disease. J Dev Biol 2018; 6:E21. [PMID: 30126171 PMCID: PMC6162566 DOI: 10.3390/jdb6030021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
An outstanding question in developmental neurobiology is how RNA processing events contribute to the regulation of neurogenesis. RNA processing events are increasingly recognized as playing fundamental roles in regulating multiple developmental events during neurogenesis, from the asymmetric divisions of neural stem cells, to the generation of complex and diverse neurite morphologies. Indeed, both asymmetric cell division and neurite morphogenesis are often achieved by mechanisms that generate asymmetric protein distributions, including post-transcriptional gene regulatory mechanisms such as the transport of translationally silent messenger RNAs (mRNAs) and local translation of mRNAs within neurites. Additionally, defects in RNA splicing have emerged as a common theme in many neurodegenerative disorders, highlighting the importance of RNA processing in maintaining neuronal circuitry. RNA-binding proteins (RBPs) play an integral role in splicing and post-transcriptional gene regulation, and mutations in RBPs have been linked with multiple neurological disorders including autism, dementia, amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Fragile X syndrome (FXS), and X-linked intellectual disability disorder. Despite their widespread nature and roles in neurological disease, the molecular mechanisms and networks of regulated target RNAs have been defined for only a small number of specific RBPs. This review aims to highlight recent studies in Drosophila that have advanced our knowledge of how RBP dysfunction contributes to neurological disease.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
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19
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Ravanidis S, Kattan FG, Doxakis E. Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors. Int J Mol Sci 2018; 19:ijms19082280. [PMID: 30081499 PMCID: PMC6121432 DOI: 10.3390/ijms19082280] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 12/13/2022] Open
Abstract
The timing, dosage and location of gene expression are fundamental determinants of brain architectural complexity. In neurons, this is, primarily, achieved by specific sets of trans-acting RNA-binding proteins (RBPs) and their associated factors that bind to specific cis elements throughout the RNA sequence to regulate splicing, polyadenylation, stability, transport and localized translation at both axons and dendrites. Not surprisingly, misregulation of RBP expression or disruption of its function due to mutations or sequestration into nuclear or cytoplasmic inclusions have been linked to the pathogenesis of several neuropsychiatric and neurodegenerative disorders such as fragile-X syndrome, autism spectrum disorders, spinal muscular atrophy, amyotrophic lateral sclerosis and frontotemporal dementia. This review discusses the roles of Pumilio, Staufen, IGF2BP, FMRP, Sam68, CPEB, NOVA, ELAVL, SMN, TDP43, FUS, TAF15, and TIA1/TIAR in RNA metabolism by analyzing their specific molecular and cellular function, the neurological symptoms associated with their perturbation, and their axodendritic transport/localization along with their target mRNAs as part of larger macromolecular complexes termed ribonucleoprotein (RNP) granules.
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Affiliation(s)
- Stylianos Ravanidis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Fedon-Giasin Kattan
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
| | - Epaminondas Doxakis
- Basic Sciences Division I, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece.
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20
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Singh KD, Zheng X, Milstein S, Keller M, Roschitzki B, Grossmann J, Hengartner MO. Differential regulation of germ line apoptosis and germ cell differentiation by CPEB family members in C. elegans. PLoS One 2017; 12:e0182270. [PMID: 28759574 PMCID: PMC5536308 DOI: 10.1371/journal.pone.0182270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/14/2017] [Indexed: 11/21/2022] Open
Abstract
Cytoplasmic polyadenylation element binding (CPEB) proteins are evolutionary conserved RNA-binding proteins that control mRNA polyadenylation and translation. Orthologs in humans and other vertebrates are mainly involved in oogenesis. This is also the case for the C. elegans CPEB family member CPB-3, whereas two further CPEB proteins (CPB-1 and FOG-1) are involved in spermatogenesis. Here we describe the characterisation of a new missense allele of cpb-3 and show that loss of cpb-3 function leads to an increase in physiological germ cell death. To better understand the interaction and effect of C. elegans CPEB proteins on processes such as physiological apoptosis, germ cell differentiation, and regulation of gene expression, we characterised changes in the transcriptome and proteome of C. elegans CPEB mutants. Our results show that, despite their sequence similarities CPEB family members tend to have distinct overall effects on gene expression (both at the transcript and protein levels). This observation is consistent with the distinct phenotypes observed in the various CPEB family mutants.
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Affiliation(s)
- Kapil Dev Singh
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stuart Milstein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Martin Keller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- PhD Program in Molecular Life Science, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Michael O. Hengartner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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21
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Nasti R, Rossi D, Amadio M, Pascale A, Unver MY, Hirsch AKH, Collina S. Compounds Interfering with Embryonic Lethal Abnormal Vision (ELAV) Protein–RNA Complexes: An Avenue for Discovering New Drugs. J Med Chem 2017; 60:8257-8267. [DOI: 10.1021/acs.jmedchem.6b01871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Rita Nasti
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Daniela Rossi
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Marialaura Amadio
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - Alessia Pascale
- Department of Drug
Sciences, Pharmacology Section, University of Pavia, Via Taramelli
14, 27100 Pavia, Italy
| | - M. Yagiz Unver
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747
AG Groningen, The Netherlands
| | - Simona Collina
- Department of Drug
Sciences, Medicinal Chemistry and Technology Section, University of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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22
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Aberrant plasticity of peripheral sensory axons in a painful neuropathy. Sci Rep 2017; 7:3407. [PMID: 28611388 PMCID: PMC5469767 DOI: 10.1038/s41598-017-03390-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/27/2017] [Indexed: 12/21/2022] Open
Abstract
Neuronal cells express considerable plasticity responding to environmental cues, in part, through subcellular mRNA regulation. Here we report on the extensive changes in distribution of mRNAs in the cell body and axon compartments of peripheral sensory neurons and the 3' untranslated region (3'UTR) landscapes after unilateral sciatic nerve entrapment (SNE) injury in rats. Neuronal cells dissociated from SNE-injured and contralateral L4 and L5 dorsal root ganglia were cultured in a compartmentalized system. Axonal and cell body RNA samples were separately subjected to high throughput RNA sequencing (RNA-Seq). The injured axons exhibited enrichment of mRNAs related to protein synthesis and nerve regeneration. Lengthening of 3'UTRs was more prevalent in the injured axons, including the newly discovered alternative cleavage and polyadenylation of NaV1.8 mRNA. Alternative polyadenylation was largely independent from the relative abundance of axonal mRNAs; but they were highly clustered in functional pathways related to RNA granule formation in the injured axons. These RNA-Seq data analyses indicate that peripheral nerve injury may result in highly selective mRNA enrichment in the affected axons with 3'UTR alterations potentially contributing to the mechanism of neuropathic pain.
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23
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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: 47] [Impact Index Per Article: 5.9] [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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24
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Carbone SE, Jovanovska V, Brookes SJH, Nurgali K. Electrophysiological and morphological changes in colonic myenteric neurons from chemotherapy-treated patients: a pilot study. Neurogastroenterol Motil 2016; 28:975-84. [PMID: 26909894 PMCID: PMC5215581 DOI: 10.1111/nmo.12795] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/14/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Patients receiving anticancer chemotherapy experience a multitude of gastrointestinal side-effects. However, the causes of these symptoms are uncertain and whether these therapeutics directly affect the enteric nervous system is unknown. Our aim was to determine whether the function and morphology of myenteric neurons are altered in specimens of the colon from chemotherapy-treated patients. METHODS Colon specimens were compared from chemotherapy-treated and non-treated patients following colorectal resections for removal of carcinoma. Intracellular electrophysiological recordings from myenteric neurons and immunohistochemistry were performed in whole mount preparations. KEY RESULTS Myenteric S neurons from chemotherapy-treated patients were hyperexcitable; more action potentials (11.4 ± 9.4, p < 0.05) were fired in response to depolarising current pulses than in non-treated patients (1.4 ± 0.5). The rheobase and the threshold to evoke action potentials were significantly lower for neurons from chemotherapy-treated patients compared to neurons from non-treated patients (p < 0.01). Fast excitatory postsynaptic potential reversal potential was more positive in neurons from chemotherapy-treated patients (p < 0.05). An increase in the number of neurons with translocation of Hu protein from the cytoplasm to the nucleus was observed in specimens from chemotherapy-treated patients (103 ± 25 neurons/mm(2) , 37.2 ± 7.0%, n = 8) compared to non-treated (26 ± 5 neurons/mm(2) , 11.9 ± 2.7%, n = 12, p < 0.01). An increase in the soma size of neuronal nitric oxide synthase-immunoreactive neurons was also observed in these specimens. CONCLUSIONS & INFERENCES This is the first study suggesting functional and structural changes in human myenteric neurons in specimens of colon from patients receiving anticancer chemotherapy. These changes may contribute to the causation of gastrointestinal symptoms experienced by chemotherapy-treated patients.
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Affiliation(s)
- S. E. Carbone
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
| | - V. Jovanovska
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
| | - S. J. H. Brookes
- Discipline of Human Physiology and Centre for NeuroscienceFlinders UniversityAdelaideSAAustralia
| | - K. Nurgali
- Centre for Chronic DiseaseCollege of Health and BiomedicineVictoria UniversityMelbourneVICAustralia
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25
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Aschrafi A, Kar AN, Gale JR, Elkahloun AG, Vargas JNS, Sales N, Wilson G, Tompkins M, Gioio AE, Kaplan BB. A heterogeneous population of nuclear-encoded mitochondrial mRNAs is present in the axons of primary sympathetic neurons. Mitochondrion 2016; 30:18-23. [PMID: 27318271 DOI: 10.1016/j.mito.2016.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/18/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
Abstract
Mitochondria are enriched in subcellular regions of high energy consumption, such as axons and pre-synaptic nerve endings. Accumulating evidence suggests that mitochondrial maintenance in these distal structural/functional domains of the neuron depends on the "in-situ" translation of nuclear-encoded mitochondrial mRNAs. In support of this notion, we recently provided evidence for the axonal targeting of several nuclear-encoded mRNAs, such as cytochrome c oxidase, subunit 4 (COXIV) and ATP synthase, H+ transporting and mitochondrial Fo complex, subunit C1 (ATP5G1). Furthermore, we showed that axonal trafficking and local translation of these mRNAs plays a critical role in the generation of axonal ATP. Using a global gene expression analysis, this study identified a highly diverse population of nuclear-encoded mRNAs that were enriched in the axon and presynaptic nerve terminals. Among this population of mRNAs, fifty seven were found to be at least two-fold more abundant in distal axons, as compared with the parental cell bodies. Gene ontology analysis of the nuclear-encoded mitochondrial mRNAs suggested functions for these gene products in molecular and biological processes, including but not limited to oxidoreductase and electron carrier activity and proton transport. Based on these results, we postulate that local translation of nuclear-encoded mitochondrial mRNAs present in the axons may play an essential role in local energy production and maintenance of mitochondrial function.
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Affiliation(s)
- Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amar N Kar
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenna R Gale
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel G Elkahloun
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jose Noberto S Vargas
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naomi Sales
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gabriel Wilson
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Miranda Tompkins
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anthony E Gioio
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barry B Kaplan
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA.
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26
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Albu RF, Chan GT, Zhu M, Wong ETC, Taghizadeh F, Hu X, Mehran AE, Johnson JD, Gsponer J, Mayor T. A feature analysis of lower solubility proteins in three eukaryotic systems. J Proteomics 2014; 118:21-38. [PMID: 25451012 DOI: 10.1016/j.jprot.2014.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/11/2014] [Accepted: 10/18/2014] [Indexed: 11/27/2022]
Abstract
UNLABELLED Because misfolded and damaged proteins can form potentially harmful aggregates, all living organisms have evolved a wide variety of quality control mechanisms. However, the timely clearance of aggregation-prone species may not always be achieved, potentially leading to the accumulation of low solubility proteins. At the same time, promiscuity, which can be a driving force for aggregation, is also important to the functionality of certain proteins which have a large number of interaction partners. Considerable efforts have been made towards characterizing why some proteins appear to be more aggregation-prone than others. In this study, we analyze the features of proteins which precipitate following centrifugation in unstressed yeast cells, human SH-SY5Y cells and mouse brain tissue. By normalizing for protein abundance, we devised an approach whereby lower solubility proteins are reliably identified. Our findings indicate that these tend to be longer, low abundance proteins, which contain fewer hydrophobic amino acids. Furthermore, low solubility proteins also contain more low complexity and disordered regions. Overall, we observed an increase in features that link low solubility proteins to functional aggregates. Our results indicate that lower solubility proteins from three biologically distinct model systems share several common traits, shedding light on potentially universal solubility determinants. BIOLOGICAL SIGNIFICANCE We set up a novel approach to identify lower solubility proteins in unstressed cells by comparing precipitated proteins with those that remain soluble after centrifugation. By analyzing three eukaryotic model systems in parallel, we were able to identify traits which cross the species barrier, as well as species-specific characteristics. Notably, our analyses revealed a number of primary and secondary structural features that set apart lower solubility proteins, a number of which connected them to a greater potential for promiscuity. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
- Razvan F Albu
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Gerard T Chan
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Mang Zhu
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Eric T C Wong
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Farnaz Taghizadeh
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
| | - Xiaoke Hu
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
| | - Arya E Mehran
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
| | - James D Johnson
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3 Canada
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Thibault Mayor
- Department of Biochemistry and Molecular Biology and Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada.
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27
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Reyes-Herrera PH, Ficarra E. Computational Methods for CLIP-seq Data Processing. Bioinform Biol Insights 2014; 8:199-207. [PMID: 25336930 PMCID: PMC4196881 DOI: 10.4137/bbi.s16803] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action. As a result of recent evolution of experimental techniques, it is now possible to obtain the RNA regions recognized by RBPs on a transcriptome-wide scale. In fact, CLIP-seq protocols use the joint action of CLIP, crosslinking immunoprecipitation, and high-throughput sequencing to recover the transcriptome-wide set of interaction regions for a particular protein. Nevertheless, computational methods are necessary to process CLIP-seq experimental data and are a key to advancement in the understanding of gene regulatory mechanisms. Considering the importance of computational methods in this area, we present a review of the current status of computational approaches used and proposed for CLIP-seq data.
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Affiliation(s)
- Paula H Reyes-Herrera
- Facultad de Ingeniería Electrónica y Biomédica, Universidad Antonio Nariño, Bogotá, Colombia
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, TO, Italy
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28
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Ho MS. Neurodevelopment and degeneration. Neurosci Bull 2014; 30:539-41. [PMID: 25082533 DOI: 10.1007/s12264-014-1455-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Margaret S Ho
- Department of Anatomy and Neurobiology, School of Medicine, Tongji University, Shanghai, 200092, China,
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