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Ollà I, Pardiñas AF, Parras A, Hernández IH, Santos-Galindo M, Picó S, Callado LF, Elorza A, Rodríguez-López C, Fernández-Miranda G, Belloc E, Walters JTR, O'Donovan MC, Méndez R, Toma C, Meana JJ, Owen MJ, Lucas JJ. Pathogenic Mis-splicing of CPEB4 in Schizophrenia. Biol Psychiatry 2023; 94:341-351. [PMID: 36958377 DOI: 10.1016/j.biopsych.2023.03.010] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/16/2023] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND Schizophrenia (SCZ) is caused by an interplay of polygenic risk and environmental factors, which may alter regulators of gene expression leading to pathogenic misexpression of SCZ risk genes. The CPEB family of RNA-binding proteins (CPEB1-4) regulates translation of target RNAs (approximately 40% of overall genes). We previously identified CPEB4 as a key dysregulated translational regulator in autism spectrum disorder (ASD) because its neuronal-specific microexon (exon 4) is mis-spliced in ASD brains, causing underexpression of numerous ASD risk genes. The genetic factors and pathogenic mechanisms shared between SCZ and ASD led us to hypothesize CPEB4 mis-splicing in SCZ leading to underexpression of multiple SCZ-related genes. METHODS We performed MAGMA-enrichment analysis on Psychiatric Genomics Consortium genome-wide association study data and analyzed RNA sequencing data from the PsychENCODE Consortium. Reverse transcriptase polymerase chain reaction and Western blot were performed on postmortem brain tissue, and the presence/absence of antipsychotics was assessed through toxicological analysis. Finally, mice with mild overexpression of exon 4-lacking CPEB4 (CPEB4Δ4) were generated and analyzed biochemically and behaviorally. RESULTS First, we found enrichment of SCZ-associated genes for CPEB4-binder transcripts. We also found decreased usage of CPEB4 microexon in SCZ probands, which was correlated with decreased protein levels of CPEB4-target SCZ-associated genes only in antipsychotic-free individuals. Interestingly, differentially expressed genes fit those reported for SCZ, specifically in the SCZ probands with decreased CPEB4-microexon inclusion. Finally, we demonstrated that mice with mild overexpression of CPEB4Δ4 showed decreased protein levels of CPEB4-target SCZ genes and SCZ-linked behaviors. CONCLUSIONS We identified aberrant CPEB4 splicing and downstream misexpression of SCZ risk genes as a novel etiological mechanism in SCZ.
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Affiliation(s)
- Ivana Ollà
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio F Pardiñas
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Alberto Parras
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Ivó H Hernández
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - María Santos-Galindo
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Picó
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis F Callado
- Department of Pharmacology, University of the Basque Country, UPV/EHU, Biocruces Bizkaia Health Research Institute and Networking Research Center on Mental Health (Centro de investigación Biomédica en Red | Salud Mental), Leioa, Bizkaia, Spain
| | - Ainara Elorza
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Claudia Rodríguez-López
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain
| | - Gonzalo Fernández-Miranda
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Eulàlia Belloc
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - James T R Walters
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Raúl Méndez
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de RIcerca i Estudis Avançats, Barcelona, Spain
| | - Claudio Toma
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Neuroscience Research Australia, Sydney, New South Wales, Australia; School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - J Javier Meana
- Department of Pharmacology, University of the Basque Country, UPV/EHU, Biocruces Bizkaia Health Research Institute and Networking Research Center on Mental Health (Centro de investigación Biomédica en Red | Salud Mental), Leioa, Bizkaia, Spain
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - José J Lucas
- Center for Molecular Biology "Severo Ochoa," Spanish National Research Council/Autonomous University of Madrid, Madrid, Spain; Networking Research Center on Neurodegenerative Diseases (Centro de Investigación Biomédica en Red|Enfermedades Neurodegenerativas), Instituto de Salud Carlos III, Madrid, Spain.
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Huang YS, Mendez R, Fernandez M, Richter JD. CPEB and translational control by cytoplasmic polyadenylation: impact on synaptic plasticity, learning, and memory. Mol Psychiatry 2023; 28:2728-2736. [PMID: 37131078 PMCID: PMC10620108 DOI: 10.1038/s41380-023-02088-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/04/2023]
Abstract
The late 1990s were banner years in molecular neuroscience; seminal studies demonstrated that local protein synthesis, at or near synapses, was necessary for synaptic plasticity, the underlying cellular basis of learning and memory [1, 2]. The newly made proteins were proposed to "tag" the stimulated synapse, distinguishing it from naive synapses, thereby forming a cellular memory [3]. Subsequent studies demonstrated that the transport of mRNAs from soma to dendrite was linked with translational unmasking at synapses upon synaptic stimulation. It soon became apparent that one prevalent mechanism governing these events is cytoplasmic polyadenylation, and that among the proteins that control this process, CPEB, plays a central role in synaptic plasticity, and learning and memory. In vertebrates, CPEB is a family of four proteins, all of which regulate translation in the brain, that have partially overlapping functions, but also have unique characteristics and RNA binding properties that make them control different aspects of higher cognitive function. Biochemical analysis of the vertebrate CPEBs demonstrate them to respond to different signaling pathways whose output leads to specific cellular responses. In addition, the different CPEBs, when their functions go awry, result in pathophysiological phenotypes resembling specific human neurological disorders. In this essay, we review key aspects of the vertebrate CPEB proteins and cytoplasmic polyadenylation within the context of brain function.
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Affiliation(s)
- Yi-Shuian Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Raul Mendez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
| | | | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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Duran-Arqué B, Cañete M, Castellazzi CL, Bartomeu A, Ferrer-Caelles A, Reina O, Caballé A, Gay M, Arauz-Garofalo G, Belloc E, Mendez R. Comparative analyses of vertebrate CPEB proteins define two subfamilies with coordinated yet distinct functions in post-transcriptional gene regulation. Genome Biol 2022; 23:192. [PMID: 36096799 PMCID: PMC9465852 DOI: 10.1186/s13059-022-02759-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Vertebrate CPEB proteins bind mRNAs at cytoplasmic polyadenylation elements (CPEs) in their 3' UTRs, leading to cytoplasmic changes in their poly(A) tail lengths; this can promote translational repression or activation of the mRNA. However, neither the regulation nor the mechanisms of action of the CPEB family per se have been systematically addressed to date. RESULTS Based on a comparative analysis of the four vertebrate CPEBs, we determine their differential regulation by phosphorylation, the composition and properties of their supramolecular assemblies, and their target mRNAs. We show that all four CPEBs are able to recruit the CCR4-NOT deadenylation complex to repress the translation. However, their regulation, mechanism of action, and target mRNAs define two subfamilies. Thus, CPEB1 forms ribonucleoprotein complexes that are remodeled upon a single phosphorylation event and are associated with mRNAs containing canonical CPEs. CPEB2-4 are regulated by multiple proline-directed phosphorylations that control their liquid-liquid phase separation. CPEB2-4 mRNA targets include CPEB1-bound transcripts, with canonical CPEs, but also a specific subset of mRNAs with non-canonical CPEs. CONCLUSIONS Altogether, these results show how, globally, the CPEB family of proteins is able to integrate cellular cues to generate a fine-tuned adaptive response in gene expression regulation through the coordinated actions of all four members.
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Affiliation(s)
- Berta Duran-Arqué
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Manuel Cañete
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Chiara Lara Castellazzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Bartomeu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Ferrer-Caelles
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Adrià Caballé
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Eulalia Belloc
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Raúl Mendez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Balvey A, Fernandez M. Translational Control in Liver Disease. Front Physiol 2021; 12:795298. [PMID: 34912244 PMCID: PMC8667601 DOI: 10.3389/fphys.2021.795298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic liver disease is one of the biggest threats to public health worldwide. Worryingly, the incidence of liver disease is dramatically rising due to the aging of the population and the global epidemics of obesity. Both are major risk factors for chronic liver disease and adverse prognostic factors, causing an increase in mortality rate. It is of great concern that 80–95% of obese people have non-alcoholic fatty liver disease, the major precursor for liver failure and a global health challenge. Currently, the only curative treatment for advanced chronic liver disease is liver transplantation, which is, however, hampered by high treatment costs and the scarcity of donor organs. New strategies are therefore urgently needed to prevent and reverse chronic liver disease. And for that it is essential to understand better the molecular mechanisms underlying human disease. This review focuses on the abnormalities in the regulation of translation by RNA-binding proteins during chronic liver disease and their pathological impact on portal hypertension, fibrosis, steatosis, neovascularization, and cancer development.
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Affiliation(s)
- Alexandra Balvey
- Laboratory of Translational Control in Liver Disease and Cancer, IDIBAPS Biomedical Research Institute, University of Barcelona, Barcelona, Spain
| | - Mercedes Fernandez
- Laboratory of Translational Control in Liver Disease and Cancer, IDIBAPS Biomedical Research Institute, University of Barcelona, Barcelona, Spain
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Bao X, Song Y, Li T, Zhang S, Huang L, Zhang S, Cao J, Liu X, Zhang J. Comparative Transcriptome Profiling of Ovary Tissue between Black Muscovy Duck and White Muscovy Duck with High- and Low-Egg Production. Genes (Basel) 2020; 12:57. [PMID: 33396489 PMCID: PMC7824526 DOI: 10.3390/genes12010057] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/25/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022] Open
Abstract
The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGFβ2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of "circadian sleep/wake cycle process," "negative regulation of transforming growth factor-β secretion," "positive regulation of calcium ion transport" in BH-vs-WH and "cell surface receptor signaling pathway," "Notch signaling pathway" and "calcium ion transport" in BL-vs-BH. Besides, "steroid biosynthetic process," "granulosa cell development" and "egg coat formation" were mainly enriched in BL-vs-WL and "reproduction," "MAPK cascade" and "mitotic cell cycle" were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jianqin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (X.B.); (Y.S.); (T.L.); (S.Z.); (L.H.); (S.Z.); (J.C.); (X.L.)
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Zhou Q, Xie Y, Wang L, Xu T, Gao Y. LncRNA EWSAT1 upregulates CPEB4 via miR-330-5p to promote cervical cancer development. Mol Cell Biochem 2020; 471:177-188. [PMID: 32556917 DOI: 10.1007/s11010-020-03778-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022]
Abstract
Long non-coding RNA (lncRNA) Ewing sarcoma associated transcript 1 (EWSAT1) is an oncogene in a variety of tumors. Here, we planned to demonstrate EWSAT1 function in cervical cancer and further illustrate its underlying mechanism. EWSAT1 expression in cervical cancer was evaluated through qRT-PCR. Colony forming capacity was measured by colony formation assay and cell proliferation ability was measured by CCK-8 kit. Wound healing experiment was applied to test the cell migration and transwell assay was applied to test the invasion ability. Luciferase assay was employed to demonstrate EWSAT1 and miR-330-5p interaction. In cervical cancer, the expression of EWSAT1 was enhanced and contributed to the poor prognosis. Downregulated EWSAT1 expression inhibited Hela cell migration, proliferation, and invasion. EWSAT1 targeted to miR-330-5p and upregulated cytoplasmic polyadenylation element-binding protein 4 (CPEB4) expression by sponging miR-330-5p. Our study revealed that EWSAT1 enhances CPEB4 expression through sponging miR-330-5p, thereby promoting cervical cancer development, which might provide potential therapeutic targets for clinically cervical cancer patients.
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Affiliation(s)
- Qingyan Zhou
- Department of Gynecology, Dongchangfu District, Liaocheng Dongchangfu People's Hospital, No. 128 Songgui Road, Liaocheng, 252000, Shandong, China.
| | - Yuan Xie
- Department of Gynecology, Dongchangfu District, Liaocheng Dongchangfu People's Hospital, No. 128 Songgui Road, Liaocheng, 252000, Shandong, China
| | - Li Wang
- Department of Gynecology, Dongchangfu District, Liaocheng Dongchangfu People's Hospital, No. 128 Songgui Road, Liaocheng, 252000, Shandong, China
| | - Tao Xu
- Delivery Room, Dongchangfu District, Liaocheng Dongchangfu People's Hospital, No. 128 Songgui Road, Liaocheng, 252000, Shandong, China
| | - Yongbin Gao
- Department of Gynecology, Dongchangfu District, Liaocheng Dongchangfu People's Hospital, No. 128 Songgui Road, Liaocheng, 252000, Shandong, China
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A Comparative Analysis of Oocyte Development in Mammals. Cells 2020; 9:cells9041002. [PMID: 32316494 PMCID: PMC7226043 DOI: 10.3390/cells9041002] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/06/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Sexual reproduction requires the fertilization of a female gamete after it has undergone optimal development. Various aspects of oocyte development and many molecular actors in this process are shared among mammals, but phylogeny and experimental data reveal species specificities. In this chapter, we will present these common and distinctive features with a focus on three points: the shaping of the oocyte transcriptome from evolutionarily conserved and rapidly evolving genes, the control of folliculogenesis and ovulation rate by oocyte-secreted Growth and Differentiation Factor 9 and Bone Morphogenetic Protein 15, and the importance of lipid metabolism.
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Prochazkova B, Komrskova P, Kubelka M. CPEB2 Is Necessary for Proper Porcine Meiotic Maturation and Embryonic Development. Int J Mol Sci 2018; 19:ijms19103138. [PMID: 30322039 PMCID: PMC6214008 DOI: 10.3390/ijms19103138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/02/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
Oocyte meiotic maturation and embryogenesis are some of the most important physiological processes that occur in organisms, playing crucial roles in the preservation of life in all species. The post-transcriptional regulation of maternal messenger ribonucleic acids (mRNAs) and the post-translational regulation of proteins are critical in the control of oocyte maturation and early embryogenesis. Translational control affects the basic mechanism of protein synthesis, thus, knowledge of the key components included in this machinery is required in order to understand its regulation. Cytoplasmic polyadenylation element binding proteins (CPEBs) bind to the 3′-end of mRNAs to regulate their localization and translation and are necessary for proper development. In this study we examined the expression pattern of cytoplasmic polyadenylation element binding protein 2 (CPEB2) both on the mRNA (by real-time quantitative reverse transcription polymerase chain reaction, qRT-PCR) and protein (by Western blotting, WB) level, as well as its localization during the meiotic maturation of porcine oocytes and early embryonic development by immunocytochemistry (ICC). For the elucidation of its functions, CPEB2 knockdown by double-strand RNA (dsRNA) was used. We discovered that CPEB2 is expressed during all stages of porcine meiotic maturation and embryonic development. Moreover, we found that it is necessary to enable a high percentage of oocytes to reach the metaphase II (MII) stage, as well as for the production of good-quality parthenogenetic blastocysts.
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Affiliation(s)
- Barbora Prochazkova
- Department of Veterinary Sciences, Czech University of Life Sciences, Kamycka 129, 165 00 Prague, Czech Republic.
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic.
| | - Pavla Komrskova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic.
| | - Michal Kubelka
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 277 21 Libechov, Czech Republic.
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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10
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Lou WPK, Mateos A, Koch M, Klussman S, Yang C, Lu N, Kumar S, Limpert S, Göpferich M, Zschaetzsch M, Sliwinski C, Kenzelmann M, Seedorf M, Maillo C, Senis E, Grimm D, Puttagunta R, Mendez R, Liu K, Hassan BA, Martin-Villalba A. Regulation of Adult CNS Axonal Regeneration by the Post-transcriptional Regulator Cpeb1. Front Mol Neurosci 2018; 10:445. [PMID: 29379413 PMCID: PMC5770975 DOI: 10.3389/fnmol.2017.00445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022] Open
Abstract
Adult mammalian central nervous system (CNS) neurons are unable to regenerate following axonal injury, leading to permanent functional impairments. Yet, the reasons underlying this regeneration failure are not fully understood. Here, we studied the transcriptome and translatome shortly after spinal cord injury. Profiling of the total and ribosome-bound RNA in injured and naïve spinal cords identified a substantial post-transcriptional regulation of gene expression. In particular, transcripts associated with nervous system development were down-regulated in the total RNA fraction while remaining stably loaded onto ribosomes. Interestingly, motif association analysis of post-transcriptionally regulated transcripts identified the cytoplasmic polyadenylation element (CPE) as enriched in a subset of these transcripts that was more resistant to injury-induced reduction at the transcriptome level. Modulation of these transcripts by overexpression of the CPE binding protein, Cpeb1, in mouse and Drosophila CNS neurons promoted axonal regeneration following injury. Our study uncovered a global evolutionarily conserved post-transcriptional mechanism enhancing regeneration of injured CNS axons.
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Affiliation(s)
- Wilson Pak-Kin Lou
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Alvaro Mateos
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
| | - Marta Koch
- VIB Center for the Biology of Disease and Center for Human Genetics, VIB and KU Leuven, Leuven, Belgium
| | - Stefan Klussman
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Chao Yang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Na Lu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Sachin Kumar
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Stefanie Limpert
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
| | - Manuel Göpferich
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany
| | - Marlen Zschaetzsch
- VIB Center for the Biology of Disease and Center for Human Genetics, VIB and KU Leuven, Leuven, Belgium
| | - Christopher Sliwinski
- Department of Neuroregeneration, University Hospital Heidelberg, Heidelberg, Germany
| | - Marc Kenzelmann
- Division of Molecular Biology of the Cell I, German Cancer Research Center, Heidelberg, Germany
| | - Matthias Seedorf
- Zentrum für Molekulare Biologie, University of Heidelberg, Heidelberg, Germany
| | - Carlos Maillo
- Translational Control of Cell Cycle and Differentiation, Institute for Research in Biomedicine, Barcelona, Spain
| | - Elena Senis
- Virus Host Interaction, Heidelberg University Hospital, Center for Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant, Heidelberg, Germany
| | - Dirk Grimm
- Virus Host Interaction, Heidelberg University Hospital, Center for Infectious Diseases/Virology, Cluster of Excellence CellNetworks, BioQuant, Heidelberg, Germany
| | - Radhika Puttagunta
- Department of Neuroregeneration, University Hospital Heidelberg, Heidelberg, Germany
| | - Raul Mendez
- Translational Control of Cell Cycle and Differentiation, Institute for Research in Biomedicine, Barcelona, Spain
| | - Kai Liu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
- Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Bassem A. Hassan
- VIB Center for the Biology of Disease and Center for Human Genetics, VIB and KU Leuven, Leuven, Belgium
- Sorbonne Universités, UPMC Univ Paris 06, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut du Cerveau et de la Moelle epiniere - Hôpital Pitié-Salpêtrière, Paris, France
| | - Ana Martin-Villalba
- Division of Molecular Neurobiology, German Cancer Research Center, Heidelberg, Germany
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11
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Translational reprogramming in tumour cells can generate oncoselectivity in viral therapies. Nat Commun 2017; 8:14833. [PMID: 28300077 PMCID: PMC5357308 DOI: 10.1038/ncomms14833] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/02/2017] [Indexed: 01/06/2023] Open
Abstract
Systemic treatment of cancer requires tumour-selective therapies that eliminate cancer cells yet preserve healthy tissues from undesired damage. Tumoral transformation is associated with profound effects in translational reprogramming of gene expression, such that tumour-specific translational regulation presents an attractive possibility for generating oncoselective therapies. We recently discovered that mRNA translational control by cytoplasmic polyadenylation element-binding proteins (CPEBs) is reactivated in cancer. Here we present a novel approach to restrict genetic-engineered therapies to malignant tissues based on CPEB translational regulation of target mRNAs. We demonstrate that tumour reprogramming of CPEB-mediated mRNA stability and translational regulation modulates tumour-specific expression of viral proteins. For oncolytic adenoviruses, insertion of CPE regulatory sequences in the 3'-untranslated region of the E1A gene provides oncoselectivity, with full potency in cancer cells but attenuated in normal tissues. Our results demonstrate the potential of this strategy to improve oncolytic virus design and provide a framework for exploiting CPE-regulated transgenes for therapy.
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12
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Circadian- and UPR-dependent control of CPEB4 mediates a translational response to counteract hepatic steatosis under ER stress. Nat Cell Biol 2017; 19:94-105. [PMID: 28092655 DOI: 10.1038/ncb3461] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 12/09/2016] [Indexed: 12/18/2022]
Abstract
The cytoplasmic polyadenylation element-binding (CPEB) proteins regulate pre-mRNA processing and translation of CPE-containing mRNAs in early embryonic development and synaptic activity. However, specific functions in adult organisms are poorly understood. Here we show that CPEB4 is required for adaptation to high-fat-diet- and ageing-induced endoplasmic reticulum (ER) stress, and subsequent hepatosteatosis. Stress-activated liver CPEB4 expression is dual-mode regulated. First, Cpeb4 mRNA transcription is controlled by the circadian clock, and then its translation is regulated by the unfolded protein response (UPR) through upstream open reading frames within the 5'UTR. Thus, the CPEB4 protein is synthesized only following ER stress but the induction amplitude is circadian. In turn, CPEB4 activates a second wave of UPR translation required to maintain ER and mitochondrial homeostasis. Our results suggest that combined transcriptional and translational Cpeb4 regulation generates a 'circadian mediator', which coordinates hepatic UPR activity with periods of high ER-protein-folding demand. Accordingly, CPEB4 deficiency results in non-alcoholic fatty liver disease.
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13
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Abstract
Fully grown oocytes arrest meiosis at prophase I and deposit maternal RNAs. A subset of maternal transcripts is stored in a dormant state in the oocyte, and the timely driven translation of specific mRNAs guides meiotic progression, the oocyte-embryo transition, and early embryo development. In the absence of transcription, the regulation of gene expression in oocytes is controlled almost exclusively at the level of transcriptome and proteome stabilization and at the level of protein synthesis.This chapter focuses on the recent findings on RNA distribution related to the temporal and spatial translational control of the meiotic cycle progression in mammalian oocytes. We discuss the most relevant mechanisms involved in the organization of the oocyte's maternal transcriptome storage and localization, and the regulation of translation, in correlation with the regulation of oocyte meiotic progression.
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14
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Guillén-Boixet J, Buzon V, Salvatella X, Méndez R. CPEB4 is regulated during cell cycle by ERK2/Cdk1-mediated phosphorylation and its assembly into liquid-like droplets. eLife 2016; 5. [PMID: 27802129 PMCID: PMC5089860 DOI: 10.7554/elife.19298] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
Abstract
The four members of the vertebrate CPEB family of RNA-binding proteins share similar RNA-binding domains by which they regulate the translation of CPE-containing mRNAs, thereby controlling cell cycle and differentiation or synaptic plasticity. However, the N-terminal domains of CPEBs are distinct and contain specific regulatory post-translational modifications that presumably differentially integrate extracellular signals. Here we show that CPEB4 activity is regulated by ERK2- and Cdk1-mediated hyperphosphorylation. These phosphorylation events additively activate CPEB4 in M-phase by maintaining it in its monomeric state. In contrast, unphosphorylated CPEB4 phase separates into inactive, liquid-like droplets through its intrinsically disordered regions in the N-terminal domain. This dynamic and reversible regulation of CPEB4 is coordinated with that of CPEB1 through Cdk1, which inactivates CPEB1 while activating CPEB4, thereby integrating phase-specific signal transduction pathways to regulate cell cycle progression.
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Affiliation(s)
- Jordina Guillén-Boixet
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Víctor Buzon
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Raúl Méndez
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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15
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Skubal M, Gielen GH, Waha A, Gessi M, Kaczmarczyk L, Seifert G, Freihoff D, Freihoff J, Pietsch T, Simon M, Theis M, Steinhäuser C, Waha A. Altered splicing leads to reduced activation of CPEB3 in high-grade gliomas. Oncotarget 2016; 7:41898-41912. [PMID: 27256982 PMCID: PMC5173104 DOI: 10.18632/oncotarget.9735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 05/13/2016] [Indexed: 12/19/2022] Open
Abstract
Cytoplasmic polyadenylation element binding proteins (CPEBs) are auxiliary translational factors that associate with consensus sequences present in 3'UTRs of mRNAs, thereby activating or repressing their translation. Knowing that CPEBs are players in cell cycle regulation and cellular senescence prompted us to investigate their contribution to the molecular pathology of gliomas-most frequent of intracranial tumors found in humans. To this end, we performed methylation analyses in the promoter regions of CPEB1-4 and identified the CPEB1 gene to be hypermethylated in tumor samples. Decreased expression of CPEB1 protein in gliomas correlated with the rising grade of tumor malignancy. Abundant expression of CPEBs2-4 was observed in several glioma specimens. Interestingly, expression of CPEB3 positively correlated with tumor progression and malignancy but negatively correlated with protein phosphorylation in the alternatively spliced region. Our data suggest that loss of CPEB3 activity in high-grade gliomas is caused by expression of alternatively spliced variants lacking the B-region that overlaps with the kinase recognition site. We conclude that deregulation of CPEB proteins may be a frequent phenomenon in gliomas and occurs on the level of transcription involving epigenetic mechanism as well as on the level of mRNA splicing, which generates isoforms with compromised biological properties.
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Affiliation(s)
- Magdalena Skubal
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Gerrit H. Gielen
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Anke Waha
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Marco Gessi
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Lech Kaczmarczyk
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53105 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Gerald Seifert
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Dorothee Freihoff
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Johannes Freihoff
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Torsten Pietsch
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Matthias Simon
- Institute of Neurosurgery, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Martin Theis
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Christian Steinhäuser
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, 53105 Bonn, Germany
| | - Andreas Waha
- Institute of Neuropathology, Medical Faculty, University of Bonn, 53105 Bonn, Germany
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16
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Cytoplasmic polyadenylation element-binding protein 4 is highly expressed in human glioma. Neuroreport 2016; 27:593-9. [DOI: 10.1097/wnr.0000000000000577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Biphasic and Stage-Associated Expression of CPEB4 in Hepatocellular Carcinoma. PLoS One 2016; 11:e0155025. [PMID: 27158894 PMCID: PMC4861299 DOI: 10.1371/journal.pone.0155025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 04/22/2016] [Indexed: 01/16/2023] Open
Abstract
Cytoplasmic polyadenylation element binding protein 4 (CPEB4) is a sequence-specific RNA-binding protein and translational regulator, with expression associated with tumor progression. Nevertheless, CPEB4 seems to play paradoxical roles in cancers–an oncogenic promoter in pancreatic ductal adenocarcinoma (PDA) and glioblastomas but a tumor suppressor in hepatocellular carcinoma (HCC). To assess whether CPEB4-regulated carcinogenesis is tissue-specific, we reevaluated the role of CPEB4 in HCC. Although proliferation of hepatocytes appeared normal in CPEB4-knockout (KO) mice after partial hepatectomy, knockdown (KD) of CPEB4 in HepG2 liver cancer cells promoted colony formation in vitro. Moreover, the growth of CPEB4-KD cells was accelerated in an in vivo xenograft mouse model. In tumorous and adjacent non-tumorous paired liver specimens from 49 HCC patients, the protein level of CPEB4 was significantly upregulated in early-stage HCC but decreased toward late-stage HCC. This finding agrees with changes in CPEB4 mRNA level from analysis of two sets of HCC microarray data from the Gene Expression Omnibus (GEO) database. Taken together, downregulation of CPEB4 likely occurs at the late cancer stage to facilitate HCC progression. Biphasic alteration of CPEB4 expression during HCC progression suggests its complicated role in tumorigenesis.
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18
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Kaczmarczyk L, Labrie-Dion É, Sehgal K, Sylvester M, Skubal M, Josten M, Steinhäuser C, De Koninck P, Theis M. New Phosphospecific Antibody Reveals Isoform-Specific Phosphorylation of CPEB3 Protein. PLoS One 2016; 11:e0150000. [PMID: 26915047 PMCID: PMC4767366 DOI: 10.1371/journal.pone.0150000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/08/2016] [Indexed: 11/23/2022] Open
Abstract
Cytoplasmic Polyadenylation Element Binding proteins (CPEBs) are a family of polyadenylation factors interacting with 3’UTRs of mRNA and thereby regulating gene expression. Various functions of CPEBs in development, synaptic plasticity, and cellular senescence have been reported. Four CPEB family members of partially overlapping functions have been described to date, each containing a distinct alternatively spliced region. This region is highly conserved between CPEBs-2-4 and contains a putative phosphorylation consensus, overlapping with the exon seven of CPEB3. We previously found CPEBs-2-4 splice isoforms containing exon seven to be predominantly present in neurons, and the isoform expression pattern to be cell type-specific. Here, focusing on the alternatively spliced region of CPEB3, we determined that putative neuronal isoforms of CPEB3 are phosphorylated. Using a new phosphospecific antibody directed to the phosphorylation consensus we found Protein Kinase A and Calcium/Calmodulin-dependent Protein Kinase II to robustly phosphorylate CPEB3 in vitro and in primary hippocampal neurons. Interestingly, status epilepticus induced by systemic kainate injection in mice led to specific upregulation of the CPEB3 isoforms containing exon seven. Extensive analysis of CPEB3 phosphorylation in vitro revealed two other phosphorylation sites. In addition, we found plethora of potential kinases that might be targeting the alternatively spliced kinase consensus site of CPEB3. As this site is highly conserved between the CPEB family members, we suggest the existence of a splicing-based regulatory mechanism of CPEB function, and describe a robust phosphospecific antibody to study it in future.
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Affiliation(s)
- Lech Kaczmarczyk
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
- * E-mail:
| | | | - Kapil Sehgal
- Institut universitaire en santé mentale de Québec, Québec, QC, Canada
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Magdalena Skubal
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Michele Josten
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Christian Steinhäuser
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Paul De Koninck
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC, Canada
- Institut universitaire en santé mentale de Québec, Québec, QC, Canada
| | - Martin Theis
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
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19
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Sun HT, Wen X, Han T, Liu ZH, Li SB, Wang JG, Liu XP. Expression of CPEB4 in invasive ductal breast carcinoma and its prognostic significance. Onco Targets Ther 2015; 8:3499-506. [PMID: 26648741 PMCID: PMC4664518 DOI: 10.2147/ott.s87587] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aims Cytoplasmic polyadenylation element binding proteins (CPEBs) are RNA-binding proteins that regulate translation by inducing cytoplasmic polyadenylation. CPEB4 has been reported in association with tumor growth, vascularization, and invasion in several cancers. To date, the expression of CPEB4 with clinical prognosis of breast cancer was never reported before. We aim to investigate the expression of CPEB4 and its prognostic significance in invasive ductal breast carcinoma. Methods Immunohistochemical staining of CPEB4 and estrogen receptor, progesterone receptor, and human epidermal growth factor receptor was performed in 107 invasive ductal carcinoma (IDC) samples, and prognostic significance was evaluated. Results High expression of CPEB4 was observed in 48.6% of IDC samples. Elevated CPEB4 expression was possibly related to increased histological grading (P=0.037) and N stage (P<0.001). Patients with high expression of CPEB4 showed shorter overall survival (P=0.001). High CPEB4 expression was an independent prognostic factor for overall survival (P=0.022, hazard ratio =4.344, 95% confidence interval =1.235–15.283). Conclusion High CPEB4 expression is associated with increased histological grading and N stage, and it can serve as an independent prognostic factor in IDC.
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Affiliation(s)
- Hao-Ting Sun
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China ; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Xin Wen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Canton, Guangdong Province, People's Republic of China
| | - Tian Han
- Key Lab of Myopia, Ministry of Health, Department of Ophthalmology, Eye & ENT Hospital of Fudan University, Shanghai, People's Republic of China
| | - Zhen-Hua Liu
- Urology Department and Institute of Urology, Peking University First Hospital, Peking University, Beijing, People's Republic of China
| | - Shao-Bo Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Ji-Gang Wang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Xiu-Ping Liu
- Department of Pathology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, People's Republic of China
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20
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Turimella SL, Bedner P, Skubal M, Vangoor VR, Kaczmarczyk L, Karl K, Zoidl G, Gieselmann V, Seifert G, Steinhäuser C, Kandel E, Theis M. Characterization of cytoplasmic polyadenylation element binding 2 protein expression and its RNA binding activity. Hippocampus 2014; 25:630-42. [DOI: 10.1002/hipo.22399] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/30/2022]
Affiliation(s)
| | - Peter Bedner
- Institute of Cellular Neurosciences, University of Bonn; Bonn Germany
| | - Magdalena Skubal
- Institute of Cellular Neurosciences, University of Bonn; Bonn Germany
| | | | - Lech Kaczmarczyk
- Institute of Cellular Neurosciences, University of Bonn; Bonn Germany
| | - Kevin Karl
- HHMI; Center for Neurobiology and Behavior; Columbia University; New York New York
| | - Georg Zoidl
- Department of Psychology; Faculty of Health; York University; Toronto Canada
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, University of Bonn; Bonn Germany
| | - Gerald Seifert
- Institute of Cellular Neurosciences, University of Bonn; Bonn Germany
| | | | - Eric Kandel
- HHMI; Center for Neurobiology and Behavior; Columbia University; New York New York
| | - Martin Theis
- Institute of Cellular Neurosciences, University of Bonn; Bonn Germany
- HHMI; Center for Neurobiology and Behavior; Columbia University; New York New York
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21
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Afroz T, Skrisovska L, Belloc E, Guillén-Boixet J, Méndez R, Allain FHT. A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins. Genes Dev 2014; 28:1498-514. [PMID: 24990967 PMCID: PMC4083092 DOI: 10.1101/gad.241133.114] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
How CPEB RNA-binding proteins regulate cytoplasmic polyadenylation and translation is poorly understood. Allain and colleagues report the structures of the tandem RNA recognition motifs (RRMs) of two human paralogs (CPEB1 and CPEB4) in their free and RNA-bound states. Structural and functional studies reveal how RNA binding by CPEB proteins leads to an optimal positioning of the N-terminal and zinc-binding domains at the 3′ UTR, which favors the nucleation of ribonucleoprotein complexes for translation regulation. This study provides the molecular basis for the translational regulatory circuit established by CPEB proteins. Cytoplasmic changes in polyA tail length is a key mechanism of translational control and is implicated in germline development, synaptic plasticity, cellular proliferation, senescence, and cancer progression. The presence of a U-rich cytoplasmic polyadenylation element (CPE) in the 3′ untranslated regions (UTRs) of the responding mRNAs gives them the selectivity to be regulated by the CPE-binding (CPEB) family of proteins, which recognizes RNA via the tandem RNA recognition motifs (RRMs). Here we report the solution structures of the tandem RRMs of two human paralogs (CPEB1 and CPEB4) in their free and RNA-bound states. The structures reveal an unprecedented arrangement of RRMs in the free state that undergo an original closure motion upon RNA binding that ensures high fidelity. Structural and functional characterization of the ZZ domain (zinc-binding domain) of CPEB1 suggests a role in both protein–protein and protein–RNA interactions. Together with functional studies, the structures reveal how RNA binding by CPEB proteins leads to an optimal positioning of the N-terminal and ZZ domains at the 3′ UTR, which favors the nucleation of the functional ribonucleoprotein complexes for translation regulation.
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Affiliation(s)
- Tariq Afroz
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
| | - Lenka Skrisovska
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
| | - Eulàlia Belloc
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | | | - Raúl Méndez
- Institute for Research in Biomedicine, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zurich, CH-8093 Zürich, Switzerland
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22
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Schelhorn C, Gordon JMB, Ruiz L, Alguacil J, Pedroso E, Macias MJ. RNA recognition and self-association of CPEB4 is mediated by its tandem RRM domains. Nucleic Acids Res 2014; 42:10185-95. [PMID: 25081215 PMCID: PMC4150798 DOI: 10.1093/nar/gku700] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/19/2014] [Indexed: 11/12/2022] Open
Abstract
Cytoplasmic polyadenylation is regulated by the interaction of the cytoplasmic polyadenylation element binding proteins (CPEB) with cytoplasmic polyadenylation element (CPE) containing mRNAs. The CPEB family comprises four paralogs, CPEB1-4, each composed of a variable N-terminal region, two RNA recognition motif (RRM) and a C-terminal ZZ-domain. We have characterized the RRM domains of CPEB4 and their binding properties using a combination of biochemical, biophysical and NMR techniques. Isothermal titration calorimetry, NMR and electrophoretic mobility shift assay experiments demonstrate that both the RRM domains are required for an optimal CPE interaction and the presence of either one or two adenosines in the two most commonly used consensus CPE motifs has little effect on the affinity of the interaction. Both the single RRM1 and the tandem RRM1-RRM2 have the ability to dimerize, although representing a minor population. Self-association does not affect the proteins' ability to interact with RNA as demonstrated by ion mobility-mass spectrometry. Chemical shift effects measured by NMR of the apo forms of the RRM1-RRM2 samples indicate that the two domains are orientated toward each other. NMR titration experiments show that residues on the β-sheet surface on RRM1 and at the C-terminus of RRM2 are affected upon RNA binding. We propose a model of the CPEB4 RRM1-RRM2-CPE complex that illustrates the experimental data.
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Affiliation(s)
- Constanze Schelhorn
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - James M B Gordon
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Javier Alguacil
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Enrique Pedroso
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, Barcelona 08010, Spain
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Grudzien-Nogalska E, Reed BC, Rhoads RE. CPEB1 promotes differentiation and suppresses EMT in mammary epithelial cells. J Cell Sci 2014; 127:2326-38. [PMID: 24634508 DOI: 10.1242/jcs.144956] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Downregulation of CPEB1, a sequence-specific RNA-binding protein, in a mouse mammary epithelial cell line (CID-9) causes epithelial-to-mesenchymal transition (EMT), based on several criteria. First, CPEB1 knockdown decreases protein levels of E-cadherin and β-catenin but increases those of vimentin and Twist1. Second, the motility of CPEB1-depleted cells is increased. Third, CID-9 cells normally form growth-arrested, polarized and three-dimensional acini upon culture in extracellular matrix, but CPEB1-deficient CID-9 cells form nonpolarized proliferating colonies lacking a central cavity. CPEB1 downregulates Twist1 expression by binding to its mRNA, shortening its poly(A) tract and repressing its translation. CID-9 cultures contain both myoepithelial and luminal epithelial cells. CPEB1 increases during CID-9 cell differentiation, is predominantly expressed in myoepithelial cells, and its knockdown prevents expression of the myoepithelial marker p63. CPEB1 is present in proliferating subpopulations of pure luminal epithelial cells (SCp2) and myoepithelial cells (SCg6), but its depletion increases Twist1 only in SCg6 cells and fails to downregulate E-cadherin in SCp2 cells. We propose that myoepithelial cells prevent EMT by influencing the polarity and proliferation of luminal epithelial cells in a mechanism that requires translational silencing of myoepithelial Twist1 by CPEB1.
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Affiliation(s)
- Ewa Grudzien-Nogalska
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Brent C Reed
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
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24
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Charlesworth A, Meijer HA, de Moor CH. Specificity factors in cytoplasmic polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 4:437-61. [PMID: 23776146 PMCID: PMC3736149 DOI: 10.1002/wrna.1171] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/12/2022]
Abstract
Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3' untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.
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Affiliation(s)
- Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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Fernández-Miranda G, Méndez R. The CPEB-family of proteins, translational control in senescence and cancer. Ageing Res Rev 2012; 11:460-72. [PMID: 22542725 DOI: 10.1016/j.arr.2012.03.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/14/2012] [Accepted: 03/27/2012] [Indexed: 12/31/2022]
Abstract
Cytoplasmic elongation of the poly(A) tail was originally identified as a mechanism to activate maternal mRNAs, stored as silent transcripts with short poly(A) tails, during meiotic progression. A family of RNA-binding proteins named CPEBs, which recruit the translational repression or cytoplasmic polyadenylation machineries to their target mRNAs, directly mediates cytoplasmic polyadenylation. Recent years have witnessed an explosion of studies showing that CPEBs are not only expressed in a variety of somatic tissues, but have essential functions controlling gene expression in time and space in the adult organism. These "new" functions of the CPEBs include regulating the balance between senescence and proliferation and its pathological manifestation, tumor development. In this review, we summarize current knowledge on the functions of the CPEB-family of proteins in the regulation of cell proliferation, their target mRNAs and the mechanism controlling their activities.
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Weill L, Belloc E, Bava FA, Méndez R. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat Struct Mol Biol 2012; 19:577-85. [PMID: 22664985 DOI: 10.1038/nsmb.2311] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Beyond the well-known function of poly(A) tail length in mRNA stability, recent years have witnessed an explosion of information about how changes in tail length and the selection of alternative polyadenylation sites contribute to the translational regulation of a large portion of the genome. The mechanisms and factors mediating nuclear and cytoplasmic changes in poly(A) tail length have been studied in great detail, the targets of these mechanisms have been identified--in some cases by genome-wide screenings--and changes in poly(A) tail length are now implicated in a number of physiological and pathological processes. However, in very few cases have all three levels--mechanisms, targets and functions--been studied together.
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Affiliation(s)
- Laure Weill
- Institute for Research in Biomedicine-IRB Barcelona, Barcelona, Spain
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Sinnamon JR, Czaplinski K. mRNA trafficking and local translation: the Yin and Yang of regulating mRNA localization in neurons. Acta Biochim Biophys Sin (Shanghai) 2011; 43:663-70. [PMID: 21749992 DOI: 10.1093/abbs/gmr058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Localized translation and the requisite trafficking of the mRNA template play significant roles in the nervous system including the establishment of dendrites and axons, axon path-finding, and synaptic plasticity. We provide a brief review on the regulation of localizing mRNA in mammalian neurons through critical post-translational modifications of the factors involved. These examples highlight the relationship between mRNA trafficking and the translational regulation of trafficked mRNAs and provide insight into how extracellular signals target these events during signal transduction.
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Affiliation(s)
- John R Sinnamon
- Program in Neuroscience, Stony Brook University, NY 11794, USA
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