1
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Luo J, Zhu WC, Chen QX, Yang CF, Huang BJ, Zhang SJ. A prognostic model based on DNA methylation-related gene expression for predicting overall survival in hepatocellular carcinoma. Front Oncol 2024; 13:1171932. [PMID: 38304027 PMCID: PMC10830715 DOI: 10.3389/fonc.2023.1171932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) continues to increase in morbidity and mortality among all types of cancer. DNA methylation, an important epigenetic modification, is associated with cancer occurrence and progression. The objective of this study was to establish a model based on DNA methylation risk scores for identifying new potential therapeutic targets in HCC and preventing cancer progression. Methods Transcriptomic, clinical, and DNA methylation data on 374 tumor tissues and 50 adjacent normal tissues were downloaded from The Cancer Genome Atlas-Liver Hepatocellular Carcinoma database. The gene expression profiles of the GSE54236 liver cancer dataset, which contains data on 161 liver tissue samples, were obtained from the Gene Expression Omnibus database. We analyzed the relationship between DNA methylation and gene expression levels after identifying the differentially methylated and expressed genes. Then, we developed and validated a risk score model based on the DNA methylation-driven genes. A tissue array consisting of 30 human hepatocellular carcinoma samples and adjacent normal tissues was used to assess the protein and mRNA expression levels of the marker genes by immunohistochemistry and qRT-PCR, respectively. Results Three methylation-related differential genes were identified in our study: GLS, MEX3B, and GNA14. The results revealed that their DNA methylation levels were negatively correlated with local gene expression regulation. The gene methylation levels correlated strongly with the prognosis of patients with liver cancer. This was confirmed by qRT-PCR and immunohistochemical verification of the expression of these genes or proteins in tumors and adjacent tissues. These results revealed the relationship between the level of relevant gene methylation and the prognosis of patients with liver cancer as well as the underlying cellular and biological mechanisms. This allows our gene signature to provide more accurate and appropriate predictions for clinical applications. Conclusion Through bioinformatics analysis and experimental validation, we obtained three DNA methylation marker: GLS, MEX3B, and GNA14. This helps to predict the prognosis and may be a potential therapeutic target for HCC patients.
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Affiliation(s)
- Jin Luo
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Traditional Chinese Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Wan-Cui Zhu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qiu-Xia Chen
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang-Fu Yang
- Department of Oncology, The People’s Hospital of Gaozhou, Gaozhou, China
| | - Bi-Jun Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Shi-Jun Zhang
- Department of Traditional Chinese Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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2
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Frith MC, Ni S. DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development. Mol Biol Evol 2023; 40:msad275. [PMID: 38085182 PMCID: PMC10735318 DOI: 10.1093/molbev/msad275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
DNA that controls gene expression (e.g. enhancers, promoters) has seemed almost never to be conserved between distantly related animals, like vertebrates and arthropods. This is mysterious, because development of such animals is partly organized by homologous genes with similar complex expression patterns, termed "deep homology." Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone). They control developmental genes (e.g. Nr2f, Ptch, Rfx1/3, Sall, Smad6, Sp5, Tbx2/3), including six homeobox genes: Gsx, Hmx, Meis, Msx, Six1/2, and Zfhx3/4. The segments contain perfectly or near-perfectly conserved CCAAT boxes, E-boxes, and other sequences recognized by regulatory proteins. More such DNA conservation will surely be found soon, as more genomes are published and sequence comparison is optimized. This reveals a control system for animal development conserved since the Precambrian.
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Affiliation(s)
- Martin C Frith
- Artificial Intelligence Research Center, AIST, Tokyo, Japan
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Computational Bio Big Data Open Innovation Laboratory, AIST, Tokyo, Japan
| | - Shengliang Ni
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
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3
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Domingo-Muelas A, Duart-Abadia P, Morante-Redolat JM, Jordán-Pla A, Belenguer G, Fabra-Beser J, Paniagua-Herranz L, Pérez-Villalba A, Álvarez-Varela A, Barriga FM, Gil-Sanz C, Ortega F, Batlle E, Fariñas I. Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis. Nat Commun 2023; 14:373. [PMID: 36690670 PMCID: PMC9871011 DOI: 10.1038/s41467-023-36054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Neural stem cells (NSCs) in the adult murine subependymal zone balance their self-renewal capacity and glial identity with the potential to generate neurons during the lifetime. Adult NSCs exhibit lineage priming via pro-neurogenic fate determinants. However, the protein levels of the neural fate determinants are not sufficient to drive direct differentiation of adult NSCs, which raises the question of how cells along the neurogenic lineage avoid different conflicting fate choices, such as self-renewal and differentiation. Here, we identify RNA-binding protein MEX3A as a post-transcriptional regulator of a set of stemness associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A regulates a quiescence-related RNA signature in activated NSCs that is needed for their return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A is a pivotal regulator of adult murine neurogenesis acting as a translational remodeller.
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Grants
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-119917RB-I00.
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-117937GB-I00, PID2020-119917RB-I00, PID 2019-109155RB-I00, PID2020-114227RB-I00, RyC-2015-19058, PRE2018-084838. Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED, Spain) - MICINN- CB06/05/0086.
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Affiliation(s)
- Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Pere Duart-Abadia
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jose Manuel Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Germán Belenguer
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jaime Fabra-Beser
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Lucía Paniagua-Herranz
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Ana Pérez-Villalba
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Gil-Sanz
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Felipe Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain.
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain.
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4
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Yang Y, Wang SY. Mex3B inhibits DC-STAMP mRNA level and osteoclastogenesis. CELL INSIGHT 2022; 1:100002. [PMID: 37192984 PMCID: PMC10120280 DOI: 10.1016/j.cellin.2021.100002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 05/18/2023]
Abstract
Bone homeostasis is maintained through continuous remodeling by osteoclast-driven bone resorption and osteoblast-mediated bone formation. Osteoclasts are multinucleated giant cells (MNCs) differentiated from myeloid progenitors of the monocytic lineage. During osteoclast maturation, DC-STAMP (dendritic cell specific transmembrane protein) has been shown as a master determinant of osteoclast cell fusion. In this study, we demonstrate that Mex3B inhibits osteoclast fusion protein DCSTAMP expression and osteoclastogenesis. During differentiation of osteoclasts, the expression of Mex3B is down-regulated by cytokines such as RANKL and TNFa, resulting in relief of Mex3B-mediated down-regulation of DC-STAMP mRNA level. Our findings not only reveal critical mechanisms on regulation of DC-STAMP-mediated osteoclastogenesis, but also point to Mex3B as a potential therapeutic target for the treatment of human bone diseases.
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5
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Naef V, De Sarlo M, Testa G, Corsinovi D, Azzarelli R, Borello U, Ori M. The Stemness Gene Mex3A Is a Key Regulator of Neuroblast Proliferation During Neurogenesis. Front Cell Dev Biol 2020; 8:549533. [PMID: 33072742 PMCID: PMC7536324 DOI: 10.3389/fcell.2020.549533] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/31/2020] [Indexed: 01/31/2023] Open
Abstract
Mex3A is an RNA binding protein that can also act as an E3 ubiquitin ligase to control gene expression at the post-transcriptional level. In intestinal adult stem cells, MEX3A is required for cell self-renewal and when overexpressed, MEX3A can contribute to support the proliferation of different cancer cell types. In a completely different context, we found mex3A among the genes expressed in neurogenic niches of the embryonic and adult fish brain and, notably, its expression was downregulated during brain aging. The role of mex3A during embryonic and adult neurogenesis in tetrapods is still unknown. Here, we showed that mex3A is expressed in the proliferative region of the developing brain in both Xenopus and mouse embryos. Using gain and loss of gene function approaches, we showed that, in Xenopus embryos, mex3A is required for neuroblast proliferation and its depletion reduced the neuroblast pool, leading to microcephaly. The tissue-specific overexpression of mex3A in the developing neural plate enhanced the expression of sox2 and msi-1 keeping neuroblasts into a proliferative state. It is now clear that the stemness property of mex3A, already demonstrated in adult intestinal stem cells and cancer cells, is a key feature of mex3a also in developing brain, opening new lines of investigation to better understand its role during brain aging and brain cancer development.
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Affiliation(s)
- Valentina Naef
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Miriam De Sarlo
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Giovanna Testa
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Debora Corsinovi
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Roberta Azzarelli
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Ugo Borello
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Michela Ori
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
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6
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Cox DC, Guan X, Xia Z, Cooper TA. Increased nuclear but not cytoplasmic activities of CELF1 protein leads to muscle wasting. Hum Mol Genet 2020; 29:1729-1744. [PMID: 32412585 PMCID: PMC7322576 DOI: 10.1093/hmg/ddaa095] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/16/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
mRNA processing is highly regulated during development through changes in RNA-binding protein (RBP) activities. CUG-BP, Elav-like family member 1 (CELF1, also called CUGBP1) is an RBP, the expression of which decreases in skeletal muscle soon after birth. CELF1 regulates multiple nuclear and cytoplasmic RNA processing events. In the nucleus, CELF1 regulates networks of postnatal alternative splicing (AS) transitions, while in the cytoplasm, CELF1 regulates mRNA stability and translation. Stabilization and misregulation of CELF1 has been implicated in human diseases including myotonic dystrophy type 1, Alzheimer's disease and multiple cancers. To understand the contribution of nuclear and cytoplasmic CELF1 activity to normal and pathogenic skeletal muscle biology, we generated transgenic mice for doxycycline-inducible and skeletal muscle-specific expression of active CELF1 mutants engineered to be localized predominantly to either the nucleus or the cytoplasm. Adult mice expressing nuclear, but not cytoplasmic, CELF1 are characterized by strong histopathological defects, muscle loss within 10 days and changes in AS. In contrast, mice expressing cytoplasmic CELF1 display changes in protein levels of targets known to be regulated at the level of translation by CELF1, with minimal changes in AS. These changes are in the absence of overt histopathological changes or muscle loss. RNA-sequencing revealed extensive gene expression and AS changes in mice overexpressing nuclear and naturally localized CELF1 protein, with affected genes involved in cytoskeleton dynamics, membrane dynamics, RNA processing and zinc ion binding. These results support a stronger role for nuclear CELF1 functions as compared to cytoplasmic CELF1 functions in skeletal muscle wasting.
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Affiliation(s)
- Diana C Cox
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Biochemistry & Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xiangnan Guan
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239 USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239 USA
| | - Thomas A Cooper
- Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Molecular & Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston TX, 77030 USA
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7
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Rocha de Almeida T, Alix M, Le Cam A, Klopp C, Montfort J, Toomey L, Ledoré Y, Bobe J, Chardard D, Schaerlinger B, Fontaine P. Domestication may affect the maternal mRNA profile in unfertilized eggs, potentially impacting the embryonic development of Eurasian perch (Perca fluviatilis). PLoS One 2019; 14:e0226878. [PMID: 31891603 PMCID: PMC6938363 DOI: 10.1371/journal.pone.0226878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 12/06/2019] [Indexed: 12/18/2022] Open
Abstract
Domestication is an evolutionary process during which we expect populations to progressively adapt to an environment controlled by humans. It is accompanied by genetic and presumably epigenetic changes potentially leading to modifications in the transcriptomic profile in various tissues. Reproduction is a key function often affected by this process in numerous species, regardless of the mechanism. The maternal mRNA in fish eggs is crucial for the proper embryogenesis. Our working hypothesis is that modifications of maternal mRNAs may reflect potential genetic and/or epigenetic modifications occurring during domestication and could have consequences during embryogenesis. Consequently, we investigated the trancriptomic profile of unfertilized eggs from two populations of Eurasian perch. These two populations differed by their domestication histories (F1 vs. F7+-at least seven generations of reproduction in captivity) and were genetically differentiated (FST = 0.1055, p<0.05). A broad follow up of the oogenesis progression failed to show significant differences during oogenesis between populations. However, the F1 population spawned earlier with embryos presenting an overall higher survivorship than those from the F7+ population. The transcriptomic profile of unfertilized eggs showed 358 differentially expressed genes between populations. In conclusion, our data suggests that the domestication process may influence the regulation of the maternal transcripts in fish eggs, which could in turn explain differences of developmental success.
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Affiliation(s)
| | - Maud Alix
- UR AFPA, University of Lorraine, INRA, Nancy, France
| | - Aurélie Le Cam
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
| | | | - Jérôme Montfort
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
| | - Lola Toomey
- UR AFPA, University of Lorraine, INRA, Nancy, France
| | | | - Julien Bobe
- LPGP, UR1037 Fish Physiology and Genomics, INRA, Rennes, France
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8
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Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1. Genes Dev 2019; 33:1221-1235. [PMID: 31371437 PMCID: PMC6719626 DOI: 10.1101/gad.328492.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 01/19/2023]
Abstract
In this study, Welte et al. investigated the dual roles of mammalian TRIM71, a phylogenetically conserved regulator of development, in the control of stem cell fate. They demonstrate that TRIM71 shapes the transcriptome of mESCs predominantly through its RNA-binding activity and identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1/Muscleblind. TRIM71/LIN-41, a phylogenetically conserved regulator of development, controls stem cell fates. Mammalian TRIM71 exhibits both RNA-binding and protein ubiquitylation activities, but the functional contribution of either activity and relevant primary targets remain poorly understood. Here, we demonstrate that TRIM71 shapes the transcriptome of mouse embryonic stem cells (mESCs) predominantly through its RNA-binding activity. We reveal that TRIM71 binds targets through 3′ untranslated region (UTR) hairpin motifs and that it acts predominantly by target degradation. TRIM71 mutations implicated in etiogenesis of human congenital hydrocephalus impair target silencing. We identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1 (Muscleblind-like protein 1). MBNL1 promotes cell differentiation through regulation of alternative splicing, and we demonstrate that TRIM71 promotes embryonic splicing patterns through MBNL1 repression. Hence, repression of MBNL1-dependent alternative splicing may contribute to TRIM71's function in regulating stem cell fates.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
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9
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Yasuoka Y, Taira M. Microinjection of DNA Constructs into Xenopus Embryos for Gene Misexpression and cis-Regulatory Module Analysis. Cold Spring Harb Protoc 2019; 2019:pdb.prot097279. [PMID: 30131366 DOI: 10.1101/pdb.prot097279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introducing exogenous DNA into an embryo can promote misexpression of a gene of interest via transcription regulated by an attached enhancer-promoter. This protocol describes plasmid DNA microinjection into Xenopus embryos for misexpression of genes after zygotic gene expression begins. It also describes a method for coinjecting a reporter plasmid with mRNA or antisense morpholinos to perform luciferase reporter assays, which are useful for quantitative analysis of cis-regulatory sequences responding to endogenous or exogenous stimuli in embryos.
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Affiliation(s)
- Yuuri Yasuoka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa 904-0495, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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10
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Huang L, Malu S, McKenzie JA, Andrews MC, Talukder AH, Tieu T, Karpinets T, Haymaker C, Forget MA, Williams LJ, Wang Z, Mbofung RM, Wang ZQ, Davis RE, Lo RS, Wargo JA, Davies MA, Bernatchez C, Heffernan T, Amaria RN, Korkut A, Peng W, Roszik J, Lizée G, Woodman SE, Hwu P. The RNA-binding Protein MEX3B Mediates Resistance to Cancer Immunotherapy by Downregulating HLA-A Expression. Clin Cancer Res 2018; 24:3366-3376. [PMID: 29496759 PMCID: PMC9872773 DOI: 10.1158/1078-0432.ccr-17-2483] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/30/2017] [Accepted: 02/21/2018] [Indexed: 01/27/2023]
Abstract
Purpose: Cancer immunotherapy has shown promising clinical outcomes in many patients. However, some patients still fail to respond, and new strategies are needed to overcome resistance. The purpose of this study was to identify novel genes and understand the mechanisms that confer resistance to cancer immunotherapy.Experimental Design: To identify genes mediating resistance to T-cell killing, we performed an open reading frame (ORF) screen of a kinome library to study whether overexpression of a gene in patient-derived melanoma cells could inhibit their susceptibility to killing by autologous tumor-infiltrating lymphocytes (TIL).Results: The RNA-binding protein MEX3B was identified as a top candidate that decreased the susceptibility of melanoma cells to killing by TILs. Further analyses of anti-PD-1-treated melanoma patient tumor samples suggested that higher MEX3B expression is associated with resistance to PD-1 blockade. In addition, significantly decreased levels of IFNγ were secreted from TILs incubated with MEX3B-overexpressing tumor cells. Interestingly, this phenotype was rescued upon overexpression of exogenous HLA-A2. Consistent with this, we observed decreased HLA-A expression in MEX3B-overexpressing tumor cells. Finally, luciferase reporter assays and RNA-binding protein immunoprecipitation assays suggest that this is due to MEX3B binding to the 3' untranslated region (UTR) of HLA-A to destabilize the mRNA.Conclusions: MEX3B mediates resistance to cancer immunotherapy by binding to the 3' UTR of HLA-A to destabilize the HLA-A mRNA and thus downregulate HLA-A expression on the surface of tumor cells, thereby making the tumor cells unable to be recognized and killed by T cells. Clin Cancer Res; 24(14); 3366-76. ©2018 AACRSee related commentary by Kalbasi and Ribas, p. 3239.
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Affiliation(s)
- Lu Huang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A. McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miles C. Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amjad H. Talukder
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J. Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhe Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina M. Mbofung
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhi-Qiang Wang
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roger S. Lo
- Department of Medicine, The University of California, Los Angeles, Los Angeles, California
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N. Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott E. Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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11
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Hildebrandt A, Alanis-Lobato G, Voigt A, Zarnack K, Andrade-Navarro MA, Beli P, König J. Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Sci Rep 2017; 7:16582. [PMID: 29185492 PMCID: PMC5707401 DOI: 10.1038/s41598-017-16695-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/14/2017] [Indexed: 11/09/2022] Open
Abstract
RNA-binding ubiquitin ligases (RBULs) have the potential to link RNA-mediated mechanisms to protein ubiquitylation. Despite this, the cellular functions, substrates and interaction partners of most RBULs remain poorly characterized. Affinity purification (AP) combined with quantitative mass spectrometry (MS)-based proteomics is a powerful approach for analyzing protein functions. Mapping the physiological interaction partners of RNA-binding proteins has been hampered by their intrinsic properties, in particular the existence of low-complexity regions, which are prone to engage in non-physiological interactions. Here, we used an adapted AP approach to identify the interaction partners of human RBULs harboring different RNA-binding domains. To increase the likelihood of recovering physiological interactions, we combined control and bait-expressing cells prior to lysis. In this setup, only stable interactions that were originally present in the cell will be identified. We exploit gene function similarity between the bait proteins and their interactors to benchmark our approach in its ability to recover physiological interactions. We reveal that RBULs engage in stable interactions with RNA-binding proteins involved in different steps of RNA metabolism as well as with components of the ubiquitin conjugation machinery and ubiquitin-binding proteins. Our results thus demonstrate their capacity to link posttranscriptional regulation with the ubiquitin system.
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Affiliation(s)
- Andrea Hildebrandt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Gregorio Alanis-Lobato
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Gresemundweg 2, 55128, Mainz, Germany
| | - Petra Beli
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
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12
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Jeremias WDJ, Araújo FMG, Queiroz FR, Pais FSM, de Mattos ACA, Salim ACDM, Coelho PMZ, Oliveira GC, Kusel JR, Guerra-Sá R, Coimbra RS, Babá ÉH. Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum. PLoS One 2017. [PMID: 28622369 PMCID: PMC5473564 DOI: 10.1371/journal.pone.0178829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Once inside a vertebrate host after infection, individual schistosomula of the parasite Schistosoma mansoni find a new and complex environment, which requires quick adjustments for survival, such as those that allow it to avoid the innate immune response of the host. Thus, it is very important for the parasite to remain within the skin after entering the host for a period of about 3 days, at which time it can then reach the venous system, migrate to the lungs and, by the end of eighth day post-infection, it reach the portal venous system, while undergoing minimal changes in morphology. However, after just a few days in the portal blood system, the parasite experiences an extraordinary increase in biomass and significant morphological alterations. Therefore, determining the constituents of the portal venous system that may trigger these changes that causes the parasite to consolidate its development inside the vertebrate host, thus causing the disease schistosomiasis, is essential. The present work simulated the conditions found in the portal venous system of the vertebrate host by exposing schistosomula of S. mansoni to in vitro culture in the presence of portal serum of the hamster, Mesocricetus auratus. Two different incubation periods were evaluated, one of 3 hours and one of 12 hours. These time periods were used to mimic the early contact of the parasite with portal serum during the course of natural infection. As a control, parasites were incubated in presence of hamster peripheral serum, in order to compare gene expression signatures between the two conditions. The mRNA obtained from parasites cultured under both conditions were submitted to a whole transcriptome library preparation and sequenced with a next generation platform. On average, nearly 15 million reads were produced per sample and, for the purpose of gene expression quantification, only reads mapped to one location of the transcriptome were considered. After statistical analysis, we found 103 genes differentially expressed by schistosomula cultured for 3 hours and 12 hours in the presence of hamster portal serum. After the subtraction of a second list of genes, also differentially expressed between schistosomula cultured for 3 hours and 12 hours in presence of peripheral serum, a set of 58 genes was finally established. This pattern was further validated for a subset of 17 genes, by measuring gene expression through quantitative real time polymerase chain reaction (qPCR). Processes that were activated by the portal serum stimulus include response to stress, membrane transport, protein synthesis and folding/degradation, signaling, cytoskeleton arrangement, cell adhesion and nucleotide synthesis. Additionally, a smaller number of genes down-regulated under the same condition act on cholinergic signaling, inorganic cation and organic anion membrane transport, cell adhesion and cytoskeleton arrangement. Considering the role of these genes in triggering processes that allow the parasite to quickly adapt, escape the immune response of the host and start maturation into an adult worm after contact with the portal serum, this work may point to unexplored molecular targets for drug discovery and vaccine development against schistosomiasis.
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Affiliation(s)
- Wander de Jesus Jeremias
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
- Centro Universitário de Belo Horizonte – UNIBH, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
| | | | - Fábio Ribeiro Queiroz
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Guilherme Correa Oliveira
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - John Robert Kusel
- Glasgow University, Centre for Open Studies, Glasgow, United Kingdom
| | - Renata Guerra-Sá
- Federal University of Ouro Preto, Institute of Exact and Biological Sciences, Ouro Preto, Minas Gerais, Brazil
| | - Roney Santos Coimbra
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
| | - Élio Hideo Babá
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
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13
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Song KY, Choi HS, Law PY, Wei LN, Loh HH. Post-Transcriptional Regulation of the Human Mu-Opioid Receptor (MOR) by Morphine-Induced RNA Binding Proteins hnRNP K and PCBP1. J Cell Physiol 2016; 232:576-584. [PMID: 27292014 DOI: 10.1002/jcp.25455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/10/2016] [Indexed: 01/18/2023]
Abstract
Expression of the mu-opioid receptor (MOR) protein is controlled by extensive transcriptional and post-transcriptional processing. MOR gene expression has previously been shown to be altered by a post-transcriptional mechanism involving the MOR mRNA untranslated region (UTR). Here, we demonstrate for the first time the role of heterogeneous nuclear ribonucleic acids (hnRNA)-binding protein (hnRNP) K and poly(C)-binding protein 1 (PCBP1) as post-transcriptional inducers in MOR gene regulation. In the absence of morphine, a significant level of MOR mRNA is sustained in its resting state and partitions in the translationally inactive polysomal fraction. Morphine stimulation activates the downstream targets hnRNP K and PCPB1 and induces partitioning of the MOR mRNA to the translationally active fraction. Using reporter and ligand binding assays, as well as RNA EMSA, we reveal potential RNP binding sites located in the 5'-untranslated region of human MOR mRNA. In addition, we also found that morphine-induced RNPs could regulate MOR expression. Our results establish the role of hnRNP K and PCPB1 in the translational control of morphine-induced MOR expression in human neuroblastoma (NMB) cells as well as cells stably expressing MOR (NMB1). J. Cell. Physiol. 232: 576-584, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Kyu Young Song
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Hack Sun Choi
- Subtropical Horticulture Research Institute, College of Applied Life Science, Jeju National University, Jeju, Jeju, Republic of Korea
| | - Ping-Yee Law
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Li-Na Wei
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Horace H Loh
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota
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14
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Li X, Li Y, Liu C, Jin M, Lu B. Oocyte-Specific Expression of Mouse MEX3C652AA in the Ovary and Its Potential Role in Regulating Maternal Fos mRNA. Biol Reprod 2016; 94:115. [PMID: 27053362 DOI: 10.1095/biolreprod.115.136630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/29/2016] [Indexed: 12/31/2022] Open
Abstract
Currently, the human MEX3C gene is known to encode an RNA-binding protein of 659 amino acid residues. Here we show that the MEX3C gene has alternative splicing forms giving rise to multiple MEX3C variants, and some cells express MEX3C transcripts coding for short MEX3C isoforms but not transcripts for MEX3C(659AA) MEX3C(659AA) functions as an adaptor protein for Exportin 1 (XPO1)-mediated nuclear export since it increases the cytoplasmic distribution of poly(A)(+) RNA and since addition of the nuclear export signal (NES) sequence to a short MEX3C isoform MEX3C(464AA) confers similar cytoplasmic poly(A)(+) RNA accumulation activity as MEX3C(659AA) FOS mRNA is a potential MEX3C target mRNA. One mechanism by which MEX3C(659AA) could regulate FOS mRNA is by promoting its nuclear export. Overexpressing MEX3C(659AA) significantly increased FOS mRNA expression, whereas mutating the NES of MEX3C(659AA) and treating cells with leptomycin B to inhibit XPO1-mediated nuclear export attenuated FOS upregulation. FOS mRNA is unstable in somatic cells but less so in oocytes; how it is stabilized in the oocytes is unknown. Transcripts for the mouse counterpart of human MEX3C(659AA) (MEX3C(652AA)) are specifically expressed in developing oocytes in the ovary, although total Mex3c transcripts are expressed in both granulosa cells and oocytes. The specific expression of this long MEX3C isoform in oocytes and its ability to enhance FOS mRNA nuclear export and stability all suggest that MEX3C(659AA) is an RNA-binding protein that preserves maternal FOS mRNA in oocytes.
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Affiliation(s)
- Xue Li
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina
| | - Yan Li
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina General Hospital, Ningxia Medical University, Ningxia, People's Republic of China
| | - Chunlian Liu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina General Hospital, Ningxia Medical University, Ningxia, People's Republic of China
| | - Mulan Jin
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Baisong Lu
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina
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15
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Rodríguez-Cazorla E, Ripoll JJ, Andújar A, Bailey LJ, Martínez-Laborda A, Yanofsky MF, Vera A. K-homology nuclear ribonucleoproteins regulate floral organ identity and determinacy in arabidopsis. PLoS Genet 2015; 11:e1004983. [PMID: 25658099 PMCID: PMC4450054 DOI: 10.1371/journal.pgen.1004983] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/05/2015] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional control is nowadays considered a main checking point for correct gene regulation during development, and RNA binding proteins actively participate in this process. Arabidopsis thaliana FLOWERING LOCUS WITH KH DOMAINS (FLK) and PEPPER (PEP) genes encode RNA-binding proteins that contain three K-homology (KH)-domain, the typical configuration of Poly(C)-binding ribonucleoproteins (PCBPs). We previously demonstrated that FLK and PEP interact to regulate FLOWERING LOCUS C (FLC), a central repressor of flowering time. Now we show that FLK and PEP also play an important role in the maintenance of the C-function during floral organ identity by post-transcriptionally regulating the MADS-box floral homeotic gene AGAMOUS (AG). Previous studies have indicated that the KH-domain containing protein HEN4, in concert with the CCCH-type RNA binding protein HUA1 and the RPR-type protein HUA2, facilitates maturation of the AG pre-mRNA. In this report we show that FLK and PEP genetically interact with HEN4, HUA1, and HUA2, and that the FLK and PEP proteins physically associate with HUA1 and HEN4. Taken together, these data suggest that HUA1, HEN4, PEP and FLK are components of the same post-transcriptional regulatory module that ensures normal processing of the AG pre-mRNA. Our data better delineates the roles of PEP in plant development and, for the first time, links FLK to a morphogenetic process. Unlike animals, angiosperms (flowering plants) lack a germline that is set-aside early in embryo development. Contrariwise, reproductive success relies on the formation of flowers during adult life, which provide the germ cells and the means for fertilization. Therefore, timing of flowering and flower organ morphogenesis are critical developmental operations that must be finely regulated and coordinated to complete reproduction. Arabidopsis thaliana FLOWERING LOCUS WITH KH DOMAINS (FLK) and PEPPER (PEP) encode two KH-domain RNA-binding proteins phylogenetically related to human proteins characterized by their high developmental versatility. FLK and PEP modulate the mRNA expression of the MADS-box gene FLOWERING LOCUS C, key in flowering control. In this work we have found that FLK and PEP also play a pivotal role in flower organogenesis by post-transcriptionally regulating the MADS-box floral organ identity gene AGAMOUS (AG). Interestingly, FLK and PEP physically interact with proteins involved in AG pre-mRNA processing to secure correct AG function in the floral meristem and flower. Taken together, our results reveal the existence of a post-transcriptional regulatory activity controlling key master genes for floral timing and flower morphogenesis, which might be instrumental for coordinating both developmental phases.
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Affiliation(s)
| | - Juan José Ripoll
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Alfonso Andújar
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Lindsay J. Bailey
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Antonio Martínez-Laborda
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
| | - Martin F. Yanofsky
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - Antonio Vera
- Área de Genética, Universidad Miguel Hernández, Campus de Sant Joan d’Alacant, Sant Joan d’Alacant, Alicante, Spain
- * E-mail:
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16
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Mawaribuchi S, Ikeda N, Fujitani K, Ito Y, Onuma Y, Komiya T, Takamatsu N, Ito M. Cell-mass structures expressing the aromatase gene Cyp19a1 lead to ovarian cavities in Xenopus laevis. Endocrinology 2014; 155:3996-4005. [PMID: 25051437 DOI: 10.1210/en.2014-1096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The African clawed frog, Xenopus laevis, has a ZZ/ZW-type sex-determination system. We previously reported that a W-linked gene, Dm-W, can determine development as a female. However, the mechanisms of early sex differentiation remain unclear. We used microarrays to screen for genes with sexually dimorphic expression in ZZ and ZW gonads during early sex differentiation in X laevis and found several steroidogenic genes. Importantly, the steroid 17α-hydroxylase gene Cyp17a1 and the aromatase gene Cyp19a1 were highly expressed in ZZ and ZW gonads, respectively, just after sex determination. At this stage, we found that Cyp17a1, Cyp19a1, or both were expressed in the ZZ and ZW gonads in a unique mass-in-line structure, in which several masses of cells, each surrounded by a basement membrane, were aligned along the anteroposterior axis. In fact, during sex differentiation, ovarian cavities formed inside each mass of Cyp17a1- and Cyp19a1-positive cells in the ZW gonads. However, the mass-in-line structure disappeared during testicular development in the ZZ testes. These results suggested that the mass-in-line structure found in both ZZ and ZW gonads just after sex determination might be formed in advance to produce ovarian cavities and then oocytes. Consequently, we propose a view that the default sex may be female in the morphological aspect of gonads in X laevis.
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Affiliation(s)
- Shuuji Mawaribuchi
- Department of Biosciences (S.M., N.I., K.F., N.T., M.I.), School of Science, Kitasato University, Sagamihara 252-0373, Japan; Research Center for Stem Cell Engineering (Y.I., Y.O.), National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, Tsukuba 305-8562, Japan; and Department of Biological Function (T.K.), Osaka City University, Sumiyoshi 558-8585, Japan
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17
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Song KY, Choi HS, Law PY, Wei LN, Loh HH. Vimentin interacts with the 5'-untranslated region of mouse mu opioid receptor (MOR) and is required for post-transcriptional regulation. RNA Biol 2013; 10:256-66. [PMID: 23353576 PMCID: PMC3594284 DOI: 10.4161/rna.23022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The opioid receptors are among the most highly studied members of the superfamily of G-protein coupled receptors. Morphine and endogenous mu opioid peptides exert their pharmacological actions mainly through the mu opioid receptor (MOR). Expression of opioid receptor proteins is controlled by extensive transcriptional and post-transcriptional processing. Previously, the 5′-untranslated region (UTR) of the mouse MOR was found to be important for post-transcriptional regulation of the MOR gene in neuronal cells. Here, we demonstrate for the first time the role of vimentin as a post-transcriptional repressor in MOR gene regulation. To identify potential regulators of the mouse MOR gene, we performed affinity column chromatography using 5′-UTR-specific RNA oligonucleotides using neuroblastoma NS20Y cells. Chromatography was followed by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry. We identified an intermediate filament protein, vimentin, which bound specifically to the region between -175 and -150 (175–150) of the MOR 5′-UTR. Binding was confirmed by western blot analysis and RNA supershift assay. Furthermore, a cotransfection study demonstrated that the presence of vimentin resulted in reduced expression of the mouse MOR. Our data suggest that vimentin functions as a repressor of MOR translation, dependent on 175–150 of the MOR 5′-UTR.
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Affiliation(s)
- Kyu Young Song
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, USA.
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