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Aya F, Lanuza-Gracia P, González-Pérez A, Bonnal S, Mancini E, López-Bigas N, Arance A, Valcárcel J. Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Rep 2024; 43:114048. [PMID: 38614086 DOI: 10.1016/j.celrep.2024.114048] [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: 08/29/2023] [Revised: 02/06/2024] [Accepted: 03/19/2024] [Indexed: 04/15/2024] Open
Abstract
Resistance to MAPK inhibitors (MAPKi), the main cause of relapse in BRAF-mutant melanoma, is associated with the production of alternative BRAF mRNA isoforms (altBRAFs) in up to 30% of patients receiving BRAF inhibitor monotherapy. These altBRAFs have been described as being generated by alternative pre-mRNA splicing, and splicing modulation has been proposed as a therapeutic strategy to overcome resistance. In contrast, we report that altBRAFs are generated through genomic deletions. Using different in vitro models of altBRAF-mediated melanoma resistance, we demonstrate the production of altBRAFs exclusively from the BRAF V600E allele, correlating with corresponding genomic deletions. Genomic deletions are also detected in tumor samples from melanoma and breast cancer patients expressing altBRAFs. Along with the identification of altBRAFs in BRAF wild-type and in MAPKi-naive melanoma samples, our results represent a major shift in our understanding of mechanisms leading to the generation of BRAF transcripts variants associated with resistance in melanoma.
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Affiliation(s)
- Francisco Aya
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pablo Lanuza-Gracia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Abel González-Pérez
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Estefania Mancini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria López-Bigas
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ana Arance
- Medical Oncology Department, Hospital Clinic, Barcelona, Spain; Institut de Investigacions Biomedicas August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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2
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Fotouhi M, Worrall D, Ayoubi R, Southern K, McPherson PS, Laflamme C. A guide to selecting high-performing antibodies for RNA-binding protein TIA1 for use in Western Blot, immunoprecipitation and immunofluorescence. F1000Res 2024; 12:745. [PMID: 38638178 PMCID: PMC11024596 DOI: 10.12688/f1000research.133645.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
A member of the RNA-binding protein family, T-cell intracellular antigen-1 (TIA1) regulates mRNA translation and splicing as well as cellular stress by promoting stress granule formation. Variants of the TIA1 gene have implications in neurogenerative disorders including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Reproducible research on TIA1 would be enhanced with the availability of high-quality anti-TIA1 antibodies. In this study, we characterized twelve TIA1 commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.
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Affiliation(s)
- Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | - Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | - Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
| | | | - ABIF Consortium
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada
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3
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Ramos-Velasco B, Naranjo R, Izquierdo JM. Bibliometric Overview on T-Cell Intracellular Antigens and Their Pathological Implications. BIOLOGY 2024; 13:195. [PMID: 38534464 DOI: 10.3390/biology13030195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024]
Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation regulation, linking them to a wide range of diseases including neuronal disorders, cancer and other pathologies. From their discovery to the present day, many studies have focused on the behavior of these proteins in order to understand their impact on molecular and cellular processes and to understand their relationship to human pathologies. The volume of research on these proteins in various fields, including molecular biology, biochemistry, cell biology, immunology and cancer, has steadily increased, indicating a growing interest in these gene expression regulators among researchers. This information can be used to know the most productive institutions working in the field, understand the focus of research, identify key areas of involvement, delve deeper into their relationship and impact on different diseases, and to establish the level of study associated with them.
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Affiliation(s)
- Beatriz Ramos-Velasco
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Rocío Naranjo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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4
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Wu H, Liu X, Fang Y, Yang Y, Huang Y, Pan X, Shen HB. Decoding protein binding landscape on circular RNAs with base-resolution transformer models. Comput Biol Med 2024; 171:108175. [PMID: 38402841 DOI: 10.1016/j.compbiomed.2024.108175] [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: 12/02/2023] [Revised: 01/16/2024] [Accepted: 02/18/2024] [Indexed: 02/27/2024]
Abstract
Circular RNAs (circRNAs), a class of endogenous RNA with a covalent loop structure, can regulate gene expression by serving as sponges for microRNAs and RNA-binding proteins (RBPs). To date, most computational methods for predicting RBP binding sites on circRNAs focus on circRNA fragments instead of circRNAs. These methods detect whether a circRNA fragment contains binding sites, but cannot determine where are the binding sites and how many binding sites are on the circRNA transcript. We report a hybrid deep learning-based tool, CircSite, to predict RBP binding sites at single-nucleotide resolution and detect key contributed nucleotides on circRNA transcripts. CircSite takes advantage of convolutional neural networks (CNNs) and Transformer for learning local and global representations of circRNAs binding to RBPs, respectively. We construct 37 datasets of circRNAs interacting with proteins for benchmarking and the experimental results show that CircSite offers accurate predictions of RBP binding nucleotides and detects key subsequences aligning well with known binding motifs. CircSite is an easy-to-use online webserver for predicting RBP binding sites on circRNA transcripts and freely available at http://www.csbio.sjtu.edu.cn/bioinf/CircSite/.
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Affiliation(s)
- Hehe Wu
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, And Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Xiaojian Liu
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, And Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yi Fang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, And Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yang Yang
- Center for Brain-Like Computing and Machine Intelligence, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Huang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics Chinese Academy of Sciences, 500 Yutian Road, Shanghai, 200083, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, And Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, And Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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5
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Fuentes-Jiménez DA, Salinas LS, Morales-Oliva E, Ramírez-Ramírez VA, Arciniega M, Navarro RE. Two predicted α-helices within the prion-like domain of TIAR-1 play a crucial role in its association with stress granules in Caenorhabditis elegans. Front Cell Dev Biol 2023; 11:1265104. [PMID: 38161334 PMCID: PMC10757852 DOI: 10.3389/fcell.2023.1265104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Stress granules (SGs) are sites for mRNA storage, protection, and translation repression. TIA1 and TIAR1 are two RNA-binding proteins that are key players in SGs formation in mammals. TIA1/TIAR have a prion-like domain (PrD) in their C-terminal that promotes liquid-phase separation. Lack of any TIA1/TIAR has severe consequences in mice. However, it is not clear whether the failure to form proper SGs is the cause of any of these problems. We disrupted two predicted α-helices within the prion-like domain of the Caenohabditis elegans TIA1/TIAR homolog, TIAR-1, to test whether its association with SGs is important for the nematode. We found that tiar-1 PrD mutant animals continued to form TIAR-1 condensates under stress in the C. elegans gonad. Nonetheless, TIAR-1 condensates appeared fragile and disassembled quickly after stress. Apparently, the SGs continued to associate regularly as observed with CGH-1, an SG marker. Like tiar-1-knockout nematodes, tiar-1 PrD mutant animals exhibited fertility problems and a shorter lifespan. Notwithstanding this, tiar-1 PrD mutant nematodes were no sensitive to stress. Our data demonstrate that the predicted prion-like domain of TIAR-1 is important for its association with stress granules. Moreover, this domain may also play a significant role in various TIAR-1 functions unrelated to stress, such as fertility, embryogenesis and lifespan.
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Affiliation(s)
- D. A. Fuentes-Jiménez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - L. S. Salinas
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - E. Morales-Oliva
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - V. A. Ramírez-Ramírez
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - M. Arciniega
- Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - R. E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
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6
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Sung HM, Schott J, Boss P, Lehmann JA, Hardt MR, Lindner D, Messens J, Bogeski I, Ohler U, Stoecklin G. Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing. J Cell Biol 2023; 222:e202111151. [PMID: 37956386 PMCID: PMC10641589 DOI: 10.1083/jcb.202111151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 11/15/2023] Open
Abstract
Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate posttranscriptional mRNA processing. Here, we discovered that ribotoxic stress induces a profound reorganization of NSs with enhanced recruitment of factors required for splice-site recognition, including the RNA-binding protein TIAR, U1 snRNP proteins and U2-associated factor 65, as well as serine 2 phosphorylated RNA polymerase II. NS reorganization relies on the stress-activated p38 mitogen-activated protein kinase (MAPK) pathway and coincides with splicing activation of both pre-existing and newly synthesized pre-mRNAs. In particular, ribotoxic stress causes targeted excision of retained introns from pre-mRNAs of immediate early genes (IEGs), whose transcription is induced during the stress response. Importantly, enhanced splicing of the IEGs ZFP36 and FOS is accompanied by relocalization of the corresponding nuclear mRNA foci to NSs. Our study reveals NSs as a dynamic compartment that is remodeled under stress conditions, whereby NSs appear to become sites of IEG transcription and efficient cotranscriptional splicing.
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Affiliation(s)
- Hsu-Min Sung
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Johanna Schott
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Philipp Boss
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Janina A. Lehmann
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Marius Roland Hardt
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Doris Lindner
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Joris Messens
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Brussels Center for Redox Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Department of Biology, Humboldt University, Berlin, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
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7
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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8
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Liu K, Dai W, Ju J, Li W, Chen Q, Li J, Liu H. Depletion of TIAR impairs embryogenesis via inhibiting zygote genome transcribe. Reprod Domest Anim 2023; 58:1456-1467. [PMID: 37667420 DOI: 10.1111/rda.14461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
T cell intracellular antigen 1 related protein (TIAR), an RNA-binding protein (RBP), regulates pre-messenger RNA (pre-mRNA) alternative splicing, has been suggested to affect the maturation of primordial germ cells and early mouse embryo development. However, the underlying mechanism remains elusive. In this study, we revealed that TIAR was primarily located in the nucleus at the 2-cell stage embryo, accompanied by highly active transcription. Using immunofluorescence staining and western blotting, we first described the localization and expression level of TIAR during the whole period of oocyte matured and embryogenesis. Knocked down of TIAR could significantly inhibit transcribed and blocked the early mouse embryo development. Combined with RNAP II inhibitor and pre-RNA splicing inhibitor treatment, we further supposed that TIAR might affect transcription at 2-cell via regulating pre-mRNA splicing, and then regulate early mouse embryo development. Collectively, our results provided a novel and potential understanding of TIAR in embryogenesis, suggesting TIAR is required for transcription and embryonic development.
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Affiliation(s)
- Ke Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weilong Dai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jiaqian Ju
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weijian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qianqian Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Juan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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9
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Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
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Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
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10
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He S, Valkov E, Cheloufi S, Murn J. The nexus between RNA-binding proteins and their effectors. Nat Rev Genet 2023; 24:276-294. [PMID: 36418462 DOI: 10.1038/s41576-022-00550-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) regulate essentially every event in the lifetime of an RNA molecule, from its production to its destruction. Whereas much has been learned about RNA sequence specificity and general functions of individual RBPs, the ways in which numerous RBPs instruct a much smaller number of effector molecules, that is, the core engines of RNA processing, as to where, when and how to act remain largely speculative. Here, we survey the known modes of communication between RBPs and their effectors with a particular focus on converging RBP-effector interactions and their roles in reducing the complexity of RNA networks. We discern the emerging unifying principles and discuss their utility in our understanding of RBP function, regulation of biological processes and contribution to human disease.
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Affiliation(s)
- Shiyang He
- Department of Biochemistry, University of California, Riverside, CA, USA
- Center for RNA Biology and Medicine, Riverside, CA, USA
| | - Eugene Valkov
- RNA Biology Laboratory & Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD, USA
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
- Stem Cell Center, University of California, Riverside, CA, USA.
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Center for RNA Biology and Medicine, Riverside, CA, USA.
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11
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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12
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Westcott CE, Isom CM, Karki D, Sokoloski KJ. Dancing with the Devil: A Review of the Importance of Host RNA-Binding Proteins to Alphaviral RNAs during Infection. Viruses 2023; 15:164. [PMID: 36680204 PMCID: PMC9865062 DOI: 10.3390/v15010164] [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: 10/17/2022] [Revised: 12/02/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Alphaviruses are arthropod-borne, single-stranded positive sense RNA viruses that rely on the engagement of host RNA-binding proteins to efficiently complete the viral lifecycle. Because of this reliance on host proteins, the identification of host/pathogen interactions and the subsequent characterization of their importance to viral infection has been an intensive area of study for several decades. Many of these host protein interaction studies have evaluated the Protein:Protein interactions of viral proteins during infection and a significant number of host proteins identified by these discovery efforts have been RNA Binding Proteins (RBPs). Considering this recognition, the field has shifted towards discovery efforts involving the direct identification of host factors that engage viral RNAs during infection using innovative discovery approaches. Collectively, these efforts have led to significant advancements in the understanding of alphaviral molecular biology; however, the precise extent and means by which many RBPs influence viral infection is unclear as their specific contributions to infection, as per any RNA:Protein interaction, have often been overlooked. The purpose of this review is to summarize the discovery of host/pathogen interactions during alphaviral infection with a specific emphasis on RBPs, to use new ontological analyses to reveal potential functional commonalities across alphaviral RBP interactants, and to identify host RBPs that have, and have yet to be, evaluated in their native context as RNA:Protein interactors.
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Affiliation(s)
- Claire E. Westcott
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Cierra M. Isom
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Deepa Karki
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Kevin J. Sokoloski
- Department of Microbiology and Immunology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
- Center for Predictive Medicine for Biodefense and Emerging Infectious Disease (CPM), University of Louisville, Louisville, KY 40202, USA
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13
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Osma-Garcia IC, Capitan-Sobrino D, Mouysset M, Aubert Y, Maloudi O, Turner M, Diaz-Muñoz MD. The splicing regulators TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis. Cell Rep 2022; 41:111869. [PMID: 36543128 PMCID: PMC9794549 DOI: 10.1016/j.celrep.2022.111869] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
B cell lymphopoiesis requires dynamic modulation of the B cell transcriptome for timely coordination of somatic mutagenesis and DNA repair in progenitor B (pro-B) cells. Here, we show that, in pro-B cells, the RNA-binding proteins T cell intracellular antigen 1 (TIA1) and TIA1-like protein (TIAL1) act redundantly to enable developmental progression. They are global splicing regulators that control the expression of hundreds of mRNAs, including those involved in DNA damage repair. Mechanistically, TIA1 and TIAL1 bind to 5' splice sites for exon definition, splicing, and expression of DNA damage sensors, such as Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression, and increased cell death. Our study uncovers the importance of tight regulation of RNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs that control DNA damage sensing and repair during B cell development.
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Affiliation(s)
- Ines C. Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Orlane Maloudi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Manuel D. Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France,Corresponding author
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14
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Espinosa S, De Bortoli F, Li X, Rossi J, Wagley ME, Lo HYG, Taliaferro JM, Zhao R. Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites. RNA (NEW YORK, N.Y.) 2022; 29:rna.079320.122. [PMID: 36316087 PMCID: PMC9808567 DOI: 10.1261/rna.079320.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Human PRPF39 is a homolog of the yeast Prp39 and Prp42 paralogs. We have previously shown that human PRPF39 forms a homodimer that interacts with the CTD of U1C, mirroring the yeast Prp39/Prp42 heterodimer. We demonstrate here that PRPF39 knockdown in HEK293 cells affects many alternative splicing events primarily by reducing the usage of weak 5'ss. Additionally, PRPF39 preferentially binds to a GC-rich RNA, likely at the interface between its NTD and CTD. These data indicate that PRPF39 potentially recruits U1 snRNP to a weak 5' ss, serving as a previously unrecognized alternative splicing factor. We further demonstrate that human TIA1 binds to U1C through its RRM1 and RRM3+Q domains but has no significant binding to PRPF39. Finally, all three human LUC7L isoforms directly interact with U1C. These results reveal significant parallels to the yeast U1 snRNP structure and support the use of yeast U1 snRNP as a model for understanding the mechanism of human alternative splicing.
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Affiliation(s)
- Sara Espinosa
- University of Colorado Denver Anschutz Medical Campus
| | | | - Xueni Li
- University of Colorado Denver Anschutz Medical Campus
| | - John Rossi
- University of Colorado Denver Anschutz Medical Campus
| | | | - Hei-Yong G Lo
- University of Colorado Denver Anschutz Medical Campus
| | | | - Rui Zhao
- University of Colorado Denver Anschutz Medical Campus
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15
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Chen M, Wang L, Li M, Budai MM, Wang J. Mitochondrion-Mediated Cell Death through Erk1-Alox5 Independent of Caspase-9 Signaling. Cells 2022; 11:cells11193053. [PMID: 36231015 PMCID: PMC9564198 DOI: 10.3390/cells11193053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial disruption leads to the release of cytochrome c to activate caspase-9 and the downstream caspase cascade for the execution of apoptosis. However, cell death can proceed efficiently in the absence of caspase-9 following mitochondrial disruption, suggesting the existence of caspase-9-independent cell death mechanisms. Through a genome-wide siRNA library screening, we identified a network of genes that mediate caspase-9-independent cell death, through ROS production and Alox5-dependent membrane lipid peroxidation. Erk1-dependent phosphorylation of Alox5 is critical for targeting Alox5 to the nuclear membrane to mediate lipid peroxidation, resulting in nuclear translocation of cytolytic molecules to induce DNA damage and cell death. Consistently, double knockouts of caspase-9 and Alox5 in mice, but not deletion of either gene alone, led to significant T cell expansion with inhibited cell death, indicating that caspase-9- and Alox5-dependent pathways function in parallel to regulate T cell death in vivo. This unbiased whole-genome screening reveals an Erk1-Alox5-mediated pathway that promotes membrane lipid peroxidation and nuclear translocation of cytolytic molecules, leading to the execution of cell death in parallel to the caspase-9 signaling cascade.
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Affiliation(s)
- Min Chen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (M.C.); (J.W.)
| | - Lei Wang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Min Li
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Marietta M. Budai
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jin Wang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Correspondence: (M.C.); (J.W.)
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16
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Velasco BR, Izquierdo JM. T-Cell Intracellular Antigen 1-Like Protein in Physiology and Pathology. Int J Mol Sci 2022; 23:ijms23147836. [PMID: 35887183 PMCID: PMC9318959 DOI: 10.3390/ijms23147836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
T-cell intracellular antigen 1 (TIA1)-related/like (TIAR/TIAL1) protein is a multifunctional RNA-binding protein (RBP) involved in regulating many aspects of gene expression, independently or in combination with its paralog TIA1. TIAR was first described in 1992 by Paul Anderson’s lab in relation to the development of a cell death phenotype in immune system cells, as it possesses nucleolytic activity against cytotoxic lymphocyte target cells. Similar to TIA1, it is characterized by a subcellular nucleo-cytoplasmic localization and ubiquitous expression in the cells of different tissues of higher organisms. In this paper, we review the relevant structural and functional information available about TIAR from a triple perspective (molecular, cellular and pathophysiological), paying special attention to its expression and regulation in cellular events and processes linked to human pathophysiology.
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17
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Dolicka D, Zahoran S, Correia de Sousa M, Gjorgjieva M, Sempoux C, Fournier M, Maeder C, Collart MA, Foti M, Sobolewski C. TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14071704. [PMID: 35406476 PMCID: PMC8997004 DOI: 10.3390/cancers14071704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations in specific RNA-binding protein expression/activity importantly contribute to the development of fatty liver disease (FLD) and hepatocellular carcinoma (HCC). In particular, adenylate–uridylate-rich element binding proteins (AUBPs) were reported to control the post-transcriptional regulation of genes involved in both metabolic and cancerous processes. Herein, we investigated the pathophysiological functions of the AUBP, T-cell-restricted intracellular antigen-1 (TIA1) in the development of FLD and HCC. Analysis of TIA1 expression in mouse and human models of FLD and HCC indicated that TIA1 is downregulated in human HCC. In vivo silencing of TIA1 using AAV8-delivered shRNAs in mice worsens hepatic steatosis and fibrosis induced by a methionine and choline-deficient diet and increases the hepatic tumor burden in liver-specific PTEN knockout (LPTENKO) mice. In contrast, our in vitro data indicated that TIA1 expression promoted proliferation and migration in HCC cell lines, thus suggesting a dual and context-dependent role for TIA1 in tumor initiation versus progression. Consistent with a dual function of TIA1 in tumorigenesis, translatome analysis revealed that TIA1 appears to control the expression of both pro- and anti-tumorigenic factors in hepatic cancer cells. This duality of TIA1′s function in hepatocarcinogenesis calls for cautiousness when considering TIA1 as a therapeutic target or biomarker in HCC.
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland;
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Martine A. Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
- Correspondence: or
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18
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Fernández-Gómez A, Velasco BR, Izquierdo JM. Dynamics of T-Cell Intracellular Antigen 1-Dependent Stress Granules in Proteostasis and Welander Distal Myopathy under Oxidative Stress. Cells 2022; 11:cells11050884. [PMID: 35269506 PMCID: PMC8909843 DOI: 10.3390/cells11050884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is primarily involved in the post-transcriptional regulation of cellular RNAs. Furthermore, it is a key component of stress granules (SGs), RNA, and protein aggregates that are formed in response to stressful stimuli to reduce cellular activity as a survival mechanism. TIA1 p.E384K mutation is the genetic cause of Welander distal myopathy (WDM), a late-onset muscular dystrophy whose pathogenesis has been related to modifying SG dynamics. In this study, we present the results obtained by analyzing two specific aspects: (i) SGs properties and dynamics depending on the amino acid at position 384 of TIA1; and (ii) the formation/disassembly time-course of TIA1WT/WDM-dependent SGs under oxidative stress. The generation of TIA1 variants—in which the amino acid mutated in WDM and the adjacent ones were replaced by lysines, glutamic acids, or alanines—allowed us to verify that the inclusion of a single lysine is necessary and sufficient to alter SGs dynamics. Moreover, time-lapse microscopy analysis allowed us to establish in vivo the dynamics of TIA1WT/WDM-dependent SG formation and disassembly, after the elimination of the oxidizing agent, for 1 and 3 h, respectively. Our observations show distinct dynamics between the formation and disassembly of TIA1WT/WDM-dependent SGs. Taken together, this study has allowed us to expand the existing knowledge on the role of TIA1 and the WDM mutation in SG formation.
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19
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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20
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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21
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AU-Rich Element RNA Binding Proteins: At the Crossroads of Post-Transcriptional Regulation and Genome Integrity. Int J Mol Sci 2021; 23:ijms23010096. [PMID: 35008519 PMCID: PMC8744917 DOI: 10.3390/ijms23010096] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 12/14/2022] Open
Abstract
Genome integrity must be tightly preserved to ensure cellular survival and to deter the genesis of disease. Endogenous and exogenous stressors that impose threats to genomic stability through DNA damage are counteracted by a tightly regulated DNA damage response (DDR). RNA binding proteins (RBPs) are emerging as regulators and mediators of diverse biological processes. Specifically, RBPs that bind to adenine uridine (AU)-rich elements (AREs) in the 3' untranslated region (UTR) of mRNAs (AU-RBPs) have emerged as key players in regulating the DDR and preserving genome integrity. Here we review eight established AU-RBPs (AUF1, HuR, KHSRP, TIA-1, TIAR, ZFP36, ZFP36L1, ZFP36L2) and their ability to maintain genome integrity through various interactions. We have reviewed canonical roles of AU-RBPs in regulating the fate of mRNA transcripts encoding DDR genes at multiple post-transcriptional levels. We have also attempted to shed light on non-canonical roles of AU-RBPs exploring their post-translational modifications (PTMs) and sub-cellular localization in response to genotoxic stresses by various factors involved in DDR and genome maintenance. Dysfunctional AU-RBPs have been increasingly found to be associated with many human cancers. Further understanding of the roles of AU-RBPS in maintaining genomic integrity may uncover novel therapeutic strategies for cancer.
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22
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Carrascoso I, Velasco BR, Izquierdo JM. Deficiency of T-Cell Intracellular Antigen 1 in Murine Embryonic Fibroblasts Is Associated with Changes in Mitochondrial Morphology and Respiration. Int J Mol Sci 2021; 22:ijms222312775. [PMID: 34884582 PMCID: PMC8657690 DOI: 10.3390/ijms222312775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is a multifunctional RNA-binding protein involved in regulating gene expression and splicing during development and in response to environmental stress, to maintain cell homeostasis and promote survival. Herein, we used TIA1-deficient murine embryonic fibroblasts (MEFs) to study their role in mitochondria homeostasis. We found that the loss of TIA1 was associated with changes in mitochondrial morphology, promoting the appearance of elongated mitochondria with heterogeneous cristae density and size. The proteomic patterns of TIA1-deficient MEFs were consistent with expression changes in molecular components related to mitochondrial dynamics/organization and respiration. Bioenergetics analysis illustrated that TIA1 deficiency enhances mitochondrial respiration. Overall, our findings shed light on the role of TIA1 in mitochondrial dynamics and highlight a point of crosstalk between potential pro-survival and pro-senescence pathways.
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23
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Blake D, Lynch KW. The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function. Immunol Rev 2021; 304:30-50. [PMID: 34368964 DOI: 10.1111/imr.13018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The latest advances in next-generation sequencing studies and transcriptomic profiling over the past decade have highlighted a surprising frequency of genes regulated by RNA processing mechanisms in the immune system. In particular, two control steps in mRNA maturation, namely alternative splicing and alternative polyadenylation, are now recognized to occur in the vast majority of human genes. Both have the potential to alter the identity of the encoded protein, as well as control protein abundance or even protein localization or association with other factors. In this review, we will provide a summary of the general mechanisms by which alternative splicing (AS) and alternative polyadenylation (APA) occur, their regulation within cells of the immune system, and their impact on immunobiology. In particular, we will focus on how control of apoptosis by AS and APA is used to tune cell fate during an immune response.
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Affiliation(s)
- Davia Blake
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen W Lynch
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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24
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Vivori C, Papasaikas P, Stadhouders R, Di Stefano B, Rubio AR, Balaguer CB, Generoso S, Mallol A, Sardina JL, Payer B, Graf T, Valcárcel J. Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. Genome Biol 2021; 22:171. [PMID: 34082786 PMCID: PMC8173870 DOI: 10.1186/s13059-021-02372-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. RESULTS We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enables the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNA-binding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes. CONCLUSIONS Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.
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Affiliation(s)
- Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
| | - Panagiotis Papasaikas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66/Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Ralph Stadhouders
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Departments of Pulmonary Medicine and Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Bruno Di Stefano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Alkek Bldg Room N1020, Houston, TX 77030 USA
| | - Anna Ribó Rubio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Serena Generoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna Mallol
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - José Luis Sardina
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Savarese M, Sarparanta J, Vihola A, Jonson PH, Johari M, Rusanen S, Hackman P, Udd B. Panorama of the distal myopathies. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2020; 39:245-265. [PMID: 33458580 PMCID: PMC7783427 DOI: 10.36185/2532-1900-028] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/15/2022]
Abstract
Distal myopathies are genetic primary muscle disorders with a prominent weakness at onset in hands and/or feet. The age of onset (from early childhood to adulthood), the distribution of muscle weakness (upper versus lower limbs) and the histological findings (ranging from nonspecific myopathic changes to myofibrillar disarrays and rimmed vacuoles) are extremely variable. However, despite being characterized by a wide clinical and genetic heterogeneity, the distal myopathies are a category of muscular dystrophies: genetic diseases with progressive loss of muscle fibers. Myopathic congenital arthrogryposis is also a form of distal myopathy usually caused by focal amyoplasia. Massive parallel sequencing has further expanded the long list of genes associated with a distal myopathy, and contributed identifying as distal myopathy-causative rare variants in genes more often related with other skeletal or cardiac muscle diseases. Currently, almost 20 genes (ACTN2, CAV3, CRYAB, DNAJB6, DNM2, FLNC, HNRNPA1, HSPB8, KHLH9, LDB3, MATR3, MB, MYOT, PLIN4, TIA1, VCP, NOTCH2NLC, LRP12, GIPS1) have been associated with an autosomal dominant form of distal myopathy. Pathogenic changes in four genes (ADSSL, ANO5, DYSF, GNE) cause an autosomal recessive form; and disease-causing variants in five genes (DES, MYH7, NEB, RYR1 and TTN) result either in a dominant or in a recessive distal myopathy. Finally, a digenic mechanism, underlying a Welander-like form of distal myopathy, has been recently elucidated. Rare pathogenic mutations in SQSTM1, previously identified with a bone disease (Paget disease), unexpectedly cause a distal myopathy when combined with a common polymorphism in TIA1. The present review aims at describing the genetic basis of distal myopathy and at summarizing the clinical features of the different forms described so far.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Center, Department of Genetics, Fimlab Laboratories, Tampere, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Salla Rusanen
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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26
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Baeza-Centurion P, Miñana B, Valcárcel J, Lehner B. Mutations primarily alter the inclusion of alternatively spliced exons. eLife 2020; 9:59959. [PMID: 33112234 PMCID: PMC7673789 DOI: 10.7554/elife.59959] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Genetic analyses and systematic mutagenesis have revealed that synonymous, non-synonymous and intronic mutations frequently alter the inclusion levels of alternatively spliced exons, consistent with the concept that altered splicing might be a common mechanism by which mutations cause disease. However, most exons expressed in any cell are highly-included in mature mRNAs. Here, by performing deep mutagenesis of highly-included exons and by analysing the association between genome sequence variation and exon inclusion across the transcriptome, we report that mutations only very rarely alter the inclusion of highly-included exons. This is true for both exonic and intronic mutations as well as for perturbations in trans. Therefore, mutations that affect splicing are not evenly distributed across primary transcripts but are focussed in and around alternatively spliced exons with intermediate inclusion levels. These results provide a resource for prioritising synonymous and other variants as disease-causing mutations.
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Affiliation(s)
- Pablo Baeza-Centurion
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Belén Miñana
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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27
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Abstract
To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively-spliced GFP reporter gene in Arabidopsis thaliana. This effort generated a collection of sixteen mutants impaired in various splicing-related proteins, many of which had not been recovered in any prior genetic screen or implicated in splicing in plants. The factors are predicted to act at different steps of the spliceosomal cycle, snRNP biogenesis pathway, transcription, and mRNA transport. We have described eleven of the mutants in recent publications. Here we present the final five mutants, which are defective, respectively, in RNA-BINDING PROTEIN 45D (rbp45d), DIGEORGE SYNDROME CRITICAL REGION 14 (dgcr14), CYCLIN-DEPENDENT KINASE G2 (cdkg2), INTERACTS WITH SPT6 (iws1) and CAP BINDING PROTEIN 80 (cbp80). We provide RNA-sequencing data and analyses of differential gene expression and alternative splicing patterns for the cbp80 mutant and for several previously published mutants, including smfa and new alleles of cwc16a, for which such information was not yet available. Sequencing of small RNAs from the cbp80 mutant highlighted the necessity of wild-type CBP80 for processing of microRNA (miRNA) precursors into mature miRNAs. Redundancy tests of paralogs encoding several of the splicing factors revealed their functional non-equivalence in the GFP reporter gene system. We discuss the cumulative findings and their implications for the regulation of pre-mRNA splicing efficiency and alternative splicing in plants. The mutant collection provides a unique resource for further studies on a coherent set of splicing factors and their roles in gene expression, alternative splicing and plant development.
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28
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Huertas CS, Bonnal S, Soler M, Escuela AM, Valcárcel J, Lechuga LM. Site-Specific mRNA Cleavage for Selective and Quantitative Profiling of Alternative Splicing with Label-Free Optical Biosensors. Anal Chem 2019; 91:15138-15146. [DOI: 10.1021/acs.analchem.9b03898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cesar S. Huertas
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
- Integrated Photonics and Applications Centre, School of Engineering, RMIT University, Melbourne, VIC 3001, Australia
| | - Sophie Bonnal
- Centre de Regulació Genòmica and BIST, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Maria Soler
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain
| | - Alfonso M. Escuela
- Institute for Applied Microelectronics (IUMA). University of Las Palmas de Gran Canaria, E-35017 Las Palmas, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica and BIST, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Laura M. Lechuga
- Nanobiosensors and Bioanalytical Applications Group, Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, BIST and CIBER-BBN, 08193 Bellaterra, Barcelona, Spain
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Lourou N, Gavriilidis M, Kontoyiannis DL. Lessons from studying the AU-rich elements in chronic inflammation and autoimmunity. J Autoimmun 2019; 104:102334. [PMID: 31604649 DOI: 10.1016/j.jaut.2019.102334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 09/09/2019] [Indexed: 12/12/2022]
Abstract
AU-rich elements (AREs) comprise one of the most widely studied families of regulatory RNA structures met in RNAs engaged in complex immunological reactions. A multitude of genetic, molecular, holistic and functional studies have been utilized for the analyses of the AREs and their interactions to proteins that bind to them. Data stemming from these studies brought forth a world of RNA-related check-points against infection, chronic inflammation, tumor associated immunity, and autoimmunity; and the interest to capitalize the interactions of AREs for clinical management and therapy. They also provided lessons on the cellular capabilities of post-transcriptional control. Originally thought as transcript-restricted regulators of turnover and translation, ARE-binding proteins do in fact harbor great versatility and interactivity across nuclear and cytoplasmic compartments; and act as functional coordinators of immune-cellular programs. Harnessing these deterministic functions requires extensive knowledge of their synergies or antagonisms at a cell-specific level; but holds great promise since it can provide the efficacy of combinatorial therapies with single agents.
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Affiliation(s)
- Niki Lourou
- School of Biology, Department of Development, Genetics and Molecular Biology, Aristotle University of Thessaloniki, Greece
| | - Maxim Gavriilidis
- School of Biology, Department of Development, Genetics and Molecular Biology, Aristotle University of Thessaloniki, Greece; Division of Immunology, Alexander Fleming Biomedical Sciences Research Center, Greece
| | - Dimitris L Kontoyiannis
- School of Biology, Department of Development, Genetics and Molecular Biology, Aristotle University of Thessaloniki, Greece; Division of Immunology, Alexander Fleming Biomedical Sciences Research Center, Greece.
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Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning. Genes (Basel) 2019; 10:genes10080587. [PMID: 31374967 PMCID: PMC6722613 DOI: 10.3390/genes10080587] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/20/2019] [Accepted: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavior and regulation using computational models known as “Splicing Codes”. The final goal of these algorithms is to make an in-silico prediction of AS outcome from genomic sequence. Here, we develop a deep learning approach, called Deep Splicing Code (DSC), for categorizing the well-studied classes of AS namely alternatively skipped exons, alternative 5’ss, alternative 3’ss, and constitutively spliced exons based only on the sequence of the exon junctions. The proposed approach significantly improves the prediction and the obtained results reveal that constitutive exons have distinguishable local characteristics from alternatively spliced exons. Using the motif visualization technique, we show that the trained models learned to search for competitive alternative splice sites as well as motifs of important splicing factors with high precision. Thus, the proposed approach greatly expands the opportunities to improve alternative splicing modeling. In addition, a web-server for AS events prediction has been developed based on the proposed method.
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31
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Ostareck DH, Ostareck-Lederer A. RNA-Binding Proteins in the Control of LPS-Induced Macrophage Response. Front Genet 2019; 10:31. [PMID: 30778370 PMCID: PMC6369361 DOI: 10.3389/fgene.2019.00031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 01/17/2019] [Indexed: 12/18/2022] Open
Abstract
Innate immune response is triggered by pathogen components, like lipopolysaccharides (LPS) of gram-negative bacteria. LPS initiates Toll-like receptor 4 (TLR4) signaling, which involves mitogen activated protein kinases (MAPK) and nuclear factor kappa B (NFκB) in different pathway branches and ultimately induces inflammatory cytokine and chemokine expression, macrophage migration and phagocytosis. Timely gene transcription and post-transcriptional control of gene expression confer the adequate synthesis of signaling molecules. As trans-acting factors RNA binding proteins (RBPs) contribute significantly to the surveillance of gene expression. RBPs are involved in the regulation of mRNA processing, localization, stability and translation. Thereby they enable rapid cellular responses to inflammatory mediators and facilitate a coordinated systemic immune response. Specific RBP binding to conserved sequence motifs in their target mRNAs is mediated by RNA binding domains, like Zink-finger domains, RNA recognition motifs (RRM), and hnRNP K homology domains (KH), often arranged in modular arrays. In this review, we focus on RBPs Tristetraprolin (TTP), human antigen R (HUR), T-cell intracellular antigen 1 related protein (TIAR), and heterogeneous ribonuclear protein K (hnRNP K) in LPS induced macrophages as primary responding immune cells. We discuss recent experiments employing RNA immunoprecipitation and microarray analysis (RIP-Chip) and newly developed individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP), photoactivatable ribonucleoside-enhanced crosslinking (PAR-iCLIP) and RNA sequencing techniques (RNA-Seq). The global mRNA interaction profile analysis of TTP, HUR, TIAR, and hnRNP K exhibited valuable information about the post-transcriptional control of inflammation related gene expression with a broad impact on intracellular signaling and temporal cytokine expression.
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Affiliation(s)
- Dirk H Ostareck
- Department of Intensive Care Medicine, University Hospital RWTH Aachen, Aachen, Germany
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32
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Grymová T, Grodecká L, Souček P, Freiberger T. SERPING1 exon 3 splicing variants using alternative acceptor splice sites. Mol Immunol 2019; 107:91-96. [PMID: 30685616 DOI: 10.1016/j.molimm.2019.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/03/2019] [Accepted: 01/11/2019] [Indexed: 11/26/2022]
Abstract
Mutations in the C1 inhibitor (C1INH) encoding gene, SERPING1, are associated with hereditary angioedema (HAE) which manifests as recurrent submucosal and subcutaneous edema episodes. The major C1INH function is the complement system inhibition, preventing its spontaneous activation. The presented study is focused on SERPING1 exon 3, an alternative and extraordinarily long exon (499 bp). Endogenous expression analysis performed in the HepG2, human liver, and human peripheral blood cells revealed several exon 3 splicing variants alongside exon inclusion: a highly prevalent exon skipping variant and less frequent +38 and -15 variants with alternative 3' splice sites (ss) located 38 and 15 nucleotides downstream and upstream from the authentic 3' ss, respectively. An exon skipping variant introducing a premature stop codon, represented nearly one third of all splicing variants and surprisingly appeared not to be degraded by NMD. The alternative -15 3' ss was used to a small extent, although predicted to be extremely weak. Its use was shown to be independent of its strength and highly sensitive to any changes in the surrounding sequence. -15 3' ss seems to be co-regulated with the authentic 3' ss, whose use is dependent mainly on its strength and less on the presence of intronic regulatory motifs. Subtle SERPING1 exon 3 splicing regulation can contribute to overall C1INH plasma levels and HAE pathogenesis.
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Affiliation(s)
- Tereza Grymová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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33
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Butti Z, Patten SA. RNA Dysregulation in Amyotrophic Lateral Sclerosis. Front Genet 2019; 9:712. [PMID: 30723494 PMCID: PMC6349704 DOI: 10.3389/fgene.2018.00712] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/20/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common adult-onset motor neuron disease and is characterized by the degeneration of upper and lower motor neurons. It has become increasingly clear that RNA dysregulation is a key contributor to ALS pathogenesis. The major ALS genes SOD1, TARDBP, FUS, and C9orf72 are involved in aspects of RNA metabolism processes such as mRNA transcription, alternative splicing, RNA transport, mRNA stabilization, and miRNA biogenesis. In this review, we highlight the current understanding of RNA dysregulation in ALS pathogenesis involving these major ALS genes and discuss the potential of therapeutic strategies targeting disease RNAs for treating ALS.
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Affiliation(s)
- Zoe Butti
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
| | - Shunmoogum A Patten
- INRS-Institut Armand-Frappier, National Institute of Scientific Research, Laval, QC, Canada
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Baeza-Centurion P, Miñana B, Schmiedel JM, Valcárcel J, Lehner B. Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing. Cell 2019; 176:549-563.e23. [PMID: 30661752 DOI: 10.1016/j.cell.2018.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
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Affiliation(s)
- Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jörn M Schmiedel
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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35
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Meyer C, Garzia A, Mazzola M, Gerstberger S, Molina H, Tuschl T. The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. Mol Cell 2019; 69:622-635.e6. [PMID: 29429924 DOI: 10.1016/j.molcel.2018.01.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/05/2017] [Accepted: 01/09/2018] [Indexed: 12/11/2022]
Abstract
TIA1 and TIAL1 encode a family of U-rich element mRNA-binding proteins ubiquitously expressed and conserved in metazoans. Using PAR-CLIP, we determined that both proteins bind target sites with identical specificity in 3' UTRs and introns proximal to 5' as well as 3' splice sites. Double knockout (DKO) of TIA1 and TIAL1 increased target mRNA abundance proportional to the number of binding sites and also caused accumulation of aberrantly spliced mRNAs, most of which are subject to nonsense-mediated decay. Loss of PRKRA by mis-splicing triggered the activation of the double-stranded RNA (dsRNA)-activated protein kinase EIF2AK2/PKR and stress granule formation. Ectopic expression of PRKRA cDNA or knockout of EIF2AK2 in DKO cells rescued this phenotype. Perturbation of maturation and/or stability of additional targets further compromised cell cycle progression. Our study reveals the essential contributions of the TIA1 protein family to the fidelity of mRNA maturation, translation, and RNA-stress-sensing pathways in human cells.
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Affiliation(s)
- Cindy Meyer
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Aitor Garzia
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Michael Mazzola
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Stefanie Gerstberger
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Thomas Tuschl
- Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA.
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36
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Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5'-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.
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Affiliation(s)
- Tucker J Carrocci
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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Carrascoso I, Alcalde J, Tabas-Madrid D, Oliveros JC, Izquierdo JM. Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response. PLoS One 2018; 13:e0208526. [PMID: 30533021 PMCID: PMC6289441 DOI: 10.1371/journal.pone.0208526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR, and of HuR in HEK293 cells. Our gene profiling analysis identified several hundred differentially expressed genes (DEGs) and tens of alternative splicing events associated with TIA1b, TIARb and HuR overexpression. Gene ontology analysis revealed that the controlled expression of these proteins strongly influences the patterns of DEGs and RNA variants preferentially associated with development, reproduction, cell cycle, metabolism, autophagy and apoptosis. Mechanistically, TIA1b and TIARb isoforms display both common and differential effects on the regulation of gene expression, involving systematic perturbations of cell biosynthetic machineries (splicing and translation). The transcriptome outputs were validated using functional assays of the targeted cellular processes as well as expression analysis for selected genes. Collectively, our observations suggest that early TIA1b and TIARb expression operates to connect the regulatory crossroads to protective proteostasis responses associated with a survival quiescence phenotype.
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Affiliation(s)
- Isabel Carrascoso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - José Alcalde
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - Daniel Tabas-Madrid
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - Juan Carlos Oliveros
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
- * E-mail:
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A Heterologous Cell Model for Studying the Role of T-Cell Intracellular Antigen 1 in Welander Distal Myopathy. Mol Cell Biol 2018; 39:MCB.00299-18. [PMID: 30348840 DOI: 10.1128/mcb.00299-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/09/2018] [Indexed: 11/20/2022] Open
Abstract
Welander distal myopathy (WDM) is a muscle dystrophy characterized by adult-onset distal muscle weakness, prevalently impacting the distal long extensors of the hands and feet. WDM is an autosomal dominant disorder caused by a missense mutation (c.1362G>A; p.E384K) in the TIA1 (T-cell intracellular antigen 1) gene, which encodes an RNA-binding protein basically required for the posttranscriptional regulation of RNAs. We have developed a heterologous cell model of WDM to study the molecular and cellular events associated with mutated TIA1 expression. Specifically, we analyzed how this mutation affects three regulatory functions mediated by TIA1: (i) control of alternative SMN2 (survival motor neuron 2) splicing; (ii) formation, assembly, and disassembly of stress granules; and (iii) mitochondrial dynamics and its consequences for mitophagy, autophagy, and apoptosis. Our results show that whereas WDM-associated TIA1 expression had only a mild effect on SMN2 splicing, it led to suboptimal adaptation to environmental stress, with exacerbated stress granule formation that was accompanied by mitochondrial dysfunction and autophagy. Overall, our observations indicate that some aspects of the cell phenotype seen in muscle of patients with WDM can be recapitulated by ectopic expression of WDM-TIA1 in embryonic kidney cells, highlighting the potential of this model to investigate the pathogenesis of this degenerative disease and possible therapeutics.
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Hepatitis B Spliced Protein (HBSP) Suppresses Fas-Mediated Hepatocyte Apoptosis via Activation of PI3K/Akt Signaling. J Virol 2018; 92:JVI.01273-18. [PMID: 30209179 DOI: 10.1128/jvi.01273-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B spliced protein (HBSP) is known to associate with viral persistence and pathogenesis; however, its biological and clinical significance remains poorly defined. Acquired resistance to Fas-mediated apoptosis is thought to be one of the major promotors for hepatitis B virus (HBV) chronicity and malignancy. The purpose of this study was to investigate whether HBSP could protect hepatocytes against Fas-initiated apoptosis. We showed here that HBSP mediated resistance of hepatoma cells or primary human hepatocytes (PHH) to agonistic anti-Fas antibody (CH11)- or FasL-induced apoptosis. Under Fas signaling stimulation, expression of HBSP inhibited Fas aggregation and prevented recruitment of the adaptor molecule Fas-associated death domain (FADD) and procaspase-8 (or FADD-like interleukin-1β-converting enzyme [FLICE]) into the death-inducing signaling complex (DISC) while increasing recruitment of cellular FLICE-inhibitory protein L (FLIPL) into the DISC. Those effects may be mediated through activation of the phosphoinositide 3-kinase (PI3K)/Akt pathway as evidenced by increased cellular phosphatidylinositol (3,4,5)-trisphosphate (PIP3) content and PI3K activity and enhanced phosphorylation of mTORC2 and PDPK1 as well as Akt itself. Confirmedly, inhibition of PI3K by LY294002 reversed the effect of HBSP on Fas aggregation, FLIPL expression, and cellular apoptosis. These results indicate that HBSP functions to prevent hepatocytes from Fas-induced apoptosis by enhancing PI3K/Akt activity, which may contribute to the survival and persistence of infected hepatocytes during chronic infection.IMPORTANCE Our study revealed a previously unappreciated role of HBSP in Fas-mediated apoptosis. The antiapoptotic activity of HBSP is important for understanding hepatitis B virus pathogenesis. In particular, HBV variants associated with hepatoma carcinoma may downregulate apoptosis of hepatocytes through enhanced HBSP expression. Our study also found that Akt is centrally involved in Fas-induced hepatocyte apoptosis and revealed that interventions directed at inhibiting the activation or functional activity of Akt may be of therapeutic value in this process.
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40
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Jang HN, Liu Y, Choi N, Oh J, Ha J, Zheng X, Shen H. Binding of SRSF4 to a novel enhancer modulates splicing of exon 6 of Fas pre-mRNA. Biochem Biophys Res Commun 2018; 506:703-708. [PMID: 30376989 DOI: 10.1016/j.bbrc.2018.10.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/20/2018] [Indexed: 11/29/2022]
Abstract
Alternative splicing of exon 6 in Fas pre-mRNA generates a membrane bound pro-apoptotic isoform or soluble anti-apoptotic isoform. SRSF4 is a member of Arginine-Serine rich (SR) protein family. Here we demonstrate that increased SRSF4 expression stimulates exon 6 inclusion, and that reduced SRSF4 expression promotes exon 6 exclusion. We also show that weaker but not stronger 5' splice-site strength of exon 6 abolishes the SRSF4 effects on exon 6 splicing. Furthermore, we identified a novel enhancer on exon 6, on which SRSF4 interacts functionally and physically. Our results illustrate a novel regulatory mechanism of Fas pre-mRNA splicing.
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Affiliation(s)
- Ha Na Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Yongchao Liu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea.
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, South Korea.
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41
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Zhao M, Kim JR, van Bruggen R, Park J. RNA-Binding Proteins in Amyotrophic Lateral Sclerosis. Mol Cells 2018; 41:818-829. [PMID: 30157547 PMCID: PMC6182225 DOI: 10.14348/molcells.2018.0243] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/23/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022] Open
Abstract
Significant research efforts are ongoing to elucidate the complex molecular mechanisms underlying amyotrophic lateral sclerosis (ALS), which may in turn pinpoint potential therapeutic targets for treatment. The ALS research field has evolved with recent discoveries of numerous genetic mutations in ALS patients, many of which are in genes encoding RNA binding proteins (RBPs), including TDP-43, FUS, ATXN2, TAF15, EWSR1, hnRNPA1, hnRNPA2/B1, MATR3 and TIA1. Accumulating evidence from studies on these ALS-linked RBPs suggests that dysregulation of RNA metabolism, cytoplasmic mislocalization of RBPs, dysfunction in stress granule dynamics of RBPs and increased propensity of mutant RBPs to aggregate may lead to ALS pathogenesis. Here, we review current knowledge of the biological function of these RBPs and the contributions of ALS-linked mutations to disease pathogenesis.
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Affiliation(s)
- Melody Zhao
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
| | - Jihye Rachel Kim
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
| | - Rebekah van Bruggen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
| | - Jeehye Park
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Canada
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42
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Sun Y, Zhang P, Zheng H, Dong L, Tan L, Song C, Qiu X, Liao Y, Meng C, Yu S, Ding C. Chicken RNA-binding protein T-cell internal antigen-1 contributes to stress granule formation in chicken cells and tissues. J Vet Sci 2018; 19:3-12. [PMID: 28693298 PMCID: PMC5799397 DOI: 10.4142/jvs.2018.19.1.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/10/2017] [Accepted: 03/26/2017] [Indexed: 11/30/2022] Open
Abstract
T-cell internal antigen-1 (TIA-1) has roles in regulating alternative pre-mRNA splicing, mRNA translation, and stress granule (SG) formation in human cells. As an evolutionarily conserved response to environmental stress, SGs have been reported in various species. However, SG formation in chicken cells and the role of chicken TIA-1 (cTIA-1) in SG assembly has not been elucidated. In the present study, we cloned cTIA-1 and showed that it facilitates the assembly of canonical SGs in both human and chicken cells. Overexpression of the chicken prion-related domain (cPRD) of cTIA-1 that bore an N-terminal green fluorescent protein (GFP) tag (pntGFP-cPRD) or Flag tag (pFlag-cPRD) induced the production of typical SGs. However, C-terminal GFP-tagged cPRD induced notably large cytoplasmic granules that were devoid of endogenous G3BP1 and remained stable when exposed to cycloheximide, indicating that these were not typical SGs, and that the pntGFP tag influences cPRD localization. Finally, endogenous cTIA-1 was recruited to SGs in chicken cells and tissues under environmental stress. Taken together, our study provide evidence that cTIA-1 has a role in canonical SG formation in chicken cells and tissues. Our results also indicate that cPRD is necessary for SG aggregation.
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Affiliation(s)
- Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Pin Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271018, China
| | - Hang Zheng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Luna Dong
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Lei Tan
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Cuiping Song
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Xusheng Qiu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Ying Liao
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Chunchun Meng
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Shengqing Yu
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China
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43
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Moschall R, Strauss D, García-Beyaert M, Gebauer F, Medenbach J. Drosophila Sister-of-Sex-lethal is a repressor of translation. RNA (NEW YORK, N.Y.) 2018; 24:149-158. [PMID: 29089381 PMCID: PMC5769743 DOI: 10.1261/rna.063776.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
The RNA-binding protein Sex-lethal (Sxl) is an important post-transcriptional regulator of sex determination and dosage compensation in female Drosophila To prevent the assembly of the MSL dosage compensation complex in female flies, Sxl acts as a repressor of male-specific lethal-2 (msl-2) mRNA translation. It uses two distinct and mutually reinforcing blocks to translation that operate on the 5' and 3' untranslated regions (UTRs) of msl-2 mRNA, respectively. While 5' UTR-mediated translational control involves an upstream open reading frame, 3' UTR-mediated regulation strictly requires the co-repressor protein Upstream of N-ras (Unr), which is recruited to the transcript by Sxl. We have identified the protein Sister-of-Sex-lethal (Ssx) as a novel repressor of translation with Sxl-like activity. Both proteins have a comparable RNA-binding specificity and can associate with uracil-rich RNA regulatory elements present in msl-2 mRNA. Moreover, both repress translation when bound to the 5' UTR of msl-2 However, Ssx is inactive in 3' UTR-mediated regulation, as it cannot engage the co-repressor protein Unr. The difference in activity maps to the first RNA-recognition motif (RRM) of Ssx. Conversion of three amino acids within this domain into their Sxl counterpart results in a gain of function and repression via the 3' UTR, allowing detailed insights into the evolutionary origin of the two proteins and into the molecular requirements of an important translation regulatory pathway.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Marina García-Beyaert
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
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44
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Yuan Z, Jiao B, Hou L, Xiao T, Liu X, Wang J, Xu J, Zhou L, Yan X, Tang B, Shen L. Mutation analysis of the TIA1 gene in Chinese patients with amyotrophic lateral sclerosis and frontotemporal dementia. Neurobiol Aging 2017; 64:160.e9-160.e12. [PMID: 29370934 DOI: 10.1016/j.neurobiolaging.2017.12.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/18/2017] [Indexed: 11/27/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons in the brain and spinal cord. Frontotemporal dementia (FTD) is a group of dementia syndromes characterized by the progressive deterioration of behaviors, executive dysfunction, and verbal impairment. Increasing evidence indicates that these 2 diseases share a common genetic etiology and pathophysiological mechanism. Recently, rare mutations in the low-complexity domain of the RNA-binding protein T-cell-restricted intracellular antigen-1 (TIA1) gene were identified in Caucasian ALS and ALS-FTD patients. However, no comprehensive mutation analysis of the TIA1 gene has been performed in Chinese patients with ALS and FTD. In this study, we screened the low-complexity domain of TIA1 in a cohort of 241 ALS and 51 FTD patients in mainland China. As a result, 2 novel missense mutations (p.P352L and p.I300T) were identified in 2 sporadic patients with ALS, while no mutation was found in FTD cases. To the best of our knowledge, this report presented the first mutation analysis of the TIA1 gene in patients with ALS and FTD in Chinese population. Our findings broaden the known mutational spectrum in patients with ALS and further confirm TIA1 as a novel causative gene of ALS.
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Affiliation(s)
- Zhenhua Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lihua Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jun Xu
- Department of Neurology, Brain Center, Neurological Institute, Northern Jiangsu Province Hospital, Yangzhou, China
| | - Lin Zhou
- National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Department of Geriatrics Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; Parkinson's Disease Center of Beijing Institute for Brain Disorders, Beijing, China; Collaborative Innovation Center for Brain Science, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China.
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45
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Henning LM, Santos KF, Sticht J, Jehle S, Lee CT, Wittwer M, Urlaub H, Stelzl U, Wahl MC, Freund C. A new role for FBP21 as regulator of Brr2 helicase activity. Nucleic Acids Res 2017; 45:7922-7937. [PMID: 28838205 PMCID: PMC5570060 DOI: 10.1093/nar/gkx535] [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: 02/10/2017] [Accepted: 06/19/2017] [Indexed: 02/01/2023] Open
Abstract
Splicing of eukaryotic pre-mRNA is carried out by the spliceosome, which assembles stepwise on each splicing substrate. This requires the concerted action of snRNPs and non-snRNP accessory proteins, the functions of which are often not well understood. Of special interest are B complex factors that enter the spliceosome prior to catalytic activation and may alter splicing kinetics and splice site selection. One of these proteins is FBP21, for which we identified several spliceosomal binding partners in a yeast-two-hybrid screen, among them the RNA helicase Brr2. Biochemical and biophysical analyses revealed that an intrinsically disordered region of FBP21 binds to an extended surface of the C-terminal Sec63 unit of Brr2. Additional contacts in the C-terminal helicase cassette are required for allosteric inhibition of Brr2 helicase activity. Furthermore, the direct interaction between FBP21 and the U4/U6 di-snRNA was found to reduce the pool of unwound U4/U6 di-snRNA. Our results suggest FBP21 as a novel key player in the regulation of Brr2.
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Affiliation(s)
- Lisa M Henning
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Karine F Santos
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany
| | - Jana Sticht
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany.,BioSupraMol Gerätezentrum, Freie Universität Berlin, Takustr. 3, Berlin 14195, Germany
| | - Stefanie Jehle
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Chung-Tien Lee
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Malte Wittwer
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Henning Urlaub
- Max-Planck-Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, Göttingen 37077, Germany.,University Medical Center Goettingen, Bioanalytics, Department of Clinical Chemistry, Robert Koch Strasse 40, Göttingen 37075, Germany
| | - Ulrich Stelzl
- Max-Planck-Insitute for Molecular Genetics, Ihnestraße 63-74, Berlin 14195, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry, Freie Universität Berlin, Takustr. 6, Berlin 14195, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert- Einstein-Straße 15, Berlin 12489, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
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46
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Waris S, García-Mauriño SM, Sivakumaran A, Beckham SA, Loughlin FE, Gorospe M, Díaz-Moreno I, Wilce MCJ, Wilce JA. TIA-1 RRM23 binding and recognition of target oligonucleotides. Nucleic Acids Res 2017; 45:4944-4957. [PMID: 28184449 PMCID: PMC5416816 DOI: 10.1093/nar/gkx102] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/07/2017] [Indexed: 01/01/2023] Open
Abstract
TIA-1 (T-cell restricted intracellular antigen-1) is an RNA-binding protein involved in splicing and translational repression. It mainly interacts with RNA via its second and third RNA recognition motifs (RRMs), with specificity for U-rich sequences directed by RRM2. It has recently been shown that RRM3 also contributes to binding, with preferential binding for C-rich sequences. Here we designed UC-rich and CU-rich 10-nt sequences for engagement of both RRM2 and RRM3 and demonstrated that the TIA-1 RRM23 construct preferentially binds the UC-rich RNA ligand (5΄-UUUUUACUCC-3΄). Interestingly, this binding depends on the presence of Lys274 that is C-terminal to RRM3 and binding to equivalent DNA sequences occurs with similar affinity. Small-angle X-ray scattering was used to demonstrate that, upon complex formation with target RNA or DNA, TIA-1 RRM23 adopts a compact structure, showing that both RRMs engage with the target 10-nt sequences to form the complex. We also report the crystal structure of TIA-1 RRM2 in complex with DNA to 2.3 Å resolution providing the first atomic resolution structure of any TIA protein RRM in complex with oligonucleotide. Together our data support a specific mode of TIA-1 RRM23 interaction with target oligonucleotides consistent with the role of TIA-1 in binding RNA to regulate gene expression.
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Affiliation(s)
- Saboora Waris
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Andrew Sivakumaran
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simone A Beckham
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Fionna E Loughlin
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ)-Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla-Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute, Department of Biochemistry & Molecular Biology, Monash University, Victoria 3800, Australia
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47
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Ohe K, Yoshida M, Nakano-Kobayashi A, Hosokawa M, Sako Y, Sakuma M, Okuno Y, Usui T, Ninomiya K, Nojima T, Kataoka N, Hagiwara M. RBM24 promotes U1 snRNP recognition of the mutated 5' splice site in the IKBKAP gene of familial dysautonomia. RNA (NEW YORK, N.Y.) 2017; 23:1393-1403. [PMID: 28592461 PMCID: PMC5558909 DOI: 10.1261/rna.059428.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
The 5' splice site mutation (IVS20+6T>C) of the inhibitor of κ light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene in familial dysautonomia (FD) is at the sixth intronic nucleotide of the 5' splice site. It is known to weaken U1 snRNP recognition and result in an aberrantly spliced mRNA product in neuronal tissue, but normally spliced mRNA in other tissues. Aberrantly spliced IKBKAP mRNA abrogates IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1) expression and results in a defect of neuronal cell development in FD. To elucidate the tissue-dependent regulatory mechanism, we screened an expression library of major RNA-binding proteins (RBPs) with our mammalian dual-color splicing reporter system and identified RBM24 as a regulator. RBM24 functioned as a cryptic intronic splicing enhancer binding to an element (IVS20+13-29) downstream from the intronic 5' splice site mutation in the IKBKAP gene and promoted U1 snRNP recognition only to the mutated 5' splice site (and not the wild-type 5' splice site). Our results show that tissue-specific expression of RBM24 can explain the neuron-specific aberrant splicing of IKBKAP exon 20 in familial dysautonomia, and that ectopic expression of RBM24 in neuronal tissue could be a novel therapeutic target of the disease.
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Affiliation(s)
- Kenji Ohe
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
- Training Program of Leaders for Integrated Medical System for Fruitful Healthy-Longevity Society (LIMS), Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mayumi Yoshida
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akiko Nakano-Kobayashi
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukiya Sako
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Maki Sakuma
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukiko Okuno
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomomi Usui
- Laboratory of Gene Expression, School of Biomedical Science, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kensuke Ninomiya
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Naoyuki Kataoka
- Laboratory for Malignancy Control Research, Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8507, Japan
- Laboratory of Cell Regulation, Departments of Applied Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto 606-8501, Japan
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Srivastava S, Syed SB, Kumar V, Islam A, Ahmad F, Hassan MI. Fas-activated serine/threonine kinase: Structure and function. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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T-Cell Intracellular Antigens and Hu Antigen R Antagonistically Modulate Mitochondrial Activity and Dynamics by Regulating Optic Atrophy 1 Gene Expression. Mol Cell Biol 2017. [PMID: 28630277 DOI: 10.1128/mcb.00174-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondria undergo frequent morphological changes to control their function. We show here that T-cell intracellular antigens (TIA1b/TIARb) and Hu antigen R (HuR) have antagonistic roles in mitochondrial function by modulating the expression of mitochondrial shaping proteins. Expression of TIA1b/TIARb alters the mitochondrial dynamic network by enhancing fission and clustering, which is accompanied by a decrease in respiration. In contrast, HuR expression promotes fusion and cristae remodeling and increases respiratory activity. Mechanistically, TIA proteins downregulate the expression of optic atrophy 1 (OPA1) protein via switching of the splicing patterns of OPA1 to facilitate the production of OPA1 variant 5 (OPA1v5). Conversely, HuR enhances the expression of OPA1 mRNA isoforms through increasing steady-state levels and targeting translational efficiency at the 3' untranslated region. Knockdown of TIA1/TIAR or HuR partially reversed the expression profile of OPA1, whereas knockdown of OPA1 or overexpression of OPA1v5 provoked mitochondrial clustering. Middle-term expression of TIA1b/TIARb triggers reactive oxygen species production and mitochondrial DNA damage, which is accompanied by mitophagy, autophagy, and apoptosis. In contrast, HuR expression promotes mitochondrion-dependent cell proliferation. Collectively, these results provide molecular insights into the antagonistic functions of TIA1b/TIARb and HuR in mitochondrial activity dynamics and suggest that their balance might contribute to mitochondrial physiopathology.
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Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M. Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Miriam Sonntag
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Pravin Kumar Ankush Jagtap
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Bernd Simon
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ); Forschungszentrum Jülich GmbH; Lichtenbergstr. 1 85748 Garching Germany
| | - Arie Geerlof
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
| | - Frank Gabel
- Univ. Grenoble Alpes; CEA, CNRS, IBS; 38000 Grenoble France
- Institut Laue-Langevin (ILL); Avenue des Martyrs 38042 Grenoble France
| | - Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Structural and Computational Biology Unit; European Molecular Biology Laboratory (EMBL) Heidelberg; 69117 Heidelberg Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy; Department Chemie; Technische Universität München; Lichtenbergstr. 4 85747 Garching Germany
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