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Covello G, Ibrahim GH, Bacchi N, Casarosa S, Denti MA. Exon Skipping Through Chimeric Antisense U1 snRNAs to Correct Retinitis Pigmentosa GTPase-Regulator ( RPGR) Splice Defect. Nucleic Acid Ther 2022; 32:333-349. [PMID: 35166581 PMCID: PMC9416563 DOI: 10.1089/nat.2021.0053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal dystrophies are caused by mutations in more than 250 genes, each of them carrying several types of mutations that can lead to different clinical phenotypes. Mutations in Retinitis Pigmentosa GTPase-Regulator (RPGR) cause X-linked Retinitis pigmentosa (RP). A nucleotide substitution in intron 9 of RPGR causes the increase of an alternatively spliced isoform of the mature mRNA, bearing exon 9a (E9a). This introduces a stop codon, leading to truncation of the protein. Aiming at restoring impaired gene expression, we developed an antisense RNA-based therapeutic approach for the skipping of RPGR E9a. We designed a set of specific U1 antisense snRNAs (U1_asRNAs) and tested their efficacy in vitro, upon transient cotransfection with RPGR minigene reporter systems in HEK-293T, 661W, and PC-12 cell lines.
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Affiliation(s)
- Giuseppina Covello
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Gehan H Ibrahim
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Niccolò Bacchi
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Simona Casarosa
- Neural Development and Regeneration Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,Centre for Medical Science - CIS Med, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
| | - Michela Alessandra Denti
- RNA Biology and Biotechnology Laboratory, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.,CNR Neuroscience Institute, Pisa, Italy
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2
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Hooper JE, Jones KL, Smith FJ, Williams T, Li H. An Alternative Splicing Program for Mouse Craniofacial Development. Front Physiol 2020; 11:1099. [PMID: 33013468 PMCID: PMC7498679 DOI: 10.3389/fphys.2020.01099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Alternative splicing acts as a fundamental mechanism to increase the number of functional transcripts that can be derived from the genome - and its appropriate regulation is required to direct normal development, differentiation, and physiology, in many species. Recent studies have highlighted that mutation of splicing factors, resulting in the disruption of alternative splicing, can have profound consequences for mammalian craniofacial development. However, there has been no systematic analysis of the dynamics of differential splicing during the critical period of face formation with respect to age, tissue layer, or prominence. Here we used deep RNA sequencing to profile transcripts expressed in the developing mouse face for both ectodermal and mesenchymal tissues from the three facial prominences at critical ages for facial development, embryonic days 10.5, 11.5, and 12.5. We also derived separate expression data from the nasal pit relating to the differentiation of the olfactory epithelium for a total of 60 independent datasets. Analysis of these datasets reveals the differential expression of multiple genes, but we find a similar number of genes are regulated only via differential splicing, indicating that alternative splicing is a major source of transcript diversity during facial development. Notably, splicing changes between tissue layers and over time are more prevalent than between prominences, with exon skipping the most common event. We next examined how the variation in splicing correlated with the expression of RNA binding proteins across the various datasets. Further, we assessed how binding sites for splicing regulatory molecules mapped with respect to intron exon boundaries. Overall these studies help define an alternative splicing regulatory program that has important consequences for facial development.
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Affiliation(s)
- Joan E. Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kenneth L. Jones
- Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, United States
| | - Francis J. Smith
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, United States
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3
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Siam A, Baker M, Amit L, Regev G, Rabner A, Najar RA, Bentata M, Dahan S, Cohen K, Araten S, Nevo Y, Kay G, Mandel-Gutfreund Y, Salton M. Regulation of alternative splicing by p300-mediated acetylation of splicing factors. RNA (NEW YORK, N.Y.) 2019; 25:813-824. [PMID: 30988101 PMCID: PMC6573785 DOI: 10.1261/rna.069856.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/08/2019] [Indexed: 05/23/2023]
Abstract
Splicing of precursor mRNA (pre-mRNA) is an important regulatory step in gene expression. Recent evidence points to a regulatory role of chromatin-related proteins in alternative splicing regulation. Using an unbiased approach, we have identified the acetyltransferase p300 as a key chromatin-related regulator of alternative splicing. p300 promotes genome-wide exon inclusion in both a transcription-dependent and -independent manner. Using CD44 as a paradigm, we found that p300 regulates alternative splicing by modulating the binding of splicing factors to pre-mRNA. Using a tethering strategy, we found that binding of p300 to the CD44 promoter region promotes CD44v exon inclusion independently of RNAPII transcriptional elongation rate. Promoter-bound p300 regulates alternative splicing by acetylating splicing factors, leading to exclusion of hnRNP M from CD44 pre-mRNA and activation of Sam68. p300-mediated CD44 alternative splicing reduces cell motility and promotes epithelial features. Our findings reveal a chromatin-related mechanism of alternative splicing regulation and demonstrate its impact on cellular function.
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Affiliation(s)
- Ahmad Siam
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mai Baker
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Leah Amit
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gal Regev
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Alona Rabner
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Rauf Ahmad Najar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Sara Dahan
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Klil Cohen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Sarah Araten
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Yuval Nevo
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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4
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Liao S, Sun H, Xu C. YTH Domain: A Family of N 6-methyladenosine (m 6A) Readers. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:99-107. [PMID: 29715522 PMCID: PMC6112328 DOI: 10.1016/j.gpb.2018.04.002] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/24/2018] [Accepted: 04/03/2018] [Indexed: 12/31/2022]
Abstract
Like protein and DNA, different types of RNA molecules undergo various modifications. Accumulating evidence suggests that these RNA modifications serve as sophisticated codes to mediate RNA behaviors and many important biological functions. N6-methyladenosine (m6A) is the most abundant internal RNA modification found in a variety of eukaryotic RNAs, including but not limited to mRNAs, tRNAs, rRNAs, and long non-coding RNAs (lncRNAs). In mammalian cells, m6A can be incorporated by a methyltransferase complex and removed by demethylases, which ensures that the m6A modification is reversible and dynamic. Moreover, m6A is recognized by the YT521-B homology (YTH) domain-containing proteins, which subsequently direct different complexes to regulate RNA signaling pathways, such as RNA metabolism, RNA splicing, RNA folding, and protein translation. Herein, we summarize the recent progresses made in understanding the molecular mechanisms underlying the m6A recognition by YTH domain-containing proteins, which would shed new light on m6A-specific recognition and provide clues to the future identification of reader proteins of many other RNA modifications.
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Affiliation(s)
- Shanhui Liao
- Heifei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Hongbin Sun
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China.
| | - Chao Xu
- Heifei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei 230027, China.
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5
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Matsumoto Y, Itou J, Sato F, Toi M. SALL4 - KHDRBS3 network enhances stemness by modulating CD44 splicing in basal-like breast cancer. Cancer Med 2018; 7:454-462. [PMID: 29356399 PMCID: PMC5806117 DOI: 10.1002/cam4.1296] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/22/2017] [Accepted: 11/26/2017] [Indexed: 02/06/2023] Open
Abstract
Understanding the mechanism by which cancer cells enhance stemness facilitates cancer therapies. Here, we revealed that a stem cell transcription factor, SALL4, functions to enhance stemness in basal-like breast cancer cells. We used shRNA-mediated knockdown and gene overexpression systems to analyze gene functions. To evaluate stemness, we performed a sphere formation assay. In SALL4 knockdown cells, the sphere formation ability was reduced, indicating that SALL4 enhances stemness. CD44 is a membrane protein and is known as a stemness factor in cancer. CD44 splicing variants are involved in cancer stemness. We discovered that SALL4 modulates CD44 alternative splicing through the upregulation of KHDRBS3, a splicing factor for CD44. We cloned the KHDRBS3-regulated CD44 splicing isoform (CD44v), which lacks exons 8 and 9. CD44v overexpression prevented a reduction in the sphere formation ability by KHDRBS3 knockdown, indicating that CD44v is positively involved in cancer stemness. In addition, CD44v enhanced anoikis resistance under the control of the SALL4 - KHDRBS3 network. Basal-like breast cancer is an aggressive subtype among breast cancers, and there is no effective therapy so far. Our findings provide molecular targets for basal-like breast cancer therapy. In the future, this study may contribute to the establishment of drugs targeting cancer stemness.
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Affiliation(s)
- Yoshiaki Matsumoto
- Department of Breast SurgeryGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Junji Itou
- Department of Breast SurgeryGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Fumiaki Sato
- Department of Breast SurgeryGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Masakazu Toi
- Department of Breast SurgeryGraduate School of MedicineKyoto UniversityKyotoJapan
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6
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Mukohyama J, Shimono Y, Minami H, Kakeji Y, Suzuki A. Roles of microRNAs and RNA-Binding Proteins in the Regulation of Colorectal Cancer Stem Cells. Cancers (Basel) 2017; 9:cancers9100143. [PMID: 29064439 PMCID: PMC5664082 DOI: 10.3390/cancers9100143] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/17/2017] [Accepted: 10/17/2017] [Indexed: 12/28/2022] Open
Abstract
Colorectal cancer stem cells (CSCs) are responsible for the initiation, progression and metastasis of human colorectal cancers, and have been characterized by the expression of cell surface markers, such as CD44, CD133, CD166 and LGR5. MicroRNAs (miRNAs) are differentially expressed between CSCs and non-tumorigenic cancer cells, and play important roles in the maintenance and regulation of stem cell properties of CSCs. RNA binding proteins (RBPs) are emerging epigenetic regulators of various RNA processing events, such as splicing, localization, stabilization and translation, and can regulate various types of stem cells. In this review, we summarize current evidences on the roles of miRNA and RBPs in the regulation of colorectal CSCs. Understanding the epigenetic regulation of human colorectal CSCs will help to develop biomarkers for colorectal cancers and to identify targets for CSC-targeting therapies.
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Affiliation(s)
- Junko Mukohyama
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Department of Pathology and Cell Biology, Department of Medicine (Division of Digestive and Liver Diseases) and Herbert Irving Comprehensive Cancer Center (HICCC), Columbia University, New York, NY 10032, USA.
| | - Yohei Shimono
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Hyogo 6500017, Japan.
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Hyogo 6500017, Japan.
| | - Yoshihiro Kakeji
- Division of Gastrointestinal Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
| | - Akira Suzuki
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo 650-0017, Japan.
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7
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Chapat C, Chettab K, Simonet P, Wang P, De La Grange P, Le Romancer M, Corbo L. Alternative splicing of CNOT7 diversifies CCR4-NOT functions. Nucleic Acids Res 2017; 45:8508-8523. [PMID: 28591869 PMCID: PMC5737658 DOI: 10.1093/nar/gkx506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/26/2017] [Indexed: 12/11/2022] Open
Abstract
The CCR4-associated factor CAF1, also called CNOT7, is a catalytic subunit of the CCR4–NOT complex, which has been implicated in all aspects of the mRNA life cycle, from mRNA synthesis in the nucleus to degradation in the cytoplasm. In human cells, alternative splicing of the CNOT7 gene yields a second CNOT7 transcript leading to the formation of a shorter protein, CNOT7 variant 2 (CNOT7v2). Biochemical characterization indicates that CNOT7v2 interacts with CCR4–NOT subunits, although it does not bind to BTG proteins. We report that CNOT7v2 displays a distinct expression profile in human tissues, as well as a nuclear sub-cellular localization compared to CNOT7v1. Despite a conserved DEDD nuclease domain, CNOT7v2 is unable to degrade a poly(A) tail in vitro and preferentially associates with the protein arginine methyltransferase PRMT1 to regulate its activity. Using both in vitro and in cellulo systems, we have also demonstrated that CNOT7v2 regulates the inclusion of CD44 variable exons. Altogether, our findings suggest a preferential involvement of CNOT7v2 in nuclear processes, such as arginine methylation and alternative splicing, rather than mRNA turnover. These observations illustrate how the integration of a splicing variant inside CCR4–NOT can diversify its cell- and tissue-specific functions.
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Affiliation(s)
- Clément Chapat
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Kamel Chettab
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Pierre Simonet
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Peng Wang
- McGill University, Department of Biochemistry, 1160 Pine Avenue West, Montreal, QC H3A 1A3, Canada
| | | | - Muriel Le Romancer
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
| | - Laura Corbo
- Univ. Lyon, Université Lyon 1, Inserm U1052, CNRS UMR5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon 69008, France
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8
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Murphy D, Cieply B, Carstens R, Ramamurthy V, Stoilov P. The Musashi 1 Controls the Splicing of Photoreceptor-Specific Exons in the Vertebrate Retina. PLoS Genet 2016; 12:e1006256. [PMID: 27541351 PMCID: PMC4991804 DOI: 10.1371/journal.pgen.1006256] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/22/2016] [Indexed: 01/08/2023] Open
Abstract
Alternative pre-mRNA splicing expands the coding capacity of eukaryotic genomes, potentially enabling a limited number of genes to govern the development of complex anatomical structures. Alternative splicing is particularly prevalent in the vertebrate nervous system, where it is required for neuronal development and function. Here, we show that photoreceptor cells, a type of sensory neuron, express a characteristic splicing program that affects a broad set of transcripts and is initiated prior to the development of the light sensing outer segments. Surprisingly, photoreceptors lack prototypical neuronal splicing factors and their splicing profile is driven to a significant degree by the Musashi 1 (MSI1) protein. A striking feature of the photoreceptor splicing program are exons that display a "switch-like" pattern of high inclusion levels in photoreceptors and near complete exclusion outside of the retina. Several ubiquitously expressed genes that are involved in the biogenesis and function of primary cilia produce highly photoreceptor specific isoforms through use of such "switch-like" exons. Our results suggest a potential role for alternative splicing in the development of photoreceptors and the conversion of their primary cilia to the light sensing outer segments.
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Affiliation(s)
- Daniel Murphy
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Benjamin Cieply
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Russ Carstens
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Visvanathan Ramamurthy
- Departments of Biochemistry, Ophthalmology and Center for Neuroscience, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Peter Stoilov
- Department of Biochemistry and Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
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9
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Sam68 Mediates the Activation of Insulin and Leptin Signalling in Breast Cancer Cells. PLoS One 2016; 11:e0158218. [PMID: 27415018 PMCID: PMC4944952 DOI: 10.1371/journal.pone.0158218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 06/13/2016] [Indexed: 12/23/2022] Open
Abstract
Obesity is a well-known risk factor for breast cancer development in postmenopausal women. High insulin and leptin levels seem to have a role modulating the growth of these tumours. Sam68 is an RNA-binding protein with signalling functions that has been found to be overexpressed in breast cancer. Moreover, Sam68 may be recruited to insulin and leptin signalling pathways, mediating its effects on survival, growth and proliferation in different cellular types. We aimed to study the expression of Sam68 and its phosphorylation level upon insulin and leptin stimulation, and the role of Sam68 in the proliferative effect and signalling pathways that are activated by insulin or leptin in human breast adenocarcinoma cells. In the human breast adenocarcinoma cell lines MCF7, MDA-MB-231 and BT-474, Sam68 protein quantity and gene expression were increased upon leptin or insulin stimulation, as it was checked by qPCR and immunoblot. Moreover, both insulin and leptin stimulation promoted an increase in Sam68 tyrosine phosphorylation and negatively regulated its RNA binding capacity. siRNA was used to downregulate Sam68 expression, which resulted in lower proliferative effects of both insulin and leptin, as well as a lower activation of MAPK and PI3K pathways promoted by both hormones. These effects may be partly explained by the decrease in IRS-1 expression by down-regulation of Sam68. These results suggest the participation of Sam68 in both leptin and insulin receptor signaling in human breast cancer cells, mediating the trophic effects of these hormones in proliferation and cellular growth.
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10
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Feracci M, Foot JN, Grellscheid SN, Danilenko M, Stehle R, Gonchar O, Kang HS, Dalgliesh C, Meyer NH, Liu Y, Lahat A, Sattler M, Eperon IC, Elliott DJ, Dominguez C. Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68. Nat Commun 2016; 7:10355. [PMID: 26758068 PMCID: PMC4735526 DOI: 10.1038/ncomms10355] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/01/2015] [Indexed: 11/13/2022] Open
Abstract
Sam68 and T-STAR are members of the STAR family of proteins that directly link signal transduction with post-transcriptional gene regulation. Sam68 controls the alternative splicing of many oncogenic proteins. T-STAR is a tissue-specific paralogue that regulates the alternative splicing of neuronal pre-mRNAs. STAR proteins differ from most splicing factors, in that they contain a single RNA-binding domain. Their specificity of RNA recognition is thought to arise from their property to homodimerize, but how dimerization influences their function remains unknown. Here, we establish at atomic resolution how T-STAR and Sam68 bind to RNA, revealing an unexpected mode of dimerization different from other members of the STAR family. We further demonstrate that this unique dimerization interface is crucial for their biological activity in splicing regulation, and suggest that the increased RNA affinity through dimer formation is a crucial parameter enabling these proteins to select their functional targets within the transcriptome. Sam68 and T-STAR are members of the STAR family of proteins, which regulate various aspects of RNA metabolism. Here, the authors reveal structural features required for alternative splicing regulation by these proteins.
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Affiliation(s)
- Mikael Feracci
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Jaelle N Foot
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Sushma N Grellscheid
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Ralf Stehle
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany
| | - Oksana Gonchar
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Hyun-Seo Kang
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - N Helge Meyer
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Albert Lahat
- School of Biological and Biomedical Sciences, University of Durham, South Road, Durham DH1 3LE, UK
| | - Michael Sattler
- Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, DE-85747 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, DE-85764 Oberschleißheim, Germany
| | - Ian C Eperon
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle NE1 3BZ, UK
| | - Cyril Dominguez
- Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester LE1 9HN, UK
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11
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Zhang B, Shao X, Zhou J, Qiu J, Wu Y, Cheng J. YT521 promotes metastases of endometrial cancer by differential splicing of vascular endothelial growth factor A. Tumour Biol 2015; 37:15543-15549. [PMID: 26289848 DOI: 10.1007/s13277-015-3908-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/05/2015] [Indexed: 01/17/2023] Open
Abstract
The malignancy of endometrial carcinoma (EC) largely results from its high invasive feature. The regulation of the mRNA splicing of vascular endothelial growth factor A (VEGF-A) is critical for EC-associated cancer vascularization and invasion. Recently, we have reported that poorly prognostic EC had high levels of YT521, a newly defined RNA splicing protein. However, whether YT521 may similarly regulate the splicing of VEGF-A in EC is unknown. Here, we showed that EC specimens contained significantly higher levels of YT521, compared to the adjacent non-tumor endometrial tissue. Higher levels of YT521 were detected in EC specimens with metastases. High-YT521 EC is associated with poor patient survival. In order to examine whether YT521 may regulate VEGF-A mRNA splicing in EC, we transfected an EC cell line HEC-1A with different doses of YT521 mimics. We found that YT521 dose-dependently increased the ratio of VEGF-165 vs VEGF-121 at both mRNA and protein level, suggesting that YT521 may promote VEGF-A mRNA splicing to favor a VEGF-165 isoform. Moreover, the increases in the ratio of VEGF-165 vs VEGF-121 by YT521 overexpression resulted in increases in EC cell invasion, while decreases in the ratio of VEGF-165 vs VEGF-121 by YT521 depletion resulted in decreases in EC cell invasion in a transwell cell migration assay. Further, overexpression of VEGF-165, but not overexpression of VEGF-121, increased EC cell invasiveness. Finally, a strong correlation was detected between the ratio of VEGF-165 vs VEGF-121 and the levels of YT521 in EC specimens. Together, these data suggest that YT521 may promote EC metastases by regulating mRNA splicing of VEGF-A.
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Affiliation(s)
- Bo Zhang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University, 301 Yanchang Zhong Rd, Shanghai, 200072, China
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12
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Beadell AV, Haag ES. Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol 2014; 7:314-35. [PMID: 25502909 PMCID: PMC4316625 DOI: 10.1093/gbe/evu272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 12/17/2022] Open
Abstract
Given the large number of RNA-binding proteins and regulatory RNAs within genomes, posttranscriptional regulation may be an underappreciated aspect of cis-regulatory evolution. Here, we focus on nematode germ cells, which are known to rely heavily upon translational control to regulate meiosis and gametogenesis. GLD-1 belongs to the STAR-domain family of RNA-binding proteins, conserved throughout eukaryotes, and functions in Caenorhabditis elegans as a germline-specific translational repressor. A phylogenetic analysis across opisthokonts shows that GLD-1 is most closely related to Drosophila How and deuterostome Quaking, both implicated in alternative splicing. We identify messenger RNAs associated with C. briggsae GLD-1 on a genome-wide scale and provide evidence that many participate in aspects of germline development. By comparing our results with published C. elegans GLD-1 targets, we detect nearly 100 that are conserved between the two species. We also detected several hundred Cbr-GLD-1 targets whose homologs have not been reported to be associated with C. elegans GLD-1 in either of two independent studies. Low expression in C. elegans may explain the failure to detect most of them, but a highly expressed subset are strong candidates for Cbr-GLD-1-specific targets. We examine GLD-1-binding motifs among targets conserved in C. elegans and C. briggsae and find that most, but not all, display evidence of shared ancestral binding sites. Our work illustrates both the conservative and the dynamic character of evolution at the posttranslational level of gene regulation, even between congeners.
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Affiliation(s)
- Alana V Beadell
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Present address: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL
| | - Eric S Haag
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Department of Biology, University of Maryland, College Park
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A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nat Methods 2013; 10:1219-24. [PMID: 24162923 PMCID: PMC3852148 DOI: 10.1038/nmeth.2701] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/27/2013] [Indexed: 12/17/2022]
Abstract
Imaging RNA in living cells is a challenging problem in cell biology. One strategy for genetically encoding fluorescent RNAs is to express them as fusions with Spinach, an 'RNA mimic of GFP'. We found that Spinach was dimmer than expected when used to tag constructs in living cells owing to a combination of thermal instability and a propensity for misfolding. Using systematic mutagenesis, we generated Spinach2 that overcomes these issues and can be used to image diverse RNAs. Using Spinach2, we detailed the dynamics of the CGG trinucleotide repeat-containing 'toxic RNA' associated with Fragile X-associated tremor/ataxia syndrome, and show that these RNAs form nuclear foci with unexpected morphological plasticity that is regulated by the cell cycle and by small molecules. Together, these data demonstrate that Spinach2 exhibits improved versatility for fluorescently labeling RNAs in living cells.
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Schmid R, Grellscheid SN, Ehrmann I, Dalgliesh C, Danilenko M, Paronetto MP, Pedrotti S, Grellscheid D, Dixon RJ, Sette C, Eperon IC, Elliott DJ. The splicing landscape is globally reprogrammed during male meiosis. Nucleic Acids Res 2013; 41:10170-84. [PMID: 24038356 PMCID: PMC3905889 DOI: 10.1093/nar/gkt811] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5′ splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle.
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Affiliation(s)
- Ralf Schmid
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK, Department of Health Sciences, University of 00135 Rome 'Foro Italico', Rome, Italy, Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy, Department of Public Health and Cell Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Institute of Particle Physics Phenomenology, Durham University, Durham, DH1 3LE, UK and Life Technologies Ltd., Paisley PA4 9RF, UK
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15
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Ehrmann I, Dalgliesh C, Liu Y, Danilenko M, Crosier M, Overman L, Arthur HM, Lindsay S, Clowry GJ, Venables JP, Fort P, Elliott DJ. The tissue-specific RNA binding protein T-STAR controls regional splicing patterns of neurexin pre-mRNAs in the brain. PLoS Genet 2013; 9:e1003474. [PMID: 23637638 PMCID: PMC3636136 DOI: 10.1371/journal.pgen.1003474] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
The RNA binding protein T-STAR was created following a gene triplication 520-610 million years ago, which also produced its two parologs Sam68 and SLM-1. Here we have created a T-STAR null mouse to identify the endogenous functions of this RNA binding protein. Mice null for T-STAR developed normally and were fertile, surprisingly, given the high expression of T-STAR in the testis and the brain, and the known infertility and pleiotropic defects of Sam68 null mice. Using a transcriptome-wide search for splicing targets in the adult brain, we identified T-STAR protein as a potent splicing repressor of the alternatively spliced segment 4 (AS4) exons from each of the Neurexin1-3 genes, and exon 23 of the Stxbp5l gene. T-STAR protein was most highly concentrated in forebrain-derived structures like the hippocampus, which also showed maximal Neurexin1-3 AS4 splicing repression. In the absence of endogenous T-STAR protein, Nrxn1-3 AS4 splicing repression dramatically decreased, despite physiological co-expression of Sam68. In transfected cells Neurexin3 AS4 alternative splicing was regulated by either T-STAR or Sam68 proteins. In contrast, Neurexin2 AS4 splicing was only regulated by T-STAR, through a UWAA-rich response element immediately downstream of the regulated exon conserved since the radiation of bony vertebrates. The AS4 exons in the Nrxn1 and Nrxn3 genes were also associated with distinct patterns of conserved UWAA repeats. Consistent with an ancient mechanism of splicing control, human T-STAR protein was able to repress splicing inclusion of the zebrafish Nrxn3 AS4 exon. Although Neurexin1-3 and Stxbp5l encode critical synaptic proteins, T-STAR null mice had no detectable spatial memory deficits, despite an almost complete absence of AS4 splicing repression in the hippocampus. Our work identifies T-STAR as an ancient and potent tissue-specific splicing regulator that uses a concentration-dependent mechanism to co-ordinately regulate regional splicing patterns of the Neurexin1-3 AS4 exons in the mouse brain.
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Affiliation(s)
- Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina Danilenko
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Moira Crosier
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lynn Overman
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Helen M. Arthur
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gavin J. Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Julian P. Venables
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippe Fort
- Universités Montpellier 2 et 1, UMR 5237, Centre de Recherche de Biochimie Macromoléculaire, CNRS, Montpellier, France
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
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16
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Frese KS, Katus HA, Meder B. Next-generation sequencing: from understanding biology to personalized medicine. BIOLOGY 2013; 2:378-98. [PMID: 24832667 PMCID: PMC4009863 DOI: 10.3390/biology2010378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 01/21/2013] [Accepted: 02/04/2013] [Indexed: 12/11/2022]
Abstract
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.
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Affiliation(s)
- Karen S Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
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17
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Miyagawa R, Mizuno R, Watanabe K, Ijiri K. Formation of tRNA granules in the nucleus of heat-induced human cells. Biochem Biophys Res Commun 2012; 418:149-55. [PMID: 22244871 DOI: 10.1016/j.bbrc.2011.12.150] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 12/30/2011] [Indexed: 10/14/2022]
Abstract
The stress response, which can trigger various physiological phenomena, is important for living organisms. For instance, a number of stress-induced granules such as P-body and stress granule have been identified. These granules are formed in the cytoplasm under stress conditions and are associated with translational inhibition and mRNA decay. In the nucleus, there is a focus named nuclear stress body (nSB) that distinguishes these structures from cytoplasmic stress granules. Many splicing factors and long non-coding RNA species localize in nSBs as a result of stress. Indeed, tRNAs respond to several kinds of stress such as heat, oxidation or starvation. Although nuclear accumulation of tRNAs occurs in starved Saccharomyces cerevisiae, this phenomenon is not found in mammalian cells. We observed that initiator tRNA(Met) (Meti) is actively translocated into the nucleus of human cells under heat stress. During this study, we identified unique granules of Meti that overlapped with nSBs. Similarly, elongator tRNA(Met) was translocated into the nucleus and formed granules during heat stress. Formation of tRNA granules is closely related to the translocation ratio. Then, all tRNAs may form the specific granules.
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Affiliation(s)
- Ryu Miyagawa
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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18
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Bielli P, Busà R, Paronetto MP, Sette C. The RNA-binding protein Sam68 is a multifunctional player in human cancer. Endocr Relat Cancer 2011; 18:R91-R102. [PMID: 21565971 DOI: 10.1530/erc-11-0041] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Src associated in mitosis, of 68 kDa (Sam68) is a KH domain RNA-binding protein that belongs to the signal transduction and activation of RNA family. Although ubiquitously expressed, Sam68 plays very specialized roles in different cellular environments. In most cells, Sam68 resides in the nucleus and is involved in several steps of mRNA processing, from transcription, to alternative splicing, to nuclear export. In addition, Sam68 translocates to the cytoplasm upon cell stimulation, cell cycle transitions or viral infections, where it takes part to signaling complexes and associates with the mRNA translation machinery. Recent evidence has linked Sam68 function to the onset and progression of endocrine tumors, such as prostate and breast carcinomas. Notably, all the biochemical activities reported for Sam68 seem to be implicated in carcinogenesis. Herein, we review the recent advancement in the knowledge of Sam68 function and regulation and discuss it in the frame of its participation to neoplastic transformation and tumor progression.
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Affiliation(s)
- Pamela Bielli
- Department of Public Health and Cell Biology, University of Rome Tor Vergata, Italy
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19
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Idler RK, Yan W. Control of messenger RNA fate by RNA-binding proteins: an emphasis on mammalian spermatogenesis. ACTA ACUST UNITED AC 2011; 33:309-37. [PMID: 21757510 DOI: 10.2164/jandrol.111.014167] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Posttranscriptional status of messenger RNAs (mRNA) can be affected by many factors, most of which are RNA-binding proteins (RBP) that either bind mRNA in a nonspecific manner or through specific motifs, usually located in the 3' untranslated regions. RBPs can also be recruited by small noncoding RNAs (sncRNA), which have been shown to be involved in posttranscriptional regulations and transposon repression (eg, microRNAs or P-element-induced wimpy testis-interacting RNA) as components of the sncRNA effector complex. Non-sncRNA-binding RBPs have much more diverse effects on their target mRNAs. Some can cause degradation of their target transcripts and/or repression of translation, whereas others can stabilize and/or activate translation. The splicing and exportation of transcripts from the nucleus to the cytoplasm are often mediated by sequence-specific RBPs. The mechanisms by which RBPs regulate mRNA transcripts involve manipulating the 3' poly(A) tail, targeting the transcript to polysomes or to other ribonuclear protein particles, recruiting regulatory proteins, or competing with other RBPs. Here, we briefly review the known mechanisms of posttranscriptional regulation mediated by RBPs, with an emphasis on how these mechanisms might control spermatogenesis in general.
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Affiliation(s)
- R Keegan Idler
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
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20
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Jakubauskas A, Valceckiene V, Andrekute K, Seinin D, Kanopka A, Griskevicius L. Discovery of two novel EWSR1/ATF1 transcripts in four chimerical transcripts-expressing clear cell sarcoma and their quantitative evaluation. Exp Mol Pathol 2011; 90:194-200. [DOI: 10.1016/j.yexmp.2010.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 12/10/2010] [Accepted: 12/14/2010] [Indexed: 11/25/2022]
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21
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Sellier C, Rau F, Liu Y, Tassone F, Hukema RK, Gattoni R, Schneider A, Richard S, Willemsen R, Elliott DJ, Hagerman PJ, Charlet-Berguerand N. Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients. EMBO J 2010; 29:1248-61. [PMID: 20186122 DOI: 10.1038/emboj.2010.21] [Citation(s) in RCA: 286] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 01/20/2010] [Indexed: 01/22/2023] Open
Abstract
Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder caused by expansion of 55-200 CGG repeats in the 5'-UTR of the FMR1 gene. FXTAS is characterized by action tremor, gait ataxia and impaired executive cognitive functioning. It has been proposed that FXTAS is caused by titration of RNA-binding proteins by the expanded CGG repeats. Sam68 is an RNA-binding protein involved in alternative splicing regulation and its ablation in mouse leads to motor coordination defects. Here, we report that mRNAs containing expanded CGG repeats form large and dynamic intranuclear RNA aggregates that recruit several RNA-binding proteins sequentially, first Sam68, then hnRNP-G and MBNL1. Importantly, Sam68 is sequestered by expanded CGG repeats and thereby loses its splicing-regulatory function. Consequently, Sam68-responsive splicing is altered in FXTAS patients. Finally, we found that regulation of Sam68 tyrosine phosphorylation modulates its localization within CGG aggregates and that tautomycin prevents both Sam68 and CGG RNA aggregate formation. Overall, these data support an RNA gain-of-function mechanism for FXTAS neuropathology, and suggest possible target routes for treatment options.
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Affiliation(s)
- Chantal Sellier
- Department of Neurobiology and Genetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Illkirch, France
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22
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Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FHT, Stamm S. The YTH domain is a novel RNA binding domain. J Biol Chem 2010; 285:14701-10. [PMID: 20167602 DOI: 10.1074/jbc.m110.104711] [Citation(s) in RCA: 212] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The YTH (YT521-B homology) domain was identified by sequence comparison and is found in 174 different proteins expressed in eukaryotes. It is characterized by 14 invariant residues within an alpha-helix/beta-sheet structure. Here we show that the YTH domain is a novel RNA binding domain that binds to a short, degenerated, single-stranded RNA sequence motif. The presence of the binding motif in alternative exons is necessary for YT521-B to directly influence splice site selection in vivo. Array analyses demonstrate that YT521-B predominantly regulates vertebrate-specific exons. An NMR titration experiment identified the binding surface for single-stranded RNA on the YTH domain. Structural analyses indicate that the YTH domain is related to the pseudouridine synthase and archaeosine transglycosylase (PUA) domain. Our data show that the YTH domain conveys RNA binding ability to a new class of proteins that are found in all eukaryotic organisms.
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Affiliation(s)
- Zhaiyi Zhang
- Institute for Biochemistry, Universität Erlangen-Nuremberg, Fahrstrasse 17, 91054 Erlangen, Germany
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23
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Zhang LY, Zeng M, Chen P, Sun HQ, Tao DC, Liu YQ, Lin L, Yang Y, Zhang SZ, Ma YX. Identification of messenger RNA substrates for mouse T-STAR. BIOCHEMISTRY (MOSCOW) 2010; 74:1270-7. [PMID: 19916944 DOI: 10.1134/s0006297909110145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using the method of isolation of specific nucleic acids associated with proteins (SNAAP), we have identified 10 candidate target mRNA substrates bound by mT-STAR (mouse T-STAR protein) from testis extract. Among them, our study focused on Fabp9, a gene that is essential for male gametogenesis, and showed that mT-STAR could directly bind to Fabp9 mRNAs. The binding sites are in a short sequence of the coding region and 3' untranslated region of Fabp9 mRNA. These suggest that mT-STAR can regulate the metabolism and expression of Fabp9. In conclusion, identification of mT-STAR-bound mRNA substrates might help to illustrate the potential spectrum of the process and provide valuable insight into the biological function of this RNA-binding protein in spermatogenesis.
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Affiliation(s)
- L Y Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, P. R. China
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Expression and functions of the star proteins Sam68 and T-STAR in mammalian spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 693:67-81. [PMID: 21189686 DOI: 10.1007/978-1-4419-7005-3_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Spermatogenesis is one of the few major developmental pathways which are still ongoing in the adult. In this chapter we review the properties of Sam68 and T-STAR, which are the STAR proteins functionally implicated in mammalian spermatogenesis. Sam68 is a ubiquitously expressed member of the STAR family, but has an essential role in spermatogenesis. Sam68 null mice are male infertile and at least in part this is due to a failure in important translational controls that operate during and after meiosis. The homologous T-STAR protein has a much more restricted anatomic expression pattern than Sam68, with highest levels seen in the testis and the developing brain. The focus of this chapter is the functional role of Sam68 and T-STAR proteins in male germ cell development. Since these proteins are known to have many cellular functions we extrapolate from other cell types and tissues to speculate on each of their likely functions within male germ cells, including control of alternative pre-mRNA splicing patterns in male germ cells.
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26
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Sette C. Post-translational regulation of star proteins and effects on their biological functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 693:54-66. [PMID: 21189685 DOI: 10.1007/978-1-4419-7005-3_4] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
STAR (Signal Transduction and Activation of RNA) proteins owed their name to the presence in their structure ofa RNA-binding domain and several hallmarks of their involvement in signal transduction pathways. In many members of the family, the STAR RNA-binding domain (also named GSG, an acronym for GRP33/Sam68/ GLD-1) is flanked by regulatory regions containing proline-rich sequences, which serve as docking sites for proteins containing SH3 and WW domains and also a tyrosine-rich region at the C-terminus, which can mediateprotein-protein interactions with partners through SH2 domains. These regulatory regions contain consensus sequences for additional modifications, including serine/threonine phosphorylation, methylation, acetylation and sumoylation. Since their initial description, evidence has been gathered in different cell types and model organisms that STAR proteins can indeed integrate signals from external and internal cues with changes in transcription and processing of target RNAs. The most striking example of the high versatility of STAR proteins is provided by Sam68 (KHDRBS1), whose function, subcellular localization and affinity for RNA are strongly modulated by several signaling pathways through specific modifications. Moreover, the recent development of genetic knockout models has unveiled the physiological function of some STAR proteins, pointing to a crucial role of their post-translational modifications in the biological processes regulated by these RNA-binding proteins. This chapter offers an overview of the most updated literature on the regulation of STAR proteins by post-translational modifications and illustrates examples of how signal transduction pathways can modulate their activity and affect biological processes.
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Affiliation(s)
- Claudio Sette
- Department of Public Health and Cell Biology, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy.
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27
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Ashraf S, Hoskins BE, Chaib H, Hoefele J, Pasch A, Saisawat P, Trefz F, Hacker HW, Nuernberg G, Nuernberg P, Otto EA, Hildebrandt F. Mapping of a new locus for congenital anomalies of the kidney and urinary tract on chromosome 8q24. Nephrol Dial Transplant 2009; 25:1496-501. [PMID: 20007758 DOI: 10.1093/ndt/gfp650] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Congenital anomalies of the kidney and urinary tract (CAKUT) account for the majority of end-stage renal disease in children (50%). Previous studies have mapped autosomal dominant loci for CAKUT. We here report a genome-wide search for linkage in a large pedigree of Somalian descent containing eight affected individuals with a non-syndromic form of CAKUT. METHODS Clinical data and blood samples were obtained from a Somalian family with eight individuals with CAKUT including high-grade vesicoureteral reflux and unilateral renal agenesis. Total genome search for linkage was performed using a 50K SNP Affymetric DNA microarray. As neither parent is affected, the results of the SNP array were analysed under recessive models of inheritance, with and without the assumption of consanguinity. RESULTS Using the non-consanguineous recessive model, a new gene locus (CAKUT1) for CAKUT was mapped to chromosome 8q24 with a significant maximum parametric Logarithm of the ODDs (LOD) score (LOD(max)) of 4.2. Recombinations were observed in two patients defining a critical genetic interval of 2.5 Mb physical distance flanked by markers SNP_A-1740062 and SNP_A-1653225. CONCLUSION We have thus identified a new non-syndromic recessive gene locus for CAKUT (CAKUT1) on chromosome 8q24. The identification of the disease-causing gene will provide further insights into the pathogenesis of urinary tract malformations and mechanisms of renal development.
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Affiliation(s)
- Shazia Ashraf
- 1Department of Pediatrics and of Human Genetics, University of Michigan, Ann Arbor, USA
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Rajan P, Dalgliesh C, Bourgeois CF, Heiner M, Emami K, Clark EL, Bindereif A, Stevenin J, Robson CN, Leung HY, Elliott DJ. Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies. BMC Cell Biol 2009; 10:82. [PMID: 19912651 PMCID: PMC2784748 DOI: 10.1186/1471-2121-10-82] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 11/13/2009] [Indexed: 11/25/2022] Open
Abstract
Background Active pre-mRNA splicing occurs co-transcriptionally, and takes place throughout the nucleoplasm of eukaryotic cells. Splicing decisions are controlled by networks of nuclear RNA-binding proteins and their target sequences, sometimes in response to signalling pathways. Sam68 (Src-associated in mitosis 68 kDa) is the prototypic member of the STAR (Signal Transduction and Activation of RNA) family of RNA-binding proteins, which regulate splicing in response to signalling cascades. Nuclear Sam68 protein is concentrated within subnuclear organelles called SLM/Sam68 Nuclear Bodies (SNBs), which also contain some other splicing regulators, signalling components and nucleic acids. Results We used proteomics to search for the major interacting protein partners of nuclear Sam68. In addition to Sam68 itself and known Sam68-associated proteins (heterogeneous nuclear ribonucleoproteins hnRNP A1, A2/B1 and G), we identified hnRNP L as a novel Sam68-interacting protein partner. hnRNP L protein was predominantly present within small nuclear protein complexes approximating to the expected size of monomers and dimers, and was quantitatively associated with nucleic acids. hnRNP L spatially co-localised with Sam68 as a novel component of SNBs and was also observed within the general nucleoplasm. Localisation within SNBs was highly specific to hnRNP L and was not shared by the closely-related hnRNP LL protein, nor any of the other Sam68-interacting proteins we identified by proteomics. The interaction between Sam68 and hnRNP L proteins was observed in a cell line which exhibits low frequency of SNBs suggesting that this association also takes place outside SNBs. Although ectopic expression of hnRNP L and Sam68 proteins independently affected splicing of CD44 variable exon v5 and TJP1 exon 20 minigenes, these proteins did not, however, co-operate with each other in splicing regulation of these target exons. Conclusion Here we identify hnRNP L as a novel SNB component. We show that, compared with other identified Sam68-associated hnRNP proteins and hnRNP LL, this co-localisation within SNBs is specific to hnRNP L. Our data suggest that the novel Sam68-hnRNP L protein interaction may have a distinct role within SNBs.
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Affiliation(s)
- Prabhakar Rajan
- Institute of Human Genetics, Newcastle University, Central Parkway, Newcastle-upon-Tyne, NE1 3BZ, UK.
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Wang J, Yuan Y, Zhou Y, Guo L, Zhang L, Kuai X, Deng B, Pan Z, Li D, He F. Protein Interaction Data Set Highlighted with Human Ras-MAPK/PI3K Signaling Pathways. J Proteome Res 2008; 7:3879-89. [DOI: 10.1021/pr8001645] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Longhua Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xuezhang Kuai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Binwei Deng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhi Pan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China, and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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Ohno G, Hagiwara M, Kuroyanagi H. STAR family RNA-binding protein ASD-2 regulates developmental switching of mutually exclusive alternative splicing in vivo. Genes Dev 2008; 22:360-74. [PMID: 18230701 PMCID: PMC2216695 DOI: 10.1101/gad.1620608] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 12/04/2007] [Indexed: 11/25/2022]
Abstract
Alternative splicing of pre-mRNAs greatly contributes to the spatiotemporal diversity of gene expression in metazoans. However, the molecular basis of developmental regulation and the precise sequence of alternative pre-mRNA processing in vivo are poorly understood. In the present study, we focus on the developmental switching of the mutually exclusive alternative splicing of the let-2 gene of Caenorhabditis elegans from the exon 9 form in embryos to the exon 10 form in adults. By visualizing the usage of the let-2 mutually exclusive exons through differential expression of green fluorescent protein (GFP) and red fluorescent protein (RFP), we isolated several switching-defective mutants and identified the alternative splicing defective-2 (asd-2) gene, encoding a novel member of the evolutionarily conserved STAR (signal transduction activators of RNA) family of RNA-binding proteins. Comparison of the amounts of partially spliced let-2 RNAs in synchronized wild-type and asd-2 mutant worms suggested that either of the introns downstream from the let-2 mutually exclusive exons is removed prior to the removal of the upstream ones, and that asd-2 promotes biased excision of intron 10 in the late larval stages. We propose that the developmental switching between alternative sequences of intron removal determines the ratio between the mature let-2 mRNA isoforms.
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Affiliation(s)
- Genta Ohno
- Laboratory of Gene Expression, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masatoshi Hagiwara
- Laboratory of Gene Expression, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- Department of Functional Genomics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- Department of Functional Genomics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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Skotheim RI, Nees M. Alternative splicing in cancer: Noise, functional, or systematic? Int J Biochem Cell Biol 2007; 39:1432-49. [PMID: 17416541 DOI: 10.1016/j.biocel.2007.02.016] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/13/2007] [Accepted: 02/22/2007] [Indexed: 12/22/2022]
Abstract
Pre-messenger RNA splicing is a fine-tuned process that generates multiple functional variants from individual genes. Various cell types and developmental stages regulate alternative splicing patterns differently in their generation of specific gene functions. In cancers, splicing is significantly altered, and understanding the underlying mechanisms and patterns in cancer will shed new light onto cancer biology. Cancer-specific transcript variants are promising biomarkers and targets for diagnostic, prognostic, and treatment purposes. In this review, we explore how alternative splicing cannot simply be considered as noise or an innocent bystander, but is actively regulated or deregulated in cancers. A special focus will be on aspects of cell biology and biochemistry of alternative splicing in cancer cells, addressing differences in splicing mechanisms between normal and malignant cells. The systems biology of splicing is only now applied to the field of cancer research. We explore functional annotations for some of the most intensely spliced gene classes, and provide a literature mining and clustering that reflects the most intensely investigated genes. A few well-established cancer-specific splice events, such as the CD44 antigen, are used to illustrate the potential behind the exploration of the mechanisms of their regulation. Accordingly, we describe the functional connection between the regulatory machinery (i.e., the spliceosome and its accessory proteins) and their global impact on qualitative transcript variation that are only now emerging from the use of genomic technologies such as microarrays. These studies are expected to open an entirely new level of genetic information that is currently still poorly understood.
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Affiliation(s)
- Rolf I Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
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Fu G, Condon KC, Epton MJ, Gong P, Jin L, Condon GC, Morrison NI, Dafa'alla TH, Alphey L. Female-specific insect lethality engineered using alternative splicing. Nat Biotechnol 2007; 25:353-7. [PMID: 17322873 DOI: 10.1038/nbt1283] [Citation(s) in RCA: 186] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 09/14/2006] [Indexed: 11/09/2022]
Abstract
The Sterile Insect Technique is a species-specific and environmentally friendly method of pest control involving mass release of sterilized insects that reduce the wild population through infertile matings. Insects carrying a female-specific autocidal genetic system offer an attractive alternative to conventional sterilization methods while also eliminating females from the release population. We exploited sex-specific alternative splicing in insects to engineer female-specific autocidal genetic systems in the Mediterranean fruit fly, Ceratitis capitata. These rely on the insertion of cassette exons from the C. capitata transformer gene into a heterologous tetracycline-repressible transactivator such that the transactivator transcript is disrupted in male splice variants but not in the female-specific one. As the key components of these systems function across a broad phylogenetic range, this strategy addresses the paucity of sex-specific expression systems (e.g., early-acting, female-specific promoters) in insects other than Drosophila melanogaster. The approach may have wide applicability for regulating gene expression in other organisms, particularly for combinatorial control with appropriate promoters.
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Affiliation(s)
- Guoliang Fu
- Oxitec Limited, 71 Milton Park, Oxford OX14 4RX, UK
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Sergeant KA, Bourgeois CF, Dalgliesh C, Venables JP, Stevenin J, Elliott DJ. Alternative RNA splicing complexes containing the scaffold attachment factor SAFB2. J Cell Sci 2007; 120:309-19. [PMID: 17200140 DOI: 10.1242/jcs.03344] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The scaffold attachment factor SAFB1 and its recently discovered homologue SAFB2 might provide an important link between pre-mRNA splicing, intracellular signalling and transcription. Using novel mono-specific antisera, we found endogenous SAFB2 protein has a different spatial distribution from SAFB1 within the nucleus where it is found in much larger nuclear complexes (up to 670 kDa in size), and a distinct pattern of expression in adult human testis. By contrast, SAFB1 protein predominantly exists either as smaller complexes or as a monomeric protein. Our results suggest stable core complexes containing components comprised of SAFB1, SAFB2 and the RNA binding proteins Sam68 and hnRNPG exist in parallel with free SAFB1 protein. We found that SAFB2 protein, like SAFB1, acts as a negative regulator of a tra2β variable exon. Despite showing an involvement in splicing, we detected no stable interaction between SAFB proteins and SR or SR-related splicing regulators, although these were also found in stable higher molecular mass complexes. Each of the detected alternative splicing regulator complexes exists independently of intact nucleic acids, suggesting they might be pre-assembled and recruited to nascent transcripts as modules to facilitate alternative splicing, and/or they represent nuclear storage compartments from which active proteins are recruited.
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Affiliation(s)
- Kate A Sergeant
- Institute of Human Genetics, University of Newcastle, International Centre for Life, Central Parkway, Newcastle, NE1 3BZ, UK
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35
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Lynch KW. Regulation of alternative splicing by signal transduction pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:161-74. [PMID: 18380346 DOI: 10.1007/978-0-387-77374-2_10] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alternative splicing is now recognized as a ubiquitous mechanism for controlling gene expression in a tissue-specific manner. A growing body of work from the past few years as begun to also highlight the existence of networks of signal-responsive alternative splicing in a variety of cell types. While the mechanisms by which signal transduction pathways influence the splicing machinery are relatively poorly understood, a few themes have begun to emerge for how extracellular stimuli can be communicated to specific RNA-binding proteins that control splice site selection by the spliceosome. This chapter describes our current understanding of signal-induced alternative splicing with an emphasis on these emerging themes and the likely directions for future research.
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Affiliation(s)
- Kristen W Lynch
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75390-9038, USA.
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36
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Hoebeke I, De Smedt M, Stolz F, Pike-Overzet K, Staal FJT, Plum J, Leclercq G. T-, B- and NK-lymphoid, but not myeloid cells arise from human CD34+CD38−CD7+ common lymphoid progenitors expressing lymphoid-specific genes. Leukemia 2006; 21:311-9. [PMID: 17170726 DOI: 10.1038/sj.leu.2404488] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hematopoietic stem cells in the bone marrow (BM) give rise to all blood cells. According to the classic model of hematopoiesis, the differentiation paths leading to the myeloid and lymphoid lineages segregate early. A candidate 'common lymphoid progenitor' (CLP) has been isolated from CD34(+)CD38(-) human cord blood cells based on CD7 expression. Here, we confirm the B- and NK-differentiation potential of CD34(+)CD38(-)CD7(+) cells and show in addition that this population has strong capacity to differentiate into T cells. As CD34(+)CD38(-)CD7(+) cells are virtually devoid of myeloid differentiation potential, these cells represent true CLPs. To unravel the molecular mechanisms underlying lymphoid commitment, we performed genome-wide gene expression profiling on sorted CD34(+)CD38(-)CD7(+) and CD34(+)CD38(-)CD7(-) cells. Interestingly, lymphoid-affiliated genes were mainly upregulated in the CD7(+) population, while myeloid-specific genes were downregulated. This supports the hypothesis that lineage commitment is accompanied by the shutdown of inappropriate gene expression and the upregulation of lineage-specific genes. In addition, we identified several highly expressed genes that have not been described in hematopoiesis before.
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Affiliation(s)
- I Hoebeke
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, Ghent, Belgium
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37
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Robard C, Daviau A, Di Fruscio M. Phosphorylation status of the Kep1 protein alters its affinity for its protein binding partner alternative splicing factor ASF/SF2. Biochem J 2006; 400:91-7. [PMID: 16834570 PMCID: PMC1635453 DOI: 10.1042/bj20060384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations in the Drosophila kep1 gene, encoding a single maxi KH (K homology) domain-containing RNA-binding protein, result in a reduction of fertility in part due to the disruption of the apoptotic programme during oogenesis. This disruption is concomitant with the appearance of an alternatively spliced mRNA isoform encoding the inactive caspase dredd. We generated a Kep1 antibody and have found that the Kep1 protein is present in the nuclei of both the follicle and nurse cells during all stages of Drosophila oogenesis. We have shown that the Kep1 protein is phosphorylated in ovaries induced to undergo apoptosis following treatment with the topoisomerase I inhibitor camptothecin. We have also found that the Kep1 protein interacts specifically with the SR (serine/arginine-rich) protein family member ASF/SF2 (alternative splicing factor/splicing factor 2). This interaction is independent of the ability of Kep1 to bind RNA, but is dependent on the phosphorylation of the Kep1 protein, with the interaction between Kep1 and ASF/SF2 increasing in the presence of activated Src. Using a CD44v5 alternative splicing reporter construct, we observed 99% inclusion of the alternatively spliced exon 5 following kep1 transfection in a cell line that constitutively expresses activated Src. This modulation in splicing was not observed in the parental NIH 3T3 cell line in which we obtained 7.5% exon 5 inclusion following kep1 transfection. Our data suggest a mechanism of action in which the in vivo phosphorylation status of the Kep1 protein affects its affinity towards its protein binding partners and in turn may allow for the modulation of alternative splice site selection in Kep1-ASF/SF2-dependent target genes.
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Affiliation(s)
- Cécile Robard
- Département de biologie, Université de Sherbrooke, 2500 Boul, Sherbrooke, QC, Canada J1K 2R1
| | - Alex Daviau
- Département de biologie, Université de Sherbrooke, 2500 Boul, Sherbrooke, QC, Canada J1K 2R1
| | - Marco Di Fruscio
- Département de biologie, Université de Sherbrooke, 2500 Boul, Sherbrooke, QC, Canada J1K 2R1
- To whom correspondence should be addressed (email )
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Zhang L, Guo L, Peng Y, Chen B. Expression of T-STAR gene is associated with regulation of telomerase activity in human colon cancer cell line HCT-116. World J Gastroenterol 2006; 12:4056-60. [PMID: 16810759 PMCID: PMC4087721 DOI: 10.3748/wjg.v12.i25.4056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effects on telomerase activity of transfection of human T-STAR gene full-length sense cDNA or partial antisense cDNA into human colon cancer cell line HCT-116.
METHODS: mRNA and protein expression levels of T-STAR gene were determined by RT-PCR and western blot, and telomerase activity was measured by PCR-ELISA, after transfection of T-STAR sense or antisense gene into HCT-116 cells with lipofectamine.
RESULTS: T-STAR gene expression was enhanced or knocked down both at mRNA and protein levels, and telomerase activity was significantly increased or decreased.
CONCLUSION: The T-STAR gene may participate in regulation of telomerase activity in human colon cancer HCT-116 cells in a parallel fashion.
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Affiliation(s)
- Ling Zhang
- Department of Disease Prevention and Health Protection, Southwest Hospital, The Third Military Medical University, Chongqing 400038, China
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Scholzová E, Malík R, Sevcík J, Kleibl Z. RNA regulation and cancer development. Cancer Lett 2006; 246:12-23. [PMID: 16675105 DOI: 10.1016/j.canlet.2006.03.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 03/20/2006] [Accepted: 03/24/2006] [Indexed: 12/23/2022]
Abstract
Cancer is viewed as a genetic disease. According to the currently accepted model of carcinogenesis, several consequential mutations in oncogenes or tumor suppressor genes are necessary for cancer development. In this model, mutated DNA sequence is transcribed to mRNA that is finally translated into functionally aberrant protein. mRNA is viewed solely as an intermediate between DNA (with 'coding' potential) and protein (with 'executive' function). However, recent findings suggest that (m)RNA is actively regulated by a variety of processes including nonsense-mediated decay, alternative splicing, RNA editing or RNA interference. Moreover, RNA molecules can regulate a variety of cellular functions through interactions with RNA, DNA as well as protein molecules. Although, the precise contribution of RNA molecules by themselves and RNA-regulated processes on cancer development is currently unknown, recent data suggest their important role in carcinogenesis. Here, we summarize recent knowledge on RNA-related processes and discuss their potential role in cancer development.
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Affiliation(s)
- Eva Scholzová
- First Medical Faculty, Institute of Biochemistry and Experimental Oncology, Charles University, U Nemocnice 5, 128 53 Prague 2, Czech Republic.
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Badri KR, Modem S, Gerard HC, Khan I, Bagchi M, Hudson AP, Reddy TR. Regulation of Sam68 activity by small heat shock protein 22. J Cell Biochem 2006; 99:1353-62. [PMID: 16795043 DOI: 10.1002/jcb.21004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Sam68 associates with c-Src kinase during mitosis. We previously demonstrated that Sam68 functionally replaces and/or synergizes with HIV-1 Rev in rev response element (RRE)-mediated gene expression and virus production. Furthermore, we reported that knockdown of Sam68 inhibited Rev-mediated RNA export and it is absolutely required for HIV-1 production. In the present study, we identified small heat shock protein, hsp22, as a novel interacting partner of Sam68. Hsp22 binds to Sam68 in vitro and in vivo. Overexpression of hsp22 significantly inhibits Sam68-mediated RRE- as well as CTE (constitutive transport element)-dependent reporter gene expression. Furthermore, exposing 293T cells to heat shock inhibits Sam68/RRE function by virtue of elevating hsp22. The critical domain of hsp22 that interacts with Sam68 resides between amino acids 62 and 133. Our studies provide evidence for the first time that hsp22 specifically binds to Sam68 and modulates its activity, thus playing a role in the post-transcriptional regulation of gene expression.
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Affiliation(s)
- Kameswara R Badri
- Department of Immunology and Microbiology, Wayne State University-School of Medicine, Detroit, Michigan 48201, USA
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Lukong KE, Larocque D, Tyner AL, Richard S. Tyrosine phosphorylation of sam68 by breast tumor kinase regulates intranuclear localization and cell cycle progression. J Biol Chem 2005; 280:38639-47. [PMID: 16179349 DOI: 10.1074/jbc.m505802200] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The breast tumor kinase (BRK) is a growth promoting non-receptor tyrosine kinase overexpressed in the majority of human breast tumors. BRK is known to potentiate the epidermal growth factor (EGF) response in these cells. Although BRK is known to phosphorylate the RNA-binding protein Sam68, the specific tyrosines phosphorylated and the exact role of this phosphorylation remains unknown. Herein, we have generated Sam68 phospho-specific antibodies against C-terminal phosphorylated tyrosine residues within the Sam68 nuclear localization signal. We show that BRK phosphorylates Sam68 on all three tyrosines in the nuclear localization signal. By indirect immunofluorescence we observed that BRK and EGF treatment not only phosphorylates Sam68 but also induces its relocalization. Tyrosine 440 was identified as a principal modulator of Sam68 localization and this site was phosphorylated in response to EGF treatment in human breast tumor cell lines. Moreover, this phosphorylation event was inhibited by BRK small interfering RNA treatment, consistent with Sam68 being a physiological substrate of BRK downstream of the EGF receptor in breast cancer cells. Finally, we observed that Sam68 suppressed BRK-induced cell proliferation, suggesting that Sam68 does indeed contain anti-proliferative properties that may be neutralized in breast cancer cells by phosphorylation.
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Affiliation(s)
- Kiven Erique Lukong
- Terry Fox Molecular Oncology Group and Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research and Department of Oncology, McGill University, Montreal, Quebec H3T 1E2, Canada
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Galarneau A, Richard S. Target RNA motif and target mRNAs of the Quaking STAR protein. Nat Struct Mol Biol 2005; 12:691-8. [PMID: 16041388 DOI: 10.1038/nsmb963] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 06/20/2005] [Indexed: 11/08/2022]
Abstract
Quaking viable (Qk(v)) mice have developmental defects that result in their characteristic tremor. The quaking (Qk) locus expresses alternatively spliced RNA-binding proteins belonging to the STAR family. To characterize the RNA binding specificity of the QKI proteins, we selected for RNA species that bound QKI from random pools of RNAs and defined the QKI response element (QRE) as a bipartite consensus sequence NACUAAY-N(1-20)-UAAY. A bioinformatic analysis using the QRE identified the three known RNA targets of QKI and 1,430 new putative mRNA targets, of which 23 were validated in vivo. A large proportion of the mRNAs are implicated in development and cell differentiation, as predicted from the phenotype of the Qk(v) mice. In addition, 24% are implicated in cell growth and/or maintenance, suggesting a role for QKI in cancer.
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Affiliation(s)
- André Galarneau
- Terry Fox Molecular Oncology Group, Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Department of Oncology, McGill University, Montréal, Québec, Canada, H3T 1E2
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Zhang L, Guo L, Peng Y, Chen B. Effects of T-STAR gene on activity of telomerase in colon cancer cell line HCT-116. Shijie Huaren Xiaohua Zazhi 2005; 13:1267-1271. [DOI: 10.11569/wcjd.v13.i11.1267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effects of testis-signal transduction and activator of RNA (T-STAR) on telomerase activity in human colon cancer cell line HCT-116.
METHODS: The T-STAR sense or antisense gene was transfected into HCT-116 cells with lipofectamine. The mRNA and protein expression of T-STAR were determined by reverse transcription polymerase chain reaction (RT-PCR) and western blot, and the activity of telomerase was measured by PCR-ELISA.
RESULTS: The expression of T-STAR mRNA and protein were significantly increased in T-STAR transfected cells (296% and 180% respectively, P<0.01), while markedly decreased in antisense T-STAR transfected ones (59% and 83.8% respectively, P<0.01). The activity of telomerase was significantly increased in T-STAR transfected cells, but decreased in antisense T-STAR transfected ones. The expression of T-STAR and the activity of telomerase manifested no significant difference between HCT-116 cells transfected with empty vector and non-transfected ones.
CONCLUSION: T-STAR gene may play an important role in the positive regulation of telomerase activtity in human colon cancer HCT-116 cells.
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Cohen CD, Doran PP, Blattner SM, Merkle M, Wang GQ, Schmid H, Mathieson PW, Saleem MA, Henger A, Rastaldi MP, Kretzler M. Sam68-like mammalian protein 2, identified by digital differential display as expressed by podocytes, is induced in proteinuria and involved in splice site selection of vascular endothelial growth factor. J Am Soc Nephrol 2005; 16:1958-65. [PMID: 15901763 DOI: 10.1681/asn.2005020204] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Podocytes, the glomerular epithelial cells of the kidney, share important features with neuronal cells. In addition to phenotypical and functional similarities, a number of gene products have been found to be expressed exclusively or predominantly by both cell types. With the hypothesis of a common transcriptome shared by podocytes and neurons, digital differential display was used to identify novel podocyte-expressed gene products. Comparison of brain and kidney cDNA libraries with those of other organs identified Sam68-like mammalian protein 2 (SLM-2), a member of the STAR family of RNA processing proteins, as expressed by podocytes. SLM-2 expression was found to be restricted in the kidney to podocytes. In proteinuric diseases, SLM-2, a known regulator of neuronal mRNA splice site selection, was found significantly upregulated on mRNA and protein levels. Knockdown of SLM-2 by short interfering RNA in podocytes was performed to evaluate its biologic role. RNA splicing of vascular endothelial growth factor (VEGF), a key regulator of the filtration barrier and expressed as functionally distinct splice isoforms, was evaluated. VEGF(165) expression was found to be reduced by 25% after SLM-2 knockdown. In vivo, the glomerular expression of SLM-2 correlated with the mRNA levels of VEGF(165). This study demonstrates the power of digital differential display to predict cell type-specific gene expression by hypothesis-driven analysis of tissue cDNA libraries. SLM-2-dependent VEGF splicing indicates the importance of mRNA splice site selection for glomerular filtration barrier function.
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Affiliation(s)
- Clemens D Cohen
- Medizinische Poliklinik, Ludwig-Maximilians-University, Pettenkoferstrasse 8A, Munich, 80336, Germany.
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45
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Elliott DJ. The role of potential splicing factors including RBMY, RBMX, hnRNPG-T and STAR proteins in spermatogenesis. ACTA ACUST UNITED AC 2005; 27:328-34. [PMID: 15595951 DOI: 10.1111/j.1365-2605.2004.00496.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Investigations into the RBM gene family are uncovering networks of protein interactions which regulate RNA processing, and which might operate downstream of signal transduction pathways. Similar pathways likely operate in germ cells and somatic cells, with RBMY, hnRNPGT and T-STAR proteins providing germ cell-specific components. These pathways may be important for normal germ cell development, and might be compromised in men with Y chromosome deletions affecting RBMY gene expression. The STAR proteins have multiple functions in pre-mRNA splicing, signalling and cell cycle control. These processes might have to be very finely regulated during germ cell development, which involves both two sequential meiotic divisions (meiosis I and II) as well as mitotic (spermatogonial) cell divisions, and which is controlled by paracrine signalling within the testis from Sertoli cells.
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Affiliation(s)
- David J Elliott
- Institute of Human Genetics, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 3BZ, UK.
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Modem S, Badri KR, Holland TC, Reddy TR. Sam68 is absolutely required for Rev function and HIV-1 production. Nucleic Acids Res 2005; 33:873-9. [PMID: 15701759 PMCID: PMC549398 DOI: 10.1093/nar/gki231] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Revised: 05/27/2004] [Accepted: 01/19/2005] [Indexed: 11/12/2022] Open
Abstract
Sam68 functionally complements for, as well as synergizes with, HIV-1 Rev in Rev response element (RRE)-mediated gene expression and virus production. Furthermore, C-terminal deletion/point mutants of Sam68 (Sam68DeltaC/Sam68-P21) exert a transdominant negative phenotype for Rev function and HIV-1 production. However, the relevance of Sam68 in Rev/RRE function is not well defined. To gain more insight into the mechanism of Sam68 in Rev function, we used an RNAi (RNA interference) strategy to create stable Sam68 knockdown HeLa (SSKH) cells. In SSKH cells, Rev failed to activate both RRE-mediated reporter gene [chloramphenicol acetyltransferase (CAT) and/or gag] expressions. Importantly, reduction of Sam68 expression led to a dramatic inhibition of HIV-1 production. Inhibition of the reporter gene expression and HIV production correlated with the failure to export RRE-containing CAT mRNA and unspliced viral mRNAs to the cytoplasm, confirming that SSKH cells are defective for Rev-mediated RNA export. Taken together, these results suggest that Sam68 is involved in Rev-mediated RNA export and is absolutely required for HIV production.
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Affiliation(s)
- Suhasini Modem
- Department of Immunology and Microbiology, Wayne State University-School of MedicineDetroit, MI 48201, USA
| | - Kameswara R. Badri
- Department of Immunology and Microbiology, Wayne State University-School of MedicineDetroit, MI 48201, USA
| | - Thomas C. Holland
- Department of Immunology and Microbiology, Wayne State University-School of MedicineDetroit, MI 48201, USA
| | - Thipparthi R. Reddy
- Department of Immunology and Microbiology, Wayne State University-School of MedicineDetroit, MI 48201, USA
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Andreadis A. Tau gene alternative splicing: expression patterns, regulation and modulation of function in normal brain and neurodegenerative diseases. Biochim Biophys Acta Mol Basis Dis 2005; 1739:91-103. [PMID: 15615629 DOI: 10.1016/j.bbadis.2004.08.010] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Accepted: 08/27/2004] [Indexed: 12/12/2022]
Abstract
Organization of cytoskeletal elements is critical for cellular migration and maintenance of morphology. Tau protein, which binds to and organizes microtubules, is instrumental in forming and maintaining the neuronal axon. Disturbances in tau expression result in disruption of the neuronal cytoskeleton and formation of pathological tau structures (neurofibrillary tangles, NFTs) found in brains of dementia sufferers. Null tau mice, although viable, exhibit developmental and cognitive defects and transgenic mice which overexpress tau develop severe neuropathies. The neuron-specific tau transcript produces multiple isoforms by intricately regulated alternative splicing. These isoforms modulate tau function in normal brain. Moreover, aberrations in tau splicing regulation directly cause several neurodegenerative diseases. Thus, tau splicing regulation is vital to neuronal health and correct brain function. This review briefly presents our cumulative knowledge of tau splicing-cis elements and trans factors which influence it at the RNA level, its effect on the structure and roles of the tau protein and its repercussions on neuronal morphology and neurodegeneration.
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Affiliation(s)
- Athena Andreadis
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 06155, USA.
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Stoss O, Novoyatleva T, Gencheva M, Olbrich M, Benderska N, Stamm S. p59(fyn)-mediated phosphorylation regulates the activity of the tissue-specific splicing factor rSLM-1. Mol Cell Neurosci 2005; 27:8-21. [PMID: 15345239 DOI: 10.1016/j.mcn.2004.04.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 04/22/2004] [Accepted: 04/29/2004] [Indexed: 02/08/2023] Open
Abstract
The Sam68-like mammalian protein SLM-1 is a member of the STAR protein family and is related to SAM68 and SLM-2. Here, we demonstrate that rSLM-1 interacts with itself, scaffold-attachment factor B, YT521-B, SAM68, rSLM-2, SRp30c, and hnRNP G. rSLM-1 regulates splice site selection in vivo via a purine-rich enhancer. In contrast to the widely expressed SAM68 and rSLM-2 proteins, rSLM-1 is found primarily in brain and, to a much smaller degree, in testis. In the brain, rSLM-1 and rSLM-2 are predominantly expressed in different neurons. In the hippocampal formation, rSLM-1 is present only in the dentate gyrus, whereas rSLM-2 is found in the pyramidal cells of the CA1, CA3, and CA4 regions. rSLM-1, but not rSLM-2, is phosphorylated by p59(fyn). p59(fyn)-mediated phosphorylation abolishes the ability of rSLM-1 to regulate splice site selection, but has no effect on rSLM-2 activity. This suggests that rSLM-1-positive cells could respond with a change of their splicing pattern to p59(fyn) activation, whereas rSLM-2-positive cells would not be affected. Together, our data indicate that rSLM-1 is a tissue-specific splicing factor whose activity is regulated by tyrosine phosphorylation signals emanating from p59(fyn).
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Affiliation(s)
- Oliver Stoss
- Klinikum Kassel, Pathology, Mönchebergstr. 41-43, D-34125 Kassel, Germany
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Haegebarth A, Heap D, Bie W, Derry JJ, Richard S, Tyner AL. The nuclear tyrosine kinase BRK/Sik phosphorylates and inhibits the RNA-binding activities of the Sam68-like mammalian proteins SLM-1 and SLM-2. J Biol Chem 2004; 279:54398-404. [PMID: 15471878 DOI: 10.1074/jbc.m409579200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Expression of the intracellular tyrosine kinase BRK/Sik is epithelial-specific and regulated during differentiation. Only a few substrates have been identified for BRK/Sik, including the KH domain containing RNA-binding protein Sam68 and the novel adaptor protein BKS. Although the physiological role of Sam68 is unknown, it has been shown to regulate mRNA transport, pre-mRNA splicing, and polyadenylation. Here we demonstrate that the Sam68-like mammalian proteins SLM-1 and SLM-2 but not the related KH domain containing heterogeneous nuclear ribonucleoprotein K are novel substrates of BRK/Sik. The expression of active BRK/Sik results in increased SLM-1 and SLM-2 phosphorylation and increased retention of BRK/Sik within the nucleus. The phosphorylation of SLM-1 and SLM-2 has functional relevance and leads to inhibition of their RNA-binding abilities. We show that SLM-1, SLM-2, and BRK/Sik have restricted patterns of expression unlike the ubiquitously expressed Sam68. Moreover, BRK/Sik, SLM-1, and Sam68 transcripts were coexpressed in the mouse gastrointestinal tract and skin, suggesting that SLM-1 and Sam68 could be physiologically relevant BRK/Sik targets in vivo. The ability of BRK/Sik to negatively regulate the RNA-binding activities of the KH domain RNA binding proteins SLM-1 and Sam68 may have an impact on the posttranscriptional regulation of epithelial cell gene expression.
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Affiliation(s)
- Andrea Haegebarth
- Departments of Biochemistry and Molecular Genetics, University of Illinois, Chicago, Illinois 60607, USA
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Rafalska I, Zhang Z, Benderska N, Wolff H, Hartmann AM, Brack-Werner R, Stamm S. The intranuclear localization and function of YT521-B is regulated by tyrosine phosphorylation. Hum Mol Genet 2004; 13:1535-49. [PMID: 15175272 DOI: 10.1093/hmg/ddh167] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
YT521-B is a ubiquitously expressed nuclear protein that changes alternative splice site usage in a concentration dependent manner. YT521-B is located in a dynamic nuclear compartment, the YT body. We show that YT521-B is tyrosine phosphorylated by c-Abl in the nucleus. The protein shuttles between nucleus and cytosol, where it can be phosphorylated by c-Src or p59(fyn). Tyrosine phosphorylation causes dispersion of YT521-B from YT bodies to the nucleoplasm. Whereas YT bodies are soluble in non-denaturing buffers, the phosphorylated, dispersed form is non-soluble. Non-phosphorylated YT521-B changes alternative splice site selection of the IL-4 receptor, CD44 and SRp20, but phosphorylation of c-Abl minimizes this concentration dependent effect. We propose that tyrosine phosphorylation causes sequestration of YT521-B in an insoluble nuclear form, which abolishes the ability of YT521-B to change alternative splice sites.
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Affiliation(s)
- Ilona Rafalska
- University of Erlangen, Institute for Biochemistry, Germany
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