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Carrion SA, Michal JJ, Jiang Z. Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases. Genes (Basel) 2023; 14:2051. [PMID: 38002994 PMCID: PMC10671453 DOI: 10.3390/genes14112051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Manipulation using alternative exon splicing (AES), alternative transcription start (ATS), and alternative polyadenylation (APA) sites are key to transcript diversity underlying health and disease. All three are pervasive in organisms, present in at least 50% of human protein-coding genes. In fact, ATS and APA site use has the highest impact on protein identity, with their ability to alter which first and last exons are utilized as well as impacting stability and translation efficiency. These RNA variants have been shown to be highly specific, both in tissue type and stage, with demonstrated importance to cell proliferation, differentiation and the transition from fetal to adult cells. While alternative exon splicing has a limited effect on protein identity, its ubiquity highlights the importance of these minor alterations, which can alter other features such as localization. The three processes are also highly interwoven, with overlapping, complementary, and competing factors, RNA polymerase II and its CTD (C-terminal domain) chief among them. Their role in development means dysregulation leads to a wide variety of disorders and cancers, with some forms of disease disproportionately affected by specific mechanisms (AES, ATS, or APA). Challenges associated with the genome-wide profiling of RNA variants and their potential solutions are also discussed in this review.
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Affiliation(s)
| | | | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 99164-7620, USA; (S.A.C.); (J.J.M.)
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Werner M, Dyas A, Parfentev I, Schmidt GE, Mieczkowska IK, Müller-Kirschbaum LC, Müller C, Kalkhof S, Reinhardt O, Urlaub H, Alves F, Gallwas J, Prokakis E, Wegwitz F. ROBO3s: a novel ROBO3 short isoform promoting breast cancer aggressiveness. Cell Death Dis 2022; 13:762. [PMID: 36057630 PMCID: PMC9440919 DOI: 10.1038/s41419-022-05197-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 01/21/2023]
Abstract
Basal-like breast cancer (BLBC) is a highly aggressive breast cancer subtype frequently associated with poor prognosis. Due to the scarcity of targeted treatment options, conventional cytotoxic chemotherapies frequently remain the standard of care. Unfortunately, their efficacy is limited as BLBC malignancies rapidly develop resistant phenotypes. Using transcriptomic and proteomic approaches in human and murine BLBC cells, we aimed to elucidate the molecular mechanisms underlying the acquisition of aggressive and chemotherapy-resistant phenotypes in these mammary tumors. Specifically, we identified and characterized a novel short isoform of Roundabout Guidance Receptor 3 (ROBO3s), upregulated in BLBC in response to chemotherapy and encoding for a protein variant lacking the transmembrane domain. We established an important role for the ROBO3s isoform, mediating cancer stem cell properties by stimulating the Hippo-YAP signaling pathway, and thus driving resistance of BLBC cells to cytotoxic drugs. By uncovering the conservation of ROBO3s expression across multiple cancer types, as well as its association with reduced BLBC-patient survival, we emphasize its potential as a prognostic marker and identify a novel attractive target for anti-cancer drug development.
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Affiliation(s)
- Marcel Werner
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany ,grid.4567.00000 0004 0483 2525Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Anna Dyas
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany ,grid.4372.20000 0001 2105 1091International Max-Planck Research School for Molecular Biology, Göttingen, Germany ,Early Cancer Institute, University of Cambridge, Department of Oncology, Hutchison Research Centre, Box 197 Cambridge Biomedical Campus, Cambridge, Germany
| | - Iwan Parfentev
- grid.4372.20000 0001 2105 1091Bioanalytical Mass Spectrometry group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Geske E. Schmidt
- grid.411984.10000 0001 0482 5331Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Göttingen, Göttingen, Germany
| | - Iga K. Mieczkowska
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Lukas C. Müller-Kirschbaum
- grid.411984.10000 0001 0482 5331Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Claudia Müller
- grid.418008.50000 0004 0494 3022Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Stefan Kalkhof
- grid.418008.50000 0004 0494 3022Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Oliver Reinhardt
- grid.4372.20000 0001 2105 1091Translational Molecular Imaging, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- grid.4372.20000 0001 2105 1091Bioanalytical Mass Spectrometry group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany ,grid.411984.10000 0001 0482 5331Bioanalytics, Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Frauke Alves
- grid.4372.20000 0001 2105 1091Translational Molecular Imaging, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany ,grid.411984.10000 0001 0482 5331Department of Hematology and Medical Oncology, University Medicine Goettingen, Göttingen, Germany
| | - Julia Gallwas
- grid.411984.10000 0001 0482 5331Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Evangelos Prokakis
- grid.411984.10000 0001 0482 5331Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Florian Wegwitz
- grid.411984.10000 0001 0482 5331Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
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Revealing the alternative promoter usage of SAF/MAZ gene by bichromatic fluorescent reporter construct. Biosci Rep 2019; 39:BSR20171668. [PMID: 30610159 PMCID: PMC6340948 DOI: 10.1042/bsr20171668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 11/17/2022] Open
Abstract
The large-scale identification of putative alternative promoters study shows more than 52% of human genes are regulated by alternative promoters. The human myc-associated zinc finger protein (SAF/MAZ) gene have SAF-1 and SAF-3 variants transcripted from two transcription start sites (TSSs). By using SAF/MAZ promoter as a model, we set up an approach to probe how the alternative promoters are regulated in real time. We have constructed the bichromatic fluorescent reporter driven by SAF/MAZ 5'-proximal promoter plasmids from which transactivation status of SAF-1 and SAF-3 alternative promoter could be monitored by EGFP and DsRed expression respectively. The results showed that the SAF-3 expression is regulated by alternative promoters. When the bichromatic fluorescent reporter was driven by -1692/+277 or -1401/+277 SAF/MAZ promoter the dominant expression of SAF-3 would be observed in comparison with SAF-1 expression. We also identified that Elk-1 is an inhibitory transcription factor for SAF-3 expression. The temporal diversity of SAF-1 and SAF-3 expressions can be observed via bichromatic fluorescent reporters. These imply that the bichromatic fluorescent reporter driven by alternative promoter construct might be a useful tool for decoding the temporal regulatory repertoire of alternative promoter in human genes.
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