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Jia Z, Wang J, Meng X, Yang X, Tian Y, Wang B, Chen M, Yang J, Das D, Cao Y. Evolution and stress response potential of the plant splicing factor U1C. Sci Rep 2024; 14:17212. [PMID: 39060315 PMCID: PMC11282270 DOI: 10.1038/s41598-024-68190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/22/2024] [Indexed: 07/28/2024] Open
Abstract
Alternative splicing is a crucial process in multicellular eukaryote, facilitated by the assembly of spliceosomal complexes comprising numerous small ribonucleoproteins. At an early stage, U1C is thought to be required for 5' splice site recognition and base pairing. However, a systematic analysis of the U1C gene family in response to developmental cues and stress conditions has not yet been conducted in plants. This study identified 114 U1C genes in 72 plant species using basic bioinformatics analyses. Phylogenetic analysis was used to compare gene and protein structures, promoter motifs, and tissue- and stress-specific expression levels, revealing their functional commonalities or diversity in response to developmental cues, such as embryonic expression, or stress treatments, including drought and heat. Fluorescence quantitative expression analysis showed that U1C gene expression changed under salt, low temperature, drought, and Cd stress in rice seedlings. However, gene expression in shoots and roots was not consistent under different stress conditions, suggesting a complex regulatory mechanism. This research provides foundational insights into the U1C gene family's role in plant development and stress responses, highlighting potential targets for future studies.
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Affiliation(s)
- Zichang Jia
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Junjie Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xiangfeng Meng
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Xue Yang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China
| | - Moxian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jingfang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65201, USA.
| | - Yunying Cao
- School of Life Sciences, Nantong University, 9 Seyuan Road, Nantong, 226019, Jiangsu, China.
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2
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Liang W, Xu F, Li L, Peng C, Sun H, Qiu J, Sun J. Epigenetic control of skeletal muscle atrophy. Cell Mol Biol Lett 2024; 29:99. [PMID: 38978023 PMCID: PMC11229277 DOI: 10.1186/s11658-024-00618-1] [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: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Skeletal muscular atrophy is a complex disease involving a large number of gene expression regulatory networks and various biological processes. Despite extensive research on this topic, its underlying mechanisms remain elusive, and effective therapeutic approaches are yet to be established. Recent studies have shown that epigenetics play an important role in regulating skeletal muscle atrophy, influencing the expression of numerous genes associated with this condition through the addition or removal of certain chemical modifications at the molecular level. This review article comprehensively summarizes the different types of modifications to DNA, histones, RNA, and their known regulators. We also discuss how epigenetic modifications change during the process of skeletal muscle atrophy, the molecular mechanisms by which epigenetic regulatory proteins control skeletal muscle atrophy, and assess their translational potential. The role of epigenetics on muscle stem cells is also highlighted. In addition, we propose that alternative splicing interacts with epigenetic mechanisms to regulate skeletal muscle mass, offering a novel perspective that enhances our understanding of epigenetic inheritance's role and the regulatory network governing skeletal muscle atrophy. Collectively, advancements in the understanding of epigenetic mechanisms provide invaluable insights into the study of skeletal muscle atrophy. Moreover, this knowledge paves the way for identifying new avenues for the development of more effective therapeutic strategies and pharmaceutical interventions.
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Affiliation(s)
- Wenpeng Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China
| | - Feng Xu
- Department of Endocrinology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, China
| | - Li Li
- Nantong Center for Disease Control and Prevention, Medical School of Nantong University, Nantong, 226001, China
| | - Chunlei Peng
- Department of Medical Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, 226000, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China.
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China.
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3
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Pan D, Long L, Li C, Zhou Y, Liu Q, Zhao Z, Zhao H, Lin W, Zheng Z, Peng L, Li E, Xu L. Splicing factor hnRNPA1 regulates alternative splicing of LOXL2 to enhance the production of LOXL2Δ13. J Biol Chem 2024; 300:107414. [PMID: 38810697 PMCID: PMC11259713 DOI: 10.1016/j.jbc.2024.107414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) is a member of the lysyl oxidase family and has the ability to catalyze the cross-linking of extracellular matrix collagen and elastin. High expression of LOXL2 is related to tumor cell proliferation, invasion, and metastasis. LOXL2 contains 14 exons. Previous studies have found that LOXL2 has abnormal alternative splicing and exon skipping in a variety of tissues and cells, resulting in a new alternatively spliced isoform denoted LOXL2Δ13. LOXL2Δ13 lacks LOXL2WT exon 13, but its encoded protein has greater ability to induce tumor cell proliferation, invasion, and metastasis. However, the molecular events that produce LOXL2Δ13 are still unclear. In this study, we found that overexpression of the splicing factor hnRNPA1 in cells can regulate the alternative splicing of LOXL2 and increase the expression of LOXL2Δ13. The exonic splicing silencer exists at the 3' splice site and 5' splice site of LOXL2 exon 13. HnRNPA1 can bind to the exonic splicing silencer and inhibit the inclusion of exon 13. The RRM domain of hnRNPA1 and phosphorylation of hnRNPA1 at S91 and S95 are important for the regulation of LOXL2 alternative splicing. These results show that hnRNPA1 is a splicing factor that enhances the production of LOXL2Δ13.
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Affiliation(s)
- Deyuan Pan
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Lin Long
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Chengyu Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Yingxin Zhou
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Qing Liu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, Urumqi, China
| | - Ziting Zhao
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Hui Zhao
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Wan Lin
- Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Zhenyuan Zheng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Liu Peng
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China
| | - Enmin Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China.
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Basic Medical Science, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong Province, China; Institute of Oncologic Pathology, Shantou University Medical College, Shantou, Guangdong Province, China.
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4
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Riccardi F, Romano G, Licastro D, Pagani F. Age-dependent regulation of ELP1 exon 20 splicing in Familial Dysautonomia by RNA Polymerase II kinetics and chromatin structure. PLoS One 2024; 19:e0298965. [PMID: 38829854 PMCID: PMC11146744 DOI: 10.1371/journal.pone.0298965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/01/2024] [Indexed: 06/05/2024] Open
Abstract
Familial Dysautonomia (FD) is a rare disease caused by ELP1 exon 20 skipping. Here we clarify the role of RNA Polymerase II (RNAPII) and chromatin on this splicing event. A slow RNAPII mutant and chromatin-modifying chemicals that reduce the rate of RNAPII elongation induce exon skipping whereas chemicals that create a more relaxed chromatin exon inclusion. In the brain of a mouse transgenic for the human FD-ELP1 we observed on this gene an age-dependent decrease in the RNAPII density profile that was most pronounced on the alternative exon, a robust increase in the repressive marks H3K27me3 and H3K9me3 and a decrease of H3K27Ac, together with a progressive reduction in ELP1 exon 20 inclusion level. In HEK 293T cells, selective drug-induced demethylation of H3K27 increased RNAPII elongation on ELP1 and SMN2, promoted the inclusion of the corresponding alternative exons, and, by RNA-sequencing analysis, induced changes in several alternative splicing events. These data suggest a co-transcriptional model of splicing regulation in which age-dependent changes in H3K27me3/Ac modify the rate of RNAPII elongation and affect processing of ELP1 alternative exon 20.
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Affiliation(s)
- Federico Riccardi
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Giulia Romano
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Science Park, Padriciano, Trieste, Italy
| | - Franco Pagani
- Human Molecular Genetics, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy
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5
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Zhang YE, Stuelten CH. Alternative splicing in EMT and TGF-β signaling during cancer progression. Semin Cancer Biol 2024; 101:1-11. [PMID: 38614376 PMCID: PMC11180579 DOI: 10.1016/j.semcancer.2024.04.001] [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: 05/26/2023] [Revised: 11/20/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
Epithelial to mesenchymal transition (EMT) is a physiological process during development where epithelial cells transform to acquire mesenchymal characteristics, which allows them to migrate and colonize secondary tissues. Many cellular signaling pathways and master transcriptional factors exert a myriad of controls to fine tune this vital process to meet various developmental and physiological needs. Adding to the complexity of this network are post-transcriptional and post-translational regulations. Among them, alternative splicing has been shown to play important roles to drive EMT-associated phenotypic changes, including actin cytoskeleton remodeling, cell-cell junction changes, cell motility and invasiveness. In advanced cancers, transforming growth factor-β (TGF-β) is a major inducer of EMT and is associated with tumor cell metastasis, cancer stem cell self-renewal, and drug resistance. This review aims to provide an overview of recent discoveries regarding alternative splicing events and the involvement of splicing factors in the EMT and TGF-β signaling. It will emphasize the importance of various splicing factors involved in EMT and explore their regulatory mechanisms.
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Affiliation(s)
- Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Christina H Stuelten
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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6
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Townley BA, Buerer L, Tsao N, Bacolla A, Mansoori F, Rusanov T, Clark N, Goodarzi N, Schmidt N, Srivatsan SN, Sun H, Sample RA, Brickner JR, McDonald D, Tsai MS, Walter MJ, Wozniak DF, Holehouse AS, Pena V, Tainer JA, Fairbrother WG, Mosammaparast N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 2023; 83:2258-2275.e11. [PMID: 37369199 PMCID: PMC10483886 DOI: 10.1016/j.molcel.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.
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Affiliation(s)
- Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ning Tsao
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Fadhel Mansoori
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timur Rusanov
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathanial Clark
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Negar Goodarzi
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - Nicolas Schmidt
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Hua Sun
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Reilly A Sample
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew McDonald
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David F Wozniak
- Department of Psychiatry, Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alex S Holehouse
- Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Vladimir Pena
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI 02912, USA.
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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7
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Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. Beyond transcription: compelling open questions in plant RNA biology. THE PLANT CELL 2023; 35:1626-1653. [PMID: 36477566 PMCID: PMC10226580 DOI: 10.1093/plcell/koac346] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 12/06/2022] [Indexed: 05/30/2023]
Abstract
The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
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Affiliation(s)
- Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Micaela A Godoy Herz
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Alberto R Kornblihtt
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires C1428EHA, Argentina
| | - Reed Sorenson
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Leslie E Sieburth
- School of Biological Sciences, University of UtahSalt Lake City 84112, USA
| | - Kentaro Nakaminami
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa 244-0813, Japan
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea
| | - Federico D Ariel
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Evry, Université Paris-Saclay, Bâtiment 630, Orsay 91405, France
- Institute of Plant Sciences Paris-Saclay IPS2, Université de Paris, Bâtiment 630, Orsay 91405, France
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Hailing Jin
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California 92507, USA
| | - Xiaoqi Feng
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Craig S Pikaard
- Howard Hughes Medical Institute, Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
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8
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Lim WF, Rinaldi C. RNA Transcript Diversity in Neuromuscular Research. J Neuromuscul Dis 2023:JND221601. [PMID: 37182892 DOI: 10.3233/jnd-221601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Three decades since the Human Genome Project began, scientists have now identified more then 25,000 protein coding genes in the human genome. The vast majority of the protein coding genes (> 90%) are multi-exonic, with the coding DNA being interrupted by intronic sequences, which are removed from the pre-mRNA transcripts before being translated into proteins, a process called splicing maturation. Variations in this process, i.e. by exon skipping, intron retention, alternative 5' splice site (5'ss), 3' splice site (3'ss), or polyadenylation usage, lead to remarkable transcriptome and proteome diversity in human tissues. Given its critical biological importance, alternative splicing is tightly regulated in a tissue- and developmental stage-specific manner. The central nervous system and skeletal muscle are amongst the tissues with the highest number of differentially expressed alternative exons, revealing a remarkable degree of transcriptome complexity. It is therefore not surprising that splicing mis-regulation is causally associated with a myriad of neuromuscular diseases, including but not limited to amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Duchenne muscular dystrophy (DMD), and myotonic dystrophy type 1 and 2 (DM1, DM2). A gene's transcript diversity has since become an integral and an important consideration for drug design, development and therapy. In this review, we will discuss transcript diversity in the context of neuromuscular diseases and current approaches to address splicing mis-regulation.
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Affiliation(s)
- Wooi Fang Lim
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Carlo Rinaldi
- Department of Paediatrics and Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
- MDUK Oxford Neuromuscular Centre, University of Oxford, Oxford, UK
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9
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Leung CS, Rosenzweig SJ, Yoon B, Marinelli NA, Hollingsworth EW, Maguire AM, Cowen MH, Schmidt M, Imitola J, Gamsiz Uzun ED, Lizarraga SB. Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of autism spectrum disorder. Hum Mol Genet 2023; 32:1634-1646. [PMID: 36621967 PMCID: PMC10162432 DOI: 10.1093/hmg/ddad002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/10/2023] Open
Abstract
Autism spectrum disorder (ASD) affects 1 in 44 children. Chromatin regulatory proteins are overrepresented among genes that contain high risk variants in ASD. Disruption of the chromatin environment leads to widespread dysregulation of gene expression, which is traditionally thought of as a mechanism of disease pathogenesis associated with ASD. Alternatively, alterations in chromatin dynamics could also lead to dysregulation of alternative splicing, which is understudied as a mechanism of ASD pathogenesis. The anticonvulsant valproic acid (VPA) is a well-known environmental risk factor for ASD that acts as a class I histone deacetylase inhibitor. However, the precise molecular mechanisms underlying defects in human neuronal development associated with exposure to VPA are understudied. To dissect how VPA exposure and subsequent chromatin hyperacetylation influence molecular signatures involved in ASD pathogenesis, we conducted RNA sequencing (RNA-seq) in human cortical neurons that were treated with VPA. We observed that differentially expressed genes (DEGs) were enriched for mRNA splicing, mRNA processing, histone modification and metabolism related gene sets. Furthermore, we observed widespread increases in the number and the type of alternative splicing events. Analysis of differential transcript usage (DTU) showed that exposure to VPA induces extensive alterations in transcript isoform usage across neurodevelopmentally important genes. Finally, we find that DEGs and genes that display DTU overlap with known ASD-risk genes. Altogether, these findings suggest that, in addition to differential gene expression, changes in alternative splicing correlated with alterations in the chromatin environment could act as an additional mechanism of disease in ASD.
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Affiliation(s)
- Calvin S Leung
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Shoshana J Rosenzweig
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Brian Yoon
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Nicholas A Marinelli
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Ethan W Hollingsworth
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Abbie M Maguire
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Mara H Cowen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
| | - Jaime Imitola
- UCONN Health Comprehensive Multiple Sclerosis Center, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
- Division of Multiple Sclerosis and Translational Neuroimmunology, Department of Neurology, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Academic Medical Center, Providence, RI 02903, USA
| | - Sofia B Lizarraga
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Translational Neuroscience, Carney Institute for Brain Science and Brown Institute for Translational Science (BITS), Brown University, Providence, RI 02912, USA
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10
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Marasco LE, Kornblihtt AR. The physiology of alternative splicing. Nat Rev Mol Cell Biol 2023; 24:242-254. [PMID: 36229538 DOI: 10.1038/s41580-022-00545-z] [Citation(s) in RCA: 116] [Impact Index Per Article: 116.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Moleculary Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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11
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Yeo XY, Lim YT, Chae WR, Park C, Park H, Jung S. Alterations of presynaptic proteins in autism spectrum disorder. Front Mol Neurosci 2022; 15:1062878. [DOI: 10.3389/fnmol.2022.1062878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
The expanded use of hypothesis-free gene analysis methods in autism research has significantly increased the number of genetic risk factors associated with the pathogenesis of autism. A further examination of the implicated genes directly revealed the involvement in processes pertinent to neuronal differentiation, development, and function, with a predominant contribution from the regulators of synaptic function. Despite the importance of presynaptic function in synaptic transmission, the regulation of neuronal network activity, and the final behavioral output, there is a relative lack of understanding of the presynaptic contribution to the pathology of autism. Here, we will review the close association among autism-related mutations, autism spectrum disorders (ASD) phenotypes, and the altered presynaptic protein functions through a systematic examination of the presynaptic risk genes relating to the critical stages of synaptogenesis and neurotransmission.
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12
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PARP1′s Involvement in RNA Polymerase II Elongation: Pausing and Releasing Regulation through the Integrator and Super Elongation Complex. Cells 2022; 11:cells11203202. [PMID: 36291070 PMCID: PMC9600911 DOI: 10.3390/cells11203202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
RNA polymerase elongation along the gene body is tightly regulated to ensure proper transcription and alternative splicing events. Understanding the mechanism and factors critical in regulating the rate of RNA polymerase II elongation and processivity is clearly important. Recently we showed that PARP1, a well-known DNA repair protein, when bound to chromatin, regulates RNA polymerase II elongation. However, the mechanism by which it does so is not known. In the current study, we aimed to tease out how PARP1 regulates RNAPII elongation. We show, both in vivo and in vitro, that PARP1 binds directly to the Integrator subunit 3 (IntS3), a member of the elongation Integrator complex. The association between the two proteins is mediated via the C-terminal domain of PARP1 to the C-terminal domain of IntS3. Interestingly, the occupancy of IntS3 along two PARP1 target genes mimicked that of PARP1, suggesting a role in its recruitment/assembly of elongation factors. Indeed, the knockdown of PARP1 resulted in differential chromatin association and gene occupancy of IntS3 and other key elongation factors. Most of these PARP1-mediated effects were due to the physical presence of PARP1 rather than its PARylation activity. These studies argue that PARP1 controls the progressive RNAPII elongation complexes. In summary, we present a platform to begin to decipher PARP1′s role in recruiting/scaffolding elongation factors along the gene body regions during RNA polymerase II elongation and gene regulation.
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13
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Marasco LE, Dujardin G, Sousa-Luís R, Liu YH, Stigliano JN, Nomakuchi T, Proudfoot NJ, Krainer AR, Kornblihtt AR. Counteracting chromatin effects of a splicing-correcting antisense oligonucleotide improves its therapeutic efficacy in spinal muscular atrophy. Cell 2022; 185:2057-2070.e15. [PMID: 35688133 DOI: 10.1016/j.cell.2022.04.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/17/2022] [Accepted: 04/26/2022] [Indexed: 11/19/2022]
Abstract
Spinal muscular atrophy (SMA) is a motor-neuron disease caused by mutations of the SMN1 gene. The human paralog SMN2, whose exon 7 (E7) is predominantly skipped, cannot compensate for the lack of SMN1. Nusinersen is an antisense oligonucleotide (ASO) that upregulates E7 inclusion and SMN protein levels by displacing the splicing repressors hnRNPA1/A2 from their target site in intron 7. We show that by promoting transcriptional elongation, the histone deacetylase inhibitor VPA cooperates with a nusinersen-like ASO to promote E7 inclusion. Surprisingly, the ASO promotes the deployment of the silencing histone mark H3K9me2 on the SMN2 gene, creating a roadblock to RNA polymerase II elongation that inhibits E7 inclusion. By removing the roadblock, VPA counteracts the chromatin effects of the ASO, resulting in higher E7 inclusion without large pleiotropic effects. Combined administration of the nusinersen-like ASO and VPA in SMA mice strongly synergizes SMN expression, growth, survival, and neuromuscular function.
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Affiliation(s)
- Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon, 1649-028 Lisboa, Portugal
| | - Ying Hsiu Liu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jose N Stigliano
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alberto R Kornblihtt
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), 1428 Buenos Aires, Argentina.
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14
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Öther-Gee Pohl S, Myant KB. Alternative RNA splicing in tumour heterogeneity, plasticity and therapy. Dis Model Mech 2022; 15:dmm049233. [PMID: 35014671 PMCID: PMC8764416 DOI: 10.1242/dmm.049233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected - these include processes synonymous with the hallmarks of cancer - evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Edinburgh Centre, Institute of Genetics of Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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15
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Baker M, Petasny M, Taqatqa N, Bentata M, Kay G, Engal E, Nevo Y, Siam A, Dahan S, Salton M. KDM3A regulates alternative splicing of cell-cycle genes following DNA damage. RNA (NEW YORK, N.Y.) 2021; 27:1353-1362. [PMID: 34321328 PMCID: PMC8522690 DOI: 10.1261/rna.078796.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Changes in the cellular environment result in chromatin structure alteration, which in turn regulates gene expression. To learn about the effect of the cellular environment on the transcriptome, we studied the H3K9 demethylase KDM3A. Using RNA-seq, we found that KDM3A regulates the transcription and alternative splicing of genes associated with cell cycle and DNA damage. We showed that KDM3A undergoes phosphorylation by PKA at serine 265 following DNA damage, and that the phosphorylation is important for proper cell-cycle regulation. We demonstrated that SAT1 alternative splicing, regulated by KDM3A, plays a role in cell-cycle regulation. Furthermore we found that KDM3A's demethylase activity is not needed for SAT1 alternative splicing regulation. In addition, we identified KDM3A's protein partner ARID1A, the SWI/SNF subunit, and SRSF3 as regulators of SAT1 alternative splicing and showed that KDM3A is essential for SRSF3 binding to SAT1 pre-mRNA. These results suggest that KDM3A serves as a sensor of the environment and an adaptor for splicing factor binding. Our work reveals chromatin sensing of the environment in the regulation of alternative splicing.
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Affiliation(s)
- Mai Baker
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mayra Petasny
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, 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, 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, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eden Engal
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, 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, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ahmad Siam
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, 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, 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, Hebrew University of Jerusalem, Jerusalem 91120, Israel
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16
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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17
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Liao SE, Regev O. Splicing at the phase-separated nuclear speckle interface: a model. Nucleic Acids Res 2021; 49:636-645. [PMID: 33337476 PMCID: PMC7826271 DOI: 10.1093/nar/gkaa1209] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023] Open
Abstract
Phase-separated membraneless bodies play important roles in nucleic acid biology. While current models for the roles of phase separation largely focus on the compartmentalization of constituent proteins, we reason that other properties of phase separation may play functional roles. Specifically, we propose that interfaces of phase-separated membraneless bodies could have functional roles in spatially organizing biochemical reactions. Here we propose such a model for the nuclear speckle, a membraneless body implicated in RNA splicing. In our model, sequence-dependent RNA positioning along the nuclear speckle interface coordinates RNA splicing. Our model asserts that exons are preferentially sequestered into nuclear speckles through binding by SR proteins, while introns are excluded through binding by nucleoplasmic hnRNP proteins. As a result, splice sites at exon-intron boundaries are preferentially positioned at nuclear speckle interfaces. This positioning exposes splice sites to interface-localized spliceosomes, enabling the subsequent splicing reaction. Our model provides a simple mechanism that seamlessly explains much of the complex logic of splicing. This logic includes experimental results such as the antagonistic duality between splicing factors, the position dependence of splicing sequence motifs, and the collective contribution of many motifs to splicing decisions. Similar functional roles for phase-separated interfaces may exist for other membraneless bodies.
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Affiliation(s)
- Susan E Liao
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Oded Regev
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
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18
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Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Mol Cell 2021; 81:998-1012.e7. [PMID: 33440169 DOI: 10.1016/j.molcel.2020.12.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long-read sequencing of individual nascent RNAs and precision run-on sequencing (PRO-seq) during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. Interestingly, several hundred introns displayed abundant splicing intermediates, suggesting that splicing delays can take place between the two catalytic steps. Overall, splicing efficiencies were correlated among introns within the same transcript, and intron retention was associated with inefficient 3' end cleavage. Remarkably, a thalassemia patient-derived mutation introducing a cryptic 3'SS improved both splicing and 3' end cleavage of individual β-globin transcripts, demonstrating functional coupling between the two co-transcriptional processes as a determinant of productive gene output.
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Affiliation(s)
- Kirsten A Reimer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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19
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Abstract
This review explores how different classes of drugs, including those with therapeutic and abuse potential, alter brain functions and behavior via the epigenome. Epigenetics, in its simplest interpretation, is the study of the regulation of a genes' transcriptional potential. The epigenome is established during development but is malleable throughout life by a wide variety of drugs, with both clinical utility and abuse potential. An epigenetic effect can be central to the drug's therapeutic or abuse potential, or it can be independent from the main effect but nevertheless produce beneficial or adverse side effects. Here, I discuss the various epigenetic effects of main pharmacological drug classes, including antidepressants, antiepileptics, and drugs of abuse.
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Affiliation(s)
- Miklos Toth
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA;
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20
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Linking transcription, RNA polymerase II elongation and alternative splicing. Biochem J 2020; 477:3091-3104. [DOI: 10.1042/bcj20200475] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022]
Abstract
Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.
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21
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López Soto EJ, Lipscombe D. Cell-specific exon methylation and CTCF binding in neurons regulate calcium ion channel splicing and function. eLife 2020; 9:54879. [PMID: 32213287 PMCID: PMC7124252 DOI: 10.7554/elife.54879] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/26/2020] [Indexed: 12/14/2022] Open
Abstract
Cell-specific alternative splicing modulates myriad cell functions and is disrupted in disease. The mechanisms governing alternative splicing are known for relatively few genes and typically focus on RNA splicing factors. In sensory neurons, cell-specific alternative splicing of the presynaptic CaV channel Cacna1b gene modulates opioid sensitivity. How this splicing is regulated is unknown. We find that cell and exon-specific DNA hypomethylation permits CTCF binding, the master regulator of mammalian chromatin structure, which, in turn, controls splicing in a DRG-derived cell line. In vivo, hypomethylation of an alternative exon specifically in nociceptors, likely permits CTCF binding and expression of CaV2.2 channel isoforms with increased opioid sensitivity in mice. Following nerve injury, exon methylation is increased, and splicing is disrupted. Our studies define the molecular mechanisms of cell-specific alternative splicing of a functionally validated exon in normal and disease states – and reveal a potential target for the treatment of chronic pain.
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Affiliation(s)
- Eduardo Javier López Soto
- The Robert J and Nancy D Carney Institute for Brain Science & Department of Neuroscience, Brown University, Providence, United States
| | - Diane Lipscombe
- The Robert J and Nancy D Carney Institute for Brain Science & Department of Neuroscience, Brown University, Providence, United States
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22
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Lan Y, Lou J, Hu J, Yu Z, Lyu W, Zhang B. Downregulation of SNRPG induces cell cycle arrest and sensitizes human glioblastoma cells to temozolomide by targeting Myc through a p53-dependent signaling pathway. Cancer Biol Med 2020; 17:112-131. [PMID: 32296580 PMCID: PMC7142844 DOI: 10.20892/j.issn.2095-3941.2019.0164] [Citation(s) in RCA: 20] [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: 05/17/2019] [Accepted: 08/29/2019] [Indexed: 12/17/2022] Open
Abstract
Objective: Temozolomide (TMZ) is commonly used for glioblastoma multiforme (GBM) chemotherapy. However, drug resistance limits its therapeutic effect in GBM treatment. RNA-binding proteins (RBPs) have vital roles in posttranscriptional events. While disturbance of RBP-RNA network activity is potentially associated with cancer development, the precise mechanisms are not fully known. The SNRPG gene, encoding small nuclear ribonucleoprotein polypeptide G, was recently found to be related to cancer incidence, but its exact function has yet to be elucidated. Methods:SNRPG knockdown was achieved via short hairpin RNAs. Gene expression profiling and Western blot analyses were used to identify potential glioma cell growth signaling pathways affected by SNRPG. Xenograft tumors were examined to determine the carcinogenic effects of SNRPG on glioma tissues. Results: The SNRPG-mediated inhibitory effect on glioma cells might be due to the targeted prevention of Myc and p53. In addition, the effects of SNRPG loss on p53 levels and cell cycle progression were found to be Myc-dependent. Furthermore, SNRPG was increased in TMZ-resistant GBM cells, and downregulation of SNRPG potentially sensitized resistant cells to TMZ, suggesting that SNRPG deficiency decreases the chemoresistance of GBM cells to TMZ via the p53 signaling pathway. Our data confirmed that SNRPG suppression sensitizes GBM cells to TMZ by targeting Myc via the p53 signaling cascade. Conclusions: These results indicated that SNRPG is a probable molecular target of GBM and suggested that suppressing SNRPG in resistant GBM cells might be a substantially beneficial method for overcoming essential drug resistance.
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Affiliation(s)
- Yulong Lan
- Department of Neurosurgery, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Jiacheng Lou
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
| | - Jiliang Hu
- Department of Neurosurgery, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Zhikuan Yu
- Department of Neurosurgery, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Wen Lyu
- Department of Neurosurgery, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Bo Zhang
- Department of Neurosurgery, Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
- Department of Neurosurgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China
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23
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Fiszbein A, Krick KS, Begg BE, Burge CB. Exon-Mediated Activation of Transcription Starts. Cell 2019; 179:1551-1565.e17. [PMID: 31787377 DOI: 10.1016/j.cell.2019.11.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/20/2019] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
The processing of RNA transcripts from mammalian genes occurs in proximity to their transcription. Here, we describe a phenomenon affecting thousands of genes that we call exon-mediated activation of transcription starts (EMATS), in which the splicing of internal exons impacts promoter choice and the expression level of the gene. We observed that evolutionary gain of internal exons is associated with gain of new transcription start sites (TSSs) nearby and increased gene expression. Inhibiting exon splicing reduced transcription from nearby promoters, and creation of new spliced exons activated transcription from cryptic promoters. The strongest effects occurred for weak promoters located proximal and upstream of efficiently spliced exons. Together, our findings support a model in which splicing recruits transcription machinery locally to influence TSS choice and identify exon gain, loss, and regulatory change as major contributors to the evolution of alternative promoters and gene expression in mammals.
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Affiliation(s)
- Ana Fiszbein
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Keegan S Krick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Bridget E Begg
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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24
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Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019; 11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
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Affiliation(s)
- Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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25
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Van Acker HH, Van Acker ZP, Versteven M, Ponsaerts P, Pende D, Berneman ZN, Anguille S, Van Tendeloo VF, Smits EL. CD56 Homodimerization and Participation in Anti-Tumor Immune Effector Cell Functioning: A Role for Interleukin-15. Cancers (Basel) 2019; 11:E1029. [PMID: 31336622 PMCID: PMC6678613 DOI: 10.3390/cancers11071029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
A particularly interesting marker to identify anti-tumor immune cells is the neural cell adhesion molecule (NCAM), also known as cluster of differentiation (CD)56. Namely, hematopoietic expression of CD56 seems to be confined to powerful effector immune cells. Here, we sought to elucidate its role on various killer immune cells. First, we identified the high motility NCAM-120 molecule to be the main isoform expressed by immune cells. Next, through neutralization of surface CD56, we were able to (1) demonstrate the direct involvement of CD56 in tumor cell lysis exerted by CD56-expressing killer cells, such as natural killer cells, gamma delta (γδ) T cells, and interleukin (IL)-15-cultured dendritic cells (DCs), and (2) reveal a putative crosstalk mechanism between IL-15 DCs and CD8 T cells, suggesting CD56 as a co-stimulatory molecule in their cell-to-cell contact. Moreover, by means of a proximity ligation assay, we visualized the CD56 homophilic interaction among cancer cells and between immune cells and cancer cells. Finally, by blocking the mitogen-activated protein kinase (MAPK) pathway and the phosphoinositide 3-kinase (PI3K)-Akt pathway, we showed that IL-15 stimulation directly led to CD56 upregulation. In conclusion, these results underscore the previously neglected importance of CD56 expression on immune cells, benefiting current and future immune therapeutic options.
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Affiliation(s)
- Heleen H Van Acker
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Zoë P Van Acker
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling, University of Antwerp, 2610 Antwerp, Belgium
- Laboratory of Membrane Trafficking, VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium
| | - Maarten Versteven
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology, Experimental Cell Transplantation Group (ECTG), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Daniela Pende
- Immunology Laboratory, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
| | - Zwi N Berneman
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling, University of Antwerp, 2610 Antwerp, Belgium
- Division of Hematology, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Sébastien Anguille
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Division of Hematology, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Viggo F Van Tendeloo
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium.
| | - Evelien L Smits
- Laboratory of Experimental Hematology, Tumor Immunology Group (TIGR), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Center for Oncological Research (CORE), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
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26
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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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27
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Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation. Mol Cell 2019; 73:1066-1074.e3. [DOI: 10.1016/j.molcel.2018.12.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/19/2018] [Accepted: 12/07/2018] [Indexed: 01/25/2023]
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28
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Matveeva EA, Al-Tinawi QMH, Rouchka EC, Fondufe-Mittendorf YN. Coupling of PARP1-mediated chromatin structural changes to transcriptional RNA polymerase II elongation and cotranscriptional splicing. Epigenetics Chromatin 2019; 12:15. [PMID: 30777121 PMCID: PMC6378753 DOI: 10.1186/s13072-019-0261-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/12/2019] [Indexed: 01/02/2023] Open
Abstract
Background Recently, we showed that PARP1 is involved in cotranscriptional splicing, possibly by bridging chromatin to RNA and recruiting splicing factors. It also can influence alternative splicing decisions through the regulation of RNAPII elongation. In this study, we investigated the effect of PARP1-mediated chromatin changes on RNAPII movement, during transcription and alternative splicing. Results We show that RNAPII pauses at PARP1–chromatin structures within the gene body. Knockdown of PARP1 abolishes this RNAPII pausing, suggesting that PARP1 may regulate RNAPII elongation. Additionally, PARP1 alters nucleosome deposition and histone post-translational modifications at specific exon–intron boundaries, thereby affecting RNAPII movement. Lastly, genome-wide analyses confirmed that PARP1 influences changes in RNAPII elongation by either reducing or increasing the rate of RNAPII elongation depending on the chromatin context. Conclusions These studies suggest a context-specific effect of PARP1–chromatin binding on RNA polymerase movement and provide a platform to delineate PARP1’s role in RNA biogenesis and processing. Electronic supplementary material The online version of this article (10.1186/s13072-019-0261-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Qamar M H Al-Tinawi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.,Alfaisal University, Al Maather' Riyadh, 12714, Saudi Arabia
| | - Eric C Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, 522 East Gray Street, Louisville, KY, 40292, USA.,Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY, 40292, USA
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29
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Sexual dimorphism in brain transcriptomes of Amami spiny rats (Tokudaia osimensis): a rodent species where males lack the Y chromosome. BMC Genomics 2019; 20:87. [PMID: 30683046 PMCID: PMC6347839 DOI: 10.1186/s12864-019-5426-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Background Brain sexual differentiation is sculpted by precise coordination of steroid hormones during development. Programming of several brain regions in males depends upon aromatase conversion of testosterone to estrogen. However, it is not clear the direct contribution that Y chromosome associated genes, especially sex-determining region Y (Sry), might exert on brain sexual differentiation in therian mammals. Two species of spiny rats: Amami spiny rat (Tokudaia osimensis) and Tokunoshima spiny rat (T. tokunoshimensis) lack a Y chromosome/Sry, and these individuals possess an XO chromosome system in both sexes. Both Tokudaia species are highly endangered. To assess the neural transcriptome profile in male and female Amami spiny rats, RNA was isolated from brain samples of adult male and female spiny rats that had died accidentally and used for RNAseq analyses. Results RNAseq analyses confirmed that several genes and individual transcripts were differentially expressed between males and females. In males, seminal vesicle secretory protein 5 (Svs5) and cytochrome P450 1B1 (Cyp1b1) genes were significantly elevated compared to females, whereas serine (or cysteine) peptidase inhibitor, clade A, member 3 N (Serpina3n) was upregulated in females. Many individual transcripts elevated in males included those encoding for zinc finger proteins, e.g. zinc finger protein X-linked (Zfx). Conclusions This method successfully identified several genes and transcripts that showed expression differences in the brain of adult male and female Amami spiny rat. The functional significance of these findings, especially differential expression of transcripts encoding zinc finger proteins, in this unusual rodent species remains to be determined. Electronic supplementary material The online version of this article (10.1186/s12864-019-5426-6) contains supplementary material, which is available to authorized users.
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30
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Hinkle ER, Wiedner HJ, Black AJ, Giudice J. RNA processing in skeletal muscle biology and disease. Transcription 2019; 10:1-20. [PMID: 30556762 DOI: 10.1080/21541264.2018.1558677] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.
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Affiliation(s)
- Emma R Hinkle
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Hannah J Wiedner
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Adam J Black
- b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA
| | - Jimena Giudice
- a Curriculum in Genetics and Molecular Biology (GMB) , University of North Carolina , Chapel Hill , USA.,b Department of Cell Biology & Physiology , University of North Carolina , Chapel Hill , USA.,c McAllister Heart Institute , University of North Carolina , Chapel Hill , USA
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31
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Carrocci TJ, Neugebauer KM. Pre-mRNA Splicing in the Nuclear Landscape. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2019; 84:11-20. [PMID: 32493763 PMCID: PMC7384967 DOI: 10.1101/sqb.2019.84.040402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Eukaryotic gene expression requires the cumulative activity of multiple molecular machines to synthesize and process newly transcribed pre-messenger RNA. Introns, the noncoding regions in pre-mRNA, must be removed by the spliceosome, which assembles on the pre-mRNA as it is transcribed by RNA polymerase II (Pol II). The assembly and activity of the spliceosome can be modulated by features including the speed of transcription elongation, chromatin, post-translational modifications of Pol II and histone tails, and other RNA processing events like 5'-end capping. Here, we review recent work that has revealed cooperation and coordination among co-transcriptional processing events and speculate on new avenues of research. We anticipate new mechanistic insights capable of unraveling the relative contribution of coupled processing to gene expression.
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Affiliation(s)
- Tucker J Carrocci
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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32
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Godoy Herz MA, Kornblihtt AR. Alternative Splicing and Transcription Elongation in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:309. [PMID: 30972082 PMCID: PMC6443983 DOI: 10.3389/fpls.2019.00309] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
Abstract
Alternative splicing and transcription elongation by RNA polymerase II (RNAPII) are two processes which are tightly connected. Splicing is a co-transcriptional process, and different experimental approaches show that splicing is coupled to transcription in Drosophila, yeast and mammals. However, little is known about coupling of transcription and alternative splicing in plants. The kinetic coupling explains how changes in RNAPII elongation rate influence alternative splicing choices. Recent work in Arabidopsis shows that expression of a dominant negative transcription elongation factor, TFIIS, enhances exon inclusion. Furthermore, the Arabidopsis transcription elongation complex has been recently described, providing new information about elongation factors that interact with elongating RNAPII. Light regulates alternative splicing in plants through a chloroplast retrograde signaling. We have recently shown that light promotes RNAPII elongation in the affected genes, while in darkness elongation is lower. These changes in transcription are consistent with elongation causing the observed changes in alternative splicing. Altogether, these findings provide evidence that coupling between transcription and alternative splicing is an important layer of gene expression regulation in plants.
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Affiliation(s)
- Micaela A. Godoy Herz
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
| | - Alberto R. Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, Argentina
- *Correspondence: Alberto R. Kornblihtt,
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33
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Vander Borght A, Duysinx M, Broers JLV, Ummelen M, Falkenberg FW, Hahnel C, van der Zeijst BAM. The 180 splice variant of NCAM-containing exon 18-is specifically expressed in small cell lung cancer cells. Transl Lung Cancer Res 2018; 7:376-388. [PMID: 30050775 DOI: 10.21037/tlcr.2018.03.03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background The Neural Cell Adhesion Molecule (NCAM) is a glycoprotein expressed as 120, 140 and/or 180 kDa isoforms, all derived through alternative splicing of a single gene. NCAM 120 contains no intracellular domain, whereas NCAM 140 and 180 have different intracellular domains determined by alternative splicing of exon 18. NCAM has been described as a biomarker to discriminate small cell lung cancer (SCLC) from non-SCLC (NSCLC). However, peripheral blood mononuclear cells (PBMC) also express NCAM. We studied the expression of NCAM splice variants in cell lines, tumor tissues and control cells. Methods Using reverse transcriptase-PCR we evaluated the expression of NCAM exon 18 splice variants in lung cancers cell lines, control cell lines, PBMC of healthy controls and SCLC tissue. In addition we studied the expression of the NCAM exon 18 encoded protein (E18) in SCLC by immunocytochemistry and flow cytometry using an E18-specific monoclonal antibody obtained by hybridoma fusion of E18-immunized mouse spleen cells. Finally we looked at immune responses to E18 in mice. Results We found expression of RNA encoding the NCAM 180 variant in all SCLC cell lines. NCAM exon 18 was not expressed in 23/28 (82%) of the other tumor and leukemia cell lines tested and PBMC. Next, we also evaluated the expression of NCAM exon 18 in human SCLC tissue. Expression of NCAM exon 18 in 8 of the 10 (80%) SCLC biopsy samples was found. The newly raised E18-specific antibodies stained NCAM at the adherent junctions between adjacent cells in SCLC cell lines. The data demonstrate the intracellular location of E18 in SCLC. Furthermore, a specific cytotoxic T cell (CTL) response and significant antibody titers were found in mice upon immunization with recombinant E18 and its encoding DNA. Conclusions The results of this study can be applied in the diagnosis and immunotherapy of SCLC. A larger study investigating E18 as a marker for SCLC is indicated.
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Affiliation(s)
- Ann Vander Borght
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands.,MUbio Products BV, Maastricht, The Netherlands
| | | | - Jos L V Broers
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Monique Ummelen
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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Romero-Barrios N, Legascue MF, Benhamed M, Ariel F, Crespi M. Splicing regulation by long noncoding RNAs. Nucleic Acids Res 2018; 46:2169-2184. [PMID: 29425321 PMCID: PMC5861421 DOI: 10.1093/nar/gky095] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/05/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Massive high-throughput sequencing techniques allowed the identification of thousands of noncoding RNAs (ncRNAs) and a plethora of different mRNA processing events occurring in higher organisms. Long ncRNAs can act directly as long transcripts or can be processed into active small si/miRNAs. They can modulate mRNA cleavage, translational repression or the epigenetic landscape of their target genes. Recently, certain long ncRNAs have been shown to play a crucial role in the regulation of alternative splicing in response to several stimuli or during disease. In this review, we focus on recent discoveries linking gene regulation by alternative splicing and its modulation by long and small ncRNAs.
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Affiliation(s)
- Natali Romero-Barrios
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Maria Florencia Legascue
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
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35
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He R, Kidder BL. H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells. Nucleic Acids Res 2017; 45:6427-6441. [PMID: 28402433 PMCID: PMC5499819 DOI: 10.1093/nar/gkx251] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 02/04/2023] Open
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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36
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Sánchez-Hernández N, Prieto-Sánchez S, Moreno-Castro C, Muñoz-Cobo JP, El Yousfi Y, Boyero-Corral S, Suñé-Pou M, Hernández-Munain C, Suñé C. Targeting proteins to RNA transcription and processing sites within the nucleus. Int J Biochem Cell Biol 2017; 91:194-202. [DOI: 10.1016/j.biocel.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
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37
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Kornblihtt AR. Epigenetics at the base of alternative splicing changes that promote colorectal cancer. J Clin Invest 2017; 127:3281-3283. [PMID: 28825597 DOI: 10.1172/jci96497] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromatin modification influences gene expression by either repressing or activating genes, depending on the specific histone mark. Chromatin structure can also influence alternative splicing of transcripts; however, the mechanisms by which epigenetic marks influence splicing are poorly understood. A report in the current issue of the JCI highlights the biological importance of the coordinated control of alternative pre-mRNA splicing by chromatin structure and transcriptional elongation. Yuan et al. found that mutation of the histone methyl transferase SEDT2 affects alternative splicing fates of several key regulatory genes, including those involved in Wnt signaling. As a consequence, loss of SEDT2 in the intestine aggravated Wnt/β-catenin signaling effects, thereby leading to colorectal cancer.
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38
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Herzel L, Ottoz DSM, Alpert T, Neugebauer KM. Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. Nat Rev Mol Cell Biol 2017; 18:637-650. [PMID: 28792005 DOI: 10.1038/nrm.2017.63] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Diana S M Ottoz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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39
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Neuronal activity-regulated alternative mRNA splicing. Int J Biochem Cell Biol 2017; 91:184-193. [PMID: 28591617 DOI: 10.1016/j.biocel.2017.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/24/2017] [Accepted: 06/01/2017] [Indexed: 11/20/2022]
Abstract
Activity-regulated gene transcription underlies plasticity-dependent changes in the molecular composition and structure of neurons. Numerous genes whose expression is induced by different neuronal plasticity inducing pathways have been identified, but the alteration of gene expression levels represents only part of the complexity of the activity-regulated transcriptional program. Alternative splicing of precursor mRNA is an additional mechanism that modulates the activity-dependent transcriptional signature. Recently developed splicing sensitive transcriptome wide analyses improve our understanding of the underlying mechanisms and demonstrate to what extend the activity regulated transcriptome is alternatively spliced. So far, only for a small group of differentially spliced mRNAs of synaptic proteins, the functional implications have been studied in detail. These include examples in which differential exon usage can result in the expression of alternative proteins which interfere with or alter the function of preexisting proteins and cause a dominant negative functional block of constitutively expressed variants. Such altered proteins contribute to the structural and functional reorganization of pre- and postsynaptic terminals and to the maintenance and formation of synapses. In addition, activity-induced alternative splicing can affect the untranslated regions (UTRs) and generates mRNAs harboring different cis-regulatory elements. Such differential UTRs can influence mRNA stability, translation, and can change the targeting of mRNAs to subcellular compartments. Here, we summarize different categories of alternative splicing which are thought to contribute to synaptic remodeling, give an overview of activity-regulated alternatively spliced mRNAs of synaptic proteins that impact synaptic functions, and discuss splicing factors and epigenetic modifications as regulatory determinants.
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40
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Abstract
Alternative splicing (AS) greatly expands the coding capacities of genomes by allowing the generation of multiple mature mRNAs from a limited number of genes. Although the massive switch in AS profiles that often accompanies variations in gene expression patterns occurring during cell differentiation has been characterized for a variety of models, their causes and mechanisms remain largely unknown. Here, we integrate foundational and recent studies indicating the AS switches that govern the processes of cell fate determination. We include some distinct AS events in pluripotent cells and somatic reprogramming and discuss new progresses on alternative isoform expression in adipogenesis, myogenic differentiation and stimulation of immune cells. Finally, we cover novel insights on AS mechanisms during neuronal differentiation, paying special attention to the role of chromatin structure.
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Affiliation(s)
- Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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41
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Zhao JX, Li XW, Shi BY, Wang F, Xu ZR, Meng HL, Su YY, Wang JM, Xiao N, He Q, Wang YP, Fan YM. Effect of histone modifications on hMLH1 alternative splicing in gastric cancer. Tumour Biol 2017; 39:1010428317697546. [PMID: 28381181 DOI: 10.1177/1010428317697546] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
hMLH1 is one of the mismatch genes closely related to the occurrence of gastric cancer. Epigenetic regulation may play more important roles than gene mutations in DNA damage repair genes to drive carcinogenesis. In this article, we discuss the role of epigenetic changes, especially histone modifications in the regulation of hMLH1 alternative splicing. Our results showed that hMLH1 delEx10, delEx11, delEx10-11, delEx16 and delEx17 transcripts were ubiquitous in sporadic Chinese gastric cancer patients and gastric cancer cell lines. Lower level of H4K16ac and H3ac was detected in hMLH1 exon 10-11 region in gastric cancer cell lines when compared with human gastric mucosal epithelial cell line GES-1. A significant decrease of hMLH1 delEx11 and delEx10-11 was observed in gastric cancer cell lines after trichostatin A treatment. H3K36me3 and H3K4me2 levels were lower in hMLH1 exon 10-11 and exon 16-17 regions in gastric cancer lines when compared with GES-1. Aberrant transcripts such as hMLH1 delEx11 and delEx10-11 were significantly higher in gastric cancer cell lines after small interfering RNA-mediated knockdown of SETD2 (the specific methyltransferase of H3K36). The hMLH1 delEx10 and delEx10-11 transcripts were increased after interference of SRSF2. Taken together, our study demonstrates that lower level of histone acetylation and specific histone methylation such as H3K36me3 correlate with aberrant transcripts in hMLH1 exon 10-11 region. SRSF2 may be involved in these specific exons skipping as well.
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Affiliation(s)
- Jin-Xuan Zhao
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Xiao-Wei Li
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Bing-Yu Shi
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Fang Wang
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Zheng-Rong Xu
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Hai-Lan Meng
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Yun-Yan Su
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Jing-Mei Wang
- 2 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Nong Xiao
- 3 Lujiang People's Hospital, Anhui, China
| | - Qiong He
- 3 Lujiang People's Hospital, Anhui, China
| | - Ya-Ping Wang
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
| | - Yi-Mei Fan
- 1 Jiangsu Key Laboratory of Molecular Medicine and Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
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42
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A saga of cancer epigenetics: linking epigenetics to alternative splicing. Biochem J 2017; 474:885-896. [PMID: 28270561 DOI: 10.1042/bcj20161047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 12/14/2022]
Abstract
The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by 'cis' RNA-binding sites and 'trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression.
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Hollander D, Naftelberg S, Lev-Maor G, Kornblihtt AR, Ast G. How Are Short Exons Flanked by Long Introns Defined and Committed to Splicing? Trends Genet 2016; 32:596-606. [PMID: 27507607 DOI: 10.1016/j.tig.2016.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/19/2022]
Abstract
The splice sites (SSs) delimiting an intron are brought together in the earliest step of spliceosome assembly yet it remains obscure how SS pairing occurs, especially when introns are thousands of nucleotides long. Splicing occurs in vivo in mammals within minutes regardless of intron length, implying that SS pairing can instantly follow transcription. Also, factors required for SS pairing, such as the U1 small nuclear ribonucleoprotein (snRNP) and U2AF65, associate with RNA polymerase II (RNAPII), while nucleosomes preferentially bind exonic sequences and associate with U2 snRNP. Based on recent publications, we assume that the 5' SS-bound U1 snRNP can remain tethered to RNAPII until complete synthesis of the downstream intron and exon. An additional U1 snRNP then binds the downstream 5' SS, whereas the RNAPII-associated U2AF65 binds the upstream 3' SS to facilitate SS pairing along with exon definition. Next, the nucleosome-associated U2 snRNP binds the branch site to advance splicing complex assembly. This may explain how RNAPII and chromatin are involved in spliceosome assembly and how introns lengthened during evolution with a relatively minimal compromise in splicing.
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Affiliation(s)
- Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Shiran Naftelberg
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Alberto R Kornblihtt
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel.
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44
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TALE-directed local modulation of H3K9 methylation shapes exon recognition. Sci Rep 2016; 6:29961. [PMID: 27439481 PMCID: PMC4954949 DOI: 10.1038/srep29961] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/28/2016] [Indexed: 12/12/2022] Open
Abstract
In search for the function of local chromatin environment on pre-mRNA processing we established a new tool, which allows for the modification of chromatin using a targeted approach. Using Transcription Activator-Like Effector domains fused to histone modifying enzymes (TALE-HME), we show locally restricted alteration of histone methylation modulates the splicing of target exons. We provide evidence that a local increase in H3K9 di- and trimethylation promotes inclusion of the target alternative exon, while demethylation by JMJD2D leads to exon skipping. We further demonstrate that H3K9me3 is localized on internal exons genome-wide suggesting a general role in splicing. Consistently, targeting of the H3K9 demethylase to a weak constitutive exon reduced co-transcriptional splicing. Together our data show H3K9 methylation within the gene body is a factor influencing recognition of both constitutive and alternative exons.
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45
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Dębski KJ, Pitkanen A, Puhakka N, Bot AM, Khurana I, Harikrishnan KN, Ziemann M, Kaspi A, El-Osta A, Lukasiuk K, Kobow K. Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy. Sci Rep 2016; 6:25668. [PMID: 27157830 PMCID: PMC4860710 DOI: 10.1038/srep25668] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pilocarpine injection, or lateral fluid-percussion induced traumatic brain injury (TBI) in rats. In the models studies, DNA methylation and gene expression profiles distinguished controls from injured animals. We observed consistent increased methylation in gene bodies and hypomethylation at non-genic regions. We did not find a common methylation signature in all three different models and few regions common to any two models. Our data provide evidence that genome-wide alteration of DNA methylation signatures is a general pathomechanism associated with epileptogenesis and epilepsy in experimental animal models, but the broad pathophysiological differences between models (i.e. pilocarpine, amygdala stimulation, and post-TBI) are reflected in distinct etiology-dependent DNA methylation patterns.
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Affiliation(s)
- Konrad J. Dębski
- Laboratory of Epileptogenesis, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Asla Pitkanen
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Noora Puhakka
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Anna M. Bot
- Laboratory of Epileptogenesis, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Ishant Khurana
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia
| | - KN Harikrishnan
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC, Australia
| | - Katarzyna Lukasiuk
- Laboratory of Epileptogenesis, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
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46
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Sun T, Li T, Davies H, Li W, Yang J, Li S, Ling S. Altered Morphologies and Functions of the Olfactory Bulb and Hippocampus Induced by miR-30c. Front Neurosci 2016; 10:207. [PMID: 27242411 PMCID: PMC4860400 DOI: 10.3389/fnins.2016.00207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/25/2016] [Indexed: 11/17/2022] Open
Abstract
Adult neurogenesis is considered to contribute to a certain degree of plasticity for the brain. However, the effects of adult-born neurons on the brain are still largely unknown. Here, we specifically altered the expression of miR-30c in the subventricular zone (SVZ) and dentate gyrus (DG) by stereotaxic injection with their respective up- and down-regulated lentiviruses. Results showed an increased level of miR-30c enhanced adult neurogenesis by prompting cell-cycles of stem cells, whereas down-regulated miR-30c led to the opposite results. When these effects of miR-30c lasted for 3 months, we detected significant morphological changes in the olfactory bulb (OB) and lineage alteration in the hippocampus. Tests of olfactory sensitivity and associative and spatial memory showed that a certain amount of adult-born neurons are essential for the normal functions of the OB and hippocampus, but there also exist redundant newborn neurons that do not further improve the functioning of these areas. Our study revealed the interactions between miRNA, adult neurogenesis, brain morphology and function, and this provides a novel insight into understanding the role of newborn neurons in the adult brain.
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Affiliation(s)
- Tingting Sun
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine Hangzhou, China
| | - Tianpeng Li
- College of Environment Science and Engineering, Donghua University Shanghai, China
| | - Henry Davies
- Institute of Neuroscience, Zhejiang University School of Medicine Hangzhou, China
| | - Weiyun Li
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine Hangzhou, China
| | - Jing Yang
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine Hangzhou, China
| | - Shanshan Li
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine Hangzhou, China
| | - Shucai Ling
- Institute of Neuroscience and Anatomy, Zhejiang University School of Medicine Hangzhou, China
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47
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Fiszbein A, Giono LE, Quaglino A, Berardino BG, Sigaut L, von Bilderling C, Schor IE, Enriqué Steinberg JH, Rossi M, Pietrasanta LI, Caramelo JJ, Srebrow A, Kornblihtt AR. Alternative Splicing of G9a Regulates Neuronal Differentiation. Cell Rep 2016; 14:2797-808. [PMID: 26997278 DOI: 10.1016/j.celrep.2016.02.063] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/25/2016] [Accepted: 02/12/2016] [Indexed: 01/08/2023] Open
Abstract
Chromatin modifications are critical for the establishment and maintenance of differentiation programs. G9a, the enzyme responsible for histone H3 lysine 9 dimethylation in mammalian euchromatin, exists as two isoforms with differential inclusion of exon 10 (E10) through alternative splicing. We find that the G9a methyltransferase is required for differentiation of the mouse neuronal cell line N2a and that E10 inclusion increases during neuronal differentiation of cultured cells, as well as in the developing mouse brain. Although E10 inclusion greatly stimulates overall H3K9me2 levels, it does not affect G9a catalytic activity. Instead, E10 increases G9a nuclear localization. We show that the G9a E10(+) isoform is necessary for neuron differentiation and regulates the alternative splicing pattern of its own pre-mRNA, enhancing E10 inclusion. Overall, our findings indicate that by regulating its own alternative splicing, G9a promotes neuron differentiation and creates a positive feedback loop that reinforces cellular commitment to differentiation.
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Affiliation(s)
- Ana Fiszbein
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Luciana E Giono
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Ana Quaglino
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Bruno G Berardino
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Lorena Sigaut
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-CONICET, Cuidad Universitaria Pabellón I, C1428EHA Buenos Aires, Argentina
| | - Catalina von Bilderling
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-CONICET, Cuidad Universitaria Pabellón I, C1428EHA Buenos Aires, Argentina
| | - Ignacio E Schor
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Juliana H Enriqué Steinberg
- Instituto de Investigación en Biomedicina de Buenos Aires CONICET, Partner Institute of the Max Planck Society, C1425FQD Buenos Aires, Argentina
| | - Mario Rossi
- Instituto de Investigación en Biomedicina de Buenos Aires CONICET, Partner Institute of the Max Planck Society, C1425FQD Buenos Aires, Argentina
| | - Lía I Pietrasanta
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-CONICET, Cuidad Universitaria Pabellón I, C1428EHA Buenos Aires, Argentina; Centro de Microscopías Avanzadas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Cuidad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Julio J Caramelo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina; Fundación Instituto Leloir, C1405BWE Buenos Aires, Argentina
| | - Anabella Srebrow
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Ciudad Universitaria Pabellón II, C1428EHA Buenos Aires, Argentina.
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48
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Wang HLV, Chekanova JA. Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:356-81. [PMID: 26924473 DOI: 10.1002/wrna.1340] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes produce thousands of diverse small RNAs (smRNAs), which play vital roles in regulating gene expression in all conditions, including in survival of biotic and abiotic environmental stresses. SmRNA pathways intersect with most of the pathways regulating different steps in the life of a messenger RNA (mRNA), starting from transcription and ending at mRNA decay. SmRNAs function in both nuclear and cytoplasmic compartments; the regulation of mRNA stability and translation in the cytoplasm and the epigenetic regulation of gene expression in the nucleus are the main and best-known modes of smRNA action. However, recent evidence from animal systems indicates that smRNAs and RNA interference (RNAi) also participate in the regulation of alternative pre-mRNA splicing, one of the most crucial steps in the fast, efficient global reprogramming of gene expression required for survival under stress. Emerging evidence from bioinformatics studies indicates that a specific class of plant smRNAs, induced by various abiotic stresses, the sutr-siRNAs, has the potential to target regulatory regions within introns and thus may act in the regulation of splicing in response to stresses. This review summarizes the major types of plant smRNAs in the context of their mechanisms of action and also provides examples of their involvement in regulation of gene expression in response to environmental cues and developmental stresses. In addition, we describe current advances in our understanding of how smRNAs function in the regulation of pre-mRNA splicing. WIREs RNA 2016, 7:356-381. doi: 10.1002/wrna.1340 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hsiao-Lin V Wang
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Julia A Chekanova
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
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Marina RJ, Sturgill D, Bailly MA, Thenoz M, Varma G, Prigge MF, Nanan KK, Shukla S, Haque N, Oberdoerffer S. TET-catalyzed oxidation of intragenic 5-methylcytosine regulates CTCF-dependent alternative splicing. EMBO J 2015; 35:335-55. [PMID: 26711177 DOI: 10.15252/embj.201593235] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/25/2015] [Indexed: 01/09/2023] Open
Abstract
Intragenic 5-methylcytosine and CTCF mediate opposing effects on pre-mRNA splicing: CTCF promotes inclusion of weak upstream exons through RNA polymerase II pausing, whereas 5-methylcytosine evicts CTCF, leading to exon exclusion. However, the mechanisms governing dynamic DNA methylation at CTCF-binding sites were unclear. Here, we reveal the methylcytosine dioxygenases TET1 and TET2 as active regulators of CTCF-mediated alternative splicing through conversion of 5-methylcytosine to its oxidation derivatives. 5-hydroxymethylcytosine and 5-carboxylcytosine are enriched at an intragenic CTCF-binding sites in the CD45 model gene and are associated with alternative exon inclusion. Reduced TET levels culminate in increased 5-methylcytosine, resulting in CTCF eviction and exon exclusion. In vitro analyses establish the oxidation derivatives are not sufficient to stimulate splicing, but efficiently promote CTCF association. We further show genomewide that reciprocal exchange of 5-hydroxymethylcytosine and 5-methylcytosine at downstream CTCF-binding sites is a general feature of alternative splicing in naïve and activated CD4(+) T cells. These findings significantly expand our current concept of the pre-mRNA "splicing code" to include dynamic intragenic DNA methylation catalyzed by the TET proteins.
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Affiliation(s)
- Ryan J Marina
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - David Sturgill
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Marc A Bailly
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Morgan Thenoz
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Garima Varma
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Maria F Prigge
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Kyster K Nanan
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Sanjeev Shukla
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Nazmul Haque
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
| | - Shalini Oberdoerffer
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, USA
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50
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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