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Zhou H, Zeng H, Yan T, Chen S, Fu Y, Qin G, Zhao X, Heng Y, Li J, Lin F, Xu D, Wei N, Deng XW. Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis. Nat Commun 2024; 15:5130. [PMID: 38879536 PMCID: PMC11180117 DOI: 10.1038/s41467-024-49571-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/10/2024] [Indexed: 06/19/2024] Open
Abstract
Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.
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Affiliation(s)
- Hua Zhou
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Haiyue Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Tingting Yan
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Fu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
| | - Guochen Qin
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China
| | - Xianhai Zhao
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yueqin Heng
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fang Lin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xing Wang Deng
- Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Southern University of Science and Technology, Shenzhen, 518055, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, 61000, Shandong, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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2
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Zhang X, Zhan X, Bian T, Yang F, Li P, Lu Y, Xing Z, Fan R, Zhang QC, Shi Y. Structural insights into branch site proofreading by human spliceosome. Nat Struct Mol Biol 2024; 31:835-845. [PMID: 38196034 DOI: 10.1038/s41594-023-01188-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5.
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Affiliation(s)
- Xiaofeng Zhang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Xiechao Zhan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Tong Bian
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Fenghua Yang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Pan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yichen Lu
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Zhihan Xing
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Rongyan Fan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Qiangfeng Cliff Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
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3
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Hong W, Yang H, Wang X, Shi J, Zhang J, Xie J. The Role of mRNA Alternative Splicing in Macrophages Infected with Mycobacterium tuberculosis: A Field Needing to Be Discovered. Molecules 2024; 29:1798. [PMID: 38675618 PMCID: PMC11052237 DOI: 10.3390/molecules29081798] [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: 01/19/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the major causes of human death. In its battle with humans, Mtb has fully adapted to its host and developed ways to evade the immune system. At the same time, the human immune system has developed ways to respond to Mtb. The immune system responds to viral and bacterial infections through a variety of mechanisms, one of which is alternative splicing. In this study, we summarized the overall changes in alternative splicing of the transcriptome after macrophages were infected with Mtb. We found that after infection with Mtb, cells undergo changes, including (1) directly reducing the expression of splicing factors, which affects the regulation of gene expression, (2) altering the original function of proteins through splicing, which can involve gene truncation or changes in protein domains, and (3) expressing unique isoforms that may contribute to the identification and development of tuberculosis biomarkers. Moreover, alternative splicing regulation of immune-related genes, such as IL-4, IL-7, IL-7R, and IL-12R, may be an important factor affecting the activation or dormancy state of Mtb. These will help to fully understand the immune response to Mtb infection, which is crucial for the development of tuberculosis biomarkers and new drug targets.
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Affiliation(s)
- Weiling Hong
- Jinhua Advanced Research Institute, Jinhua 321019, China; (W.H.); (H.Y.); (X.W.); (J.S.)
| | - Hongxing Yang
- Jinhua Advanced Research Institute, Jinhua 321019, China; (W.H.); (H.Y.); (X.W.); (J.S.)
| | - Xiao Wang
- Jinhua Advanced Research Institute, Jinhua 321019, China; (W.H.); (H.Y.); (X.W.); (J.S.)
| | - Jingyi Shi
- Jinhua Advanced Research Institute, Jinhua 321019, China; (W.H.); (H.Y.); (X.W.); (J.S.)
| | - Jian Zhang
- Zhejiang University Medical Center, Hangzhou 311113, China;
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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Zhang Z, Kumar V, Dybkov O, Will CL, Urlaub H, Stark H, Lührmann R. Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. EMBO J 2024; 43:1065-1088. [PMID: 38383864 PMCID: PMC10943123 DOI: 10.1038/s44318-024-00052-1] [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: 09/27/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB molecular model, we determined the cryo-EM structure of B complex dimers formed in the presence of ATP γ S. The enhanced resolution of these complexes allows a finer molecular dissection of how the 5' splice site (5'ss) is recognized in hB, and new insights into molecular interactions of FBP21, SNU23 and PRP38 with the U6/5'ss helix and with each other. It also reveals that SMU1 and RED are present as a heterotetrameric complex and are located at the interface of the B dimer protomers. We further show that MFAP1 and UBL5 form a 5' exon binding channel in hB, and elucidate the molecular contacts stabilizing the 5' exon at this stage. Our studies thus yield more accurate models of protein and RNA components of hB complexes. They further allow the localization of additional proteins and protein domains (such as SF3B6, BUD31 and TCERG1) whose position was not previously known, thereby uncovering new functions for B-specific and other hB proteins during pre-mRNA splicing.
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Affiliation(s)
- Zhenwei Zhang
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Vinay Kumar
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Cindy L Will
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
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5
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Blázquez-Encinas R, García-Vioque V, Caro-Cuenca T, Moreno-Montilla MT, Mangili F, Alors-Pérez E, Ventura S, Herrera-Martínez AD, Moreno-Casado P, Calzado MA, Salvatierra Á, Gálvez-Moreno MA, Fernandez-Cuesta L, Foll M, Luque RM, Alcala N, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery. J Transl Med 2023; 21:879. [PMID: 38049848 PMCID: PMC10696873 DOI: 10.1186/s12967-023-04754-8] [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: 05/05/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Lung neuroendocrine neoplasms (LungNENs) comprise a heterogeneous group of tumors ranging from indolent lesions with good prognosis to highly aggressive cancers. Carcinoids are the rarest LungNENs, display low to intermediate malignancy and may be surgically managed, but show resistance to radiotherapy/chemotherapy in case of metastasis. Molecular profiling is providing new information to understand lung carcinoids, but its clinical value is still limited. Altered alternative splicing is emerging as a novel cancer hallmark unveiling a highly informative layer. METHODS We primarily examined the status of the splicing machinery in lung carcinoids, by assessing the expression profile of the core spliceosome components and selected splicing factors in a cohort of 25 carcinoids using a microfluidic array. Results were validated in an external set of 51 samples. Dysregulation of splicing variants was further explored in silico in a separate set of 18 atypical carcinoids. Selected altered factors were tested by immunohistochemistry, their associations with clinical features were assessed and their putative functional roles were evaluated in vitro in two lung carcinoid-derived cell lines. RESULTS The expression profile of the splicing machinery was profoundly dysregulated. Clustering and classification analyses highlighted five splicing factors: NOVA1, SRSF1, SRSF10, SRSF9 and PRPF8. Anatomopathological analysis showed protein differences in the presence of NOVA1, PRPF8 and SRSF10 in tumor versus non-tumor tissue. Expression levels of each of these factors were differentially related to distinct number and profiles of splicing events, and were associated to both common and disparate functional pathways. Accordingly, modulating the expression of NOVA1, PRPF8 and SRSF10 in vitro predictably influenced cell proliferation and colony formation, supporting their functional relevance and potential as actionable targets. CONCLUSIONS These results provide primary evidence for dysregulation of the splicing machinery in lung carcinoids and suggest a plausible functional role and therapeutic targetability of NOVA1, PRPF8 and SRSF10.
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Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Teresa Caro-Cuenca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Pathology Service, Reina Sofía University Hospital, Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Federica Mangili
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Emilia Alors-Pérez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastian Ventura
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Paula Moreno-Casado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - Marco A Calzado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Ángel Salvatierra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Lynnette Fernandez-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Raúl M Luque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Sergio Pedraza-Arevalo
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain.
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Chen L, Xu Z, Huang J, Shu H, Hui Y, Zhu D, Wu Y, Dong S, Wu Z. Plant immunity suppressor SKRP encodes a novel RNA-binding protein that targets exon 3' end of unspliced RNA. THE NEW PHYTOLOGIST 2023; 240:1467-1483. [PMID: 37658678 DOI: 10.1111/nph.19236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/01/2023] [Indexed: 09/03/2023]
Abstract
The regulatory roles of RNA splicing in plant immunity are emerging but still largely obscure. We reported previously that Phytophthora pathogen effector Avr3c targets a soybean protein SKRP (serine/lysine/arginine-rich protein) to impair soybean basal immunity by regulating host pre-mRNA alternative splicing, while the biochemical nature of SKRP remains unknown. Here, by using Arabidopsis as a model, we studied the mechanism of SKRP in regulating pre-mRNA splicing and plant immunity. AtSKRP confers impaired plant immunity against Phytophthora capsici and associates with spliceosome component PRP8 and splicing factor SR45, which positively and negatively regulate plant immunity, respectively. Enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) showed AtSKRP is a novel RNA-binding protein that targets exon 3' end of unspliced RNA. Such position-specific binding of SKRP is associated with its activity in suppressing intron retention, including at positive immune regulatory genes UBP25 and RAR1. In addition, we found AtSKRP self-interact and forms oligomer, and these properties are associated with its function in plant immunity. Overall, our findings reveal that the immune repressor SKRP is a spliceosome-associated protein that targets exon 3' end to regulate pre-mRNA splicing in Arabidopsis.
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Affiliation(s)
- Ling Chen
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhihui Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jie Huang
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yufan Hui
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yufeng Wu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), and The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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7
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Vorobeva MA, Skvortsov DA, Pervouchine DD. Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing. Acta Naturae 2023; 15:23-31. [PMID: 38234601 PMCID: PMC10790352 DOI: 10.32607/actanaturae.26826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 01/19/2024] Open
Abstract
The regulation of alternative splicing in eukaryotic cells is carried out through the coordinated action of a large number of factors, including RNA-binding proteins and RNA structure. The RNA structure influences alternative splicing by blocking cis-regulatory elements, or bringing them closer or farther apart. In combination with RNA-binding proteins, it generates transcript conformations that help to achieve the necessary splicing outcome. However, the binding of regulatory proteins depends on RNA structure and, vice versa, the formation of RNA structure depends on the interaction with regulators. Therefore, RNA structure and RNA-binding proteins are inseparable components of common regulatory mechanisms. This review highlights examples of alternative splicing regulation by RNA-binding proteins, the regulation through local and long-range RNA structures, as well as how these elements work together, cooperate, and compete.
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Affiliation(s)
- M. A. Vorobeva
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. A. Skvortsov
- M.V. Lomonosov Moscow State University, Moscow, 119192 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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8
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Yan Y, Ren Y, Bao Y, Wang Y. RNA splicing alterations in lung cancer pathogenesis and therapy. CANCER PATHOGENESIS AND THERAPY 2023; 1:272-283. [PMID: 38327600 PMCID: PMC10846331 DOI: 10.1016/j.cpt.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 02/09/2024]
Abstract
RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy. Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide. Large-scale multi-omics studies have not only characterized the mutational landscapes but also discovered a plethora of transcriptional and post-transcriptional changes in lung cancer. Such resources have greatly facilitated the development of new diagnostic markers and therapeutic options over the past two decades. Intriguingly, altered RNA splicing has emerged as an important molecular feature and therapeutic target of lung cancer. In this review, we provide a brief overview of splicing dysregulation in lung cancer and summarize the recent progress on key splicing events and splicing factors that contribute to lung cancer pathogenesis. Moreover, we describe the general strategies targeting splicing alterations in lung cancer and highlight the potential of combining splicing modulation with currently approved therapies to combat this deadly disease. This review provides new mechanistic and therapeutic insights into splicing dysregulation in cancer.
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Affiliation(s)
- Yueren Yan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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9
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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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10
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Wang H, Lu J, Stevens T, Roberts A, Mandel J, Avula R, Ma B, Wu Y, Wang J, Land CV, Finkel T, Vockley JE, Airik M, Airik R, Muzumdar R, Gong Z, Torbenson MS, Prochownik EV. Premature aging and reduced cancer incidence associated with near-complete body-wide Myc inactivation. Cell Rep 2023; 42:112830. [PMID: 37481724 PMCID: PMC10591215 DOI: 10.1016/j.celrep.2023.112830] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
MYC proto-oncogene dysregulation alters metabolism, translation, and other functions in ways that support tumor induction and maintenance. Although Myc+/- mice are healthier and longer-lived than control mice, the long-term ramifications of more complete Myc loss remain unknown. We now describe the chronic consequences of body-wide Myc inactivation initiated postnatally. "MycKO" mice acquire numerous features of premature aging, including altered body composition and habitus, metabolic dysfunction, hepatic steatosis, and dysregulation of gene sets involved in functions that normally deteriorate with aging. Yet, MycKO mice have extended lifespans that correlate with a 3- to 4-fold lower lifetime cancer incidence. Aging tissues from normal mice and humans also downregulate Myc and gradually alter many of the same Myc target gene sets seen in MycKO mice. Normal aging and its associated cancer predisposition are thus highly linked via Myc.
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Affiliation(s)
- Huabo Wang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jie Lu
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Taylor Stevens
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Alexander Roberts
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jordan Mandel
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Raghunandan Avula
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; The University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Bingwei Ma
- Tongji University School of Medicine, Shanghai, China
| | - Yijen Wu
- Department of Developmental Biology, The University of Pittsburgh, Pittsburgh, PA, USA
| | - Jinglin Wang
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Central South University, Xiangya School of Medicine, Changsha, Hunan 410013, P.R. China
| | - Clinton Van't Land
- Division of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Toren Finkel
- Division of Cardiology, The Department of Internal Medicine and the UPMC Aging Institute, Pittsburgh, PA 15224, USA
| | - Jerry E Vockley
- Division of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Merlin Airik
- Division of Nephrology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Rannar Airik
- Division of Nephrology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Radhika Muzumdar
- Division of Endocrinology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Zhenwei Gong
- Division of Endocrinology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Michel S Torbenson
- Division of Laboratory Medicine and Pathology, The Mayo Clinic, Rochester, MN 55905, USA
| | - Edward V Prochownik
- Division of Hematology/Oncology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA 15261, USA; Hillman Cancer Center of UPMC, Pittsburgh, PA 15232, USA; Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA 15261, USA.
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11
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Prochownik EV, Wang H. Lessons in aging from Myc knockout mouse models. Front Cell Dev Biol 2023; 11:1244321. [PMID: 37621775 PMCID: PMC10446843 DOI: 10.3389/fcell.2023.1244321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Despite MYC being among the most intensively studied oncogenes, its role in normal development has not been determined as Myc-/- mice do not survival beyond mid-gestation. Myc ± mice live longer than their wild-type counterparts and are slower to accumulate many age-related phenotypes. However, Myc haplo-insufficiency likely conceals other important phenotypes as many high-affinity Myc targets genes continue to be regulated normally. By delaying Myc inactivation until after birth it has recently been possible to study the consequences of its near-complete total body loss and thus to infer its normal function. Against expectation, these "MycKO" mice lived significantly longer than control wild-type mice but manifested a marked premature aging phenotype. This seemingly paradoxical behavior was potentially explained by a >3-fold lower lifetime incidence of cancer, normally the most common cause of death in mice and often Myc-driven. Myc loss accelerated the accumulation of numerous "Aging Hallmarks", including the loss of mitochondrial and ribosomal structural and functional integrity, the generation of reactive oxygen species, the acquisition of genotoxic damage, the detrimental rewiring of metabolism and the onset of senescence. In both mice and humans, normal aging in many tissues was accompaniued by the downregulation of Myc and the loss of Myc target gene regulation. Unlike most mouse models of premature aging, which are based on monogenic disorders of DNA damage recognition and repair, the MycKO mouse model directly impacts most Aging Hallmarks and may therefore more faithfully replicate the normal aging process of both mice and humans. It further establishes that the strong association between aging and cancer can be genetically separated and is maintained by a single gene.
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Affiliation(s)
- Edward V. Prochownik
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
- The Department of Microbiology and Molecular Genetics, UPMC, Pittsburgh, PA, United States
- The Hillman Cancer Center of UPMC, Pittsburgh, PA, United States
- The Pittsburgh Liver Research Center, UPMC, Pittsburgh, PA, United States
| | - Huabo Wang
- Division of Hematology/Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
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12
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Enders M, Neumann P, Dickmanns A, Ficner R. Structure and function of spliceosomal DEAH-box ATPases. Biol Chem 2023; 404:851-866. [PMID: 37441768 DOI: 10.1515/hsz-2023-0157] [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: 03/10/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Splicing of precursor mRNAs is a hallmark of eukaryotic cells, performed by a huge macromolecular machine, the spliceosome. Four DEAH-box ATPases are essential components of the spliceosome, which play an important role in the spliceosome activation, the splicing reaction, the release of the spliced mRNA and intron lariat, and the disassembly of the spliceosome. An integrative approach comprising X-ray crystallography, single particle cryo electron microscopy, single molecule FRET, and molecular dynamics simulations provided deep insights into the structure, dynamics and function of the spliceosomal DEAH-box ATPases.
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Affiliation(s)
- Marieke Enders
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
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13
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Schmitzová J, Cretu C, Dienemann C, Urlaub H, Pena V. Structural basis of catalytic activation in human splicing. Nature 2023; 617:842-850. [PMID: 37165190 PMCID: PMC10208982 DOI: 10.1038/s41586-023-06049-w] [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: 05/29/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
Pre-mRNA splicing follows a pathway driven by ATP-dependent RNA helicases. A crucial event of the splicing pathway is the catalytic activation, which takes place at the transition between the activated Bact and the branching-competent B* spliceosomes. Catalytic activation occurs through an ATP-dependent remodelling mediated by the helicase PRP2 (also known as DHX16)1-3. However, because PRP2 is observed only at the periphery of spliceosomes3-5, its function has remained elusive. Here we show that catalytic activation occurs in two ATP-dependent stages driven by two helicases: PRP2 and Aquarius. The role of Aquarius in splicing has been enigmatic6,7. Here the inactivation of Aquarius leads to the stalling of a spliceosome intermediate-the BAQR complex-found halfway through the catalytic activation process. The cryogenic electron microscopy structure of BAQR reveals how PRP2 and Aquarius remodel Bact and BAQR, respectively. Notably, PRP2 translocates along the intron while it strips away the RES complex, opens the SF3B1 clamp and unfastens the branch helix. Translocation terminates six nucleotides downstream of the branch site through an assembly of PPIL4, SKIP and the amino-terminal domain of PRP2. Finally, Aquarius enables the dissociation of PRP2, plus the SF3A and SF3B complexes, which promotes the relocation of the branch duplex for catalysis. This work elucidates catalytic activation in human splicing, reveals how a DEAH helicase operates and provides a paradigm for how helicases can coordinate their activities.
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Affiliation(s)
- Jana Schmitzová
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Constantin Cretu
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK
- Cluster of Excellence Multiscale Bioimaging (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany
| | - Christian Dienemann
- Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, Bioanalytics, University Medical Center Sciences, Göttingen, Germany
| | - Vladimir Pena
- Macromolecular Crystallography, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.
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14
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Du J, Li Y, Su Y, Zhi W, Zhang J, Zhang C, Wang J, Deng W, Zhao S. LncRNA Pnky Positively Regulates Neural Stem Cell Migration by Modulating mRNA Splicing and Export of Target Genes. Cell Mol Neurobiol 2023; 43:1199-1218. [PMID: 35748966 DOI: 10.1007/s10571-022-01241-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Directed migration of neural stem cells (NSCs) is critical for embryonic neurogenesis and the healing of neurological injuries. The long noncoding RNA (lncRNA) Pnky has been reported to regulate neuronal differentiation of NSCs by interacting with PTBP1. However, its regulatory effect on NSC migration remains to be determined. Herein, we identified that Pnky is also a key regulator of NSC migration in mice, as underscored by the finding that Pnky silencing suppressed but Pnky overexpression promoted the in vitro migration of both C17.2 and NE4C murine NSCs. Additionally, in vivo cell tracking demonstrated that Pnky depletion attenuated but Pnky overexpression facilitated the migration of NE4C cells in the spinal canal after transplantation via injection into the spinal canal. Mechanistically, Pnky regulated the expression of a core set of critical regulators that direct NSC migration, including MMP2, MMP9, Connexin43, Paxillin, AKT, ERK, and P38MAPK. Using catRAPID, a web server for large-scale prediction of protein-RNA interactions, the splicing factors U2AF1 and U2AF1L4, as well as the mRNA export adaptors SARNP, Aly/Ref, and THOC7, were predicted to interact strongly with Pnky. Further investigations using colocalization and RNA immunoprecipitation (RIP) assays confirmed the direct binding of Pnky to U2AF1, SARNP, Aly/Ref, and THOC7. Transcriptomic profiling revealed that as many as 5319 differential splicing events of 3848 genes, which were highly enriched in focal adhesion, PI3K-Akt and MAPK signaling pathways, were affected by Pnky depletion. The predominant subtype of differential splicing by Pnky depletion is intron retention, followed by alternative 5' and 3' splice sites and mutually exclusive exons. Moreover, Pnky knockdown substantially blocked but Pnky overexpression facilitated the export of MMP2, Paxillin, AKT, p38MAPK, and other mRNAs to the cytosol. Collectively, our data showed that through interacting with U2AF1, SARNP, Aly/Ref, and THOC7, Pnky couples and modulates the splicing and export of target mRNAs, which consequently controlling NSC migration. These findings provide a possible theoretical basis of NSC migration regulation.
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Affiliation(s)
- Jiannan Du
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Yuan Li
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Yuting Su
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Wenqian Zhi
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Jiale Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Cheng Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Juan Wang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Wensheng Deng
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China.
| | - Shasha Zhao
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China.
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15
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Choudhry M, Gamallat Y, Khosh Kish E, Seyedi S, Gotto G, Ghosh S, Bismar TA. Downregulation of BUD31 Promotes Prostate Cancer Cell Proliferation and Migration via Activation of p-AKT and Vimentin In Vitro. Int J Mol Sci 2023; 24:ijms24076055. [PMID: 37047027 PMCID: PMC10094631 DOI: 10.3390/ijms24076055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Among men, prostate cancer (PCa) is the second most frequently diagnosed cancer subtype and has demonstrated a high degree of prevalence globally. BUD31, also known as Functional Spliceosome-Associated Protein 17, is a protein that works at the level of the spliceosome; it is functionally implicated in pre-mRNA splicing as well as processing, while also acting as a transcriptional regulator of androgen receptor (AR) target genes. Clinically, the expression of BUD31 and its functions in the development and progression of PCa is yet to be elucidated. The BUD31 expression was assessed using IHC in a tissue microarray (TMA) constructed from a cohort of 284 patient samples. In addition, we analyzed the prostate adenocarcinoma (TCGAPRAD-) database. Finally, we used PCa cell lines to knockdown BUD31 to study the underlying mechanisms in vitro.Assesment of BUD31 protein expression revealed lower expression in incidental and advanced PCa, and significantly lower expression was observed in patients diagnosed with castrate-resistant prostate cancer. Additionally, bioinformatic analysis and GSEA revealed that BUD31 increased processes related to cancer cell migration and proliferation. In vitro results made evident that BUD31 knockdown in PC3 cells led to an increase in the G2 cell population, indicating a more active and proliferative state. Additionally, an investigation of metastatic processes revealed that knockdown of BUD31 significantly enhanced the ability of PC3 cells to migrate and invade. Our in vitro results showed BUD31 knockdown promotes cell proliferation and migration of prostate cancer cells via activation of p-AKT and vimentin. These results support the clinical data, where low expression of BUD31 was correlated to more advanced stages of PCa.
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Affiliation(s)
- Muhammad Choudhry
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Departments of Oncology, Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Yaser Gamallat
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Departments of Oncology, Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Ealia Khosh Kish
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Departments of Oncology, Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sima Seyedi
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Geoffrey Gotto
- Department of Surgery, Division of Urology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sunita Ghosh
- Department of Medical Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada
- Departments of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB T6G 2G1, Canada
| | - Tarek A Bismar
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Departments of Oncology, Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute and Tom Baker Cancer Center, Calgary, AB T2N 4N1, Canada
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16
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Mushtaq A, Zahoor AF, Bilal M, Hussain SM, Irfan M, Akhtar R, Irfan A, Kotwica-Mojzych K, Mojzych M. Sharpless Asymmetric Dihydroxylation: An Impressive Gadget for the Synthesis of Natural Products: A Review. Molecules 2023; 28:2722. [PMID: 36985698 PMCID: PMC10051988 DOI: 10.3390/molecules28062722] [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: 01/26/2023] [Revised: 02/21/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Sharpless asymmetric dihydroxylation is an important reaction in the enantioselective synthesis of chiral vicinal diols that involves the treatment of alkene with osmium tetroxide along with optically active quinine ligand. Sharpless introduced this methodology after considering the importance of enantioselectivity in the total synthesis of medicinally important compounds. Vicinal diols, produced as a result of this reaction, act as intermediates in the synthesis of different naturally occurring compounds. Hence, Sharpless asymmetric dihydroxylation plays an important role in synthetic organic chemistry due to its undeniable contribution to the synthesis of biologically active organic compounds. This review emphasizes the significance of Sharpless asymmetric dihydroxylation in the total synthesis of various natural products, published since 2020.
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Affiliation(s)
- Aqsa Mushtaq
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Bilal
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Syed Makhdoom Hussain
- Department of Zoology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan
- Department of Pharmaceutics, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Rabia Akhtar
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
- Department of Chemistry, Superior University, Faisalabad 38000, Pakistan
| | - Ali Irfan
- Medicinal Chemistry Research Lab, Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Katarzyna Kotwica-Mojzych
- Laboratory of Experimental Cytology, Medical University of Lublin, Radziwiłłowska 11, 20-080 Lublin, Poland
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3-Go Maja 54, 08-110 Siedlce, Poland
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17
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Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Nat Commun 2023; 14:897. [PMID: 36797247 PMCID: PMC9935549 DOI: 10.1038/s41467-023-36489-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Three RNA helicases - DDX42, DDX46 and DHX15 - are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations.
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18
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Hong Y, Gao Y, Pang J, Shi H, Li T, Meng H, Kong D, Chen Y, Zhu JK, Wang Z. The Sm core protein SmEb regulates salt stress responses through maintaining proper splicing of RCD1 pre-mRNA in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36661041 DOI: 10.1111/jipb.13457] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Salt stress adversely impacts crop production. Several spliceosome components have been implicated in regulating salt stress responses in plants, however, the underlying molecular basis is still unclear. Here we report that the spliceosomal core protein SmEb is essential to salt tolerance in Arabidopsis. Transcriptome analysis showed that SmEb modulates alternative splicing of hundreds of pre-mRNAs in plant response to salt stress. Further study revealed that SmEb is crucial in maintaining proper ratio of two RCD1 splicing variants (RCD1.1/RCD1.2) important for salt stress response. In addition, RCD1.1 but not RCD1.2 is able to interact with the stress regulators and attenuates salt-sensitivity by decreasing salt-induced cell death in smeb-1 mutant. Together, our findings uncovered the essential role of SmEb in the regulation of alternative pre-mRNA splicing in salt stress response.
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Affiliation(s)
- Yechun Hong
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yang Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Jia Pang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, 79409, USA
| | - Tingting Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Huiying Meng
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yunjuan Chen
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhen Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
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19
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Mehta Z, Touma M. Post-Transcriptional Modification by Alternative Splicing and Pathogenic Splicing Variants in Cardiovascular Development and Congenital Heart Defects. Int J Mol Sci 2023; 24:ijms24021555. [PMID: 36675070 PMCID: PMC9862068 DOI: 10.3390/ijms24021555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Advancements in genomics, bioinformatics, and genome editing have uncovered new dimensions in gene regulation. Post-transcriptional modifications by the alternative splicing of mRNA transcripts are critical regulatory mechanisms of mammalian gene expression. In the heart, there is an expanding interest in elucidating the role of alternative splicing in transcriptome regulation. Substantial efforts were directed toward investigating this process in heart development and failure. However, few studies shed light on alternative splicing products and their dysregulation in congenital heart defects (CHDs). While elegant reports showed the crucial roles of RNA binding proteins (RBPs) in orchestrating splicing transitions during heart development and failure, the impact of RBPs dysregulation or genetic variation on CHDs has not been fully addressed. Herein, we review the current understanding of alternative splicing and RBPs' roles in heart development and CHDs. Wediscuss the impact of perinatal splicing transition and its dysregulation in CHDs. We further summarize the discoveries made of causal splicing variants in key transcription factors that are implicated in CHDs. An improved understanding of the roles of alternative splicing in heart development and CHDs may potentially inform novel preventive and therapeutic advancements for newborn infants with CHDs.
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Affiliation(s)
- Zubin Mehta
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marlin Touma
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Correspondence:
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20
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Wang H, Lu X, Zheng H, Wang W, Zhang G, Wang S, Lin P, Zhuang Y, Chen C, Chen Q, Qu J, Xu L. RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects. Comput Struct Biotechnol J 2023; 21:965-973. [PMID: 36733704 PMCID: PMC9876829 DOI: 10.1016/j.csbj.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
RNA structure plays a crucial role in gene regulation, in RNA stability and the essential biological processes. RNA secondary structure (RSS) motifs are the basic building blocks for investigating the biological mechanisms of structure. Here, we present a strategy for structural motif-based dynamic alignment, namely, RNA secondary-structural motif-comparing (RNAsmc), to identify structural motifs and quantitatively evaluate their underlying molecular functions. RNAsmc also has strong robustness to sequence length, folding protocol and RNA structural profile by chemical probing. Notably, it is also applicable to quantify structural variation in special RNA editing events (SNVs or SNPs, fragment insertion or deletion, etc.). The findings indicate that RNAsmc can uncover the heterogeneity of RNA secondary structure and score for similarities among components, which provides an impetus to cluster RNA families and evaluate allosteric effects. We find that RNAsmc exhibits remarkable detection efficiency for experimentally-derived RiboSNitches. Finally, the pipeline was assembled into an R software package to serve as an automated toolkit to explore, align, and cluster RSS. It is freely available for download at https://CRAN.R-project.org/package=RNAsmc.
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Affiliation(s)
- Hong Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou 325027, China
| | - Xiaoyan Lu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Hewei Zheng
- Wekemo Tech Group Co., Ltd. Shenzhen 518000, China
| | - Wencan Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Wenzhou Realdata Medical Research Co., Ltd, Wenzhou 325027, China
| | - Guosi Zhang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Siyu Wang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Peng Lin
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Youyuan Zhuang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Chong Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qi Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou 325027, China
- Corresponding authors at: National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Liangde Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
- Center of Optometry International Innovation of Wenzhou, Eye Valley, Wenzhou 325027, China
- Corresponding authors at: National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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21
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Fu X, Kaur H, Rodgers ML, Montemayor EJ, Butcher SE, Hoskins AA. Identification of transient intermediates during spliceosome activation by single molecule fluorescence microscopy. Proc Natl Acad Sci U S A 2022; 119:e2206815119. [PMID: 36417433 PMCID: PMC9860250 DOI: 10.1073/pnas.2206815119] [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: 04/23/2022] [Accepted: 10/05/2022] [Indexed: 11/24/2022] Open
Abstract
Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA 3'-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release. We have used colocalization single molecule spectroscopy (CoSMoS) to visualize Lsm2-8 dynamics during activation of Saccharomyces cerevisiae spliceosomes in vitro. Lsm2-8 is recruited as a component of the tri-snRNP and is released after integration of the Prp19-containing complex (NTC). Despite Lsm2-8 and the NTC being mutually exclusive in existing cryo-EM structures of yeast B complex spliceosomes, we identify a transient intermediate containing both ([Formula: see text]) and provide a kinetic framework for its formation and transformation during activation. Prior to [Formula: see text] assembly, the NTC rapidly and reversibly samples the spliceosome suggesting a mechanism for preventing NTC sequestration by defective spliceosomes that fail to properly activate. In complementary ensemble assays, we show that a base-pairing-dependent ternary complex can form between Lsm2-8 and U2 and U6 helix II RNAs. We propose that this interaction may play a role in formation of transient spliceosome intermediates formed during activation.
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Affiliation(s)
- Xingyang Fu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Margaret L. Rodgers
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Eric J. Montemayor
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Aaron A. Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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22
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The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies. Cancers (Basel) 2022; 14:cancers14184406. [PMID: 36139566 PMCID: PMC9496927 DOI: 10.3390/cancers14184406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary U2 small nuclear RNA auxiliary factor 1 (U2AF1) is one of the most important RNA splicing genes involved in regulating the alternative splicing of pre-mRNA. U2AF1 mutation is a genetic driver event in the initiation of myelodysplastic syndromes (MDSs) and frequently occurs in myeloid malignancies. U2AF1 mutation can severely impair hematopoiesis, drive tumor progression, adversely affect disease prognosis, and promote leukemic transformation. This review summarizes the biological and clinical implications of the oncogenic role of U2AF1 mutation in myeloid tumors. Our work provides important and comprehensive insights into the development of the U2AF1 mutation as a novel prognostic biomarker and therapeutic target for myeloid malignancies. Abstract Mutations of spliceosome genes have been frequently identified in myeloid malignancies with the large-scale application of advanced sequencing technology. U2 small nuclear RNA auxiliary factor 1 (U2AF1), an essential component of U2AF heterodimer, plays a pivotal role in the pre-mRNA splicing processes to generate functional mRNAs. Over the past few decades, the mutation landscape of U2AF1 (most frequently involved S34 and Q157 hotspots) has been drawn in multiple cancers, particularly in myeloid malignancies. As a recognized early driver of myelodysplastic syndromes (MDSs), U2AF1 mutates most frequently in MDS, followed by acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). Here, for the first time, we summarize the research progress of U2AF1 mutations in myeloid malignancies, including the correlations between U2AF1 mutations with clinical and genetic characteristics, prognosis, and the leukemic transformation of patients. We also summarize the adverse effects of U2AF1 mutations on hematopoietic function, and the alterations in downstream alternative gene splicing and biological pathways, thus providing comprehensive insights into the roles of U2AF1 mutations in the myeloid malignancy pathogenesis. U2AF1 mutations are expected to be potential novel molecular markers for myeloid malignancies, especially for risk stratification, prognosis assessment, and a therapeutic target of MDS patients.
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23
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Hansen SR, White DS, Scalf M, Corrêa IR, Smith LM, Hoskins AA. Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife 2022; 11:70534. [PMID: 35959885 PMCID: PMC9436412 DOI: 10.7554/elife.70534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used colocalization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5' SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5' SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS and preferentially accumulate at these sequences rather than on close cognates.
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Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - David S White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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24
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Vorländer MK, Pacheco-Fiallos B, Plaschka C. Structural basis of mRNA maturation: Time to put it together. Curr Opin Struct Biol 2022; 75:102431. [PMID: 35930970 DOI: 10.1016/j.sbi.2022.102431] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
In eukaryotes, the expression of genetic information begins in the cell nucleus with precursor messenger RNA (pre-mRNA) transcription and processing into mature mRNA. The mRNA is subsequently recognized and packaged by proteins into an mRNA ribonucleoprotein complex (mRNP) and exported to the cytoplasm for translation. Each of the nuclear mRNA maturation steps is carried out by a dedicated molecular machine. Here, we highlight recent structural and mechanistic insights into how these machines function, including the capping enzyme, the spliceosome, the 3'-end processing machinery, and the transcription-export complex. While we increasingly understand individual steps of nuclear gene expression, many questions remain. For example, we are only beginning to reveal how mature mRNAs are recognized and packaged for nuclear export and how mRNA maturation events are coupled to transcription and to each other. Advances in the preparation of recombinant and endogenous protein-nucleic acid complexes, cryo-electron microscopy, and machine learning promise exciting insights into the mechanisms of nuclear gene expression and its spatial organization.
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Affiliation(s)
- Matthias K Vorländer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria. https://twitter.com/@MVorlandr
| | - Belén Pacheco-Fiallos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria. https://twitter.com/@bpachecofiallos
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
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25
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Athanasopoulou K, Adamopoulos PG, Daneva GN, Scorilas A. Decoding the concealed transcriptional signature of the apoptosis-related BCL2 antagonist/killer 1 (BAK1) gene in human malignancies. Apoptosis 2022; 27:869-882. [DOI: 10.1007/s10495-022-01753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
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26
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Zhan X, Lu Y, Zhang X, Yan C, Shi Y. Mechanism of exon ligation by human spliceosome. Mol Cell 2022; 82:2769-2778.e4. [PMID: 35705093 DOI: 10.1016/j.molcel.2022.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C∗ complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C∗-I and pre-C∗-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C∗-I to pre-C∗-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C∗-I, pre-C∗-II, and C∗ complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C∗ complexes, our studies recapitulate a molecular choreography of the C-to-C∗ transition, revealing mechanistic insights into exon ligation.
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Affiliation(s)
- Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; College of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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27
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Zhang L, Abendroth F, Vázquez O. A Chemical Biology Perspective to Therapeutic Regulation of RNA Splicing in Spinal Muscular Atrophy (SMA). ACS Chem Biol 2022; 17:1293-1307. [PMID: 35639849 DOI: 10.1021/acschembio.2c00161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Manipulation of RNA splicing machinery has emerged as a drug modality. Here, we illustrate the potential of this novel paradigm to correct aberrant splicing events focused on the recent therapeutic advances in spinal muscular atrophy (SMA). SMA is an incurable neuromuscular disorder and at present the primary genetic cause of early infant death. This Review summarizes the exciting journey from the first reported SMA cases to the currently approved splicing-switching treatments, i.e., antisense oligonucleotides and small-molecule modifiers. We emphasize both chemical structures and molecular bases for recognition. We briefly discuss the advantages and disadvantages of these treatments and include the remaining challenges and future directions. Finally, we also predict that these success stories will contribute to further therapies for human diseases by RNA-splicing control.
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Affiliation(s)
- Lei Zhang
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
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28
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Zhang M, Hwang IT, Li K, Bai J, Chen JF, Weissman T, Zou JY, Lu Z. Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers. Genome Res 2022; 32:968-985. [PMID: 35332099 PMCID: PMC9104705 DOI: 10.1101/gr.275979.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 01/11/2022] [Indexed: 12/04/2022]
Abstract
The recent development and application of methods based on the general principle of "crosslinking and proximity ligation" (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However, extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new strategy to map short reads with irregular gaps at high sensitivity and specificity. Analysis of previously published data reveals distinct properties and bias caused by the crosslinking reactions. We perform rigorous and exhaustive classification of alignments and discover eight types of arrangements that provide distinct information on RNA structures and interactions. To deconvolve the dense and intertwined gapped alignments, we develop a network/graph-based tool Crosslinked RNA Secondary Structure Analysis using Network Techniques (CRSSANT), which enables clustering of gapped alignments and discovery of new alternative and dynamic conformations. We discover that multiple crosslinking and ligation events can occur on the same RNA, generating multisegment alignments to report complex high-level RNA structures and multi-RNA interactions. We find that alignments with overlapped segments are produced from potential homodimers and develop a new method for their de novo identification. Analysis of overlapping alignments revealed potential new homodimers in cellular noncoding RNAs and RNA virus genomes in the Picornaviridae family. Together, this suite of computational tools enables rapid and efficient analysis of RNA structure and interaction data in living cells.
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Affiliation(s)
- Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Irena T Hwang
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - Kongpan Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California (USC), Los Angeles, California 90033, USA
| | - Tsachy Weissman
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - James Y Zou
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science and Chan-Zuckerberg Biohub, Stanford University, Palo Alto, California 94305, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
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Splicing Modulation as a Promising Therapeutic Strategy for Lysosomal Storage Disorders: The Mucopolysaccharidoses Example. Life (Basel) 2022; 12:life12050608. [PMID: 35629276 PMCID: PMC9146820 DOI: 10.3390/life12050608] [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: 03/16/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Over recent decades, the many functions of RNA have become more evident. This molecule has been recognized not only as a carrier of genetic information, but also as a specific and essential regulator of gene expression. Different RNA species have been identified and novel and exciting roles have been unveiled. Quite remarkably, this explosion of novel RNA classes has increased the possibility for new therapeutic strategies that tap into RNA biology. Most of these drugs use nucleic acid analogues and take advantage of complementary base pairing to either mimic or antagonize the function of RNAs. Among the most successful RNA-based drugs are those that act at the pre-mRNA level to modulate or correct aberrant splicing patterns, which are caused by specific pathogenic variants. This approach is particularly tempting for monogenic disorders with associated splicing defects, especially when they are highly frequent among affected patients worldwide or within a specific population. With more than 600 mutations that cause disease affecting the pre-mRNA splicing process, we consider lysosomal storage diseases (LSDs) to be perfect candidates for this type of approach. Here, we introduce the overall rationale and general mechanisms of splicing modulation approaches and highlight the currently marketed formulations, which have been developed for non-lysosomal genetic disorders. We also extensively reviewed the existing preclinical studies on the potential of this sort of therapeutic strategy to recover aberrant splicing and increase enzyme activity in our diseases of interest: the LSDs. Special attention was paid to a particular subgroup of LSDs: the mucopolysaccharidoses (MPSs). By doing this, we hoped to unveil the unique therapeutic potential of the use of this sort of approach for LSDs as a whole.
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A Quality Control Mechanism of Splice Site Selection Abrogated under Stress and in Cancer. Cancers (Basel) 2022; 14:cancers14071750. [PMID: 35406522 PMCID: PMC8996931 DOI: 10.3390/cancers14071750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Splicing and alternative splicing play a major role in regulating gene expression, and mis-regulation of splicing can lead to several diseases, including cancer. The aim of this review is to summarize the current knowledge of a quality control mechanism of splice site selection termed Suppression of Splicing (SOS), proposed to protect cells from splicing at the numerous intronic unused 5′ splice sites, and emphasize its relevance to cancer. This relevance stems from the finding that SOS is abrogated under stress and in cancer resulting in the expression of thousands of aberrant nonsense mRNAs that may be toxic to cells. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies. Abstract Latent 5’ splice sites, highly abundant in human introns, are not normally used. This led to the proposal of a quality control mechanism, Suppression of Splicing (SOS), which protects cells from splicing at the numerous intronic latent sites, and whose activation can generate nonsense mRNAs. SOS was shown to be independent of Nonsense-Mediated mRNA Decay (NMD). Efforts to decipher the SOS mechanism revealed a pivotal role for initiator-tRNA, independent of protein translation. Recently, nucleolin (a multifunctional protein) was found to directly and specifically bind the initiator-tRNA in the nucleus and was shown to be a protein component of SOS, enabling an updated model of the SOS mechanism. Importantly, SOS is abrogated under stress and in cancer (e.g., in breast cancer cells and gliomas), generating thousands of nonsense mRNAs due to activation of latent splicing. The resulting affected human genes cover a variety of functional groups, including genes involved in cell proliferation and differentiation. Furthermore, in oligodendroglioma, the extent of activation of latent splicing increases with the severity of the cancer. Interesting examples are genes expressing aberrant nonsense mRNAs in both breast cancer and glioma, due to latent splicing activation. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies.
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31
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Reprogramming RNA processing: an emerging therapeutic landscape. Trends Pharmacol Sci 2022; 43:437-454. [PMID: 35331569 DOI: 10.1016/j.tips.2022.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The production of a mature mRNA requires coordination of multiple processing steps, which ultimately control its content, localization, and stability. These steps include some of the largest macromolecular machines in the cell, which were, until recently, considered undruggable due to their biological complexity. Building from an expanded understanding of the underlying mechanisms that drive these processes, a new wave of therapeutics is seeking to target RNA processing. With a focus on impacting gene regulation at the RNA level, such modalities offer potential for sequence-specific resolution in drug design. Here, we review our current understanding of RNA-processing events and their role in gene regulation, with a focus on the therapeutic opportunities that have emerged within this landscape.
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32
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Wang C, Yang J, Song P, Zhang W, Lu Q, Yu Q, Jia G. FIONA1 is an RNA N 6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. Genome Biol 2022; 23:40. [PMID: 35101091 PMCID: PMC8802475 DOI: 10.1186/s13059-022-02612-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/14/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) mRNA modification is essential for mammalian and plant viability. The U6 m6A methyltransferases in other species regulate S-adenosylmethionine (SAM) homeostasis through installing m6A in pre-mRNAs of SAM synthetases. However, U6 m6A methyltransferase has not been characterized in Arabidopsis and little is known about its role in regulating photomorphogenesis and flowering. RESULTS Here we characterize that FIONA1 is an Arabidopsis U6 m6A methyltransferase that installs m6A in U6 snRNA and a small subset of poly(A)+ RNA. Disruption of FIONA1 leads to phytochrome signaling-dependent hypocotyl elongation and photoperiod-independent early flowering. Distinct from mammalian METTL16 and worm METT-10, FIONA1 neither installs m6A in the mRNAs of Arabidopsis SAM synthetases nor affects their transcript expression levels under normal or high SAM conditions. We confirm that FIONA1 can methylate plant mRNA m6A motifs in vitro and in vivo. We further show that FIONA1 installs m6A in several phenotypic related transcripts, thereby affecting downstream mRNA stability and regulating phytochrome signaling and floral transition. CONCLUSION FIONA1 is functional as a U6 m6A methyltransferase in Arabidopsis, distinct from mammalian METTL16 and worm METT-10. Our results demonstrate that FIONA1-mediated m6A post-transcriptional regulation is an autonomous regulator for flowering and phytochrome signaling-dependent photomorphogenesis.
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Affiliation(s)
- Chunling Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiong Yu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China.
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Kaur H, van der Feltz C, Sun Y, Hoskins AA. Network theory reveals principles of spliceosome structure and dynamics. Structure 2022; 30:190-200.e2. [PMID: 34592160 PMCID: PMC8741635 DOI: 10.1016/j.str.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/30/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Cryoelectron microscopy has revolutionized spliceosome structural biology, and structures representing much of the splicing process have been determined. Comparison of these structures is challenging due to extreme dynamics of the splicing machinery and the thousands of changing interactions during splicing. We have used network theory to analyze splicing factor interactions by constructing structure-based networks from protein-protein, protein-RNA, and RNA-RNA interactions found in eight different spliceosome structures. Our analyses reveal that connectivity dynamics result in step-specific impacts of factors on network topology. The spliceosome's connectivity is focused on the active site, in part due to contributions from nonglobular proteins. Many essential factors exhibit large shifts in centralities during splicing. Others show transiently high betweenness centralities at certain stages, thereby suggesting mechanisms for regulating splicing by briefly bridging otherwise poorly connected network nodes. These observations provide insights into organizing principles of the spliceosome and provide frameworks for comparative analysis of other macromolecular machines.
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Affiliation(s)
- Harpreet Kaur
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 USA,These authors contributed equally
| | - Clarisse van der Feltz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 USA,College of Arts and Sciences, Northwest University, Kirkland, Washington, 98033 USA,These authors contributed equally
| | - Yichen Sun
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 USA,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706 USA,Correspondence:
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34
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Karbstein K. Attacking a DEAD problem: The role of DEAD-box ATPases in ribosome assembly and beyond. Methods Enzymol 2022; 673:19-38. [PMID: 35965007 PMCID: PMC10154911 DOI: 10.1016/bs.mie.2022.03.033] [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] [Indexed: 11/30/2022]
Abstract
DEAD-box proteins are a subfamily of ATPases with similarity to RecA-type helicases that are involved in all aspects of RNA Biology. Despite their potential to regulate these processes via their RNA-dependent ATPase activity, their roles remain poorly characterized. Here I describe a roadmap to study these proteins in the context of ribosome assembly, the process that utilizes more than half of all DEAD-box proteins encoded in the yeast genome.
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Affiliation(s)
- Katrin Karbstein
- Department of Integrative Structural and Computational Biology, Scripps Florida, Jupiter, FL, United States; HHMI Faculty Scholar, Chevy Chase, MD, United States; The Skaggs Graduate School of Chemical and Biological Sciences, Scripps Florida, Jupiter, FL, United States.
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35
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Jutzi D, Ruepp MD. Alternative Splicing in Human Biology and Disease. Methods Mol Biol 2022; 2537:1-19. [PMID: 35895255 DOI: 10.1007/978-1-0716-2521-7_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] [Indexed: 06/15/2023]
Abstract
Alternative pre-mRNA splicing allows for the production of multiple mRNAs from an individual gene, which not only expands the protein-coding potential of the genome but also enables complex mechanisms for the post-transcriptional control of gene expression. Regulation of alternative splicing entails a combinatorial interplay between an abundance of trans-acting splicing factors, cis-acting regulatory sequence elements and their concerted effects on the core splicing machinery. Given the extent and biological significance of alternative splicing in humans, it is not surprising that aberrant splicing patterns can cause or contribute to a wide range of diseases. In this introductory chapter, we outline the mechanisms that govern alternative pre-mRNA splicing and its regulation and discuss how dysregulated splicing contributes to human diseases affecting the motor system and the brain.
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Affiliation(s)
- Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
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36
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Liu Y, Tian Y, Wang LX, Fan T, Zhang J, Chen MX, Liu YG. Phylogeny and conservation of plant U2A/U2A', a core splicing component in U2 spliceosomal complex. PLANTA 2021; 255:25. [PMID: 34940917 DOI: 10.1007/s00425-021-03752-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/09/2021] [Indexed: 06/14/2023]
Abstract
This study systematically identifies 112 U2A genes from 80 plant species by combinatory bioinformatics analysis, which is important for understanding their phylogenetic history, expression profiles and for predicting specific functions. In eukaryotes, a pre-mRNA can generate multiple transcripts by removing certain introns and joining corresponding exons, thus greatly expanding the transcriptome and proteome diversity. The spliceosome is a mega-Dalton ribonucleoprotein (RNP) complex that is essential for the process of splicing. In spliceosome components, the U2 small nuclear ribonucleoprotein (U2 snRNP) forms the pre-spliceosome by association with the branch site. An essential component that promotes U2 snRNP assembly, named U2A, has been extensively identified in humans, yeast and nematodes. However, studies examining U2A genes in plants are scarce. In this study, we performed a comprehensive analysis and identified a total of 112 U2A genes from 80 plant species representing dicots, monocots, mosses and algae. Comparisons of the gene structures, protein domains, and expression patterns of 112 U2A genes indicated that the conserved functions were likely retained by plant U2A genes and important for responses to internal and external stimuli. In addition, analysis of alternative transcripts and splice sites of U2A genes indicated that the fifth intron contained a conserved alternative splicing event that might be important for its molecular function. Our work provides a general understanding of this splicing factor family in terms of genes and proteins, and it will serve as a fundamental resource that will contribute to further mechanistic characterization in plants.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Lan-Xiang Wang
- Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
- Guangdong Provincial Key Laboratory of Seed and Seedling Health Management Technology, Guangdong Province, Shenzhen Noposion Agrochemical Co. Ltd, Shenzhen, 518102, China.
- Shenzhen Institutes of Advanced Technology, Shenzhen Institute of Synthetic Biology, Chinese Academy of Sciences, Shenzhen, 518055, People's Republic of China.
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China.
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Architectural and functional details of CF IA proteins involved in yeast 3'-end pre-mRNA processing and its significance for eukaryotes: A concise review. Int J Biol Macromol 2021; 193:387-400. [PMID: 34699898 DOI: 10.1016/j.ijbiomac.2021.10.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 11/22/2022]
Abstract
In eukaryotes, maturation of pre-mRNA relies on its precise 3'-end processing. This processing involves co-transcriptional steps regulated by sequence elements and other proteins. Although, it holds tremendous importance, defect in the processing machinery will result in erroneous pre-mRNA maturation leading to defective translation. Remarkably, more than 20 proteins in humans and yeast share homology and execute this processing. The defects in this processing are associated with various diseases in humans. We shed light on the CF IA subunit of yeast Saccharomyces cerevisiae that contains four proteins (Pcf11, Clp1, Rna14 and Rna15) involved in this processing. Structural details of various domains of CF IA and their roles during 3'-end processing, like cleavage and polyadenylation at 3'-UTR of pre-mRNA and other cellular events are explained. Further, the chronological development and important discoveries associated with 3'-end processing are summarized. Moreover, the mammalian homologues of yeast CF IA proteins, along with their key roles are described. This knowledge would be helpful for better comprehension of the mechanism associated with this marvel; thus opening up vast avenues in this area.
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38
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Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic analysis of mRNA splicing relevant proteins in aging HSPCs. Aging Clin Exp Res 2021; 33:3123-3134. [PMID: 32141009 DOI: 10.1007/s40520-020-01509-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/10/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND HSPC (hematopoietic stem/progenitor cell) aging was closely associated with the organism aging, senile diseases and hematopoietic related diseases. Therefore, study on HSPC aging is of great significance to further elucidate the mechanisms of aging and to treat hematopoietic disease resulting from HSPC aging. Little attention had been paid to mRNA splicing as a mechanism underlying HSPC senescence. RESULTS We used our lab's patented in vitro aging model of HSPCs to analyze mRNA splicing relevant protein alterations with iTRAQ-based proteomic analysis. We found that not only the notable mRNA splicing genes such as SR, hnRNP, WBP11, Sf3b1, Ptbp1 and U2AF1 but also the scarcely reported mRNA splicing relevant genes such as Rbmxl1, Dhx16, Pcbp2, Pabpc1 were significantly down-regulated. We further verified their gene expressions by qRT-PCR. In addition, we reported the effect of Spliceostatin A (SSA), which inhibits mRNA splicing in vivo and in vitro, on HSPC aging. CONCLUSIONS It was concluded that mRNA splicing emerged as an important factor for the vulnerability of HSPC aging. This study improved our understanding of the role of mRNA splicing in the HSPC aging process.
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Sanbonmatsu K. Getting to the bottom of lncRNA mechanism: structure-function relationships. Mamm Genome 2021; 33:343-353. [PMID: 34642784 PMCID: PMC8509902 DOI: 10.1007/s00335-021-09924-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022]
Abstract
While long non-coding RNAs are known to play key roles in disease and development, relatively few structural studies have been performed for this important class of RNAs. Here, we review functional studies of long non-coding RNAs and expose the need for high-resolution 3-D structural studies, discussing the roles of long non-coding RNAs in the cell and how structure–function relationships might be used to elucidate further understanding. We then describe structural studies of other classes of RNAs using chemical probing, nuclear magnetic resonance, small-angle X-ray scattering, X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Next, we review early structural studies of long non-coding RNAs to date and describe the way forward for the structural biology of long non-coding RNAs in terms of cryo-EM.
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40
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Internally Symmetrical Stwintrons and Related Canonical Introns in Hypoxylaceae Species. J Fungi (Basel) 2021; 7:jof7090710. [PMID: 34575748 PMCID: PMC8469720 DOI: 10.3390/jof7090710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 01/01/2023] Open
Abstract
Spliceosomal introns are pervasive in eukaryotes. Intron gains and losses have occurred throughout evolution, but the origin of new introns is unclear. Stwintrons are complex intervening sequences where one of the sequence elements (5′-donor, lariat branch point element or 3′-acceptor) necessary for excision of a U2 intron (external intron) is itself interrupted by a second (internal) U2 intron. In Hypoxylaceae, a family of endophytic fungi, we uncovered scores of donor-disrupted stwintrons with striking sequence similarity among themselves and also with canonical introns. Intron–exon structure comparisons suggest that these stwintrons have proliferated within diverging taxa but also give rise to proliferating canonical introns in some genomes. The proliferated (stw)introns have integrated seamlessly at novel gene positions. The recently proliferated (stw)introns appear to originate from a conserved ancestral stwintron characterised by terminal inverted repeats (45–55 nucleotides), a highly symmetrical structure that may allow the formation of a double-stranded intron RNA molecule. No short tandem duplications flank the putatively inserted intervening sequences, which excludes a DNA transposition-based mechanism of proliferation. It is tempting to suggest that this highly symmetrical structure may have a role in intron proliferation by (an)other mechanism(s).
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Leung AKW, Kondo Y, Krummel DAP, Li J, Price SR, van Roon AMM. Engineering Crystal Packing in RNA-Protein Complexes II: A Historical Perspective from the Structural Studies of the Spliceosome. CRYSTALS 2021; 11:948. [PMID: 35154816 PMCID: PMC7612351 DOI: 10.3390/cryst11080948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cryo-electron microscopy has greatly advanced our understanding of how the spliceosome cycles through different conformational states to conduct the chemical reactions that remove introns from pre-mRNA transcripts. The Cryo-EM structures were built upon decades of crystallographic studies of various spliceosomal RNA-protein complexes. In this review we give an overview of the crystal structures solved in the Nagai group, utilizing many of the strategies to design crystal packing as described in the accompanying paper.
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Affiliation(s)
- Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Daniel A. Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jade Li
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Stephen R. Price
- Research Department of Cell and Developmental Biology, UCL Division of Biosciences, London WC1E 6DE, UK
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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43
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Xu P, Zhang L, Xiao Y, Li W, Hu Z, Zhang R, Li J, Wu F, Xi Y, Zou Q, Wang Z, Guo R, Ma H, Dong S, Xiao M, Yang Z, Ren X, Wei C, Yu W. UHRF1 regulates alternative splicing by binding to splicing factors and U snRNAs. Hum Mol Genet 2021; 30:2110-2122. [PMID: 34196368 DOI: 10.1093/hmg/ddab178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/08/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
The well-established functions of UHRF1 converge to DNA biological processes, as exemplified by DNA methylation maintenance and DNA damage repair during cell cycles. However, the potential effect of UHRF1 on RNA metabolism is largely unexplored. Here, we revealed that UHRF1 serves as a novel alternative RNA splicing regulator. The protein interactome of UHRF1 identified various splicing factors. Among them, SF3B3 could interact with UHRF1 directly and participate in UHRF1-regulated alternative splicing events. Furthermore, we interrogated the RNA interactome of UHRF1, and surprisingly, we identified U snRNAs, the canonical spliceosome component, in the UHRF1-associated RNA components. Unexpectedly, we found H3R2 methylation status determines the binding preference of U snRNA, especially U2 snRNA. The involvement of U snRNAs in UHRF1-containing complex and their binding preference to specific chromatin configuration imply a finely orchestrated mechanism at play. Our results provided the resources and pinpointed the molecular basis of UHRF1-mediated alternative RNA splicing, which will help us better our understanding of the physiological and pathological roles of UHRF1 in disease development.
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Affiliation(s)
- Peng Xu
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Lan Zhang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, 510060, China
| | - Yao Xiao
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Wei Li
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Zhiqiang Hu
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Rukui Zhang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Jin Li
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Feizhen Wu
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Clinical Science of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Yanping Xi
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Qingping Zou
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Rui Guo
- Key Laboratory of Medical Epigenetics and Metabolism, Institute of Clinical Science of Zhongshan Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Honghui Ma
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Shihua Dong
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Min Xiao
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China.,Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Zhicong Yang
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Xiaoguang Ren
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenqiang Yu
- Shanghai Public Health Clinical Centre and Department of General Surgery, Huashan Hospital, Cancer Metastasis Institute and Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508, China
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44
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Payán-Bravo L, Fontalva S, Peñate X, Cases I, Guerrero-Martínez J, Pareja-Sánchez Y, Odriozola-Gil Y, Lara E, Jimeno-González S, Suñé C, Muñoz-Centeno M, Reyes J, Chávez S. Human prefoldin modulates co-transcriptional pre-mRNA splicing. Nucleic Acids Res 2021; 49:6267-6280. [PMID: 34096575 PMCID: PMC8216451 DOI: 10.1093/nar/gkab446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022] Open
Abstract
Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.
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Affiliation(s)
- Laura Payán-Bravo
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Fontalva
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Ildefonso Cases
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - José Antonio Guerrero-Martínez
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Yerma Pareja-Sánchez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Yosu Odriozola-Gil
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Esther Lara
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Silvia Jimeno-González
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Carles Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine “López Neyra” IPBLN-CSIC, PTS, Granada, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - José C Reyes
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Junta de Andalucia-University of Pablo de Olavide-University of Seville-CSIC, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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45
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A single m 6A modification in U6 snRNA diversifies exon sequence at the 5' splice site. Nat Commun 2021; 12:3244. [PMID: 34050143 PMCID: PMC8163875 DOI: 10.1038/s41467-021-23457-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5' splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5' exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.
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46
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Yeh FL, Chang SL, Ahmed GR, Liu HI, Tung L, Yeh CS, Lanier LS, Maeder C, Lin CM, Tsai SC, Hsiao WY, Chang WH, Chang TH. Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling. Nat Commun 2021; 12:3082. [PMID: 34035302 PMCID: PMC8149812 DOI: 10.1038/s41467-021-23459-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
Splicing, a key step in the eukaryotic gene-expression pathway, converts precursor messenger RNA (pre-mRNA) into mRNA by excising introns and ligating exons. This task is accomplished by the spliceosome, a macromolecular machine that must undergo sequential conformational changes to establish its active site. Each of these major changes requires a dedicated DExD/H-box ATPase, but how these enzymes are activated remain obscure. Here we show that Prp28, a yeast DEAD-box ATPase, transiently interacts with the conserved 5' splice-site (5'SS) GU dinucleotide and makes splicing-dependent contacts with the U1 snRNP protein U1C, and U4/U6.U5 tri-snRNP proteins, Prp8, Brr2, and Snu114. We further show that Prp28's ATPase activity is potentiated by the phosphorylated Npl3, but not the unphosphorylated Npl3, thus suggesting a strategy for regulating DExD/H-box ATPases. We propose that Npl3 is a functional counterpart of the metazoan-specific Prp28 N-terminal region, which can be phosphorylated and serves as an anchor to human spliceosome.
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Affiliation(s)
- Fu-Lung Yeh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Hsin-I Liu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Luh Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Leah Stands Lanier
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - Corina Maeder
- Department of Chemistry, Trinity University, San Antonio, TX, USA
| | - Che-Min Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Chun Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Yi Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
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47
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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48
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Rhoades D, Rheingold AL, O'Malley BW, Wang J. Expedient Total Syntheses of Pladienolide-Derived Spliceosome Modulators. J Am Chem Soc 2021; 143:4915-4920. [PMID: 33755462 DOI: 10.1021/jacs.1c01135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Atom and step economical total syntheses of spliceosome modulating natural products pladienolides A and B are described. The strategic functionalization of an unsaturated macrolide precursor enabled the most concise syntheses of these natural products to date and provides convenient, flexible access to stereodefined macrolides to streamline medicinal chemistry explorations. Notably, this synthetic route does not depend on protecting group manipulations that traditionally define synthesis planning for polyhydroxylated natural products of polyketide origin. Its utility is further demonstrated by the enantioselective total synthesis of H3B-8800, a hitherto semisynthetic pladienolide-derived spliceosome modulator undergoing clinical trials for hematological malignancies.
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Affiliation(s)
| | - Arnold L Rheingold
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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49
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Gehring NH, Roignant JY. Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends Genet 2021; 37:355-372. [DOI: 10.1016/j.tig.2020.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
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50
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021; 296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023] Open
Abstract
Some of the amazing contributions brought to the scientific community by the Protein Data Bank (PDB) are described. The focus is on nucleic acid structures with a bias toward RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects, which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.
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