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Bai Y, Cui G, Sun X, Wei M, Liu Y, Guo J, Yang Y. ANGPTL4 Stabilizes Bone Morphogenetic Protein 7 Through Deubiquitination and Promotes HCC Proliferation via the SMAD/MAPK Pathway. DNA Cell Biol 2024. [PMID: 38829105 DOI: 10.1089/dna.2024.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
This study aimed to determine the function of angiopoietin-related protein 4 (ANGPTL4) and bone morphogenetic protein 7 (BMP7) on hepatocellular carcinoma (HCC). Overexpressing plasmids were cotransfected into HepG2 cells to determine the interaction between ANGPTL4 and BMP7. The effect of ANGPTL4 on the stability of BMP7 is examined by detecting the expression and ubiquitination levels. In vitro and in vivo experiments of knocking down ANGPTL4 while overexpressing BMP7 were performed to investigate whether the effects of ANGPTL4 on HCC proliferation, migration, and downstream signaling pathways were dependent on BMP7. ANGPTL4 is able to interact with BMP7, and knockdown of ANGPTL4 increased BMP7 expression and ubiquitination. Overexpression of BMP7 reversed the inhibition of HCC proliferation and migration as well as the decrease in the expression levels of Smad1/5/8 and MAPK14 caused by knockdown of ANGPTL4. ANGPTL4 promotes the proliferation and migration of HCC by inhibiting the ubiquitination degradation of BMP7 and the Smad/MAPK pathway, providing a novel mechanism and a potential therapeutic target for the treatment of HCC.
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Affiliation(s)
- Yun Bai
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guanghua Cui
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoke Sun
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meiqi Wei
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanying Liu
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialu Guo
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Yang
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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2
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Bai Y, Cui G, Sun X, Wei M, Liu Y, Guo J, Yang Y. Angiopoietin-Related Protein 4-Transcript 3 Increases the Proliferation, Invasion, and Migration of Hepatocellular Carcinoma Cells and Inhibits Apoptosis. DNA Cell Biol 2024; 43:175-184. [PMID: 38466955 DOI: 10.1089/dna.2023.0392] [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] [Indexed: 03/13/2024] Open
Abstract
To investigate the functional differences of angiopoietin-related protein 4 (ANGPTL4) transcripts in hepatocellular carcinoma (HCC) cells. By transfecting ANGPTL4-Transcript 1 and ANGPTL4-Transcript 3 overexpression vectors into HepG2 and Huh7 cell lines with ANGPTL4 knockdown, the effects of overexpression of two transcripts on cell viability, invasion, migration, and apoptosis were analyzed. The expression of two transcripts was compared in human liver cancer tissue, and their effects on tumor development were validated in vivo experiments in mice. Compared with control, the overexpression of ANGPTL4-Transcript 1 had no significant effect on viability, invasion, healing, and apoptosis of HepG2 and Huh7 cells. However, these two cell lines overexpressing ANGPTL4-Transcript 3 showed remarkably enhanced cell viability, invasive and healing ability, and decreased apoptosis ability. Furthermore, the mRNA level of ANGPTL4-Transcript 3 was significantly increased in human HCC tissues and promoted tumor growth compared with Transcript 1. Different transcripts of gene ANGPTL4 have distinct effects on HCC. The abnormally elevated Transcript 3 with the specific ability of promoting HCC proliferation, infiltration, and migration is expected to become a new biological marker and more precise intervention target for HCC.
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Affiliation(s)
- Yun Bai
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guanghua Cui
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoke Sun
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meiqi Wei
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanying Liu
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialu Guo
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Yang
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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3
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Choi S, Lee HS, Cho N, Kim I, Cheon S, Park C, Kim EM, Kim W, Kim KK. RBFOX2-regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling. Nucleic Acids Res 2022; 50:8658-8673. [PMID: 35699208 PMCID: PMC9410899 DOI: 10.1093/nar/gkac509] [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: 10/15/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Alternative pre-mRNA splicing is key to proteome diversity; however, the biological roles of alternative splicing (AS) in signaling pathways remain elusive. Here, we focus on TEA domain transcription factor 1 (TEAD1), a YAP binding factor in the Hippo signaling pathway. Public database analyses showed that expression of YAP-TEAD target genes negatively correlated with the expression of a TEAD1 isoform lacking exon 6 (TEAD1ΔE6) but did not correlate with overall TEAD1 expression. We confirmed that the transcriptional activity and oncogenic properties of the full-length TEAD1 isoform were greater than those of TEAD1ΔE6, with the difference in transcription related to YAP interaction. Furthermore, we showed that RNA-binding Fox-1 homolog 2 (RBFOX2) promoted the inclusion of TEAD1 exon 6 via binding to the conserved GCAUG element in the downstream intron. These results suggest a regulatory mechanism of RBFOX2-mediated TEAD1 AS and provide insight into AS-specific modulation of signaling pathways.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyo Seong Lee
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Inyoung Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.,Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Wantae Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
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4
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Liu X, Pan X, Chen D, Yin C, Peng J, Shi W, Qi L, Wang R, Zhao W, Zhang Z, Yang J, Peng YL. Prp19-associated splicing factor Cwf15 regulates fungal virulence and development in the rice blast fungus. Environ Microbiol 2021; 23:5901-5916. [PMID: 34056823 DOI: 10.1111/1462-2920.15616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 11/29/2022]
Abstract
The splicing factor Cwf15 is an essential component of the Prp19-associated component of the spliceosome and regulates intron splicing in several model species, including yeasts and human cells. However, the roles of Cwf15 remain unexplored in plant pathogenic fungi. Here, we report that MoCWF15 in the rice blast fungus Magnaporthe oryzae is non-essential to viability and important to fungal virulence, growth and conidiation. MoCwf15 contains a putative nuclear localization signal (NLS) and is localized into the nucleus. The NLS sequence but not the predicted phosphorylation site or two sumoylation sites was essential for the biological functions of MoCwf15. Importantly, MoCwf15 physically interacted with the Prp19-associated splicing factors MoCwf4, MoSsa1 and MoCyp1, and negatively regulated protein accumulations of MoCyp1 and MoCwf4. Furthermore, with the deletion of MoCWF15, aberrant intron splicing occurred in near 400 genes, 20 of which were important to the fungal development and virulence. Taken together, MoCWF15 regulates fungal growth and infection-related development by modulating the intron splicing efficiency of a subset of genes in the rice blast fungus.
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Affiliation(s)
- Xinsen Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiao Pan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Deng Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Changfa Yin
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Junbo Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Wei Shi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Linlu Qi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ruijin Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Yang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - You-Liang Peng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China
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5
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Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA, Hemberg M. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biol 2021; 22:43. [PMID: 33482885 PMCID: PMC7821500 DOI: 10.1186/s13059-020-02246-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Microexons, exons that are ≤ 30 nucleotides, are a highly conserved and dynamically regulated set of cassette exons. They have key roles in nervous system development and function, as evidenced by recent results demonstrating the impact of microexons on behaviour and cognition. However, microexons are often overlooked due to the difficulty of detecting them using standard RNA-seq aligners. RESULTS Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons. We process 289 RNA-seq datasets from eighteen mouse tissues corresponding to nine embryonic and postnatal stages, providing the most comprehensive survey of microexons available for mice. We detect 2984 microexons, 332 of which are differentially spliced throughout mouse embryonic brain development, including 29 that are not present in mouse transcript annotation databases. Unsupervised clustering of microexons based on their inclusion patterns segregates brain tissues by developmental time, and further analysis suggests a key function for microexons in axon growth and synapse formation. Finally, we analyse single-cell RNA-seq data from the mouse visual cortex, and for the first time, we report differential inclusion between neuronal subpopulations, suggesting that some microexons could be cell type-specific. CONCLUSIONS MicroExonator facilitates the investigation of microexons in transcriptome studies, particularly when analysing large volumes of data. As a proof of principle, we use MicroExonator to analyse a large collection of both mouse bulk and single-cell RNA-seq datasets. The analyses enabled the discovery of previously uncharacterized microexons, and our study provides a comprehensive microexon inclusion catalogue during mouse development.
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Affiliation(s)
- Guillermo E Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Roberto Munita
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hugo J R Fernandes
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Maria Estela Andres
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric A Miska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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6
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SRRM4 Expands the Repertoire of Circular RNAs by Regulating Microexon Inclusion. Cells 2020; 9:cells9112488. [PMID: 33207694 PMCID: PMC7697094 DOI: 10.3390/cells9112488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)-which occur in 30% of functional mRNA transcripts-have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLBRA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family.
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7
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Wegener M, Müller-McNicoll M. Nuclear retention of mRNAs - quality control, gene regulation and human disease. Semin Cell Dev Biol 2017; 79:131-142. [PMID: 29102717 DOI: 10.1016/j.semcdb.2017.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
Abstract
Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of gene regulation, which enables the cell to rapidly respond to stress, viral infection, differentiation cues or changing environmental conditions. Focusing on mammalian cells, we discuss recent insights into the mechanisms and functions of nuclear retention, describe retention-promoting features in protein-coding transcripts and propose mechanisms for their regulated release into the cytoplasm. Moreover, we discuss examples of how aberrant nuclear retention of mRNAs may lead to human diseases.
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Affiliation(s)
- Marius Wegener
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany.
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8
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Kumar S, Cruz E, Joshi S, Patel A, Jahan R, Batra SK, Jain M. Genetic variants of mucins: unexplored conundrum. Carcinogenesis 2017; 38:671-679. [PMID: 27838635 DOI: 10.1093/carcin/bgw120] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 11/10/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative gene splicing, occurring ubiquitously in multicellular organisms can produce several protein isoforms with putatively different functions. The enormously extended genomic structure of mucin genes characterized by the presence of multiple exons encoding various domains may result in functionally diverse repertoire of mucin proteins due to alternative splicing. Splice variants (Svs) and mutations in mucin genes have been observed in various cancers and shown to participate in cancer progression and metastasis. Although several mucin Svs have been identified, their potential functions remain largely unexplored with the exception of the Svs of MUC1 and MUC4. A few studies have examined the expression of MUC1 and MUC4 Svs in cancer and indicated their potential involvement in promoting cancer cell proliferation, invasion, migration, angiogenesis and inflammation. Herein we review the current understanding of mucin Svs in cancer and inflammation and discuss the potential impact of splicing in generating a functionally diverse repertoire of mucin gene products. We also performed mutational analysis of mucin genes across five major cancer types in International Cancer Genome Consortium database and found unequal mutational rates across the panel of cancer-associated mucins. Although the functional role of mucins in the pathobiology of various malignancies and their utility as diagnostic and therapeutic targets remain undisputed, these attributes need to be reevaluated in light of the potentially unique functions of disease-specific genetic variants of mucins. Thus, the expressional and functional characterization of the genetic variants of mucins may provide avenues to fully exploit their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Sushil Kumar
- Department of Biochemistry and Molecular Biology
| | - Eric Cruz
- Department of Biochemistry and Molecular Biology
| | | | - Asish Patel
- Department of Biochemistry and Molecular Biology
| | - Rahat Jahan
- Department of Biochemistry and Molecular Biology
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology.,Eppley Institute for Research in Cancer and Allied Diseases.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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9
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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10
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Tarn WY, Kuo HC, Yu HI, Liu SW, Tseng CT, Dhananjaya D, Hung KY, Tu CC, Chang SH, Huang GJ, Chiu IM. RBM4 promotes neuronal differentiation and neurite outgrowth by modulating Numb isoform expression. Mol Biol Cell 2016; 27:1676-83. [PMID: 27009199 PMCID: PMC4865323 DOI: 10.1091/mbc.e15-11-0798] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/18/2016] [Indexed: 01/22/2023] Open
Abstract
RBM4 modulates alternative exon selection of Numb and up-regulates proneural Mash1 gene expression, possibly via specific Numb isoforms. RBM4 overexpression promotes neuronal cell differentiation. Moreover, RBM4 is essential for neurite outgrowth in primary cortical neurons by modulating specific Numb isoform expression. RBM4 participates in cell differentiation by regulating tissue-specific alternative pre-mRNA splicing. RBM4 also has been implicated in neurogenesis in the mouse embryonic brain. Using mouse embryonal carcinoma P19 cells as a neural differentiation model, we observed a temporal correlation between RBM4 expression and a change in splicing isoforms of Numb, a cell-fate determination gene. Knockdown of RBM4 affected the inclusion/exclusion of exons 3 and 9 of Numb in P19 cells. RBM4-deficient embryonic mouse brain also exhibited aberrant splicing of Numb pre-mRNA. Using a splicing reporter minigene assay, we demonstrated that RBM4 promoted exon 3 inclusion and exon 9 exclusion. Moreover, we found that RBM4 depletion reduced the expression of the proneural gene Mash1, and such reduction was reversed by an RBM4-induced Numb isoform containing exon 3 but lacking exon 9. Accordingly, induction of ectopic RBM4 expression in neuronal progenitor cells increased Mash1 expression and promoted cell differentiation. Finally, we found that RBM4 was also essential for neurite outgrowth from cortical neurons in vitro. Neurite outgrowth defects of RBM4-depleted neurons were rescued by RBM4-induced exon 9–lacking Numb isoforms. Therefore our findings indicate that RBM4 modulates exon selection of Numb to generate isoforms that promote neuronal cell differentiation and neurite outgrowth.
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Affiliation(s)
- Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Che Kuo
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-I Yu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Shin-Wu Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Ching-Tzu Tseng
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Dodda Dhananjaya
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kuan-Yang Hung
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Chiang Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Shuo-Hsiu Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Guo-Jen Huang
- Graduate Institute of Biomedical Sciences, Chung-Gung University, Tao-Yuan City 33302, Taiwan
| | - Ing-Ming Chiu
- National Health Research Institutes, Chu-Nan 35053, Taiwan
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11
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Gazzoli I, Pulyakhina I, Verwey NE, Ariyurek Y, Laros JFJ, 't Hoen PAC, Aartsma-Rus A. Non-sequential and multi-step splicing of the dystrophin transcript. RNA Biol 2015; 13:290-305. [PMID: 26670121 PMCID: PMC4829307 DOI: 10.1080/15476286.2015.1125074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The dystrophin protein encoding DMD gene is the longest human gene. The 2.2 Mb long human dystrophin transcript takes 16 hours to be transcribed and is co-transcriptionally spliced. It contains long introns (24 over 10kb long, 5 over 100kb long) and the heterogeneity in intron size makes it an ideal transcript to study different aspects of the human splicing process. Splicing is a complex process and much is unknown regarding the splicing of long introns in human genes. Here, we used ultra-deep transcript sequencing to characterize splicing of the dystrophin transcripts in 3 different human skeletal muscle cell lines, and explored the order of intron removal and multi-step splicing. Coverage and read pair analyses showed that around 40% of the introns were not always removed sequentially. Additionally, for the first time, we report that non-consecutive intron removal resulted in 3 or more joined exons which are flanked by unspliced introns and we defined these joined exons as an exon block. Lastly, computational and experimental data revealed that, for the majority of dystrophin introns, multistep splicing events are used to splice out a single intron. Overall, our data show for the first time in a human transcript, that multi-step intron removal is a general feature of mRNA splicing.
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Affiliation(s)
- Isabella Gazzoli
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Irina Pulyakhina
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Nisha E Verwey
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Yavuz Ariyurek
- b Leiden Genome Technology Center, Leiden University Medical Center , Leiden , The Netherlands
| | - Jeroen F J Laros
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands.,b Leiden Genome Technology Center, Leiden University Medical Center , Leiden , The Netherlands
| | - Peter A C 't Hoen
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Annemieke Aartsma-Rus
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
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12
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Le KQ, Prabhakar BS, Hong WJ, Li LC. Alternative splicing as a biomarker and potential target for drug discovery. Acta Pharmacol Sin 2015; 36:1212-8. [PMID: 26073330 DOI: 10.1038/aps.2015.43] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/15/2015] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing is a key process of multi-exonic gene expression during pre-mRNA maturation. In this process, particular exons of a gene will be included within or excluded from the final matured mRNA, and the resulting transcripts generate diverse protein isoforms. Recent evidence demonstrates that approximately 95% of human genes with multiple exons undergo alternative splicing during pre-mRNA maturation. Thus, alternative splicing plays a critical role in physiological processes and cell development programs, and.dysregulation of alternative splicing is highly associated with human diseases, such as cancer, diabetes and neurodegenerative diseases. In this review, we discuss the regulation of alternative splicing, examine the relationship between alternative splicing and human diseases, and describe several approaches that modify alternative splicing, which could aid in human disease diagnosis and therapy.
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13
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Ravi S, Schilder RJ, Kimball SR. Role of precursor mRNA splicing in nutrient-induced alterations in gene expression and metabolism. J Nutr 2015; 145:841-6. [PMID: 25761502 PMCID: PMC4408736 DOI: 10.3945/jn.114.203216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Precursor mRNA (pre-mRNA) splicing is a critical step in gene expression that results in the removal of intronic sequences from immature mRNA, leading to the production of mature mRNA that can be translated into protein. Alternative pre-mRNA splicing is the process whereby alternative exons and/or introns are selectively included or excluded, generating mature mRNAs that encode proteins that may differ in function. The resulting alterations in the pattern of protein isoform expression can result in changes in protein-protein interaction, subcellular localization, and flux through metabolic pathways. Although basic mechanisms of pre-mRNA splicing of introns and exons are reasonably well characterized, how these mechanisms are regulated remains poorly understood. The goal of this review is to highlight selected recent advances in our understanding of the regulation of pre-mRNA splicing by nutrients and modulation of nutrient metabolism that result from changes in pre-mRNA splicing.
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Affiliation(s)
- Suhana Ravi
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA; and
| | - Rudolf J Schilder
- Departments of Entomology and Biology, The Pennsylvania State University, State College, PA
| | - Scot R Kimball
- Department of Cellular and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA; and
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14
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Shi J, Pabon K, Scotto KW. Methylxanthines Increase Expression of the Splicing Factor SRSF2 by Regulating Multiple Post-transcriptional Mechanisms. J Biol Chem 2015; 290:14986-5003. [PMID: 25818199 DOI: 10.1074/jbc.m114.624254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 01/20/2023] Open
Abstract
We have previously reported that the methylxanthine caffeine increases expression of the splicing factor SRSF2, the levels of which are normally controlled by a negative autoregulatory loop. In the present study we have investigated the mechanisms by which methylxanthines induce this aberrant overexpression. RT-PCR analyses suggested little impact of caffeine on SRSF2 total mRNA levels. Instead, caffeine induced changes in the levels of SRSF2 3' UTR splice variants. Although some of these variants were substrates for nonsense-medicated decay (NMD), and could potentially have been stabilized by caffeine-mediated inhibition of NMD, down-regulation of NMD by a genetic approach was not sufficient to reproduce the phenotype. Furthermore, cell-based assays demonstrated that some of the caffeine-induced variants were intrinsically more efficiently translated than others; the addition of caffeine increased the translational efficiency of most SRSF2 transcripts. MicroRNA array analyses revealed a significant caffeine-mediated decrease in the expression of two SRSF2-targeting miRs, both of which were shown to repress translation of specific SRSF2 splice variants. These data support a complex model whereby caffeine down-regulates SRSF2-targeting microRNAs, leading to an increase in SRSF2 translation, which in turn induces SRSF2 splicing. SRSF2 splice variants are then stabilized by caffeine-mediated NMD inhibition, breaking the normal negative feedback loop and allowing the aberrant increase in SRSF2 protein levels. These findings highlight the complexity of SRSF2 gene regulation, and suggest ways in which SRSF2 expression may be dysregulated in disease.
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Affiliation(s)
- Jia Shi
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kirk Pabon
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
| | - Kathleen W Scotto
- From the Rutgers Cancer Institute of New Jersey, the Robert Wood Johnson Medical School, and the Graduate School of Biomedical Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903
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15
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Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CWJ. Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J 2015; 34:653-68. [PMID: 25599992 PMCID: PMC4365034 DOI: 10.15252/embj.201489852] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.
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Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Nicolás Bellora
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain INIBIOMA CONICET-UNComahue, Bariloche, Argentina
| | - Julian König
- MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Martina Hallegger
- Department of Biochemistry, University of Cambridge, Cambridge, UK Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Eduardo Eyras
- Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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16
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Shefer K, Sperling J, Sperling R. The Supraspliceosome - A Multi-Task Machine for Regulated Pre-mRNA Processing in the Cell Nucleus. Comput Struct Biotechnol J 2014; 11:113-22. [PMID: 25408845 PMCID: PMC4232567 DOI: 10.1016/j.csbj.2014.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/23/2023] Open
Abstract
Pre-mRNA splicing of Pol II transcripts is executed in the mammalian cell nucleus within a huge (21 MDa) and highly dynamic RNP machine — the supraspliceosome. It is composed of four splicing active native spliceosomes, each resembling an in vitro assembled spliceosome, which are connected by the pre-mRNA. Supraspliceosomes harbor protein splicing factors and all the five-spliceosomal U snRNPs. Recent analysis of specific supraspliceosomes at defined splicing stages revealed that they harbor all five spliceosomal U snRNAs at all splicing stages. Supraspliceosomes harbor additional pre-mRNA processing components, such as the 5′-end and 3′-end processing components, and the RNA editing enzymes ADAR1 and ADAR2. The structure of the native spliceosome, at a resolution of 20 Å, was determined by cryo-EM. A unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in-silico studies, localizing the five U snRNPs mostly within its large subunit, and sheltering the active core components deep within the spliceosomal cavity. The supraspliceosome provides a platform for coordinating the numerous processing steps that the pre-mRNA undergoes: 5′ and 3′-end processing activities, RNA editing, constitutive and alternative splicing, and processing of intronic microRNAs. It also harbors a quality control mechanism termed suppression of splicing (SOS) that, under normal growth conditions, suppresses splicing at abundant intronic latent 5′ splice sites in a reading frame-dependent fashion. Notably, changes in these regulatory processing activities are associated with human disease and cancer. These findings emphasize the supraspliceosome as a multi-task master regulator of pre-mRNA processing in the cell nucleus.
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Affiliation(s)
- Kinneret Shefer
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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