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Yan Z, Yang J, Wei WT, Zhou ML, Mo DX, Wan X, Ma R, Wu MM, Huang JH, Liu YJ, Lv FH, Li MH. A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues. Nat Commun 2024; 15:3970. [PMID: 38730227 PMCID: PMC11087590 DOI: 10.1038/s41467-024-48261-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: 08/23/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
High-altitude hypoxia acclimatization requires whole-body physiological regulation in highland immigrants, but the underlying genetic mechanism has not been clarified. Here we use sheep as an animal model for low-to-high altitude translocation. We generate multi-omics data including whole-genome sequences, time-resolved bulk RNA-Seq, ATAC-Seq and single-cell RNA-Seq from multiple tissues as well as phenotypic data from 20 bio-indicators. We characterize transcriptional changes of all genes in each tissue, and examine multi-tissue temporal dynamics and transcriptional interactions among genes. Particularly, we identify critical functional genes regulating the short response to hypoxia in each tissue (e.g., PARG in the cerebellum and HMOX1 in the colon). We further identify TAD-constrained cis-regulatory elements, which suppress the transcriptional activity of most genes under hypoxia. Phenotypic and transcriptional evidence indicate that antenatal hypoxia could improve hypoxia tolerance in offspring. Furthermore, we provide time-series expression data of candidate genes associated with human mountain sickness (e.g., BMPR2) and high-altitude adaptation (e.g., HIF1A). Our study provides valuable resources and insights for future hypoxia-related studies in mammals.
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Affiliation(s)
- Ze Yan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen-Tian Wei
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ming-Liang Zhou
- Sichuan Academy of Grassland Science, Chengdu, 611743, China
| | - Dong-Xin Mo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing Wan
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Rui Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mei-Ming Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ya-Jing Liu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Feng-Hua Lv
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Trink Y, Urbach A, Dekel B, Hohenstein P, Goldberger J, Kalisky T. Characterization of Alternative Splicing in High-Risk Wilms' Tumors. Int J Mol Sci 2024; 25:4520. [PMID: 38674106 PMCID: PMC11050615 DOI: 10.3390/ijms25084520] [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: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The significant heterogeneity of Wilms' tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms' tumors using a publicly available RNAseq dataset of high-risk Wilms' tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or "archetypes", resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the epithelial-to-mesenchymal transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms' tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.
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Affiliation(s)
- Yaron Trink
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute and Division of Pediatric Nephrology, Edmond and Lily Safra Children’s Hospital, Sheba Tel-HaShomer Medical Centre, Ramat Gan 5262000, Israel
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Jacob Goldberger
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Tomer Kalisky
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
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3
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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4
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Wiedner HJ, Blue RE, Sadovsky M, Mills CA, Wehrens XH, Herring LE, Giudice J. RBFOX2 regulated EYA3 isoforms partner with SIX4 or ZBTB1 to control transcription during myogenesis. iScience 2023; 26:108258. [PMID: 38026174 PMCID: PMC10665822 DOI: 10.1016/j.isci.2023.108258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/14/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Alternative splicing is a prevalent gene-regulatory mechanism, with over 95% of multi-exon human genes estimated to be alternatively spliced. Here, we describe a tissue-specific, developmentally regulated, highly conserved, and disease-associated alternative splicing event in exon 7 of the eyes absent homolog 3 (Eya3) gene. We discovered that EYA3 expression is vital to the proliferation and differentiation of myoblasts. Genome-wide transcriptomic analysis and mass spectrometry-based proteomic studies identified SIX homeobox 4 (SIX4) and zinc finger and BTB-domain containing 1 (ZBTB1), as major transcription factors that interact with EYA3 to dictate gene expression. EYA3 isoforms differentially regulate transcription, indicating that splicing aids in temporal control of gene expression during muscle cell differentiation. Finally, we identified RNA-binding fox-1 homolog 2 (RBFOX2) as the main regulator of EYA3 splicing. Together, our findings illustrate the interplay between alternative splicing and transcription during myogenesis.
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Affiliation(s)
- Hannah J. Wiedner
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - R. Eric Blue
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matheus Sadovsky
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - C. Allie Mills
- UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xander H.T. Wehrens
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Laura E. Herring
- UNC Proteomics Core Facility, Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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5
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Imbriano C, Moresi V, Belluti S, Renzini A, Cavioli G, Maretti E, Molinari S. Epitranscriptomics as a New Layer of Regulation of Gene Expression in Skeletal Muscle: Known Functions and Future Perspectives. Int J Mol Sci 2023; 24:15161. [PMID: 37894843 PMCID: PMC10606696 DOI: 10.3390/ijms242015161] [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: 09/14/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epitranscriptomics refers to post-transcriptional regulation of gene expression via RNA modifications and editing that affect RNA functions. Many kinds of modifications of mRNA have been described, among which are N6-methyladenosine (m6A), N1-methyladenosine (m1A), 7-methylguanosine (m7G), pseudouridine (Ψ), and 5-methylcytidine (m5C). They alter mRNA structure and consequently stability, localization and translation efficiency. Perturbation of the epitranscriptome is associated with human diseases, thus opening the opportunity for potential manipulations as a therapeutic approach. In this review, we aim to provide an overview of the functional roles of epitranscriptomic marks in the skeletal muscle system, in particular in embryonic myogenesis, muscle cell differentiation and muscle homeostasis processes. Further, we explored high-throughput epitranscriptome sequencing data to identify RNA chemical modifications in muscle-specific genes and we discuss the possible functional role and the potential therapeutic applications.
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Affiliation(s)
- Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy;
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy; (A.R.); (G.C.)
| | - Eleonora Maretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
| | - Susanna Molinari
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (S.B.); (E.M.)
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6
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Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis. Nat Commun 2023; 14:1329. [PMID: 36898987 PMCID: PMC10006080 DOI: 10.1038/s41467-023-37017-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
During muscle cell differentiation, the alternatively spliced, acidic β-domain potentiates transcription of Myocyte-specific Enhancer Factor 2 (Mef2D). Sequence analysis by the FuzDrop method indicates that the β-domain can serve as an interaction element for Mef2D higher-order assembly. In accord, we observed Mef2D mobile nuclear condensates in C2C12 cells, similar to those formed through liquid-liquid phase separation. In addition, we found Mef2D solid-like aggregates in the cytosol, the presence of which correlated with higher transcriptional activity. In parallel, we observed a progress in the early phase of myotube development, and higher MyoD and desmin expression. In accord with our predictions, the formation of aggregates was promoted by rigid β-domain variants, as well as by a disordered β-domain variant, capable of switching between liquid-like and solid-like higher-order states. Along these lines, NMR and molecular dynamics simulations corroborated that the β-domain can sample both ordered and disordered interactions leading to compact and extended conformations. These results suggest that β-domain fine-tunes Mef2D higher-order assembly to the cellular context, which provides a platform for myogenic regulatory factors and the transcriptional apparatus during the developmental process.
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7
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Bhat VD, Jayaraj J, Babu K. RNA and neuronal function: the importance of post-transcriptional regulation. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac011. [PMID: 38596700 PMCID: PMC10913846 DOI: 10.1093/oons/kvac011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/03/2022] [Accepted: 05/28/2022] [Indexed: 04/11/2024]
Abstract
The brain represents an organ with a particularly high diversity of genes that undergo post-transcriptional gene regulation through multiple mechanisms that affect RNA metabolism and, consequently, brain function. This vast regulatory process in the brain allows for a tight spatiotemporal control over protein expression, a necessary factor due to the unique morphologies of neurons. The numerous mechanisms of post-transcriptional regulation or translational control of gene expression in the brain include alternative splicing, RNA editing, mRNA stability and transport. A large number of trans-elements such as RNA-binding proteins and micro RNAs bind to specific cis-elements on transcripts to dictate the fate of mRNAs including its stability, localization, activation and degradation. Several trans-elements are exemplary regulators of translation, employing multiple cofactors and regulatory machinery so as to influence mRNA fate. Networks of regulatory trans-elements exert control over key neuronal processes such as neurogenesis, synaptic transmission and plasticity. Perturbations in these networks may directly or indirectly cause neuropsychiatric and neurodegenerative disorders. We will be reviewing multiple mechanisms of gene regulation by trans-elements occurring specifically in neurons.
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Affiliation(s)
- Vandita D Bhat
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Jagannath Jayaraj
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
| | - Kavita Babu
- Centre for Neuroscience, Indian Institute of Science, CV Raman Road, Bangalore 560012, Karnataka, India
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8
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Liu B, Ou WC, Fang L, Tian CW, Xiong Y. Myocyte Enhancer Factor 2A Plays a Central Role in the Regulatory Networks of Cellular Physiopathology. Aging Dis 2022; 14:331-349. [PMID: 37008050 PMCID: PMC10017154 DOI: 10.14336/ad.2022.0825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Cell regulatory networks are the determinants of cellular homeostasis. Any alteration to these networks results in the disturbance of cellular homeostasis and induces cells towards different fates. Myocyte enhancer factor 2A (MEF2A) is one of four members of the MEF2 family of transcription factors (MEF2A-D). MEF2A is highly expressed in all tissues and is involved in many cell regulatory networks including growth, differentiation, survival and death. It is also necessary for heart development, myogenesis, neuronal development and differentiation. In addition, many other important functions of MEF2A have been reported. Recent studies have shown that MEF2A can regulate different, and sometimes even mutually exclusive cellular events. How MEF2A regulates opposing cellular life processes is an interesting topic and worthy of further exploration. Here, we reviewed almost all MEF2A research papers published in English and summarized them into three main sections: 1) the association of genetic variants in MEF2A with cardiovascular disease, 2) the physiopathological functions of MEF2A, and 3) the regulation of MEF2A activity and its regulatory targets. In summary, multiple regulatory patterns for MEF2A activity and a variety of co-factors cause its transcriptional activity to switch to different target genes, thereby regulating opposing cell life processes. The association of MEF2A with numerous signaling molecules establishes a central role for MEF2A in the regulatory network of cellular physiopathology.
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Affiliation(s)
- Benrong Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
- Correspondence should be addressed to: Dr. Benrong Liu, the Second Affiliated Hospital, Guangzhou Medical University, Guangdong, China. E-mail: ; or Yujuan Xiong, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangdong, China. .
| | - Wen-Chao Ou
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Lei Fang
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Chao-Wei Tian
- General Practice, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Yujuan Xiong
- Department of Laboratory Medicine, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China.
- Correspondence should be addressed to: Dr. Benrong Liu, the Second Affiliated Hospital, Guangzhou Medical University, Guangdong, China. E-mail: ; or Yujuan Xiong, Panyu Hospital of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangdong, China. .
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9
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Liu K, Su Q, Kang K, Chen M, Wang WX, Zhang WQ, Pang R. Genome-wide Analysis of Alternative Gene Splicing Associated with Virulence in the Brown Planthopper Nilaparvata lugens (Hemiptera: Delphacidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2512-2523. [PMID: 34568947 DOI: 10.1093/jee/toab186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 06/13/2023]
Abstract
Alternative splicing of protein coding genes plays a profound role in phenotypic variation for many eukaryotic organisms. The development of high-throughput sequencing and bioinformatics algorithms provides the possibility of genome-wide identification of alternative splicing events in eukaryotes. However, for the brown planthopper Nilaparvata lugens, a destructive pest of rice crops, whole-genome distribution of alternative splicing events and the role of alternative splicing in the phenotypic plasticity of virulence have not previously been estimated. Here, we developed an analysis pipeline to identify alternative splicing events in the genome of N. lugens. Differential expression analysis and functional annotation were performed on datasets related to different virulence phenotypes. In total, 27,880 alternative splicing events corresponding to 9,787 multi-exon genes were detected in N. lugens. Among them, specifically expressed alternative splicing transcripts in the virulent Mudgo population were enriched in metabolic process categories, while transcripts in the avirulent TN1 population were enriched in regulator activity categories. In addition, genes encoding odorant receptor, secreted saliva protein and xenobiotic metabolic P450 monooxygenase showed different splicing patterns between Mudgo population and TN1 population. Host change experiment also revealed that an isoform of a P450 gene could be specially induced by the stimulation of resistant rice variety Mudgo. This research pioneered a genome-wide study of alternative gene splicing in the rice brown planthopper. Differences in alternative splicing between virulent and avirulent populations indicated that alternative splicing might play an important role in the formation of virulence phenotypes in N. lugens.
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Affiliation(s)
- Kai Liu
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qin Su
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Kui Kang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Meng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wei-Xia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Wen-Qing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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10
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Piasecka A, Sekrecki M, Szcześniak MW, Sobczak K. MEF2C shapes the microtranscriptome during differentiation of skeletal muscles. Sci Rep 2021; 11:3476. [PMID: 33568691 PMCID: PMC7875991 DOI: 10.1038/s41598-021-82706-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 01/20/2021] [Indexed: 01/04/2023] Open
Abstract
Myocyte enhancer factor 2C (MEF2C) is a transcription factor that regulates heart and skeletal muscle differentiation and growth. Several protein-encoding genes were identified as targets of this factor; however, little is known about its contribution to the microtranscriptome composition and dynamics in myogenic programs. In this report, we aimed to address this question. Deep sequencing of small RNAs of human muscle cells revealed a set of microRNAs (miRNAs), including several muscle-specific miRNAs, that are sensitive to MEF2C depletion. As expected, in cells with knockdown of MEF2C, we found mostly downregulated miRNAs; nevertheless, as much as one-third of altered miRNAs were upregulated. The majority of these changes are driven by transcription efficiency. Moreover, we found that MEF2C affects nontemplated 3′-end nucleotide addition of miRNAs, mainly oligouridylation. The rate of these modifications is associated with the level of TUT4 which mediates RNA 3′-uridylation. Finally, we found that a quarter of miRNAs which significantly changed upon differentiation of human skeletal myoblasts is inversely altered in MEF2C deficient cells. We concluded that MEF2C is an essential factor regulating both the quantity and quality of the microtranscriptome, leaving an imprint on the stability and perhaps specificity of many miRNAs during the differentiation of muscle cells.
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Affiliation(s)
- Agnieszka Piasecka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznań, Poland
| | - Michał Sekrecki
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznań, Poland
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznań, Poland.
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11
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Abstract
Skeletal muscle hypertrophy can be induced by hormones and growth factors acting directly as positive regulators of muscle growth or indirectly by neutralizing negative regulators, and by mechanical signals mediating the effect of resistance exercise. Muscle growth during hypertrophy is controlled at the translational level, through the stimulation of protein synthesis, and at the transcriptional level, through the activation of ribosomal RNAs and muscle-specific genes. mTORC1 has a central role in the regulation of both protein synthesis and ribosomal biogenesis. Several transcription factors and co-activators, including MEF2, SRF, PGC-1α4, and YAP promote the growth of the myofibers. Satellite cell proliferation and fusion is involved in some but not all muscle hypertrophy models.
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Affiliation(s)
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Italy
- Science and Research Centre Koper, Institute for Kinesiology Research, Koper, Slovenia
| | | | - Bert Blaauw
- Venetian Institute of Molecular Medicine, Padova, Italy
- Department of Biomedical Sciences, University of Padova, Italy
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12
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Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev 2020; 65:22-33. [PMID: 32535349 DOI: 10.1016/j.gde.2020.03.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of a network of highly conserved neuronal microexons has provided fundamental new insight into mechanisms underlying nervous system development and function, as well as an important basis for pathway convergence in autism spectrum disorder. In the past few years, considerable progress has been made in comprehensively determining the repertoires of factors that control neuronal microexons. These results have illuminated molecular mechanisms that activate the splicing of microexons, including those that control gene expression programs critical for neurogenesis, as well as synaptic protein translation and neuronal activity. Remarkably, individual disruption of specific microexons in these pathways results in autism-like phenotypes and cognitive impairment in mice. This review discusses these findings and their implications for delivering new therapeutic strategies for neurological disorders.
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13
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Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel-Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ. Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Mol Cell 2020; 77:1176-1192.e16. [PMID: 31999954 DOI: 10.1016/j.molcel.2020.01.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/15/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022]
Abstract
Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.
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Affiliation(s)
| | - Rieko Niibori
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Eric W Salter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Brian Tsang
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xinyi Liang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | | | - Jonathan Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Tyler Henderson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eesha Sharma
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mathieu Quesnel-Vallières
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona 08003, Spain
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John Georgiou
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; ICREA, Barcelona 08010, Spain
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Graham L Collingridge
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Melanie A Woodin
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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14
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Pereira AHM, Cardoso AC, Consonni SR, Oliveira RR, Saito A, Vaggione MLB, Matos-Souza JR, Carazzolle MF, Gonçalves A, Fernandes JL, Ribeiro GCA, Lopes MM, Molkentin JD, Franchini KG. MEF2C repressor variant deregulation leads to cell cycle re-entry and development of heart failure. EBioMedicine 2020; 51:102571. [PMID: 31911274 PMCID: PMC6948164 DOI: 10.1016/j.ebiom.2019.11.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/07/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
Background A pathophysiological link exists between dysregulation of MEF2C transcription factors and heart failure (HF), but the underlying mechanisms remain elusive. Alternative splicing of MEF2C exons α, β and γ provides transcript diversity with gene activation or repression functionalities. Methods Neonatal and adult rat ventricular myocytes were used to overexpress MEF2C splicing variants γ+ (repressor) or γ-, or the inactive MEF2Cγ+23/24 (K23T/R24L). Phenotypic alterations in cardiomyocytes were determined by confocal and electron microscopy, flow cytometry and DNA microarray. We used transgenic mice with cardiac-specific overexpression of MEF2Cγ+ or MEF2Cγ− to explore the impact of MEF2C variants in cardiac phenotype. Samples of non-infarcted areas of the left ventricle from patients and mouse model of myocardial infarction were used to detect the expression of MEF2Cγ+ in failing hearts. Findings We demonstrate a previously unrealized upregulation of the transrepressor MEF2Cγ+ isoform in human and mouse failing hearts. We show that adenovirus-mediated overexpression of MEF2Cγ+ downregulates multiple MEF2-target genes, and drives incomplete cell-cycle reentry, partial dedifferentiation and apoptosis in the neonatal and adult rat. None of these changes was observed in cardiomyocytes overexpressing MEF2Cγ-. Transgenic mice overexpressing MEF2Cγ+, but not the MEF2Cγ-, developed dilated cardiomyopathy, correlated to cell-cycle reentry and apoptosis of cardiomyocytes. Interpretation Our results provide a mechanistic link between MEF2Cγ+ and deleterious abnormalities in cardiomyocytes, supporting the notion that splicing dysregulation in MEF2C towards the selection of the MEF2Cγ+ variant contributes to the pathogenesis of HF by promoting cardiomyocyte dropout. Funding São Paulo Research Foundation (FAPESP); Brazilian National Research Council (CNPq).
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Affiliation(s)
- Ana Helena M Pereira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | - Alisson C Cardoso
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | - Silvio R Consonni
- Department of Biochemistry and Tissue Biology, University of Campinas, Campinas, Brazil
| | - Renata R Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | - Angela Saito
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | - Maria Luisa B Vaggione
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | - Jose R Matos-Souza
- Department of Internal Medicine, University of Campinas, Campinas, Brazil
| | | | - Anderson Gonçalves
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil
| | | | | | | | - Jeffery D Molkentin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, USA
| | - Kleber G Franchini
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, Sao Paulo, Brazil; Department of Internal Medicine, University of Campinas, Campinas, Brazil.
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15
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Tu Y, Wu X, Yu F, Dang J, Wang J, Wei Y, Cai Z, Zhou Z, Liao W, Li L, Zhang Y. Tristetraprolin specifically regulates the expression and alternative splicing of immune response genes in HeLa cells. BMC Immunol 2019; 20:13. [PMID: 31046669 PMCID: PMC6498542 DOI: 10.1186/s12865-019-0292-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 04/08/2019] [Indexed: 01/03/2023] Open
Abstract
Background Tristetraprolin (TTP) is an RNA binding protein that plays a critical role in regulating proinflammatory immune responses by destabilizing target mRNAs via binding to their AU-rich elements (AREs) in the 3′-UTRs of mRNAs. A recent CLIP-seq study revealed that TTP-binding sites are enriched in the intronic regions of RNA. TTP is also a nuclear protein that exhibits putative DNA-binding activity. These features suggested that TTP might regulate gene transcription and/or alternative splicing of pre-mRNAs in the absence of stimulation. Results To elucidate the regulatory pattern of TTP, we cloned and overexpressed the human TTP-encoding gene, ZFP36, in HeLa cells in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpressing cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, the expression of genes associated with innate immunity, including those in the type I interferon signaling pathway and viral response, were specifically upregulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulated the alternative splicing of genes involved in the positive regulation of the I-κB/NF-κB cascade and the TRIF-dependent toll-like receptor, MAPK, TNF, and T cell receptor signaling pathways. Conclusions Our findings indicated that TTP may regulate the immune response via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of TTP-mediated gene regulation. Electronic supplementary material The online version of this article (10.1186/s12865-019-0292-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yafang Tu
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
| | - Xiongfei Wu
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Jianzhong Dang
- Department of Geriatrics, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Juan Wang
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Yaxun Wei
- Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Zhitao Cai
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Zhipeng Zhou
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Wenliang Liao
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Lian Li
- Nephrology Department, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Yi Zhang
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.,Center for Genome Analysis, ABLife Inc., Optics Valley International Biomedical Park, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
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16
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Koh JH, Hancock CR, Han DH, Holloszy JO, Nair KS, Dasari S. AMPK and PPARβ positive feedback loop regulates endurance exercise training-mediated GLUT4 expression in skeletal muscle. Am J Physiol Endocrinol Metab 2019; 316:E931-E939. [PMID: 30888859 PMCID: PMC6580175 DOI: 10.1152/ajpendo.00460.2018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The objective of this study is to determine whether AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α), or peroxisome proliferator-activated receptor β (PPARβ) can independently mediate the increase of glucose transporter type 4 (GLUT4) expression that occurs in response to exercise training. We found that PPARβ can regulate GLUT4 expression without PGC-1α. We also found AMPK and PPARβ are important for maintaining normal physiological levels of GLUT4 protein in the sedentary condition as well following exercise training. However, AMPK and PPARβ are not essential for the increase in GLUT4 protein expression that occurs in response to exercise training. We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ. Furthermore, exercise training increases the cooperation of AMPK and PPARβ to regulate glucose uptake. In conclusion, cooperation between AMPK and PPARβ via NRF-1/MEF2A pathway enhances the exercise training mediated adaptive increase in GLUT4 expression and subsequent glucose uptake in skeletal muscle.
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Affiliation(s)
- Jin-Ho Koh
- Department of Internal Medicine, Mayo Clinic , Rochester, Minnesota
- Department of Physiology, College of Medicine, Yeungnam University , Daegu , Korea
| | - Chad R Hancock
- Department of Nutrition, Dietetics and Food Science, Brigham Young University , Provo, Utah
| | - Dong-Ho Han
- Division of Geriatrics and Nutritional Sciences, Department of Medicine, Washington University School of Medicine , St. Louis, Missouri
| | - John O Holloszy
- Division of Geriatrics and Nutritional Sciences, Department of Medicine, Washington University School of Medicine , St. Louis, Missouri
| | | | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic , Rochester, Minnesota
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17
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Xiong Y, Wang L, Jiang W, Pang L, Liu W, Li A, Zhong Y, Ou W, Liu B, Liu SM. MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells. BMC Mol Biol 2019; 20:8. [PMID: 30885136 PMCID: PMC6423757 DOI: 10.1186/s12867-019-0125-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/06/2019] [Indexed: 01/16/2023] Open
Abstract
Background Myocyte enhancer factor 2A (MEF2A) plays an important role in cell proliferation, differentiation and survival. Functional deletion or mutation in MEF2A predisposes individuals to cardiovascular disease mainly caused by vascular endothelial dysfunction. However, the effect of the inhibition of MEF2A expression on human coronary artery endothelial cells (HCAECs) is unclear. In this study, expression of MEF2A was inhibited by specific small interference RNA (siRNA), and changes in mRNA profiles in response to MEF2A knockdown were analyzed using an Agilent human mRNA array. Results Silencing of MEF2A in HCAECs accelerated cell senescence and suppressed cell proliferation. Microarray analysis identified 962 differentially expressed genes (DEGs) between the MEF2A knockdown group and the negative control group. Annotation clustering analysis showed that the DEGs were preferentially enriched in gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to proliferation, development, survival, and inflammation. Furthermore, 61 of the 578 downregulated DEGs have at least one potential MEF2A binding site in the proximal promoter and were mostly enriched in the GO terms “reproduction” and “cardiovascular.” The protein–protein interaction network analyzed for the downregulated DEGs and the DEGs in the GO terms “cardiovascular” and “aging” revealed that PIK3CG, IL1B, IL8, and PRKCB were included in hot nodes, and the regulation of the longevity-associated gene PIK3CG by MEF2A has been verified at the protein level, suggesting that PIK3CG might play a key role in MEF2A knockdown induced HCAEC senescence. Conclusions MEF2A knockdown accelerates HCAEC senescence, and the underlying molecular mechanism may be involved in down-regulation of the genes related with cell proliferation, development, inflammation and survival, in which PIK3CG may play a key role. Electronic supplementary material The online version of this article (10.1186/s12867-019-0125-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yujuan Xiong
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, 111 Dade Road, Guangzhou, 510120, People's Republic of China
| | - Lin Wang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Wenyi Jiang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Lihua Pang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Weihua Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Aiqun Li
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Yun Zhong
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Wenchao Ou
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China
| | - Benrong Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China.
| | - Shi-Ming Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, No. 250 Changgang Dong Road, Guangzhou, 510260, Guangdong, People's Republic of China.
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18
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Wu Y, Zhang J, Wang M, Yang L, Wang Y, Hu T, Liu A, Cheng Q, Fu Z, Zhang P, Cao L. Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects. J Cell Physiol 2019; 234:13544-13556. [PMID: 30635921 DOI: 10.1002/jcp.28033] [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: 05/26/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.
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Affiliation(s)
- Yun Wu
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Mei Wang
- Department of Pathology, Nanjing Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Yang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yongmei Wang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tao Hu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - An Liu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Qing Cheng
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Ziyi Fu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pingyang Zhang
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Cao
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
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19
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Yan LZ, Chen SN, He XF, Zhao Y, Zhang XY, Wu LL, Ping NN, Xu XY, Sun AN, Qiu HY, Tang XW, Han Y, Fu CC, Jin ZM, Miao M, Wu DP. [Expression level and clinical significance of MEF2C gene in adult acute myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2018; 39:682-685. [PMID: 30180473 PMCID: PMC7342833 DOI: 10.3760/cma.j.issn.0253-2727.2018.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Indexed: 11/05/2022]
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20
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Di Giorgio E, Hancock WW, Brancolini C. MEF2 and the tumorigenic process, hic sunt leones. Biochim Biophys Acta Rev Cancer 2018; 1870:261-273. [PMID: 29879430 DOI: 10.1016/j.bbcan.2018.05.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 12/14/2022]
Abstract
While MEF2 transcription factors are well known to cooperate in orchestrating cell fate and adaptive responses during development and adult life, additional studies over the last decade have identified a wide spectrum of genetic alterations of MEF2 in different cancers. The consequences of these alterations, including triggering and maintaining the tumorigenic process, are not entirely clear. A deeper knowledge of the molecular pathways that regulate MEF2 expression and function, as well as the nature and consequences of MEF2 mutations are necessary to fully understand the many roles of MEF2 in malignant cells. This review discusses the current knowledge of MEF2 transcription factors in cancer.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, Biesecker Center for Pediatric Liver Diseases, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy.
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21
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Thomas JD, Oliveira R, Sznajder ŁJ, Swanson MS. Myotonic Dystrophy and Developmental Regulation of RNA Processing. Compr Physiol 2018; 8:509-553. [PMID: 29687899 PMCID: PMC11323716 DOI: 10.1002/cphy.c170002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Myotonic dystrophy (DM) is a multisystemic disorder caused by microsatellite expansion mutations in two unrelated genes leading to similar, yet distinct, diseases. DM disease presentation is highly variable and distinguished by differences in age-of-onset and symptom severity. In the most severe form, DM presents with congenital onset and profound developmental defects. At the molecular level, DM pathogenesis is characterized by a toxic RNA gain-of-function mechanism that involves the transcription of noncoding microsatellite expansions. These mutant RNAs disrupt key cellular pathways, including RNA processing, localization, and translation. In DM, these toxic RNA effects are predominantly mediated through the modulation of the muscleblind-like and CUGBP and ETR-3-like factor families of RNA binding proteins (RBPs). Dysfunction of these RBPs results in widespread RNA processing defects culminating in the expression of developmentally inappropriate protein isoforms in adult tissues. The tissue that is the focus of this review, skeletal muscle, is particularly sensitive to mutant RNA-responsive perturbations, as patients display a variety of developmental, structural, and functional defects in muscle. Here, we provide a comprehensive overview of DM1 and DM2 clinical presentation and pathology as well as the underlying cellular and molecular defects associated with DM disease onset and progression. Additionally, fundamental aspects of skeletal muscle development altered in DM are highlighted together with ongoing and potential therapeutic avenues to treat this muscular dystrophy. © 2018 American Physiological Society. Compr Physiol 8:509-553, 2018.
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Affiliation(s)
- James D. Thomas
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Ruan Oliveira
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Łukasz J. Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Maurice S. Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida, USA
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22
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Imbriano C, Molinari S. Alternative Splicing of Transcription Factors Genes in Muscle Physiology and Pathology. Genes (Basel) 2018; 9:genes9020107. [PMID: 29463057 PMCID: PMC5852603 DOI: 10.3390/genes9020107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle formation is a multi-step process that is governed by complex networks of transcription factors. The regulation of their functions is in turn multifaceted, including several mechanisms, among them alternative splicing (AS) plays a primary role. On the other hand, altered AS has a role in the pathogenesis of numerous muscular pathologies. Despite these premises, the causal role played by the altered splicing pattern of transcripts encoding myogenic transcription factors in neuromuscular diseases has been neglected so far. In this review, we systematically investigate what has been described about the AS patterns of transcription factors both in the physiology of the skeletal muscle formation process and in neuromuscular diseases, in the hope that this may be useful in re-evaluating the potential role of altered splicing of transcription factors in such diseases.
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Affiliation(s)
- Carol Imbriano
- University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy.
| | - Susanna Molinari
- University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy.
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23
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Neuron-specific alternative splicing of transcriptional machineries: Implications for neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:35-45. [PMID: 29254826 DOI: 10.1016/j.mcn.2017.10.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/18/2017] [Accepted: 10/24/2017] [Indexed: 02/07/2023] Open
Abstract
The brain has long been known to display the most complex pattern of alternative splicing, thereby producing diverse protein isoforms compared to other tissues. Recent evidence indicates that many alternative exons are neuron-specific, evolutionarily conserved, and found in regulators of transcription including DNA-binding protein and histone modifying enzymes. This raises a possibility that neurons adopt unique mechanisms of transcription. Given that transcriptional machineries are frequently mutated in neurodevelopmental disorders with cognitive dysfunction, it is important to understand how neuron-specific alternative splicing contributes to proper transcriptional regulation in the brain. In this review, we summarize current knowledge regarding how neuron-specific splicing events alter the function of transcriptional regulators and shape unique gene expression patterns in the brain and the implications of neuronal splicing to the pathophysiology of neurodevelopmental disorders.
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24
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Taylor MV, Hughes SM. Mef2 and the skeletal muscle differentiation program. Semin Cell Dev Biol 2017; 72:33-44. [PMID: 29154822 DOI: 10.1016/j.semcdb.2017.11.020] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023]
Abstract
Mef2 is a conserved and significant transcription factor in the control of muscle gene expression. In cell culture Mef2 synergises with MyoD-family members in the activation of gene expression and in the conversion of fibroblasts into myoblasts. Amongst its in vivo roles, Mef2 is required for both Drosophila muscle development and mammalian muscle regeneration. Mef2 has functions in other cell-types too, but this review focuses on skeletal muscle and surveys key findings on Mef2 from its discovery, shortly after that of MyoD, up to the present day. In particular, in vivo functions, underpinning mechanisms and areas of uncertainty are highlighted. We describe how Mef2 sits at a nexus in the gene expression network that controls the muscle differentiation program, and how Mef2 activity must be regulated in time and space to orchestrate specific outputs within the different aspects of muscle development. A theme that emerges is that there is much to be learnt about the different Mef2 proteins (from different paralogous genes, spliced transcripts and species) and how the activity of these proteins is controlled.
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Affiliation(s)
- Michael V Taylor
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Simon M Hughes
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL UK
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25
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Pon JR, Marra MA. MEF2 transcription factors: developmental regulators and emerging cancer genes. Oncotarget 2016; 7:2297-312. [PMID: 26506234 PMCID: PMC4823036 DOI: 10.18632/oncotarget.6223] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/14/2015] [Indexed: 12/22/2022] Open
Abstract
The MEF2 transcription factors have roles in muscle, cardiac, skeletal, vascular, neural, blood and immune system cell development through their effects on cell differentiation, proliferation, apoptosis, migration, shape and metabolism. Altered MEF2 activity plays a role in human diseases and has recently been implicated in the development of several cancer types. In particular, MEF2B, the most divergent and least studied protein of the MEF2 family, has a role unique from its paralogs in non-Hodgkin lymphomas. The use of genome-scale technologies has enabled comprehensive MEF2 target gene sets to be identified, contributing to our understanding of MEF2 proteins as nodes in complex regulatory networks. This review surveys the molecular interactions of MEF2 proteins and their effects on cellular and organismal phenotypes. We include a discussion of the emerging roles of MEF2 proteins as oncogenes and tumor suppressors of cancer. Throughout this article we highlight similarities and differences between the MEF2 family proteins, including a focus on functions of MEF2B.
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Affiliation(s)
- Julia R Pon
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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26
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Baruffaldi F, Montarras D, Basile V, De Feo L, Badodi S, Ganassi M, Battini R, Nicoletti C, Imbriano C, Musarò A, Molinari S. Dynamic Phosphorylation of the Myocyte Enhancer Factor 2Cα1 Splice Variant Promotes Skeletal Muscle Regeneration and Hypertrophy. Stem Cells 2016; 35:725-738. [PMID: 27612437 DOI: 10.1002/stem.2495] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/18/2016] [Accepted: 08/21/2016] [Indexed: 12/20/2022]
Abstract
The transcription factor MEF2C (Myocyte Enhancer Factor 2C) plays an established role in the early steps of myogenic differentiation. However, the involvement of MEF2C in adult myogenesis and in muscle regeneration has not yet been systematically investigated. Alternative splicing of mammalian MEF2C transcripts gives rise to two mutually exclusive protein variants: MEF2Cα2 which exerts a positive control of myogenic differentiation, and MEF2Cα1, in which the α1 domain acts as trans-repressor of the MEF2C pro-differentiation activity itself. However, MEF2Cα1 variants are persistently expressed in differentiating cultured myocytes, suggesting a role in adult myogenesis. We found that overexpression of both MEF2Cα1/α2 proteins in a mouse model of muscle injury promotes muscle regeneration and hypertrophy, with each isoform promoting different stages of myogenesis. Besides the ability of MEF2Cα2 to increase differentiation, we found that overexpressed MEF2Cα1 enhances both proliferation and differentiation of primary myoblasts, and activates the AKT/mTOR/S6K anabolic signaling pathway in newly formed myofibers. The multiple activities of MEF2Cα1 are modulated by phosphorylation of Ser98 and Ser110, two amino acid residues located in the α1 domain of MEF2Cα1. These specific phosphorylations allow the interaction of MEF2Cα1 with the peptidyl-prolyl isomerase PIN1, a regulator of MEF2C functions. Overall, in this study we established a novel regulatory mechanism in which the expression and the phosphorylation of MEF2Cα1 are critically required to sustain the adult myogenesis. The described molecular mechanism will represent a new potential target for the development of therapeutical strategies to treat muscle-wasting diseases. Stem Cells 2017;35:725-738.
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Affiliation(s)
- Fiorenza Baruffaldi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Didier Montarras
- Département de Biologie du Développement et Cellules Souches, Institut Pasteur (CNRS URA 2578), Paris, France
| | - Valentina Basile
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Luca De Feo
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Sara Badodi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Massimo Ganassi
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Renata Battini
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Carmine Nicoletti
- Institute Pasteur-Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, IIM, Sapienza University, Rome, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Carol Imbriano
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Antonio Musarò
- Institute Pasteur-Cenci Bolognetti, DAHFMO-Unit of Histology and Medical Embryology, IIM, Sapienza University, Rome, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Susanna Molinari
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
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27
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Desjardins CA, Naya FJ. The Function of the MEF2 Family of Transcription Factors in Cardiac Development, Cardiogenomics, and Direct Reprogramming. J Cardiovasc Dev Dis 2016; 3. [PMID: 27630998 PMCID: PMC5019174 DOI: 10.3390/jcdd3030026] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Proper formation of the mammalian heart requires precise spatiotemporal transcriptional regulation of gene programs in cardiomyocytes. Sophisticated regulatory networks have evolved to not only integrate the activities of distinct transcription factors to control tissue-specific gene programs but also, in many instances, to incorporate multiple members within these transcription factor families to ensure accuracy and specificity in the system. Unsurprisingly, perturbations in this elaborate transcriptional circuitry can lead to severe cardiac abnormalities. Myocyte enhancer factor–2 (MEF2) transcription factor belongs to the evolutionarily conserved cardiac gene regulatory network. Given its central role in muscle gene regulation and its evolutionary conservation, MEF2 is considered one of only a few core cardiac transcription factors. In addition to its firmly established role as a differentiation factor, MEF2 regulates wide variety of, sometimes antagonistic, cellular processes such as cell survival and death. Vertebrate genomes encode multiple MEF2 family members thereby expanding the transcriptional potential of this core transcription factor in the heart. This review highlights the requirement of the MEF2 family and their orthologs in cardiac development in diverse animal model systems. Furthermore, we describe the recently characterized role of MEF2 in direct reprogramming and genome-wide cardiomyocyte gene regulation. A thorough understanding of the regulatory functions of the MEF2 family in cardiac development and cardiogenomics is required in order to develop effective therapeutic strategies to repair the diseased heart.
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28
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Nutter CA, Jaworski EA, Verma SK, Deshmukh V, Wang Q, Botvinnik OB, Lozano MJ, Abass IJ, Ijaz T, Brasier AR, Garg NJ, Wehrens XHT, Yeo GW, Kuyumcu-Martinez MN. Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes. Cell Rep 2016; 15:2200-2213. [PMID: 27239029 DOI: 10.1016/j.celrep.2016.05.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 01/25/2016] [Accepted: 04/27/2016] [Indexed: 12/27/2022] Open
Abstract
Alternative splicing (AS) defects that adversely affect gene expression and function have been identified in diabetic hearts; however, the mechanisms responsible are largely unknown. Here, we show that the RNA-binding protein RBFOX2 contributes to transcriptome changes under diabetic conditions. RBFOX2 controls AS of genes with important roles in heart function relevant to diabetic cardiomyopathy. RBFOX2 protein levels are elevated in diabetic hearts despite low RBFOX2 AS activity. A dominant-negative (DN) isoform of RBFOX2 that blocks RBFOX2-mediated AS is generated in diabetic hearts. DN RBFOX2 interacts with wild-type (WT) RBFOX2, and ectopic expression of DN RBFOX2 inhibits AS of RBFOX2 targets. Notably, DN RBFOX2 expression is specific to diabetes and occurs at early stages before cardiomyopathy symptoms appear. Importantly, DN RBFOX2 expression impairs intracellular calcium release in cardiomyocytes. Our results demonstrate that RBFOX2 dysregulation by DN RBFOX2 is an early pathogenic event in diabetic hearts.
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Affiliation(s)
- Curtis A Nutter
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Elizabeth A Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sunil K Verma
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vaibhav Deshmukh
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiongling Wang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olga B Botvinnik
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Mario J Lozano
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Ismail J Abass
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Talha Ijaz
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nisha J Garg
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xander H T Wehrens
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medicine/Cardiology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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29
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Basile V, Baruffaldi F, Dolfini D, Belluti S, Benatti P, Ricci L, Artusi V, Tagliafico E, Mantovani R, Molinari S, Imbriano C. NF-YA splice variants have different roles on muscle differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:627-38. [PMID: 26921500 DOI: 10.1016/j.bbagrm.2016.02.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 11/19/2022]
Abstract
The heterotrimeric CCAAT-binding factor NF-Y controls the expression of a multitude of genes involved in cell cycle progression. NF-YA is present in two alternatively spliced isoforms, NF-YAs and NF-YAl, differing in 28 aminoacids in the N-terminal Q-rich activation domain. NF-YAs has been identified as a regulator of stemness and proliferation in mouse embryonic cells (mESCs) and human hematopoietic stem cells (hHSCs), whereas the role of NF-YAl is not clear. In the muscle system, NF-YA expression is observed in proliferating cells, but barely detectable in terminally differentiated cells in vitro and adult skeletal muscle in vivo. Here, we show that NF-YA inactivation in mouse myoblasts impairs both proliferation and differentiation. The overexpression of the two NF-YA isoforms differentially affects myoblasts fate: NF-YAs enhance cell proliferation, while NF-YAl boosts differentiation. The molecular mechanisms were investigated by expression profilings, detailing the opposite programs of the two isoforms. Bioinformatic analysis of the regulated promoters failed to detect a significant presence of CCAAT boxes in the regulated genes. NF-YAl activates directly Mef2D, Six genes, and p57kip2 (Cdkn1c), and indirectly the myogenic regulatory factors (MRFs). Specifically, Cdkn1c activation is induced by NF-Y binding to its CCAAT promoter and by reducing the expression of the lncRNA Kcnq1ot1, a negative regulator of Cdkn1c transcription. Overall, our results indicate that NF-YA alternative splicing is an influential muscle cell determinant, through direct regulation of selected cell cycle blocking genes, and, directly and indirectly, of muscle-specific transcription factors.
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Affiliation(s)
- Valentina Basile
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D e Via Campi 287, Modena, Italy
| | - Fiorenza Baruffaldi
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Silvia Belluti
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D e Via Campi 287, Modena, Italy
| | - Paolo Benatti
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D e Via Campi 287, Modena, Italy
| | - Laura Ricci
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D e Via Campi 287, Modena, Italy
| | - Valentina Artusi
- Centro di Ricerche Genomiche, Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Enrico Tagliafico
- Centro di Ricerche Genomiche, Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Susanna Molinari
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D, 41125 Modena, Italy.
| | - Carol Imbriano
- Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, Via Campi 213/D e Via Campi 287, Modena, Italy.
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30
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Badodi S, Baruffaldi F, Ganassi M, Battini R, Molinari S. Phosphorylation-dependent degradation of MEF2C contributes to regulate G2/M transition. Cell Cycle 2016; 14:1517-28. [PMID: 25789873 PMCID: PMC4615021 DOI: 10.1080/15384101.2015.1026519] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Myocyte Enhancer Factor 2C (MEF2C) transcription factor plays a critical role in skeletal muscle differentiation, promoting muscle-specific gene transcription. Here we report that in proliferating cells MEF2C is degraded in mitosis by the Anaphase Promoting Complex/Cyclosome (APC/C) and that this downregulation is necessary for an efficient progression of the cell cycle. We show that this mechanism of degradation requires the presence on MEF2C of a D-box (R-X-X-L) and 2 phospho-motifs, pSer98 and pSer110. Both the D-box and pSer110 motifs are encoded by the ubiquitous alternate α1 exon. These two domains mediate the interaction between MEF2C and CDC20, a co-activator of APC/C. We further report that in myoblasts, MEF2C regulates the expression of G2/M checkpoint genes (14–3–3γ, Gadd45b and p21) and the sub-cellular localization of CYCLIN B1. The importance of controlling MEF2C levels during the cell cycle is reinforced by the observation that modulation of its expression affects the proliferation rate of colon cancer cells. Our findings show that beside the well-established role as pro-myogenic transcription factor, MEF2C can also function as a regulator of cell proliferation.
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Key Words
- APC/C
- APC/C, Anaphase Promoting Complex/Cyclosome
- CDK, Cyclin Dependent Kinase
- CHX, Cycloheximide
- CRC, ColoRectal Cancer
- Gadd45b, Growth Arrest and DNA Damage b
- HDAC, Histone Deacetylases
- MADS, Minichromosome maintenance, Agamous, Deficiens, Serum response factor
- MEF2
- MEF2, Myocyte Enhancer Factor 2
- MyHC, Myosin Heavy Chain
- UPS, Ubiquitin Proteasome System
- cell cycle
- degradation
- degron, degradation signal
- mitosis
- muscle
- phosphorylation
- proliferation
- splicing
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Affiliation(s)
- Sara Badodi
- a Dipartimento di Scienze della Vita ; Università di Modena e Reggio Emilia ; Modena , Italy
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31
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Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
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Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
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32
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Lin JC. RBM4-MEF2C network constitutes a feed-forward circuit that facilitates the differentiation of brown adipocytes. RNA Biol 2015; 12:208-20. [PMID: 25826570 DOI: 10.1080/15476286.2015.1017213] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the MEF2C gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the differentiation of brown adipocytes, upregulated RBM4 enhanced skipping of the MEF2Cγ region which functions as a transcriptional repressor. The presence of an overexpressed MEF2Cγ- isoform in turn induced transcriptional activity of the RBM4 promoter, constituting a positive feedback circuit in differentiating brown adipocytes. The RBM4-MEF2Cγ- network induced the expression of "myogenic" miR-1 to a greater extent than did PRDM17, BMP7 C/EBPβ, or UCP1 transcripts in C3H10T1/2 cells. Overexpression of miR-1 independently exerted the same activity as RBM4 and the MEF2Cγ- isoform of upregulating brown adipocyte-specific factors in C3H10T1/2 cells, which suggests a potential effect of miR-1 on brown adipocytes. These results indicated that the RBM4-MEF2C-miR-1 network constitutes a novel mechanism which programs the gene expression profile toward the development of brown adipocytes.
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Affiliation(s)
- Jung-Chun Lin
- a School of Medical Laboratory Science and Biotechnology ; College of Medical Science and Technology; Taipei Medical University ; Taipei , Taiwan
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33
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Adrião A, Conceição N, Cancela ML. MEF2C orthologues from zebrafish: Evolution, expression and promoter regulation. Arch Biochem Biophys 2015; 591:43-56. [PMID: 26705761 DOI: 10.1016/j.abb.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/24/2015] [Accepted: 12/13/2015] [Indexed: 12/26/2022]
Abstract
MEF2C is a crucial transcription factor for cranial neural crest cells development. An abnormal expression of this protein leads to severe abnormalities in craniofacial features. Recently, a human disease (MRD20) was described as a consequence of MEF2C haploinsufficiency. These patients show severe developmental delay, intellectual disability and dysmorphic features. Zebrafish presents two MEF2C orthologues, mef2ca and mef2cb. In this study we demonstrate a highly conserved pattern of chromosome localization for MEF2C between human and zebrafish, a similar protein sequence and tissue expression profile. We have focused our functional analysis on the zebrafish orthologue mef2cb. We identified three new exons through 5' RACE and described two new transcriptional start sites (TSS). These alternative TSS reflect the occurrence of two alternative promoters differentially regulated by nuclear factors related to craniofacial or neuronal development such as Sox9b, Sox10 and Runx2. We also predict that mef2cb gene may be post transcriptionally regulated by analysing the structure of its 5' UTR region, conserved throughout evolution. Our study provides new insights in MEF2C conservation and provides the first evidence of mef2cb regulation by both transcriptional and post transcriptional mechanisms, thus contributing to validate zebrafish as a good model for future studies concerning MEF2C dependent pathologies.
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Affiliation(s)
- Andreia Adrião
- Centre of Marine Sciences/CCMAR, University of Algarve, Portugal; PhD Program in Biomedical Sciences, University of Algarve, Portugal
| | - Natércia Conceição
- Centre of Marine Sciences/CCMAR, University of Algarve, Portugal; Dept of Biomedical Sciences and Medicine, University of Algarve, Portugal.
| | - M Leonor Cancela
- Centre of Marine Sciences/CCMAR, University of Algarve, Portugal; Dept of Biomedical Sciences and Medicine, University of Algarve, Portugal.
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Wei N, Cheng Y, Wang Z, Liu Y, Luo C, Liu L, Chen L, Xie Z, Lu Y, Feng Y. SRSF10 Plays a Role in Myoblast Differentiation and Glucose Production via Regulation of Alternative Splicing. Cell Rep 2015; 13:1647-57. [DOI: 10.1016/j.celrep.2015.10.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 10/12/2015] [Indexed: 12/26/2022] Open
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Raj B, Blencowe B. Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles. Neuron 2015; 87:14-27. [DOI: 10.1016/j.neuron.2015.05.004] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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36
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Crisafulli C, Drago A, Calabrò M, Spina E, Serretti A. A molecular pathway analysis informs the genetic background at risk for schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2015; 59:21-30. [PMID: 25554435 DOI: 10.1016/j.pnpbp.2014.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Schizophrenia is a complex mental disorder marked by severely impaired thinking, delusional thoughts, hallucinations and poor emotional responsiveness. The biological mechanisms that lead to schizophrenia may be related to the genetic background of patients. Thus, a genetic perspective may help to unravel the molecular pathways disrupted in schizophrenia. METHODS In the present work, we used a molecular pathway analysis to identify the molecular pathways associated with schizophrenia. We collected data of genetic loci previously associated with schizophrenia, identified the genes located in those positions and created the metabolic pathways that are related to those genes' products. These pathways were tested for enrichment (a number of SNPs associated with the phenotype significantly higher than expected by chance) in a sample of schizophrenic patients and controls (4486 and 4477, respectively). RESULTS The molecular pathway that resulted from the identification of all the genes located in the loci previously found to be associated with schizophrenia was found to be enriched, as expected (permutated p(10(6))=9.9999e-06).We found 60 SNPs amongst 30 different genes with a strong association with schizophrenia. The genes are related to the pathways related to neurodevelopment, apoptosis, vesicle traffic, immune response and MAPK cascade. CONCLUSIONS The pathway related to the toll-like receptor family seemed to play a central role in the modulation/connection of various pathways whose disruption leads to schizophrenia. This pathway is related to the innate immune system, further stressing the role of immunological-related events in increasing the risk to schizophrenia.
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Affiliation(s)
- Concetta Crisafulli
- Department of Biomedical Science and Morphological and Functional Images, University of Messina, Messina, Italy
| | - Antonio Drago
- Department of Biomedical and Neuromotor Sciences - DIBINEM, University of Bologna, Bologna, Italy; I.R.C.C.S. "San Giovanni di Dio", Fatebenefratelli, Brescia, Italy.
| | - Marco Calabrò
- Department of Biomedical Science and Morphological and Functional Images, University of Messina, Messina, Italy; Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy; IRCCS Centro Neurolesi "Bonino-Pulejo", Messina, Italy
| | - Edoardo Spina
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Alessandro Serretti
- Department of Biomedical and Neuromotor Sciences - DIBINEM, University of Bologna, Bologna, Italy
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Wei C, Qiu J, Zhou Y, Xue Y, Hu J, Ouyang K, Banerjee I, Zhang C, Chen B, Li H, Chen J, Song LS, Fu XD. Repression of the Central Splicing Regulator RBFox2 Is Functionally Linked to Pressure Overload-Induced Heart Failure. Cell Rep 2015; 10:1521-1533. [PMID: 25753418 DOI: 10.1016/j.celrep.2015.02.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/02/2014] [Accepted: 01/31/2015] [Indexed: 12/21/2022] Open
Abstract
Heart failure is characterized by the transition from an initial compensatory response to decompensation, which can be partially mimicked by transverse aortic constriction (TAC) in rodent models. Numerous signaling molecules have been shown to be part of the compensatory program, but relatively little is known about the transition to decompensation that leads to heart failure. Here, we show that TAC potently decreases the RBFox2 protein in the mouse heart, and cardiac ablation of this critical splicing regulator generates many phenotypes resembling those associated with decompensation in the failing heart. Global analysis reveals that RBFox2 regulates splicing of many genes implicated in heart function and disease. A subset of these genes undergoes developmental regulation during postnatal heart remodeling, which is reversed in TAC-treated and RBFox2 knockout mice. These findings suggest that RBFox2 may be a critical stress sensor during pressure overload-induced heart failure.
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Affiliation(s)
- Chaoliang Wei
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jinsong Qiu
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yu Zhou
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Yuanchao Xue
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Jing Hu
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Kunfu Ouyang
- Department of Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Indroneal Banerjee
- Department of Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Caimei Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Biyi Chen
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Ju Chen
- Department of Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA
| | - Long-Sheng Song
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine University of California, San Diego, La Jolla, CA 92093-0651, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0651, USA.
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Estrella NL, Desjardins CA, Nocco SE, Clark AL, Maksimenko Y, Naya FJ. MEF2 transcription factors regulate distinct gene programs in mammalian skeletal muscle differentiation. J Biol Chem 2014; 290:1256-68. [PMID: 25416778 DOI: 10.1074/jbc.m114.589838] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle differentiation requires precisely coordinated transcriptional regulation of diverse gene programs that ultimately give rise to the specialized properties of this cell type. In Drosophila, this process is controlled, in part, by MEF2, the sole member of an evolutionarily conserved transcription factor family. By contrast, vertebrate MEF2 is encoded by four distinct genes, Mef2a, -b, -c, and -d, making it far more challenging to link this transcription factor to the regulation of specific muscle gene programs. Here, we have taken the first step in molecularly dissecting vertebrate MEF2 transcriptional function in skeletal muscle differentiation by depleting individual MEF2 proteins in myoblasts. Whereas MEF2A is absolutely required for proper myoblast differentiation, MEF2B, -C, and -D were found to be dispensable for this process. Furthermore, despite the extensive redundancy, we show that mammalian MEF2 proteins regulate a significant subset of nonoverlapping gene programs. These results suggest that individual MEF2 family members are able to recognize specific targets among the entire cohort of MEF2-regulated genes in the muscle genome. These findings provide opportunities to modulate the activity of MEF2 isoforms and their respective gene programs in skeletal muscle homeostasis and disease.
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Affiliation(s)
- Nelsa L Estrella
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Cody A Desjardins
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Sarah E Nocco
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Amanda L Clark
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Yevgeniy Maksimenko
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
| | - Francisco J Naya
- From the Department of Biology, Program in Cell and Molecular Biology, Boston University, Boston, Massachusetts 02215
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39
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Zhang M, Zhu B, Davie J. Alternative splicing of MEF2C pre-mRNA controls its activity in normal myogenesis and promotes tumorigenicity in rhabdomyosarcoma cells. J Biol Chem 2014; 290:310-24. [PMID: 25404735 DOI: 10.1074/jbc.m114.606277] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. Many cellular disruptions contribute to the progression of this pediatric cancer, including aberrant alternative splicing. The MEF2 family of transcription factors regulates many developmental programs, including myogenesis. MEF2 gene transcripts are subject to alternate splicing to generate protein isoforms with divergent functions. We found that MEF2Cα1 was the ubiquitously expressed isoform that exhibited no myogenic activity and that MEF2Cα2, the muscle-specific MEF2C isoform, was required for efficient differentiation. We showed that exon α in MEF2C was aberrantly alternatively spliced in RMS cells, with the ratio of α2/α1 highly down-regulated in RMS cells compared with normal myoblasts. Compared with MEF2Cα2, MEF2Cα1 interacted more strongly with and recruited HDAC5 to myogenic gene promoters to repress muscle-specific genes. Overexpression of the MEF2Cα2 isoform in RMS cells increased myogenic activity and promoted differentiation in RMS cells. We also identified a serine protein kinase, SRPK3, that was down-regulated in RMS cells and found that expression of SRPK3 promoted the splicing of the MEF2Cα2 isoform and induced differentiation. Restoration of either MEF2Cα2 or SPRK3 inhibited both proliferation and anchorage-independent growth of RMS cells. Together, our findings indicate that the alternative splicing of MEF2C plays an important role in normal myogenesis and RMS development. An improved understanding of alternative splicing events in RMS cells will potentially reveal novel therapeutic targets for RMS treatment.
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Affiliation(s)
- Meiling Zhang
- From the Department of Biochemistry and Molecular Biology and Simmons Cancer Institute, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Bo Zhu
- From the Department of Biochemistry and Molecular Biology and Simmons Cancer Institute, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
| | - Judith Davie
- From the Department of Biochemistry and Molecular Biology and Simmons Cancer Institute, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901
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40
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Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA. Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Mol Cell 2014; 55:592-603. [PMID: 25087874 PMCID: PMC4142074 DOI: 10.1016/j.molcel.2014.06.035] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 05/15/2014] [Accepted: 06/27/2014] [Indexed: 12/29/2022]
Abstract
Alternative splicing plays important regulatory roles during periods of physiological change. During development, a large number of genes coordinately express protein isoform transitions regulated by alternative splicing; however, the mechanisms that coordinate splicing and the functional integration of the resultant tissue-specific protein isoforms are typically unknown. Here we show that the conserved Rbfox2 RNA binding protein regulates 30% of the splicing transitions observed during myogenesis and is required for the specific step of myoblast fusion. Integration of Rbfox2-dependent splicing outcomes from RNA-seq with Rbfox2 iCLIP data identified Mef2d and Rock2 as Rbfox2 splicing targets. Restored activities of Mef2d and Rock2 rescued myoblast fusion in Rbfox2-depleted cultures, demonstrating functional cooperation of protein isoforms generated by coordinated alterative splicing. The results demonstrate that coordinated alternative splicing by a single RNA binding protein modulates transcription (Mef2d) and cell signaling (Rock2) programs to drive tissue-specific functions (cell fusion) to promote a developmental transition.
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Affiliation(s)
- Ravi K. Singh
- Departments of Pathology and Immunology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Zheng Xia
- Departments of Molecular and Cellular Biology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
- Departments of Dan L. Duncan Cancer Center, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Christopher S. Bland
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Auinash Kalsotra
- Departments of Pathology and Immunology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Marissa A. Scavuzzo
- Departments of Pathology and Immunology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Tomaz Curk
- University of Ljubljana, Faculty of Computer and Information Science, Trẑaŝka cesta 25, SI-1000 Ljubljana
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Wei Li
- Departments of Molecular and Cellular Biology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
- Departments of Dan L. Duncan Cancer Center, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
| | - Thomas A. Cooper
- Departments of Pathology and Immunology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
- Departments of Molecular and Cellular Biology, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Medicine, Houston, Texas 77030, USA
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Ganassi M, Badodi S, Polacchini A, Baruffaldi F, Battini R, Hughes SM, Hinits Y, Molinari S. Distinct functions of alternatively spliced isoforms encoded by zebrafish mef2ca and mef2cb. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:559-70. [PMID: 24844180 PMCID: PMC4064114 DOI: 10.1016/j.bbagrm.2014.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 04/29/2014] [Accepted: 05/12/2014] [Indexed: 01/06/2023]
Abstract
In mammals, an array of MEF2C proteins is generated by alternative splicing (AS), yet specific functions have not been ascribed to each isoform. Teleost fish possess two MEF2C paralogues, mef2ca and mef2cb. In zebrafish, the Mef2cs function to promote cardiomyogenic differentiation and myofibrillogenesis in nascent skeletal myofibers. We found that zebrafish mef2ca and mef2cb are alternatively spliced in the coding exons 4–6 region and these splice variants differ in their biological activity. Of the two, mef2ca is more abundantly expressed in developing skeletal muscle, its activity is tuned through zebrafish development by AS. By 24 hpf, we found the prevalent expression of the highly active full length protein in differentiated muscle in the somites. The splicing isoform of mef2ca that lacks exon 5 (mef2ca 4–6), encodes a protein that has 50% lower transcriptional activity, and is found mainly earlier in development, before muscle differentiation. mef2ca transcripts including exon 5 (mef2ca 4–5–6) are present early in the embryo. Over-expression of this isoform alters the expression of genes involved in early dorso-ventral patterning of the embryo such as chordin, nodal related 1 and goosecoid, and induces severe developmental defects. AS of mef2cb generates a long splicing isoform in the exon 5 region (Mef2cbL) that predominates during somitogenesis. Mef2cbL contains an evolutionarily conserved domain derived from exonization of a fragment of intron 5, which confers the ability to induce ectopic muscle in mesoderm upon over-expression of the protein. Taken together, the data show that AS is a significant regulator of Mef2c activity. mef2ca and mef2cb gene products are alternatively spliced in zebrafish. Inclusion of exon 5 in mef2ca transcripts is regulated during zebrafish development. Exon 5 confers on Mef2ca the ability to activate early patterning genes. Mef2cb includes an extra octapeptide encoded by a region of intron 5. Inclusion of the extra-octapeptide confers on Mef2cb pro-myogenic activity.
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Affiliation(s)
- M Ganassi
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy; Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - S Badodi
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy
| | - A Polacchini
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy
| | - F Baruffaldi
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy
| | - R Battini
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy
| | - S M Hughes
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
| | - Y Hinits
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK.
| | - S Molinari
- University of Modena and Reggio Emilia, Department of Life Sciences, Italy.
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Davila JL, Goff LA, Ricupero CL, Camarillo C, Oni EN, Swerdel MR, Toro-Ramos AJ, Li J, Hart RP. A positive feedback mechanism that regulates expression of miR-9 during neurogenesis. PLoS One 2014; 9:e94348. [PMID: 24714615 PMCID: PMC3979806 DOI: 10.1371/journal.pone.0094348] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/13/2014] [Indexed: 12/21/2022] Open
Abstract
MiR-9, a neuron-specific miRNA, is an important regulator of neurogenesis. In this study we identify how miR-9 is regulated during early differentiation from a neural stem-like cell. We utilized two immortalized rat precursor clones, one committed to neurogenesis (L2.2) and another capable of producing both neurons and non-neuronal cells (L2.3), to reproducibly study early neurogenesis. Exogenous miR-9 is capable of increasing neurogenesis from L2.3 cells. Only one of three genomic loci capable of encoding miR-9 was regulated during neurogenesis and the promoter region of this locus contains sufficient functional elements to drive expression of a luciferase reporter in a developmentally regulated pattern. Furthermore, among a large number of potential regulatory sites encoded in this sequence, Mef2 stood out because of its known pro-neuronal role. Of four Mef2 paralogs, we found only Mef2C mRNA was regulated during neurogenesis. Removal of predicted Mef2 binding sites or knockdown of Mef2C expression reduced miR-9-2 promoter activity. Finally, the mRNA encoding the Mef2C binding partner HDAC4 was shown to be targeted by miR-9. Since HDAC4 protein could be co-immunoprecipitated with Mef2C protein or with genomic Mef2 binding sequences, we conclude that miR-9 regulation is mediated, at least in part, by Mef2C binding but that expressed miR-9 has the capacity to reduce inhibitory HDAC4, stabilizing its own expression in a positive feedback mechanism.
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Affiliation(s)
- Jonathan L Davila
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Loyal A Goff
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Christopher L Ricupero
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Cynthia Camarillo
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Eileen N Oni
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Mavis R Swerdel
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Alana J Toro-Ramos
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jiali Li
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
| | - Ronald P Hart
- W.M. Keck Center for Collaborative Neuroscience and the Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
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Infantino V, Convertini P, Menga A, Iacobazzi V. MEF2C exon α: Role in gene activation and differentiation. Gene 2013; 531:355-62. [DOI: 10.1016/j.gene.2013.08.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 08/06/2013] [Accepted: 08/12/2013] [Indexed: 12/20/2022]
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44
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The alternative heart: impact of alternative splicing in heart disease. J Cardiovasc Transl Res 2013; 6:945-55. [PMID: 23775418 DOI: 10.1007/s12265-013-9482-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 06/04/2013] [Indexed: 01/16/2023]
Abstract
Alternative splicing is the main driver of protein diversity and allows the production of different proteins from each gene in the genome. Changes in exon exclusion, intron retention or the use of alternative splice sites can alter protein structure, localisation, regulation and function. In the heart, alternative splicing of sarcomeric genes, ion channels and cell signalling proteins can lead to cardiomyopathies, arrhythmias and other pathologies. Also, a number of inherited conditions and heart-related diseases develop as a result of mutations affecting splicing. Here, we review the impact that changes in alternative splicing have on individual genes and on whole biological processes associated with heart disease. We also discuss promising therapeutic tools based on the manipulation of alternative splicing.
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45
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Ye J, Llorian M, Cardona M, Rongvaux A, Moubarak RS, Comella JX, Bassel-Duby R, Flavell RA, Olson EN, Smith CWJ, Sanchis D. A pathway involving HDAC5, cFLIP and caspases regulates expression of the splicing regulator polypyrimidine tract binding protein in the heart. J Cell Sci 2013; 126:1682-91. [PMID: 23424201 PMCID: PMC3647441 DOI: 10.1242/jcs.121384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2013] [Indexed: 01/07/2023] Open
Abstract
Polypyrimidine tract binding protein (PTB) regulates pre-mRNA splicing, having special relevance for determining gene expression in the differentiating muscle. We have previously shown that PTB protein abundance is progressively reduced during heart development without reduction of its own transcript. Simultaneous reduction of histone deacetylase (HDAC) expression prompted us to investigate the potential link between these events. HDAC5-deficient mice have reduced cardiac PTB protein abundance, and HDAC inhibition in myocytes causes a reduction in endogenous expression of cellular FLICE-like inhibitory protein (cFLIP) and caspase-dependent cleavage of PTB. In agreement with this, cardiac PTB expression is abnormally high in mice with cardiac-specific executioner caspase deficiency, and cFLIP overexpression prevents PTB cleavage in vitro. Caspase-dependent cleavage triggers further fragmentation of PTB, and these fragments accumulate in the presence of proteasome inhibitors. Experimental modification of the above processes in vivo and in vitro results in coherent changes in the alternative splicing of genes encoding tropomyosin-1 (TPM1), tropomyosin-2 (TPM2) and myocyte enhancer factor-2 (MEF2). Thus, we report a pathway connecting HDAC, cFLIP and caspases regulating the progressive disappearance of PTB, which enables the expression of the adult variants of proteins involved in the regulation of contraction and transcription during cardiac muscle development.
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Affiliation(s)
- Junmei Ye
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
| | - Miriam Llorian
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK
| | - Maria Cardona
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
| | - Anthony Rongvaux
- Department of Immunobiology, and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana S. Moubarak
- Ciberned, Institut de Recerca Hospital, Universitari Vall d'Hebró-UAB, Barcelona, 08035, Spain
| | - Joan X. Comella
- Ciberned, Institut de Recerca Hospital, Universitari Vall d'Hebró-UAB, Barcelona, 08035, Spain
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Richard A. Flavell
- Department of Immunobiology, and Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA
| | - Christopher W. J. Smith
- Department of Biochemistry, University of Cambridge, Building O, Downing Site, Cambridge, CB2 1QW, UK
| | - Daniel Sanchis
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida – IRBLLEIDA, Av Rovira Roure, 80, Lleida, 25198Spain
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46
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Molecular cloning of the duck MEF2C gene cDNA coding domain sequence and its expression during fetal muscle tissue development. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0086-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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47
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Myocyte enhancer factor 2C in hematopoiesis and leukemia. Oncogene 2013; 33:403-10. [PMID: 23435431 DOI: 10.1038/onc.2013.56] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/17/2013] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
MEF2C is a selectively expressed transcription factor involved in different transcriptional complexes. Originally identified as an essential regulator of muscle development, ectopic expression of MEF2C as a result of chromosomal rearrangements is now linked to leukemia. Specifically, high MEF2C expression has been linked to mixed lineage leukemia-rearranged acute myeloid leukemia as well as to the immature subgroup of T-cell acute lymphoblastic leukemia. This review focuses on the role of MEF2C in the hematopoietic system and on aberrant MEF2C expression in human leukemia.
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48
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Dietrich JB. The MEF2 family and the brain: from molecules to memory. Cell Tissue Res 2013; 352:179-90. [DOI: 10.1007/s00441-013-1565-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/10/2013] [Indexed: 12/31/2022]
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49
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Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
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Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
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50
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Dionyssiou MG, Nowacki NB, Hashemi S, Zhao J, Kerr A, Tsushima RG, McDermott JC. Cross-talk between glycogen synthase kinase 3β (GSK3β) and p38MAPK regulates myocyte enhancer factor 2 (MEF2) activity in skeletal and cardiac muscle. J Mol Cell Cardiol 2012; 54:35-44. [PMID: 23137781 DOI: 10.1016/j.yjmcc.2012.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 10/26/2012] [Accepted: 10/28/2012] [Indexed: 12/21/2022]
Abstract
Characterizing the signaling network that controls MEF2 transcription factors is crucial for understanding skeletal and cardiac muscle gene expression. Glycogen synthase kinase 3β (GSK3β) regulates MEF2 activity indirectly through reciprocal regulation of p38MAPK. Cross-talk between GSK3β and p38MAPK regulates MEF2 activity in skeletal and cardiac muscle. Understanding cross-talk in the signaling network converging at MEF2 control has therapeutic implications in cardiac and skeletal muscle pathology. Glycogen synthase kinase 3β (GSK3β) is a known regulator of striated muscle gene expression suppressing both myogenesis and cardiomyocyte hypertrophy. Since myocyte enhancer factor 2 (MEF2) proteins are key transcriptional regulators in both systems, we assessed whether MEF2 is a target for GSK3β. Pharmacological inhibition of GSK3β resulted in enhanced MEF2A/D expression and transcriptional activity in skeletal myoblasts and cardiac myocytes. Even though in silico analysis revealed GSK3β consensus (S/T)XXX(S/T) sites on MEF2A, a subsequent in vitro kinase assay revealed that MEF2A is only a weak substrate. However, we did observe a posttranslational modification in MEF2A in skeletal myoblasts treated with a GSK3β inhibitor which coincided with increased p38MAPK phosphorylation, a potent MEF2A activator, indicating that GSK3β inhibition may de-repress p38MAPK. Heart specific excision of GSK3β in mice also resulted in up-regulation of p38MAPK activity. Interestingly, upon pharmacological p38MAPK inhibition (SB203580), GSK3β inhibition loses its effect on MEF2 transcriptional activity suggesting potent cross-talk between the two pathways. Thus we have documented that cross-talk between p38MAPK and GSK3β signaling converges on MEF2 activity having potential consequences for therapeutic modulation of cardiac and skeletal muscle gene expression.
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Affiliation(s)
- M G Dionyssiou
- Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada M3J 1P3
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