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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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2
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Napier-Jameson R, Marx O, Norris A. A pair of RNA binding proteins inhibit ion transporter expression to maintain lifespan. Genetics 2024; 226:iyad212. [PMID: 38112749 PMCID: PMC10847721 DOI: 10.1093/genetics/iyad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
Regulation of lifespan by transcription factors has been well established. More recently, a role for RNA binding proteins (RBPs) in regulating lifespan has also emerged. In both cases, a major challenge is to determine which regulatory targets are functionally responsible for the observed lifespan phenotype. We recently identified a pair of neuronal RBPs, exc-7/ELAVL and mbl-1/Muscleblind, which in Caenorhabditis elegans display synthetic (nonadditive) lifespan defects: single mutants do not affect lifespan, but exc-7; mbl-1 double mutants have strongly reduced lifespan. Such a strong synthetic phenotype represented an opportunity to use transcriptomics to search for potential causative targets that are synthetically regulated. Focus on such genes would allow us to narrow our target search by ignoring the hundreds of genes altered only in single mutants, and provide a shortlist of synthetically regulated candidate targets that might be responsible for the double mutant phenotype. We identified a small handful of genes synthetically dysregulated in double mutants and systematically tested each candidate gene for functional contribution to the exc-7; mbl-1 lifespan phenotype. We identified 1 such gene, the ion transporter nhx-6, which is highly upregulated in double mutants. Overexpression of nhx-6 causes reduced lifespan, and deletion of nhx-6 in an exc-7; mbl-1 background partially restores both lifespan and healthspan. Together, these results reveal that a pair of RBPs mediate lifespan in part by inhibiting expression of an ion transporter, and provide a template for how synthetic phenotypes (including lifespan) can be dissected at the transcriptomic level to reveal potential causative genes.
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Affiliation(s)
- Rebekah Napier-Jameson
- Department of Biological Sciences, Southern Methodist University, 6501 Airline Rd, Dallas, TX 75205, USA
| | - Olivia Marx
- Department of Biological Sciences, Southern Methodist University, 6501 Airline Rd, Dallas, TX 75205, USA
| | - Adam Norris
- Department of Biological Sciences, Southern Methodist University, 6501 Airline Rd, Dallas, TX 75205, USA
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3
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Verbeeren J, Teixeira J, Garcia SMDA. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism. PLoS Genet 2023; 19:e1011109. [PMID: 38134228 PMCID: PMC10773944 DOI: 10.1371/journal.pgen.1011109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/08/2024] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The Muscleblind-like (MBNL) family is a highly conserved set of RNA-binding proteins (RBPs) that regulate RNA metabolism during the differentiation of various animal tissues. Functional insufficiency of MBNL affects muscle and central nervous system development, and contributes to the myotonic dystrophies (DM), a set of incurable multisystemic disorders. Studies on the regulation of MBNL genes are essential to provide insight into the gene regulatory networks controlled by MBNL proteins and to understand how dysregulation within these networks causes disease. In this study, we demonstrate the evolutionary conservation of an autoregulatory mechanism that governs the function of MBNL proteins by generating two distinct protein isoform types through alternative splicing. Our aim was to further our understanding of the regulatory principles that underlie this conserved feedback loop in a whole-organismal context, and to address the biological significance of the respective isoforms. Using an alternative splicing reporter, our studies show that, during development of the Caenorhabditis elegans central nervous system, the orthologous mbl-1 gene shifts production from long protein isoforms that localize to the nucleus to short isoforms that also localize to the cytoplasm. Using isoform-specific CRISPR/Cas9-generated strains, we showed that expression of short MBL-1 protein isoforms is required for healthy neuromuscular function and neurodevelopment, while expression of long MBL-1 protein isoforms is dispensable, emphasizing a key role for cytoplasmic functionalities of the MBL-1 protein. Furthermore, RNA-seq and lifespan analyses indicated that short MBL-1 isoforms are crucial regulators of miRNA expression and, in consequence, required for normal lifespan. In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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4
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Taylor K, Piasecka A, Kajdasz A, Brzęk A, Polay Espinoza M, Bourgeois CF, Jankowski A, Borowiak M, Raczyńska KD, Sznajder ŁJ, Sobczak K. Modulatory role of RNA helicases in MBNL-dependent alternative splicing regulation. Cell Mol Life Sci 2023; 80:335. [PMID: 37882878 PMCID: PMC10602967 DOI: 10.1007/s00018-023-04927-0] [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: 01/31/2023] [Revised: 07/14/2023] [Accepted: 08/17/2023] [Indexed: 10/27/2023]
Abstract
Muscleblind-like splicing regulators (MBNLs) activate or repress the inclusion of alternative splicing (AS) events, enabling the developmental transition of fetal mRNA splicing isoforms to their adult forms. Herein, we sought to elaborate the mechanism by which MBNLs mediate AS related to biological processes. We evaluated the functional role of DEAD-box (DDX) RNA helicases, DDX5 and DDX17 in MBNL-dependent AS regulation. Whole-transcriptome analysis and validation approaches revealed a handful of MBNLs-dependent AS events to be affected by DDX5 and DDX17 in mostly an opposite manner. The opposite expression patterns of these two groups of factors during muscle development and coordination of fetal-to-adult splicing transition indicate the importance of these proteins at early stages of development. The identified pathways of how the helicases modulate MBNL splicing activity include DDX5 and DDX17-dependent changes in the ratio of MBNL splicing isoforms and most likely changes in accessibility of MBNL-binding sites. Another pathway involves the mode of action of the helicases independent of MBNL activity. These findings lead to a deeper understanding of the network of interdependencies between RNA-binding proteins and constitute a valuable element in the discussion on developmental homeostasis and pathological states in which the studied protein factors play a significant role.
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Affiliation(s)
- Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Agnieszka Piasecka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Arkadiusz Kajdasz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Brzęk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Micaela Polay Espinoza
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Artur Jankowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Małgorzata Borowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Katarzyna D Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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5
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Aboouf MA, Gorr TA, Hamdy NM, Gassmann M, Thiersch M. Myoglobin in Brown Adipose Tissue: A Multifaceted Player in Thermogenesis. Cells 2023; 12:2240. [PMID: 37759463 PMCID: PMC10526770 DOI: 10.3390/cells12182240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Brown adipose tissue (BAT) plays an important role in energy homeostasis by generating heat from chemical energy via uncoupled oxidative phosphorylation. Besides its high mitochondrial content and its exclusive expression of the uncoupling protein 1, another key feature of BAT is the high expression of myoglobin (MB), a heme-containing protein that typically binds oxygen, thereby facilitating the diffusion of the gas from cell membranes to mitochondria of muscle cells. In addition, MB also modulates nitric oxide (NO•) pools and can bind C16 and C18 fatty acids, which indicates a role in lipid metabolism. Recent studies in humans and mice implicated MB present in BAT in the regulation of lipid droplet morphology and fatty acid shuttling and composition, as well as mitochondrial oxidative metabolism. These functions suggest that MB plays an essential role in BAT energy metabolism and thermogenesis. In this review, we will discuss in detail the possible physiological roles played by MB in BAT thermogenesis along with the potential underlying molecular mechanisms and focus on the question of how BAT-MB expression is regulated and, in turn, how this globin regulates mitochondrial, lipid, and NO• metabolism. Finally, we present potential MB-mediated approaches to augment energy metabolism, which ultimately could help tackle different metabolic disorders.
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Affiliation(s)
- Mostafa A. Aboouf
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Thomas A. Gorr
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
| | - Nadia M. Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Max Gassmann
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Markus Thiersch
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
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Xie J, Zou W, Tugizova M, Shen K, Wang X. MBL-1 and EEL-1 affect the splicing and protein levels of MEC-3 to control dendrite complexity. PLoS Genet 2023; 19:e1010941. [PMID: 37729192 PMCID: PMC10511122 DOI: 10.1371/journal.pgen.1010941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/28/2023] [Indexed: 09/22/2023] Open
Abstract
Transcription factors (TFs) play critical roles in specifying many aspects of neuronal cell fate including dendritic morphology. How TFs are accurately regulated during neuronal morphogenesis is not fully understood. Here, we show that LIM homeodomain protein MEC-3, the key TF for C. elegans PVD dendrite morphogenesis, is regulated by both alternative splicing and an E3 ubiquitin ligase. The mec-3 gene generates several transcripts by alternative splicing. We find that mbl-1, the orthologue of the muscular dystrophy disease gene muscleblind-like (MBNL), is required for PVD dendrite arbor formation. Our data suggest mbl-1 regulates the alternative splicing of mec-3 to produce its long isoform. Deleting the long isoform of mec-3(deExon2) causes reduction of dendrite complexity. Through a genetic modifier screen, we find that mutation in the E3 ubiquitin ligase EEL-1 suppresses mbl-1 phenotype. eel-1 mutants also suppress mec-3(deExon2) mutant but not the mec-3 null phenotype. Loss of EEL-1 alone leads to excessive dendrite branches. Together, these results indicate that MEC-3 is fine-tuned by alternative splicing and the ubiquitin system to produce the optimal level of dendrite branches.
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Affiliation(s)
- Jianxin Xie
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zou
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, California, United States of America
| | - Madina Tugizova
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, California, United States of America
| | - Kang Shen
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, California, United States of America
| | - Xiangming Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Department of Cell Biology, School of Basic Medical Science, Capital Medical University, Beijing, China
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7
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Deng K, Liu Z, Su Y, Zhang Z, Fan Y, Zhang Y, Wang F. RUNX1T1 modulates myogenic differentiation by regulating the calcium signaling pathway and the alternative splicing of ROCK2. FASEB J 2023; 37:e23044. [PMID: 37342905 DOI: 10.1096/fj.202300677r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/27/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023]
Abstract
RUNX1T1 (Runt-related transcription factor 1, translocated to 1) plays a wide-ranging and diverse role in cellular development, including hematopoiesis and adipogenesis. However, little is known about the function of RUNX1T1 in the skeletal muscle development. Here, we assessed the impact of RUNX1T1 on the proliferation and myogenic differentiation of goat primary myoblasts (GPMs). It was observed that RUNX1T1 is highly expressed during the early stages of myogenic differentiation and the fetal stage. Moreover, the knockdown of RUNX1T1 promotes the proliferation and inhibits myogenic differentiation and mitochondrial biogenesis of GPMs. RNA sequencing analysis revealed that significantly differentially expressed genes in RUNX1T1 knockdown cells were enriched in the calcium signaling pathway. Additionally, we discovered that RUNX1T1 regulates alternative splicing (AS) events involved in myogenesis. We also show that silencing RUNX1T1 blocked the Ca2+ -CAMK signaling pathway and reduced the expression levels of muscle-specific isoforms of recombinant rho associated coiled coil containing crotein kinase 2 (ROCK2) during myogenic differentiation, partially explaining why RUNX1T1 deficiency leads to the impairment of myotube formation. These findings suggest that RUNX1T1 is a novel regulator of myogenic differentiation that regulates the calcium signaling pathway and AS of ROCK2. Overall, our results highlight the critical role of RUNX1T1 in myogenesis and broaden our understanding of myogenic differentiation.
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Affiliation(s)
- Kaiping Deng
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Zhipeng Liu
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Yalong Su
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Zhen Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Yixuan Fan
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
- Institute of Haimen Goat Industry, Nanjing Agricultural University, Nanjing, China
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8
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Cao J, Yang S, Luo T, Yang R, Zhu H, Zhao T, Jiang K, Xu B, Wang Y, Chen F. TATA-box-binding protein promotes hepatocellular carcinoma metastasis through epithelial-mesenchymal transition. Hepatol Commun 2023; 7:e00155. [PMID: 37314767 DOI: 10.1097/hc9.0000000000000155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/02/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND HCC characterizes malignant metastasis with high incidence and recurrence. Thus, it is pivotal to discover the mechanisms of HCC metastasis. TATA-box-binding protein (TBP), a general transcriptional factor (TF), couples with activators and chromatin remodelers to sustain the transcriptional activity of target genes. Here, we investigate the key role of TBP in HCC metastasis. METHODS TBP expression was measured by PCR, western blot, and immunohistochemistry. RNA-sequencing was performed to identify downstream proteins. Functional assays of TBP and downstream targets were identified in HCC cell lines and xenograft models. Luciferase reporter and chromatin immunoprecipitation assays were used to demonstrate the mechanism mediated by TBP. RESULTS HCC patients showed high expression of TBP, which correlated with poor prognosis. Upregulation of TBP increased HCC metastasis in vivo and in vitro, and muscleblind-like-3 (MBNL3) was the effective factor of TBP, positively related to TBP expression. Mechanically, TBP transactivated and enhanced MBNL3 expression to stimulate exon inclusion of lncRNA-paxillin (PXN)-alternative splicing (AS1) and, thus, activated epithelial-mesenchymal transition for HCC progression through upregulation of PXN. CONCLUSIONS Our data revealed that TBP upregulation is an HCC enhancer mechanism that increases PXN expression to drive epithelial-mesenchymal transition.
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Affiliation(s)
- Jiayi Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Shaanxi, Xi'an, China
| | - Suzhen Yang
- Department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu, Nanjing, China
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Jiangsu, Nanjing, China
| | - Tingting Luo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Shaanxi, Xi'an, China
| | - Rui Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Shaanxi, Xi'an, China
| | - Hanlong Zhu
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Jiangsu, Nanjing, China
| | - Tianming Zhao
- Department of Gastroenterology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu, Nanjing, China
| | - Kang Jiang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Jiangsu, Nanjing, China
| | - Bing Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Shaanxi, Xi'an, China
| | - Yingchun Wang
- Department of Gastroenterology, the Affiliated Zhongshan Hospital of Dalian University, Liaoning, Dalian, China
| | - Fulin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Shaanxi, Xi'an, China
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9
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Ellis JA, Hale MA, Cleary JD, Wang E, Andrew Berglund J. Alternative splicing outcomes across an RNA-binding protein concentration gradient. J Mol Biol 2023:168156. [PMID: 37230319 DOI: 10.1016/j.jmb.2023.168156] [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: 01/12/2023] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered a MBNL1 and RBFOX1 inducible HEK-293 cell line. Modest induction of exogenous RBFOX1 in this cell line modulated MBNL1-dependent AS outcomes in 3 skipped exon events, despite significant levels of endogenous RBFOX1 and RBFOX2. Due to background RBFOX levels, we conducted a focused analysis of dose-dependent MBNL1 skipped exon AS outcomes and generated transcriptome wide dose-response curves. Analysis of this data demonstrates that MBNL1-regulated exclusion events may require higher concentrations of MBNL1 protein to properly regulate AS outcomes compared to inclusion events and that multiple arrangements of YGCY motifs can produce similar splicing outcomes. These results suggest that rather than a simple relationship between the organization of RBP binding sites and a specific splicing outcome, that complex interaction networks govern both AS inclusion and exclusion events across a RBP gradient.
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Affiliation(s)
- Joseph A Ellis
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Melissa A Hale
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - John D Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Eric Wang
- Department of Microbiology and Molecular Genetics & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - J Andrew Berglund
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; RNA Institute, State University of New York at Albany, LSRB-2033, 1400 Washington Avenue, Albany, New York, 12222.
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10
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Wright SE, Todd PK. Native functions of short tandem repeats. eLife 2023; 12:e84043. [PMID: 36940239 PMCID: PMC10027321 DOI: 10.7554/elife.84043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
Over a third of the human genome is comprised of repetitive sequences, including more than a million short tandem repeats (STRs). While studies of the pathologic consequences of repeat expansions that cause syndromic human diseases are extensive, the potential native functions of STRs are often ignored. Here, we summarize a growing body of research into the normal biological functions for repetitive elements across the genome, with a particular focus on the roles of STRs in regulating gene expression. We propose reconceptualizing the pathogenic consequences of repeat expansions as aberrancies in normal gene regulation. From this altered viewpoint, we predict that future work will reveal broader roles for STRs in neuronal function and as risk alleles for more common human neurological diseases.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- Neuroscience Graduate Program, University of Michigan–Ann ArborAnn ArborUnited States
- Department of Neuroscience, Picower InstituteCambridgeUnited States
| | - Peter K Todd
- Department of Neurology, University of Michigan–Ann ArborAnn ArborUnited States
- VA Ann Arbor Healthcare SystemAnn ArborUnited States
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11
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Tossetta G, Marzioni D. Targeting the NRF2/KEAP1 pathway in cervical and endometrial cancers. Eur J Pharmacol 2023; 941:175503. [PMID: 36641100 DOI: 10.1016/j.ejphar.2023.175503] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Cervical and endometrial cancers are among the most dangerous gynaecological malignancies, with high fatality and recurrence rates due to frequent diagnosis at an advanced stage and chemoresistance onset. The NRF2/KEAP1 signalling pathway plays an important role in protecting cells against oxidative damage due to increased reactive oxygen species (ROS) levels. NRF2, activated by ROS, induces the expression of antioxidant enzymes such as heme oxygenase, catalase, glutathione peroxidase and superoxide dismutase which neutralize ROS, protecting cells against oxidative stress damage. However, activation of NRF2/KEAP1 signalling in cancer cells results in chemoresistance, inactivating drug-mediated oxidative stress and protecting cancer cells from drug-induced cell death. We review the literature on the role of the NRF2/KEAP1 pathway in cervical and endometrial cancers, with a focus on the expression of its components and downstream genes. We also examine the role of the NRF2/KEAP1 pathway in chemotherapy resistance and how this pathway can be modulated by natural and synthetic modulators.
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Affiliation(s)
- Giovanni Tossetta
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126, Ancona, Italy; Clinic of Obstetrics and Gynaecology, Department of Clinical Sciences, Università Politecnica delle Marche, Salesi Hospital, Azienda Ospedaliero Universitaria, 60126, Ancona, Italy.
| | - Daniela Marzioni
- Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60126, Ancona, Italy
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12
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Hong D, Jeong S. 3'UTR Diversity: Expanding Repertoire of RNA Alterations in Human mRNAs. Mol Cells 2023; 46:48-56. [PMID: 36697237 PMCID: PMC9880603 DOI: 10.14348/molcells.2023.0003] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/27/2023] Open
Abstract
Genomic information stored in the DNA is transcribed to the mRNA and translated to proteins. The 3' untranslated regions (3'UTRs) of the mRNA serve pivotal roles in posttranscriptional gene expression, regulating mRNA stability, translation, and localization. Similar to DNA mutations producing aberrant proteins, RNA alterations expand the transcriptome landscape and change the cellular proteome. Recent global analyses reveal that many genes express various forms of altered RNAs, including 3'UTR length variants. Alternative polyadenylation and alternative splicing are involved in diversifying 3'UTRs, which could act as a hidden layer of eukaryotic gene expression control. In this review, we summarize the functions and regulations of 3'UTRs and elaborate on the generation and functional consequences of 3'UTR diversity. Given that dynamic 3'UTR length control contributes to phenotypic complexity, dysregulated 3'UTR diversity might be relevant to disease development, including cancers. Thus, 3'UTR diversity in cancer could open exciting new research areas and provide avenues for novel cancer theragnostics.
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Affiliation(s)
- Dawon Hong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
| | - Sunjoo Jeong
- Laboratory of RNA Cell Biology, Department of Bioconvergence Engineering, Dankook University Graduate School, Yongin 16892, Korea
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13
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Basri R, Awan FM, Yang BB, Awan UA, Obaid A, Naz A, Ikram A, Khan S, Haq IU, Khan SN, Aqeel MB. Brain-protective mechanisms of autophagy associated circRNAs: Kick starting self-cleaning mode in brain cells via circRNAs as a potential therapeutic approach for neurodegenerative diseases. Front Mol Neurosci 2023; 15:1078441. [PMID: 36727091 PMCID: PMC9885805 DOI: 10.3389/fnmol.2022.1078441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Altered autophagy is a hallmark of neurodegeneration but how autophagy is regulated in the brain and dysfunctional autophagy leads to neuronal death has remained cryptic. Being a key cellular waste-recycling and housekeeping system, autophagy is implicated in a range of brain disorders and altering autophagy flux could be an effective therapeutic strategy and has the potential for clinical applications down the road. Tight regulation of proteins and organelles in order to meet the needs of complex neuronal physiology suggests that there is distinct regulatory pattern of neuronal autophagy as compared to non-neuronal cells and nervous system might have its own separate regulator of autophagy. Evidence has shown that circRNAs participates in the biological processes of autophagosome assembly. The regulatory networks between circRNAs, autophagy, and neurodegeneration remains unknown and warrants further investigation. Understanding the interplay between autophagy, circRNAs and neurodegeneration requires a knowledge of the multiple steps and regulatory interactions involved in the autophagy pathway which might provide a valuable resource for the diagnosis and therapy of neurodegenerative diseases. In this review, we aimed to summarize the latest studies on the role of brain-protective mechanisms of autophagy associated circRNAs in neurodegenerative diseases (including Alzheimer's disease, Parkinson's disease, Huntington's disease, Spinal Muscular Atrophy, Amyotrophic Lateral Sclerosis, and Friedreich's ataxia) and how this knowledge can be leveraged for the development of novel therapeutics against them. Autophagy stimulation might be potential one-size-fits-all therapy for neurodegenerative disease as per considerable body of evidence, therefore future research on brain-protective mechanisms of autophagy associated circRNAs will illuminate an important feature of nervous system biology and will open the door to new approaches for treating neurodegenerative diseases.
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Affiliation(s)
- Rabea Basri
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan,*Correspondence: Faryal Mehwish Awan, ✉ ;
| | - Burton B. Yang
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, Toronto, ON, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Usman Ayub Awan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Ayesha Obaid
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Aqsa Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Suliman Khan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Ijaz ul Haq
- Department of Public Health and Nutrition, The University of Haripur (UOH), Haripur, Pakistan
| | - Sadiq Noor Khan
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
| | - Muslim Bin Aqeel
- Department of Medical Lab Technology, The University of Haripur (UOH), Haripur, Pakistan
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14
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Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Takei Y, Huang W, Blanco MR, Guttman M. 3D genome organization around nuclear speckles drives mRNA splicing efficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522632. [PMID: 36711853 PMCID: PMC9881923 DOI: 10.1101/2023.01.04.522632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The nucleus is highly organized such that factors involved in transcription and processing of distinct classes of RNA are organized within specific nuclear bodies. One such nuclear body is the nuclear speckle, which is defined by high concentrations of protein and non-coding RNA regulators of pre-mRNA splicing. What functional role, if any, speckles might play in the process of mRNA splicing remains unknown. Here we show that genes localized near nuclear speckles display higher spliceosome concentrations, increased spliceosome binding to their pre-mRNAs, and higher co-transcriptional splicing levels relative to genes that are located farther from nuclear speckles. We show that directed recruitment of a pre-mRNA to nuclear speckles is sufficient to drive increased mRNA splicing levels. Finally, we show that gene organization around nuclear speckles is highly dynamic with differential localization between cell types corresponding to differences in Pol II occupancy. Together, our results integrate the longstanding observations of nuclear speckles with the biochemistry of mRNA splicing and demonstrate a critical role for dynamic 3D spatial organization of genomic DNA in driving spliceosome concentrations and controlling the efficiency of mRNA splicing.
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15
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Peterson JAM, Cooper TA. Clinical and Molecular Insights into Gastrointestinal Dysfunction in Myotonic Dystrophy Types 1 & 2. Int J Mol Sci 2022; 23:ijms232314779. [PMID: 36499107 PMCID: PMC9737721 DOI: 10.3390/ijms232314779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Myotonic dystrophy (DM) is a highly variable, multisystemic disorder that clinically affects one in 8000 individuals. While research has predominantly focused on the symptoms and pathological mechanisms affecting striated muscle and brain, DM patient surveys have identified a high prevalence for gastrointestinal (GI) symptoms amongst affected individuals. Clinical studies have identified chronic and progressive dysfunction of the esophagus, stomach, liver and gallbladder, small and large intestine, and rectum and anal sphincters. Despite the high incidence of GI dysmotility in DM, little is known regarding the pathological mechanisms leading to GI dysfunction. In this review, we summarize results from clinical and molecular analyses of GI dysfunction in both genetic forms of DM, DM type 1 (DM1) and DM type 2 (DM2). Based on current knowledge of DM primary pathological mechanisms in other affected tissues and GI tissue studies, we suggest that misregulation of alternative splicing in smooth muscle resulting from the dysregulation of RNA binding proteins muscleblind-like and CUGBP-elav-like is likely to contribute to GI dysfunction in DM. We propose that a combinatorial approach using clinical and molecular analysis of DM GI tissues and model organisms that recapitulate DM GI manifestations will provide important insight into defects impacting DM GI motility.
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Affiliation(s)
- Janel A. M. Peterson
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas A. Cooper
- Baylor College of Medicine, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor College of Medicine, Department of Molecular & Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence:
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16
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Chang Z, Zheng YY, Mathivanan J, Valsangkar VA, Du J, Abou-Elkhair RAI, Hassan AEA, Sheng J. Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats. Int J Mol Sci 2022; 23:ijms23063321. [PMID: 35328743 PMCID: PMC8955525 DOI: 10.3390/ijms23063321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some studies have shown that aminoglycosides and their derivatives could work as potential lead compounds targeting these RNA repeats. In this work, sisomicin, previously known to bind HIV-1 TAR, is investigated as a possible ligand for CUG RNA repeats. We designed a novel fluorescence-labeled RNA sequence of r(CUG)10 to mimic cellular RNA repeats and improve the detecting sensitivity. The interaction of sisomicin with CUG RNA repeats is characterized by the change of fluorescent signal, which is initially minimized by covalently incorporating the fluorescein into the RNA bases and later increased upon ligand binding. The results show that sisomicin can bind and stabilize the folded RNA structure. We demonstrate that this new fluorescence-based binding characterization assay is consistent with the classic UV Tm technique, indicating its feasibility for high-throughput screening of ligand-RNA binding interactions and wide applications to measure the thermodynamic parameters in addition to binding constants and kinetics when probing such interactions.
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Affiliation(s)
- Zhihua Chang
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Ya Ying Zheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Johnsi Mathivanan
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Vibhav A. Valsangkar
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Jinxi Du
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
| | - Reham A. I. Abou-Elkhair
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
| | - Abdalla E. A. Hassan
- Applied Nucleic Acids Research Center & Chemistry Department, Faculty of Science, Zagazig University, Zagazig 44523, Egypt;
- Correspondence: (A.E.A.H.); (J.S.)
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA; (Z.C.); (Y.Y.Z.); (J.M.); (V.A.V.); (J.D.)
- Correspondence: (A.E.A.H.); (J.S.)
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17
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Bugg D, Bailey LRJ, Bretherton RC, Beach KE, Reichardt IM, Robeson KZ, Reese AC, Gunaje J, Flint G, DeForest CA, Stempien-Otero A, Davis J. MBNL1 drives dynamic transitions between fibroblasts and myofibroblasts in cardiac wound healing. Cell Stem Cell 2022; 29:419-433.e10. [PMID: 35176223 PMCID: PMC8929295 DOI: 10.1016/j.stem.2022.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 11/30/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022]
Abstract
Dynamic fibroblast to myofibroblast state transitions underlie the heart's fibrotic response. Because transcriptome maturation by muscleblind-like 1 (MBNL1) promotes differentiated cell states, this study investigated whether tactical control of MBNL1 activity could alter myofibroblast activity and fibrotic outcomes. In healthy mice, cardiac fibroblast-specific overexpression of MBNL1 transitioned the fibroblast transcriptome to that of a myofibroblast and after injury promoted myocyte remodeling and scar maturation. Both fibroblast- and myofibroblast-specific loss of MBNL1 limited scar production and stabilization, which was ascribed to negligible myofibroblast activity. The combination of MBNL1 deletion and injury caused quiescent fibroblasts to expand and adopt features of cardiac mesenchymal stem cells, whereas transgenic MBNL1 expression blocked fibroblast proliferation and drove the population into a mature myofibroblast state. These data suggest MBNL1 is a post-transcriptional switch, controlling fibroblast state plasticity during cardiac wound healing.
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Affiliation(s)
- Darrian Bugg
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Logan R J Bailey
- Molecular & Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Kylie E Beach
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Kalen Z Robeson
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Anna C Reese
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jagadambika Gunaje
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Galina Flint
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | | | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
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18
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The Splicing of the Mitochondrial Calcium Uniporter Genuine Activator MICU1 Is Driven by RBFOX2 Splicing Factor during Myogenic Differentiation. Int J Mol Sci 2022; 23:ijms23052517. [PMID: 35269658 PMCID: PMC8909990 DOI: 10.3390/ijms23052517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing, the process by which exons within a pre-mRNA transcript are differentially joined or skipped, is crucial in skeletal muscle since it is required both during myogenesis and in post-natal life to reprogram the transcripts of contractile proteins, metabolic enzymes, and transcription factors in functionally distinct muscle fiber types. The importance of such events is underlined by the numerosity of pathological conditions caused by alternative splicing aberrations. Importantly, many skeletal muscle Ca2+ homeostasis genes are also regulated by alternative splicing mechanisms, among which is the Mitochondrial Ca2+ Uniporter (MCU) genuine activator MICU1 which regulates MCU opening upon cell stimulation. We have previously shown that murine skeletal muscle MICU1 is subjected to alternative splicing, thereby generating a splice variant-which was named MICU1.1-that confers unique properties to the mitochondrial Ca2+ uptake and ensuring sufficient ATP production for muscle contraction. Here we extended the analysis of MICU1 alternative splicing to human tissues, finding two additional splicing variants that were characterized by their ability to regulate mitochondrial Ca2+ uptake. Furthermore, we found that MICU1 alternative splicing is induced during myogenesis by the splicing factor RBFOX2. These results highlight the complexity of the alternative splicing mechanisms in skeletal muscle and the regulation of mitochondrial Ca2+ among tissues.
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19
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Lin G, Li J, Cai J, Zhang H, Xin Q, Wang N, Xie W, Zhang Y, Xu N. RNA-binding Protein MBNL2 regulates Cancer Cell Metastasis through MiR-182-MBNL2-AKT Pathway. J Cancer 2021; 12:6715-6726. [PMID: 34659561 PMCID: PMC8518006 DOI: 10.7150/jca.62816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/06/2021] [Indexed: 12/12/2022] Open
Abstract
The aberrant expression of RNA-binding proteins (RBPs) plays important roles in the occurrence and progression of cancer. MBNL2 is a member of the RNA binding protein MBNL family that is widely expressed in mammalian cells. We report here that MBNL2 is downregulated in breast, lung and liver cancer tissues, the promoter methylation levels of MBNL2 are higher in cancer tissues than normal tissues. The enrichment analysis of MBNL2 correlated genes indicates the potential function of MBNL2 on cancer progression. MBNL2 regulates cancer cell migration and invasion by modulating PI3K/AKT-mediated epithelial-mesenchymal transition. PI3K/AKT inhibitor overcomes the promotive effect of shMBNL2 on metastasis. The expression of MBNL2 is directly targeted by miR-182. miR-182 is upregulated in breast, lung and liver cancers and has good potential for cancer diagnosis. miR-182 promotes cancer cell migration and invasion by inhibiting the expression of MBNL2. Re-introduction of exogenous MBNL2 reverses the promotive effect of miR-182 on metastasis. Collectively, these findings suggest that MBNL2 plays a tumor suppressive function through miR-182-MBNL2-AKT-EMT signaling pathways.
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Affiliation(s)
- Guanglan Lin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiao Li
- Department of Neurology, Wuhan Hankou Hospital, Wuhan 430010, China
| | - Jin Cai
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Haowei Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Qilei Xin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ningchao Wang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Weidong Xie
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yaou Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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20
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Shi DL, Grifone R. RNA-Binding Proteins in the Post-transcriptional Control of Skeletal Muscle Development, Regeneration and Disease. Front Cell Dev Biol 2021; 9:738978. [PMID: 34616743 PMCID: PMC8488162 DOI: 10.3389/fcell.2021.738978] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022] Open
Abstract
Embryonic myogenesis is a temporally and spatially regulated process that generates skeletal muscle of the trunk and limbs. During this process, mononucleated myoblasts derived from myogenic progenitor cells within the somites undergo proliferation, migration and differentiation to elongate and fuse into multinucleated functional myofibers. Skeletal muscle is the most abundant tissue of the body and has the remarkable ability to self-repair by re-activating the myogenic program in muscle stem cells, known as satellite cells. Post-transcriptional regulation of gene expression mediated by RNA-binding proteins is critically required for muscle development during embryogenesis and for muscle homeostasis in the adult. Differential subcellular localization and activity of RNA-binding proteins orchestrates target gene expression at multiple levels to regulate different steps of myogenesis. Dysfunctions of these post-transcriptional regulators impair muscle development and homeostasis, but also cause defects in motor neurons or the neuromuscular junction, resulting in muscle degeneration and neuromuscular disease. Many RNA-binding proteins, such as members of the muscle blind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) families, display both overlapping and distinct targets in muscle cells. Thus they function either cooperatively or antagonistically to coordinate myoblast proliferation and differentiation. Evidence is accumulating that the dynamic interplay of their regulatory activity may control the progression of myogenic program as well as stem cell quiescence and activation. Moreover, the role of RNA-binding proteins that regulate post-transcriptional modification in the myogenic program is far less understood as compared with transcription factors involved in myogenic specification and differentiation. Here we review past achievements and recent advances in understanding the functions of RNA-binding proteins during skeletal muscle development, regeneration and disease, with the aim to identify the fundamental questions that are still open for further investigations.
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Affiliation(s)
- De-Li Shi
- Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
| | - Raphaëlle Grifone
- Developmental Biology Laboratory, CNRS-UMR 7622, Institut de Biologie de Paris-Seine, Sorbonne University, Paris, France
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21
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Matilainen O, Ribeiro ARS, Verbeeren J, Cetinbas M, Sood H, Sadreyev RI, Garcia SMDA. Loss of muscleblind splicing factor shortens Caenorhabditis elegans lifespan by reducing the activity of p38 MAPK/PMK-1 and transcription factors ATF-7 and Nrf/SKN-1. Genetics 2021; 219:6325509. [PMID: 34849877 PMCID: PMC8633093 DOI: 10.1093/genetics/iyab114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/03/2021] [Indexed: 12/13/2022] Open
Abstract
Muscleblind-like splicing regulators (MBNLs) are RNA-binding factors that have an important role in developmental processes. Dysfunction of these factors is a key contributor of different neuromuscular degenerative disorders, including Myotonic Dystrophy type 1 (DM1). Since DM1 is a multisystemic disease characterized by symptoms resembling accelerated aging, we asked which cellular processes do MBNLs regulate that make them necessary for normal lifespan. By utilizing the model organism Caenorhabditis elegans, we found that loss of MBL-1 (the sole ortholog of mammalian MBNLs), which is known to be required for normal lifespan, shortens lifespan by decreasing the activity of p38 MAPK/PMK-1 as well as the function of transcription factors ATF-7 and SKN-1. Furthermore, we show that mitochondrial stress caused by the knockdown of mitochondrial electron transport chain components promotes the longevity of mbl-1 mutants in a partially PMK-1-dependent manner. Together, the data establish a mechanism of how DM1-associated loss of muscleblind affects lifespan. Furthermore, this study suggests that mitochondrial stress could alleviate symptoms caused by the dysfunction of muscleblind splicing factor, creating a potential approach to investigate for therapy.
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Affiliation(s)
- Olli Matilainen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ana R S Ribeiro
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Murat Cetinbas
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Heini Sood
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Susana M D A Garcia
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00790, Finland
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22
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Yang F, Zhang Z, Hu B, Yu Y, Tan A. A CCCH zinc finger gene regulates doublesex alternative splicing and male development in Bombyx mori. INSECT SCIENCE 2021; 28:1253-1261. [PMID: 33029871 DOI: 10.1111/1744-7917.12876] [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: 06/03/2020] [Revised: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Recent identification of a Piwi-interacting RNA (piRNA)-initiated sex determination cascade in the silkworm, Bombyx mori, provides novel insights into high diversity of insect sex determination pathways. In this system, the W-chromosome-derived Fem piRNA is the primary sex determination signal. A CCCH-type zinc finger gene Masculinizer (Masc), which is targeted by Fem piRNA-PIWI complex in female animals, is indispensable for male-specific splicing of B. mori doublesex (Bmdsx). Although many genes involved in this cascade have been identified, the regulatory mechanisms of silkworm sex determination remain to be elucidated. Here we show that another CCCH-type zinc finger gene, Bmznf-2, is a masculinization factor in B. mori. Bmznf-2 shows testis-abundant expression and loss of Bmznf-2 function via clustered regularly interspaced short palindromic repeats / single-guide RNA-mediated mutagenesis results in feminized differentiation and appearance of the female-specific splicing variants of Bmdsx transcripts in males. In contrast, there is no phenotypic consequence in mutant females. In mutant males, relative messenger RNA expression levels of female-dominant genes such as vitellogenin and sex-specific storage protein 1 are significantly elevated while several male-dominant genes are significantly down-regulated. Furthermore, male mutants show delayed developmental timing, smaller body sizes of larvae and malformation of moth wings. Our data thus reveal that Bmznf-2 plays an indispensable role in silkworm male sexual differentiation.
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Affiliation(s)
- Fangying Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongjie Zhang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Hu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Yu
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
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Tylock KM, Auerbach DS, Tang ZZ, Thornton CA, Dirksen RT. Biophysical mechanisms for QRS- and QTc-interval prolongation in mice with cardiac expression of expanded CUG-repeat RNA. J Gen Physiol 2021; 152:133632. [PMID: 31968060 PMCID: PMC7062505 DOI: 10.1085/jgp.201912450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/28/2019] [Accepted: 11/26/2019] [Indexed: 12/26/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1), the most common form of muscular dystrophy in adults, results from the expression of toxic gain-of-function transcripts containing expanded CUG-repeats. DM1 patients experience cardiac electrophysiological defects, including prolonged PR-, QRS-, and QT-intervals, that increase susceptibility to sudden cardiac death (SCD). However, the specific biophysical and molecular mechanisms that underlie the electrocardiograph (ECG) abnormalities and SCD in DM1 are unclear. Here, we addressed this issue using a novel transgenic mouse model that exhibits robust cardiac expression of expanded CUG-repeat RNA (LC15 mice). ECG measurements in conscious LC15 mice revealed significantly prolonged QRS- and corrected QT-intervals, but a normal PR-interval. Although spontaneous arrhythmias were not observed in conscious LC15 mice under nonchallenged conditions, acute administration of the sodium channel blocker flecainide prolonged the QRS-interval and unveiled an increased susceptibility to lethal ventricular arrhythmias. Current clamp measurements in ventricular myocytes from LC15 mice revealed significantly reduced action potential upstroke velocity at physiological pacing (9 Hz) and prolonged action potential duration at all stimulation rates (1–9 Hz). Voltage clamp experiments revealed significant rightward shifts in the voltage dependence of sodium channel activation and steady-state inactivation, as well as a marked reduction in outward potassium current density. Together, these findings indicate that expression of expanded CUG-repeat RNA in the murine heart results in reduced sodium and potassium channel activity that results in QRS- and QT-interval prolongation, respectively.
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Affiliation(s)
- Kevin M Tylock
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
| | - David S Auerbach
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY.,Department of Pharmacology, Upstate Medical University, Syracuse, NY
| | - Zhen Zhi Tang
- Department of Neurology, University of Rochester Medical Center, Rochester, NY
| | - Charles A Thornton
- Department of Neurology, University of Rochester Medical Center, Rochester, NY
| | - Robert T Dirksen
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY
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Cai J, Wang N, Lin G, Zhang H, Xie W, Zhang Y, Xu N. MBNL2 Regulates DNA Damage Response via Stabilizing p21. Int J Mol Sci 2021; 22:ijms22020783. [PMID: 33466733 PMCID: PMC7829980 DOI: 10.3390/ijms22020783] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/31/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
RNA-binding proteins are frequently dysregulated in human cancer and able to modulate tumor cell proliferation as well as tumor metastasis through post-transcriptional regulation on target genes. Abnormal DNA damage response and repair mechanism are closely related to genome instability and cell transformation. Here, we explore the function of the RNA-binding protein muscleblind-like splicing regulator 2 (MBNL2) on tumor cell proliferation and DNA damage response. Transcriptome and gene expression analysis show that the PI3K/AKT pathway is enriched in MBNL2-depleted cells, and the expression of cyclin-dependent kinase inhibitor 1A (p21CDKN1A) is significantly affected after MBNL2 depletion. MBNL2 modulates the mRNA and protein levels of p21, which is independent of its canonical transcription factor p53. Moreover, depletion of MBNL2 increases the phosphorylation levels of checkpoint kinase 1 (Chk1) serine 345 (S345) and DNA damage response, and the effect of MBNL2 on DNA damage response is p21-dependent. MBNL2 would further alter tumor cell fate after DNA damage, MBNL2 knockdown inhibiting DNA damage repair and DNA damage-induced senescence, but promoting DNA damage-induced apoptosis.
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Affiliation(s)
- Jin Cai
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Open FIESTA Center, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Ningchao Wang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Open FIESTA Center, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Guanglan Lin
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Open FIESTA Center, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Haowei Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Weidong Xie
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Yaou Zhang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (J.C.); (N.W.); (G.L.); (H.Z.); (W.X.); (Y.Z.)
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Correspondence:
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25
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Bubenik JL, Hale M, McConnell O, Wang E, Swanson MS, Spitale R, Berglund JA. RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells. RNA (NEW YORK, N.Y.) 2020; 27:rna.077263.120. [PMID: 33310817 PMCID: PMC7901844 DOI: 10.1261/rna.077263.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
In vivo RNA structure analysis has become a powerful tool in molecular biology, largely due to the coupling of an increasingly diverse set of chemical approaches with high-throughput sequencing. This has resulted in a transition from single target to transcriptome-wide approaches. However, these methods require sequencing depths that preclude studying low abundance targets, which are not sufficiently captured in transcriptome-wide approaches. Here we present a ligation-free method to enrich for low abundance RNA sequences, which improves the diversity of molecules analyzed and results in improved analysis. In addition, this method is compatible with any choice of chemical adduct or read-out approach. We utilized this approach to study an autoregulated event in the pre-mRNA of the splicing factor, muscleblind-like splicing regulator 1 (MBNL1).
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Szeto RA, Tran T, Truong J, Negraes PD, Trujillo CA. RNA processing in neurological tissue: development, aging and disease. Semin Cell Dev Biol 2020; 114:57-67. [PMID: 33077405 DOI: 10.1016/j.semcdb.2020.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 07/29/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Gene expression comprises a diverse array of enzymes, proteins, non-coding transcripts, and cellular structures to guide the transfer of genetic information to its various final products. In the brain, the coordination among genes, or lack thereof, characterizes individual brain regions, mediates a variety of brain-related disorders, and brings light to fundamental differences between species. RNA processing, occurring between transcription and translation, controls an essential portion of gene expression through splicing, editing, localization, stability, and interference. The machinery to regulate transcripts must operate with precision serving as a blueprint for proteins and non-coding RNAs to derive their identity. Therefore, RNA processing has a broad scope of influence in the brain, as it modulates cell morphogenesis during development and underlies mechanisms behind certain neurological diseases. Here, we present these ideas through recent findings on RNA processing in development and post-developmental maturity to advance therapeutic discoveries and the collective knowledge of the RNA life cycle.
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Affiliation(s)
- Ryan A Szeto
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Timothy Tran
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Justin Truong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Priscilla D Negraes
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Cleber A Trujillo
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA.
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27
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An Overview of Alternative Splicing Defects Implicated in Myotonic Dystrophy Type I. Genes (Basel) 2020; 11:genes11091109. [PMID: 32971903 PMCID: PMC7564762 DOI: 10.3390/genes11091109] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy, caused by expansion of a CTG triplet repeat in the 3′ untranslated region (3′UTR) of the myotonic dystrophy protein kinase (DMPK) gene. The pathological CTG repeats result in protein trapping by expanded transcripts, a decreased DMPK translation and the disruption of the chromatin structure, affecting neighboring genes expression. The muscleblind-like (MBNL) and CUG-BP and ETR-3-like factors (CELF) are two families of tissue-specific regulators of developmentally programmed alternative splicing that act as antagonist regulators of several pre-mRNA targets, including troponin 2 (TNNT2), insulin receptor (INSR), chloride channel 1 (CLCN1) and MBNL2. Sequestration of MBNL proteins and up-regulation of CELF1 are key to DM1 pathology, inducing a spliceopathy that leads to a developmental remodelling of the transcriptome due to an adult-to-foetal splicing switch, which results in the loss of cell function and viability. Moreover, recent studies indicate that additional pathogenic mechanisms may also contribute to disease pathology, including a misregulation of cellular mRNA translation, localization and stability. This review focuses on the cause and effects of MBNL and CELF1 deregulation in DM1, describing the molecular mechanisms underlying alternative splicing misregulation for a deeper understanding of DM1 complexity. To contribute to this analysis, we have prepared a comprehensive list of transcript alterations involved in DM1 pathogenesis, as well as other deregulated mRNA processing pathways implications.
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Bourefis AR, Campanari ML, Buee-Scherrer V, Kabashi E. Functional characterization of a FUS mutant zebrafish line as a novel genetic model for ALS. Neurobiol Dis 2020; 142:104935. [PMID: 32380281 DOI: 10.1016/j.nbd.2020.104935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/22/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Mutations in Fused in sarcoma (FUS), an RNA-binding protein, are known to cause Amyotrophic Lateral Sclerosis (ALS). However, molecular mechanisms due to loss of FUS function remain unclear and controversial. Here, we report the characterization and phenotypic analysis of a deletion mutant of the unique FUS orthologue in zebrafish where Fus protein levels are depleted. The homozygous mutants displayed a reduced lifespan as well as impaired motor abilities associated with specific cellular deficits, including decreased motor neurons length and neuromuscular junctions (NMJ) fragmentation. Furthermore, we demonstrate that these cellular impairments are linked to the misregulation of mRNA expression of acetylcholine receptor (AChR) subunits and histone deacetylase 4, markers of denervation and reinnervation processes observed in ALS patients. In addition, fus loss of function alters tau transcripts favoring the expression of small tau isoforms. Overall, this new animal model extends our knowledge on FUS and supports the relevance of FUS loss of function in ALS physiopathology.
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Affiliation(s)
- Annis-Rayan Bourefis
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | - Maria-Letizia Campanari
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France
| | | | - Edor Kabashi
- Imagine Institute, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1163, Paris Descartes Université, 75015 Paris, France; Sorbonne Université, Université Pierre et Marie Curie (UPMC), Université de Paris 06, INSERM Unité 1127, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche 7225 Institut du Cerveau et de la Moelle Épinière (ICM), 75013 Paris, France.
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29
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Santoro M, Piacentini R, Perna A, Pisano E, Severino A, Modoni A, Grassi C, Silvestri G. Resveratrol corrects aberrant splicing of RYR1 pre-mRNA and Ca 2+ signal in myotonic dystrophy type 1 myotubes. Neural Regen Res 2020; 15:1757-1766. [PMID: 32209783 PMCID: PMC7437583 DOI: 10.4103/1673-5374.276336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a spliceopathy related to the mis-splicing of several genes caused by sequestration of nuclear transcriptional RNA-binding factors from non-coding CUG repeats of DMPK pre-mRNAs. Dysregulation of ryanodine receptor 1 (RYR1), sarcoplasmatic/endoplasmatic Ca2+-ATPase (SERCA) and α1S subunit of voltage-gated Ca2+ channels (Cav1.1) is related to Ca2+ homeostasis and excitation-contraction coupling impairment. Though no pharmacological treatment for DM1 exists, aberrant splicing correction represents one major therapeutic target for this disease. Resveratrol (RES, 3,5,4′-trihydroxy-trans-stilbene) is a promising pharmacological tools for DM1 treatment for its ability to directly bind the DNA and RNA influencing gene expression and alternative splicing. Herein, we analyzed the therapeutic effects of RES in DM1 myotubes in a pilot study including cultured myotubes from two DM1 patients and two healthy controls. Our results indicated that RES treatment corrected the aberrant splicing of RYR1, and this event appeared associated with restoring of depolarization-induced Ca2+ release from RYR1 dependent on the electro-mechanical coupling between RYR1 and Cav1.1. Interestingly, immunoblotting studies showed that RES treatment was associated with a reduction in the levels of CUGBP Elav-like family member 1, while RYR1, Cav1.1 and SERCA1 protein levels were unchanged. Finally, RES treatment did not induce any major changes either in the amount of ribonuclear foci or sequestration of muscleblind-like splicing regulator 1. Overall, the results of this pilot study would support RES as an attractive compound for future clinical trials in DM1. Ethical approval was obtained from the Ethical Committee of IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy (rs9879/14) on May 20, 2014.
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Affiliation(s)
| | - Roberto Piacentini
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessia Perna
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Eugenia Pisano
- Department of Cardiovascular and Thoracic Sciences, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Anna Severino
- Department of Cardiovascular and Thoracic Sciences, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Modoni
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Gabriella Silvestri
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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30
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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31
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Huang K, Masuda A, Chen G, Bushra S, Kamon M, Araki T, Kinoshita M, Ohkawara B, Ito M, Ohno K. Inhibition of cyclooxygenase-1 by nonsteroidal anti-inflammatory drugs demethylates MeR2 enhancer and promotes Mbnl1 transcription in myogenic cells. Sci Rep 2020; 10:2558. [PMID: 32054946 PMCID: PMC7018979 DOI: 10.1038/s41598-020-59517-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Muscleblind-like 1 (MBNL1) is a ubiquitously expressed RNA-binding protein, which is highly expressed in skeletal muscle. Abnormally expanded CUG-repeats in the DMPK gene cause myotonic dystrophy type 1 (DM1) by sequestration of MBNL1 to nuclear RNA foci and by upregulation of another RNA-binding protein, CUG-binding protein 1 (CUGBP1). We previously reported that a nonsteroidal anti-inflammatory drug (NSAID), phenylbutazone, upregulates MBNL1 expression in DM1 mouse model by demethylation of MeR2, an enhancer element in Mbnl1 intron 1. NSAIDs inhibit cyclooxygenase (COX), which is comprised of COX-1 and COX-2 isoforms. In this study, we screened 29 NSAIDs in C2C12 myoblasts, and found that 13 NSAIDs enhanced Mbnl1 expression, where COX-1-selective NSAIDs upregulated Mbnl1 more than COX-2-selective NSAIDs. Consistently, knockdown of COX-1, but not of COX-2, upregulated MBNL1 expression in C2C12 myoblasts and myotubes, as well as in myotubes differentiated from DM1 patient-derived induced pluripotent stem cells (iPSCs). Luciferase assay showed that COX-1-knockdown augmented the MeR2 enhancer activity. Furthermore, bisulfite sequencing analysis demonstrated that COX-1-knockdown suppressed methylation of MeR2. These results suggest that COX-1 inhibition upregulates Mbnl1 transcription through demethylation of the MeR2 enhancer. Taken together, our study provides new insights into the transcriptional regulation of Mbnl1 by the COX-1-mediated pathway.
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Affiliation(s)
- Kun Huang
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Guiying Chen
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Samira Bushra
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masayoshi Kamon
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | | | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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32
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In-silico prediction of role of chitosan, chondroitin sulphate and agar in process of wound healing towards scaffold development. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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33
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Casci I, Krishnamurthy K, Kour S, Tripathy V, Ramesh N, Anderson EN, Marrone L, Grant RA, Oliver S, Gochenaur L, Patel K, Sterneckert J, Gleixner AM, Donnelly CJ, Ruepp MD, Sini AM, Zuccaro E, Pennuto M, Pasinelli P, Pandey UB. Muscleblind acts as a modifier of FUS toxicity by modulating stress granule dynamics and SMN localization. Nat Commun 2019; 10:5583. [PMID: 31811140 PMCID: PMC6898697 DOI: 10.1038/s41467-019-13383-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations in fused in sarcoma (FUS) lead to amyotrophic lateral sclerosis (ALS) with varying ages of onset, progression and severity. This suggests that unknown genetic factors contribute to disease pathogenesis. Here we show the identification of muscleblind as a novel modifier of FUS-mediated neurodegeneration in vivo. Muscleblind regulates cytoplasmic mislocalization of mutant FUS and subsequent accumulation in stress granules, dendritic morphology and toxicity in mammalian neuronal and human iPSC-derived neurons. Interestingly, genetic modulation of endogenous muscleblind was sufficient to restore survival motor neuron (SMN) protein localization in neurons expressing pathogenic mutations in FUS, suggesting a potential mode of suppression of FUS toxicity. Upregulation of SMN suppressed FUS toxicity in Drosophila and primary cortical neurons, indicating a link between FUS and SMN. Our data provide in vivo evidence that muscleblind is a dominant modifier of FUS-mediated neurodegeneration by regulating FUS-mediated ALS pathogenesis.
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Affiliation(s)
- Ian Casci
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Karthik Krishnamurthy
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Vadreenath Tripathy
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Nandini Ramesh
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lara Marrone
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Rogan A Grant
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stacie Oliver
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Lauren Gochenaur
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Krishani Patel
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Amanda M Gleixner
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Live Like Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Christopher J Donnelly
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Live Like Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc-David Ruepp
- UK Dementia Research Institute at King's College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9NU, UK
| | - Antonella M Sini
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
| | - Emanuela Zuccaro
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Maria Pennuto
- Department of Biomedical Sciences (DBS), University of Padova, Padova, Italy
- Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Piera Pasinelli
- Department of Neuroscience, Jefferson Weinberg ALS Center, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Udai Bhan Pandey
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA.
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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Wang T, Liu Q, Duan L. MBNL1 regulates resistance of HeLa cells to cisplatin via Nrf2. Biochem Biophys Res Commun 2019; 522:763-769. [PMID: 31791583 DOI: 10.1016/j.bbrc.2019.11.162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 11/24/2019] [Indexed: 12/30/2022]
Abstract
Chemotherapy is an important method in the treatment of cervical cancer, but some patients will face drug resistance, which often indicates a poor prognosis. Moreover, there is no complete solution at present. Therefore, it is urgent to study the drug resistance mechanism of cervical cancer. Based on sequencing data mining, we predicted that MBNL1 might be involved in the occurrence and poor prognosis of cervical cancer, and verifed that MBNL1 could regulate the resistance of HeLa cells to cisplatin via Nrf2. In addition, we demonstrated that MBNL1 up regulated the degradation of Nrf2 protein by increasing the mRNA stability of Cul3. These results can provide theoretical basis for clinical development of new diagnosis and treatment targets for cisplatin resistance.
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Affiliation(s)
- Ting Wang
- Obstetrics and Gynecology Department, Yuncheng County People's Hospital, Shandong Province, China
| | - Qiong Liu
- Clinical Laboratory, Hubei University Hospital, Hubei Province, China
| | - Lian Duan
- Surgery, Hubei University Hospital, Hubei Province, China.
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35
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An Overview of Circular RNAs and Their Implications in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20184385. [PMID: 31500099 PMCID: PMC6769675 DOI: 10.3390/ijms20184385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded covalently closed RNA rings. Biogenesis of circRNAs, which may occur co-transcriptionally and post-transcriptionally via a back-splicing mechanism, requires the presence of complementary and/or inverted repeat sequences in introns flanking back-spliced exons and is facilitated by RNA-binding proteins. CircRNAs are abundant across eukaryotes; however, their biological functions remain largely speculative. Recently, they have been emerging as new members of a gene regulatory network and contributing factors in various human diseases including cancer, neurological, muscular and cardiovascular disorders. In this review, we present an overview of the current knowledge about circRNAs biogenesis and their aberrant expression in various human disorders. In particular, we focus on the latest discovery of circRNAs global upregulation in myotonic dystrophy type 1 (DM1) skeletal muscles and the role these prospective biomarkers might have for prognosis and therapeutic response in DM1.
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36
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Taylor K, Sznajder LJ, Cywoniuk P, Thomas JD, Swanson MS, Sobczak K. MBNL splicing activity depends on RNA binding site structural context. Nucleic Acids Res 2019; 46:9119-9133. [PMID: 29955876 PMCID: PMC6158504 DOI: 10.1093/nar/gky565] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/16/2018] [Indexed: 02/02/2023] Open
Abstract
Muscleblind-like (MBNL) proteins are conserved RNA-binding factors involved in alternative splicing (AS) regulation during development. While AS is controlled by distribution of MBNL paralogs and isoforms, the affinity of these proteins for specific RNA-binding regions and their location within transcripts, it is currently unclear how RNA structure impacts MBNL-mediated AS regulation. Here, we defined the RNA structural determinants affecting MBNL-dependent AS activity using both cellular and biochemical assays. While enhanced inclusion of MBNL-regulated alternative exons is controlled by the arrangement and number of MBNL binding sites within unstructured RNA, when these sites are embedded in a RNA hairpin MBNL binds preferentially to one side of stem region. Surprisingly, binding of MBNL proteins to RNA targets did not entirely correlate with AS efficiency. Moreover, comparison of MBNL proteins revealed structure-dependent competitive behavior between the paralogs. Our results showed that the structure of targeted RNAs is a prevalent component of the mechanism of alternative splicing regulation by MBNLs.
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Affiliation(s)
- Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Lukasz J Sznajder
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Piotr Cywoniuk
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - James D Thomas
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA.,Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Maurice S Swanson
- Center for NeuroGenetics and the Genetics Institute, Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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Lee KY, Chang HC, Seah C, Lee LJ. Deprivation of Muscleblind-Like Proteins Causes Deficits in Cortical Neuron Distribution and Morphological Changes in Dendritic Spines and Postsynaptic Densities. Front Neuroanat 2019; 13:75. [PMID: 31417371 PMCID: PMC6682673 DOI: 10.3389/fnana.2019.00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Myotonic dystrophy (Dystrophia Myotonica; DM) is the most common adult-onset muscular dystrophy and its brain symptoms seriously affect patients’ quality of life. It is caused by extended (CTG)n expansions at 3′-UTR of DMPK gene (DM type 1, DM1) or (CCTG)n repeats in the intron 1 of CNBP gene (DM type 2, DM2) and the sequestration of Muscleblind-like (MBNL) family proteins by transcribed (CUG)n RNA hairpin is the main pathogenic mechanism for DM. The MBNL proteins are splicing factors regulating posttranscriptional RNA during development. Previously, Mbnl knockout (KO) mouse lines showed molecular and phenotypic evidence that recapitulate DM brains, however, detailed morphological study has not yet been accomplished. In our studies, control (Mbnl1+/+; Mbnl2cond/cond; Nestin-Cre−/−), Mbnl2 conditional KO (2KO, Mbnl1+/+; Mbnl2cond/cond; Nestin-Cre+/−) and Mbnl1/2 double KO (DKO, Mbnl1ΔE3/ΔE3; Mbnl2cond/cond; Nestin-Cre+/−) mice were generated by crossing three individual lines. Immunohistochemistry for evaluating density and distribution of cortical neurons; Golgi staining for depicting the dendrites/dendritic spines; and electron microscopy for analyzing postsynaptic ultrastructure were performed. We found distributional defects in cortical neurons, reduction in dendritic complexity, immature dendritic spines and alterations of postsynaptic densities (PSDs) in the mutants. In conclusion, loss of function of Mbnl1/2 caused fundamental defects affecting neuronal distribution, dendritic morphology and postsynaptic architectures that are reminiscent of predominantly immature and fetal phenotypes in DM patients.
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Affiliation(s)
- Kuang-Yung Lee
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ho-Ching Chang
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Carol Seah
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Li-Jen Lee
- Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
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38
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Hale MA, Richardson JI, Day RC, McConnell OL, Arboleda J, Wang ET, Berglund JA. An engineered RNA binding protein with improved splicing regulation. Nucleic Acids Res 2019; 46:3152-3168. [PMID: 29309648 PMCID: PMC5888374 DOI: 10.1093/nar/gkx1304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
The muscleblind-like (MBNL) family of proteins are key developmental regulators of alternative splicing. Sequestration of MBNL proteins by expanded CUG/CCUG repeat RNA transcripts is a major pathogenic mechanism in the neuromuscular disorder myotonic dystrophy (DM). MBNL1 contains four zinc finger (ZF) motifs that form two tandem RNA binding domains (ZF1-2 and ZF3-4) which each bind YGCY RNA motifs. In an effort to determine the differences in function between these domains, we designed and characterized synthetic MBNL proteins with duplicate ZF1-2 or ZF3-4 domains, referred to as MBNL-AA and MBNL-BB, respectively. Analysis of splicing regulation revealed that MBNL-AA had up to 5-fold increased splicing activity while MBNL-BB had 4-fold decreased activity compared to a MBNL protein with the canonical arrangement of zinc finger domains. RNA binding analysis revealed that the variations in splicing activity are due to differences in RNA binding specificities between the two ZF domains rather than binding affinity. Our findings indicate that ZF1-2 drives splicing regulation via recognition of YGCY RNA motifs while ZF3-4 acts as a general RNA binding domain. Our studies suggest that synthetic MBNL proteins with improved or altered splicing activity have the potential to be used as both tools for investigating splicing regulation and protein therapeutics for DM and other microsatellite diseases.
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Affiliation(s)
- Melissa A Hale
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Jared I Richardson
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ryan C Day
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
| | - Ona L McConnell
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Juan Arboleda
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Eric T Wang
- Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - J Andrew Berglund
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.,Center for NeuroGenetics, University of Florida, Gainesville, FL 32610, USA
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39
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Czubak K, Taylor K, Piasecka A, Sobczak K, Kozlowska K, Philips A, Sedehizadeh S, Brook JD, Wojciechowska M, Kozlowski P. Global Increase in Circular RNA Levels in Myotonic Dystrophy. Front Genet 2019; 10:649. [PMID: 31428124 PMCID: PMC6689976 DOI: 10.3389/fgene.2019.00649] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/19/2019] [Indexed: 12/24/2022] Open
Abstract
Splicing aberrations induced as a consequence of the sequestration of muscleblind-like splicing factors on the dystrophia myotonica protein kinase transcript, which contains expanded CUG repeats, present a major pathomechanism of myotonic dystrophy type 1 (DM1). As muscleblind-like factors may also be important factors involved in the biogenesis of circular RNAs (circRNAs), we hypothesized that the level of circRNAs would be decreased in DM1. To test this hypothesis, we selected 20 well-validated circRNAs and analyzed their levels in several experimental systems (e.g., cell lines, DM muscle tissues, and a mouse model of DM1) using droplet digital PCR assays. We also explored the global level of circRNAs using two RNA-Seq datasets of DM1 muscle samples. Contrary to our original hypothesis, our results consistently showed a global increase in circRNA levels in DM1, and we identified numerous circRNAs that were increased in DM1. We also identified many genes (including muscle-specific genes) giving rise to numerous (>10) circRNAs. Thus, this study is the first to show an increase in global circRNA levels in DM1. We also provided preliminary results showing the association of circRNA level with muscle weakness and alternative splicing changes that are biomarkers of DM1 severity.
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Affiliation(s)
- Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Taylor
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Agnieszka Piasecka
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Krzysztof Sobczak
- Laboratory of Gene Therapy, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Kozlowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Saam Sedehizadeh
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J. David Brook
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Queen’s Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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40
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Zhang J, Zheng Z, Wu M, Zhang L, Wang J, Fu W, Xu N, Zhao Z, Lao Y, Xu H. The natural compound neobractatin inhibits tumor metastasis by upregulating the RNA-binding-protein MBNL2. Cell Death Dis 2019; 10:554. [PMID: 31320607 PMCID: PMC6639345 DOI: 10.1038/s41419-019-1789-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022]
Abstract
Tumor metastasis is the predominant cause of lethality in cancer. We found that Neobractatin (NBT), a natural compound isolated from Garcinia bracteata, could efficiently inhibit breast and lung cancer cells metastasis. However, the mechanisms of NBT inhibiting cancer metastasis remain unclear. Based on the RNA-sequencing result and transcriptome analysis, Muscleblind-like 2 (MBNL2) was found to be significantly upregulated in the cells treated with NBT. The Cancer Genome Atlas (TCGA) database analysis indicated that the expression of MBNL2 in breast and lung carcinoma tumor tissues was significantly lower compared to normal tissues. We thus conducted to investigate the antimetastatic role of MBNL2. MBNL2 overexpression mimicked the effect of NBT on breast cancer and lung cancer cell motility and metastasis, in addition significantly enhanced the inhibition effect of NBT. MBNL2 knockdown furthermore partially eliminated the inhibitory effect of NBT on metastasis. Mechanistically, we demonstrated that NBT- and MBNL2-mediated antimetastasis regulation significantly correlated with the pAKT/epithelial-mesenchymal transition (EMT) pathway. Subsequent in vivo study showed the same metastasis inhibition effect in NBT and MBNL2 in MDA-MB-231 xenografts mouse model. This study suggest that NBT possesses significant antitumor activity in breast and lung cancer cells that is partly mediated through the MBNL2 expression and enhancement in metastasis via the pAKT/EMT signaling pathway.
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Affiliation(s)
- Juan Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Zhaoqing Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Man Wu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Li Zhang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Jing Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Wenwei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Naihan Xu
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, 518055, Shenzhen, P.R. China
| | - Zhili Zhao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China.,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China
| | - Yuanzhi Lao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China. .,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China.
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, P.R. China. .,Engineering Research Center of Shanghai Colleges for TCM New Drug Discovery, 201203, Shanghai, P.R. China.
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41
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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42
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Sznajder ŁJ, Swanson MS. Short Tandem Repeat Expansions and RNA-Mediated Pathogenesis in Myotonic Dystrophy. Int J Mol Sci 2019; 20:ijms20133365. [PMID: 31323950 PMCID: PMC6651174 DOI: 10.3390/ijms20133365] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/27/2019] [Accepted: 07/08/2019] [Indexed: 12/23/2022] Open
Abstract
Short tandem repeat (STR) or microsatellite, expansions underlie more than 50 hereditary neurological, neuromuscular and other diseases, including myotonic dystrophy types 1 (DM1) and 2 (DM2). Current disease models for DM1 and DM2 propose a common pathomechanism, whereby the transcription of mutant DMPK (DM1) and CNBP (DM2) genes results in the synthesis of CUG and CCUG repeat expansion (CUGexp, CCUGexp) RNAs, respectively. These CUGexp and CCUGexp RNAs are toxic since they promote the assembly of ribonucleoprotein (RNP) complexes or RNA foci, leading to sequestration of Muscleblind-like (MBNL) proteins in the nucleus and global dysregulation of the processing, localization and stability of MBNL target RNAs. STR expansion RNAs also form phase-separated gel-like droplets both in vitro and in transiently transfected cells, implicating RNA-RNA multivalent interactions as drivers of RNA foci formation. Importantly, the nucleation and growth of these nuclear foci and transcript misprocessing are reversible processes and thus amenable to therapeutic intervention. In this review, we provide an overview of potential DM1 and DM2 pathomechanisms, followed by a discussion of MBNL functions in RNA processing and how multivalent interactions between expanded STR RNAs and RNA-binding proteins (RBPs) promote RNA foci assembly.
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Affiliation(s)
- Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA.
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
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43
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Ubiquitination of MBNL1 Is Required for Its Cytoplasmic Localization and Function in Promoting Neurite Outgrowth. Cell Rep 2019; 22:2294-2306. [PMID: 29490267 DOI: 10.1016/j.celrep.2018.02.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/19/2017] [Accepted: 02/06/2018] [Indexed: 12/20/2022] Open
Abstract
The Muscleblind-like protein family (MBNL) plays an important role in regulating the transition between differentiation and pluripotency and in the pathogenesis of myotonic dystrophy type 1 (DM1), a CTG expansion disorder. How different MBNL isoforms contribute to the differentiation and are affected in DM1 has not been investigated. Here, we show that the MBNL1 cytoplasmic, but not nuclear, isoform promotes neurite morphogenesis and reverses the morphological defects caused by expanded CUG RNA. Cytoplasmic MBNL1 is polyubiquitinated by lysine 63 (K63). Reduced cytoplasmic MBNL1 in the DM1 mouse brain is consistent with the reduced extent of K63 ubiquitination. Expanded CUG RNA induced the deubiqutination of cytoplasmic MBNL1, which resulted in nuclear translocation and morphological impairment that could be ameliorated by inhibiting K63-linked polyubiquitin chain degradation. Our results suggest that K63-linked ubiquitination of MBNL1 is required for its cytoplasmic localization and that deubiquitination of cytoplasmic MBNL1 is pathogenic in the DM1 brain.
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44
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Gerritsma S, Jalvingh KM, van de Beld C, Beerda J, van de Zande L, Vrieling K, Wertheim B. Natural and Artificial Selection for Parasitoid Resistance in Drosophila melanogaster Leave Different Genetic Signatures. Front Genet 2019; 10:479. [PMID: 31214243 PMCID: PMC6557190 DOI: 10.3389/fgene.2019.00479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 05/03/2019] [Indexed: 12/20/2022] Open
Abstract
Adaptation of complex traits depends on standing genetic variation at multiple loci. The allelic variants that have positive fitness effects, however, can differ depending on the genetic background and the selective pressure. Previously, we interrogated the Drosophila melanogaster genome at the population level for polymorphic positions and identified 215 single nucleotide polymorphisms (SNPs) that had significantly changed in frequency after experimental evolution for increased parasitoid resistance. In the current study, we follow up on 11 of these SNPs as putative targets of the experimental selection process (Jalvingh et al., 2014). We study the patterns of genetic variation for these SNPs in several European field populations. Furthermore, we associate the genetic variation of these SNPs to variation in resistance against the parasitoid Asobara tabida, by determining the individual phenotype and SNP genotype for 144 individuals from four Selection lines and four non-selected Control lines and for 400 individuals from 12 Field lines that differ in parasitoid resistance. For the Selection lines we additionally monitored the changes in allele frequencies throughout the five generations of experimental selection. For three genes, mbl (Zn-finger protein), mthl4 (G-protein coupled receptor) and CG17287 (protein-cysteine S-palmitoyltransferase) individual SNP genotypes were significantly associated with resistance level in the Selection and Control lines. Additionally, the minor allele in mbl and mthl4 were consistently and gradually favored throughout the five generations of experimental evolution. However, none of these alleles did appear to be associated to high resistance in the Field lines. We suggest that, within field populations, selection for parasitoid resistance is a gradual process that involves co-adapted gene complexes. Fast artificial selection, however, enforces the sudden cumulating of particular alleles that confer high resistance (genetic sweep). We discuss our findings in the context of local adaptation.
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Affiliation(s)
- Sylvia Gerritsma
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Kirsten M Jalvingh
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Carmen van de Beld
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Jelmer Beerda
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Louis van de Zande
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Klaas Vrieling
- Plant Cluster, Institute of Biology, Sylvius Laboratory, Leiden University, Leiden, Netherlands
| | - Bregje Wertheim
- Evolutionary Genetics, Development and Behaviour, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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45
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André LM, van Cruchten RTP, Willemse M, Wansink DG. (CTG)n repeat-mediated dysregulation of MBNL1 and MBNL2 expression during myogenesis in DM1 occurs already at the myoblast stage. PLoS One 2019; 14:e0217317. [PMID: 31116797 PMCID: PMC6530876 DOI: 10.1371/journal.pone.0217317] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/08/2019] [Indexed: 11/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a severe neuromuscular disorder caused by the expression of trinucleotide repeat-containing DMPK transcripts. Abnormally expanded (CUG)n repeats in these transcripts form hairpin-like structures that cause the RNA to accumulate in the cell nucleus by sequestering isoforms of the Muscleblind (MBNL) family, tissue-specific regulators of developmentally programmed, post-transcriptional processes in RNA metabolism. Through this mechanism, the function of MBNL in RNA processing becomes dominantly perturbed, which eventually leads to aberrant alternative splicing and the expression of foetal splice variants of a wide variety of proteins, including the MBNL isoforms themselves. Here, we employ a patient-derived muscle cell model for DM1 to examine in detail the expression of MBNL RNA and protein variants during myogenic differentiation. This DM1 model consists of a panel of isogenic myoblast cell lines that either contain a pathogenic DMPK allele with a congenital mutation of 2600 triplets, or lack this expanded repeat through CRISPR/Cas9-mediated gene editing. We found that the temporal expression levels of MBNL1, MBNL2 and MBNL3 RNAs are not influenced by presence of the (CTG)2600 repeat during myogenesis in vitro. However, throughout myoblast proliferation and differentiation to myotubes a disproportionate inclusion of MBNL1 exon 5 and MBNL2 exons 5 and 8 occurs in cells with the (CTG)2600 repeat. As a consequence, a reduced quantity and imbalanced collection of splice variants of MBNL1 and MBNL2 accumulates in both the cytoplasm and the nucleus of DM1 myoblasts and myotubes. We thus propose that both the quantitative and qualitative changes in the intracellular partitioning of MBNL proteins are a pivotal cause of skeletal muscle problems in DM1, starting already in muscle progenitor cells.
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Affiliation(s)
- Laurène M. André
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Remco T. P. van Cruchten
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Marieke Willemse
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
| | - Derick G. Wansink
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Department of Cell Biology, Nijmegen, The Netherlands
- * E-mail:
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46
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Nikonova E, Kao SY, Ravichandran K, Wittner A, Spletter ML. Conserved functions of RNA-binding proteins in muscle. Int J Biochem Cell Biol 2019; 110:29-49. [PMID: 30818081 DOI: 10.1016/j.biocel.2019.02.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022]
Abstract
Animals require different types of muscle for survival, for example for circulation, motility, reproduction and digestion. Much emphasis in the muscle field has been placed on understanding how transcriptional regulation generates diverse types of muscle during development. Recent work indicates that alternative splicing and RNA regulation are as critical to muscle development, and altered function of RNA-binding proteins causes muscle disease. Although hundreds of genes predicted to bind RNA are expressed in muscles, many fewer have been functionally characterized. We present a cross-species view summarizing what is known about RNA-binding protein function in muscle, from worms and flies to zebrafish, mice and humans. In particular, we focus on alternative splicing regulated by the CELF, MBNL and RBFOX families of proteins. We discuss the systemic nature of diseases associated with loss of RNA-binding proteins in muscle, focusing on mis-regulation of CELF and MBNL in myotonic dystrophy. These examples illustrate the conservation of RNA-binding protein function and the marked utility of genetic model systems in understanding mechanisms of RNA regulation.
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Affiliation(s)
- Elena Nikonova
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Shao-Yen Kao
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Keshika Ravichandran
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Anja Wittner
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany
| | - Maria L Spletter
- Biomedical Center, Department of Physiological Chemistry, Ludwig-Maximilians-University München, Großhaderner Str. 9, 82152, Martinsried-Planegg, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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47
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Tang L, Zhao P, Kong D. Muscleblind‑like 1 destabilizes Snail mRNA and suppresses the metastasis of colorectal cancer cells via the Snail/E‑cadherin axis. Int J Oncol 2019; 54:955-965. [PMID: 30664186 PMCID: PMC6365040 DOI: 10.3892/ijo.2019.4691] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022] Open
Abstract
RNA-binding proteins (RBPs) play a fundamental role in the recurrence and metastasis of colorectal cancer (CRC). In this study, we identified muscleblind-like 1 (MBNL1), an RBP implicated in developmental control, as a robust suppressor of CRC cell metastasis in vitro. By using a scratch assay coupled with time-lapse live cell imaging, our findings revealed that the knockdown of MBNL1 induced epithelial-to-mesenchymal transition (EMT)-like morphological changes in the HCT-116 cells, accompanied by an enhanced cell motility, and by the downregulation of E-cadherin and the upregulation of Snail expression. By contrast, the ectopic overexpression of MBNL1 suppressed EMT, characterized by the upregulation of E-cadherin and the downregulation of Snail expression. Mechanistically, Snail rather than E-cadherin, was identified as a direct downstream target gene of MBNL1. The ectopic the overexpression of MBNL1 markedly enhanced the recruitment of Snail transcripts to processing bodies (P-bodies), leading to the increased degradation of Snail mRNA and consequent translational silencing. Furthermore, the effect of MBNL1 on CRC cell migration was confirmed in additional CRC cell lines. SW480 and HT-29 cells exhibited similar changes in migratory capacity and the expression of Snail/E-cadherin to those observed in HCT-116 cells. On the whole, this study demonstrates that MBNL1 destabilizes Snail transcripts and, in turn, suppresses the EMT of CRC cells through the Snail/E-cadherin axis in vitro. Therefore, this EMT-related MBNL1/Snail/E-cadherin axis may prove to be a novel therapeutic target for CRC metastasis.
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Affiliation(s)
- Liang Tang
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Peng Zhao
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
| | - Dalu Kong
- Department of Colorectal Cancer, Cancer Hospital of Tianjin Medical University, Key Laboratory of Cancer Prevention and Therapy, and National Clinical Research Center of Cancer, Tianjin 300060, P.R. China
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48
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Li JSS, Millard SS. Deterministic splicing of Dscam2 is regulated by Muscleblind. SCIENCE ADVANCES 2019; 5:eaav1678. [PMID: 30746474 PMCID: PMC6357765 DOI: 10.1126/sciadv.aav1678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Alternative splicing increases the proteome diversity crucial for establishing the complex circuitry between trillions of neurons. To provide individual cells with different repertoires of protein isoforms, however, this process must be regulated. Previously, we found that the mutually exclusive alternative splicing of Drosophila Dscam2 produces two isoforms (A and B) with unique binding properties. This splicing event is cell type specific, and the transmembrane proteins that it generates are crucial for the development of axons, dendrites, and synapses. Here, we show that Muscleblind (Mbl) controls Dscam2 alternative splicing. Mbl represses isoform A and promotes the selection of isoform B. Mbl mutants exhibit phenotypes also observed in flies engineered to express a single Dscam2 isoform. Consistent with this, mbl expression is cell type specific and correlates with the splicing of isoform B. Our study demonstrates how the regulated expression of a splicing factor is sufficient to provide neurons with unique protein isoforms crucial for development.
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49
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Sugino K, Clark E, Schulmann A, Shima Y, Wang L, Hunt DL, Hooks BM, Tränkner D, Chandrashekar J, Picard S, Lemire AL, Spruston N, Hantman AW, Nelson SB. Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain. eLife 2019; 8:38619. [PMID: 30977723 PMCID: PMC6499542 DOI: 10.7554/elife.38619] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/11/2019] [Indexed: 01/27/2023] Open
Abstract
Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.
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Affiliation(s)
- Ken Sugino
- Janelia Research CampusAshburnUnited States
| | | | | | | | - Lihua Wang
- Janelia Research CampusAshburnUnited States
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50
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Olesnicky EC, Wright EG. Drosophila as a Model for Assessing the Function of RNA-Binding Proteins during Neurogenesis and Neurological Disease. J Dev Biol 2018; 6:E21. [PMID: 30126171 PMCID: PMC6162566 DOI: 10.3390/jdb6030021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/15/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
An outstanding question in developmental neurobiology is how RNA processing events contribute to the regulation of neurogenesis. RNA processing events are increasingly recognized as playing fundamental roles in regulating multiple developmental events during neurogenesis, from the asymmetric divisions of neural stem cells, to the generation of complex and diverse neurite morphologies. Indeed, both asymmetric cell division and neurite morphogenesis are often achieved by mechanisms that generate asymmetric protein distributions, including post-transcriptional gene regulatory mechanisms such as the transport of translationally silent messenger RNAs (mRNAs) and local translation of mRNAs within neurites. Additionally, defects in RNA splicing have emerged as a common theme in many neurodegenerative disorders, highlighting the importance of RNA processing in maintaining neuronal circuitry. RNA-binding proteins (RBPs) play an integral role in splicing and post-transcriptional gene regulation, and mutations in RBPs have been linked with multiple neurological disorders including autism, dementia, amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Fragile X syndrome (FXS), and X-linked intellectual disability disorder. Despite their widespread nature and roles in neurological disease, the molecular mechanisms and networks of regulated target RNAs have been defined for only a small number of specific RBPs. This review aims to highlight recent studies in Drosophila that have advanced our knowledge of how RBP dysfunction contributes to neurological disease.
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Affiliation(s)
- Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
| | - Ethan G Wright
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
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