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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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2
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van Zwol W, van de Sluis B, Ginsberg HN, Kuivenhoven JA. VLDL Biogenesis and Secretion: It Takes a Village. Circ Res 2024; 134:226-244. [PMID: 38236950 DOI: 10.1161/circresaha.123.323284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/21/2023] [Indexed: 01/23/2024]
Abstract
The production and secretion of VLDLs (very-low-density lipoproteins) by hepatocytes has a direct impact on liver fat content, as well as the concentrations of cholesterol and triglycerides in the circulation and thus affects both liver and cardiovascular health, respectively. Importantly, insulin resistance, excess caloric intake, and lack of physical activity are associated with overproduction of VLDL, hepatic steatosis, and increased plasma levels of atherogenic lipoproteins. Cholesterol and triglycerides in remnant particles generated by VLDL lipolysis are risk factors for atherosclerotic cardiovascular disease and have garnered increasing attention over the last few decades. Presently, however, increased risk of atherosclerosis is not the only concern when considering today's cardiometabolic patients, as they often also experience hepatic steatosis, a prevalent disorder that can progress to steatohepatitis and cirrhosis. This duality of metabolic risk highlights the importance of understanding the molecular regulation of the biogenesis of VLDL, the lipoprotein that transports triglycerides and cholesterol out of the liver. Fortunately, there has been a resurgence of interest in the intracellular assembly, trafficking, degradation, and secretion of VLDL by hepatocytes, which has led to many exciting new molecular insights that are the topic of this review. Increasing our understanding of the biology of this pathway will aid to the identification of novel therapeutic targets to improve both the cardiovascular and the hepatic health of cardiometabolic patients. This review focuses, for the first time, on this duality.
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Affiliation(s)
- Willemien van Zwol
- Department of Paediatrics, University Medical Center Groningen, University of Groningen, the Netherlands (W.v.Z., B.v.d.S., J.A.K.)
| | - Bart van de Sluis
- Department of Paediatrics, University Medical Center Groningen, University of Groningen, the Netherlands (W.v.Z., B.v.d.S., J.A.K.)
| | - Henry N Ginsberg
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY (H.N.G.)
| | - Jan Albert Kuivenhoven
- Department of Paediatrics, University Medical Center Groningen, University of Groningen, the Netherlands (W.v.Z., B.v.d.S., J.A.K.)
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3
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Feicht J, Jansen RP. The high-density lipoprotein binding protein HDLBP is an unusual RNA-binding protein with multiple roles in cancer and disease. RNA Biol 2024; 21:1-10. [PMID: 38477883 PMCID: PMC10939154 DOI: 10.1080/15476286.2024.2313881] [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] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
The high-density lipoprotein binding protein (HDLBP) is the human member of an evolutionarily conserved family of RNA-binding proteins, the vigilin protein family. These proteins are characterized by 14 or 15 RNA-interacting KH (heterologous nuclear ribonucleoprotein K homology) domains. While mainly present at the cytoplasmic face of the endoplasmic reticulum, HDLBP and its homologs are also found in the cytosol and nucleus. HDLBP is involved in various processes, including translation, chromosome segregation, cholesterol transport and carcinogenesis. Especially, its association with the latter two has attracted specific interest in the HDLBP's molecular role. In this review, we give an overview of some of the functions of the protein as well as introduce its impact on different kinds of cancer, its connection to lipid metabolism and its role in viral infection. We also aim at addressing the possible use of HDLBP as a drug target or biomarker and discuss its future implications.
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Affiliation(s)
- Jonathan Feicht
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
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4
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Mi H, Hu F, Gebeyew K, Cheng Y, Du R, Gao M, He Z, Tan Z. Genome wide transcriptome analysis provides bases on hepatic lipid metabolism disorder affected by increased dietary grain ratio in fattening lambs. BMC Genomics 2023; 24:364. [PMID: 37386405 DOI: 10.1186/s12864-023-09465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The liver is a principal metabolic organ and has a major role in regulating lipid metabolism. With the development of rapidly fattening livestock in the modern breeding industry, the incidence of hepatic steatosis and accumulation in animals was significantly increased. However, the molecular mechanisms responsible for hepatic lipid metabolic disturbances in a high concentrate diet remain unclear. The objective of this study was to evaluate the effects of increasing concentrate level in a fattening lamb diet on biochemical indices, hepatic triglycerides (TG) concentration, and hepatic transcriptomic profiles. In the present study, 42 weaned lambs (about 3 ± 0.3 months old) were randomly assigned to the GN60 group (60% concentrate of dry matter, GN60, n = 21) or GN70 group (70% concentrate of dry matter, n = 21) for a 3-months feeding trial. RESULTS No difference was observed in the growth performance or plasma biochemical parameters between the GN60 group and the GN70 group. The hepatic TG concentration was higher in the GN70 group than GN60 group (P < 0.05). Hepatic transcriptomic analysis showed that there were 290 differentially expressed genes identified between GN60 and GN70 groups, with 125 genes up-regulated and 165 genes down-regulated in the GN70 group. The enriched Gene Ontology (GO) items and KEGG pathways and protein-protein interaction (PPI) network of differentially expressed genes (DEGs) revealed that the majority of enriched pathways were related to lipid metabolism. Further analysis revealed that the fatty acid synthesis was up-regulated, while fatty acid transport, oxidation, and TG degradation were down-regulated in the GN70 group when compared with the GN60 group. CONCLUSIONS These results indicated that GN70 induced excess lipid deposition in the liver of lambs during the fattening period, with high synthesis rates and low degradation rates of TG. The identified mechanisms may help understand hepatic metabolism in lambs with a high concentrate diet and provide insight into decreasing the risk of liver metabolism disorder in animals.
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Affiliation(s)
- Hui Mi
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Hu
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kefyalew Gebeyew
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Cheng
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruiping Du
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia, 010031, China
| | - Min Gao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia, 010031, China
| | - Zhixiong He
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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Vatandaslar H, Garzia A, Meyer C, Godbersen S, Brandt LTL, Griesbach E, Chao JA, Tuschl T, Stoffel M. In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion. Nat Commun 2023; 14:3386. [PMID: 37296170 PMCID: PMC10256721 DOI: 10.1038/s41467-023-39135-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
System-wide cross-linking and immunoprecipitation (CLIP) approaches have unveiled regulatory mechanisms of RNA-binding proteins (RBPs) mainly in cultured cells due to limitations in the cross-linking efficiency of tissues. Here, we describe viP-CLIP (in vivo PAR-CLIP), a method capable of identifying RBP targets in mammalian tissues, thereby facilitating the functional analysis of RBP-regulatory networks in vivo. We applied viP-CLIP to mouse livers and identified Insig2 and ApoB as prominent TIAL1 target transcripts, indicating an important role of TIAL1 in cholesterol synthesis and secretion. The functional relevance of these targets was confirmed by showing that TIAL1 influences their translation in hepatocytes. Mutant Tial1 mice exhibit altered cholesterol synthesis, APOB secretion and plasma cholesterol levels. Our results demonstrate that viP-CLIP can identify physiologically relevant RBP targets by finding a factor implicated in the negative feedback regulation of cholesterol biosynthesis.
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Affiliation(s)
- Hasan Vatandaslar
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Svenja Godbersen
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Laura T L Brandt
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10021, USA
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093, Zürich, Switzerland.
- Medical Faculty, University of Zürich, 8091, Zürich, Switzerland.
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6
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Mushtaq A, Mir US, Altaf M. Multifaceted functions of RNA-binding protein vigilin in gene silencing, genome stability, and autism-related disorders. J Biol Chem 2023; 299:102988. [PMID: 36758804 PMCID: PMC10011833 DOI: 10.1016/j.jbc.2023.102988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important players in regulating eukaryotic gene expression and genome stability. Specific RBPs have been shown to mediate various chromatin-associated processes ranging from transcription to gene silencing and DNA repair. One of the prominent classes of RBPs is the KH domain-containing proteins. Vigilin, an evolutionarily conserved KH domain-containing RBP has been shown to be associated with diverse biological processes like RNA transport and metabolism, sterol metabolism, chromosome segregation, and carcinogenesis. We have previously reported that vigilin is essential for heterochromatin-mediated gene silencing in fission yeast. More recently, we have identified that vigilin in humans plays a critical role in efficient repair of DNA double-stranded breaks and functions in homology-directed DNA repair. In this review, we highlight the multifaceted functions of vigilin and discuss the findings in the context of gene expression, genome organization, cancer, and autism-related disorders.
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Affiliation(s)
- Arjamand Mushtaq
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India.
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7
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Zinnall U, Milek M, Minia I, Vieira-Vieira CH, Müller S, Mastrobuoni G, Hazapis OG, Del Giudice S, Schwefel D, Bley N, Voigt F, Chao JA, Kempa S, Hüttelmaier S, Selbach M, Landthaler M. HDLBP binds ER-targeted mRNAs by multivalent interactions to promote protein synthesis of transmembrane and secreted proteins. Nat Commun 2022; 13:2727. [PMID: 35585045 PMCID: PMC9117268 DOI: 10.1038/s41467-022-30322-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 04/13/2022] [Indexed: 01/09/2023] Open
Abstract
The biological role of RNA-binding proteins in the secretory pathway is not well established. Here, we describe that human HDLBP/Vigilin directly interacts with more than 80% of ER-localized mRNAs. PAR-CLIP analysis reveals that these transcripts represent high affinity HDLBP substrates and are specifically bound in their coding sequences (CDS), in contrast to CDS/3’UTR-bound cytosolic mRNAs. HDLBP crosslinks strongly to long CU-rich motifs, which frequently reside in CDS of ER-localized mRNAs and result in high affinity multivalent interactions. In addition to HDLBP-ncRNA interactome, quantification of HDLBP-proximal proteome confirms association with components of the translational apparatus and the signal recognition particle. Absence of HDLBP results in decreased translation efficiency of HDLBP target mRNAs, impaired protein synthesis and secretion in model cell lines, as well as decreased tumor growth in a lung cancer mouse model. These results highlight a general function for HDLBP in the translation of ER-localized mRNAs and its relevance for tumor progression. RNA binding protein HDLBP (or Vigilin) localizes in the endoplasmic reticulum (ER) membrane. Here the authors show that HDLBP contributes to translation of ER-targeted mRNAs.
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Affiliation(s)
- Ulrike Zinnall
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Miha Milek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,National Institute of Chemistry, Ljubljana, Slovenia. .,Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany.
| | - Igor Minia
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simon Müller
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Guido Mastrobuoni
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Orsalia-Georgia Hazapis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Simone Del Giudice
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - David Schwefel
- Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, Switzerland
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Medical Faculty, Martin Luther University, Halle, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany.,Charite-Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Markus Landthaler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology, Berlin, Germany. .,IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication. J Virol 2022; 96:e0196221. [PMID: 35266803 DOI: 10.1128/jvi.01962-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.
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9
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Yildirim Z, Baboo S, Hamid SM, Dogan AE, Tufanli O, Robichaud S, Emerton C, Diedrich JK, Vatandaslar H, Nikolos F, Gu Y, Iwawaki T, Tarling E, Ouimet M, Nelson DL, Yates JR, Walter P, Erbay E. Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression. EMBO Mol Med 2022; 14:e15344. [PMID: 35191199 PMCID: PMC8988208 DOI: 10.15252/emmm.202115344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022] Open
Abstract
Fragile X Mental Retardation protein (FMRP), widely known for its role in hereditary intellectual disability, is an RNA‐binding protein (RBP) that controls translation of select mRNAs. We discovered that endoplasmic reticulum (ER) stress induces phosphorylation of FMRP on a site that is known to enhance translation inhibition of FMRP‐bound mRNAs. We show ER stress‐induced activation of Inositol requiring enzyme‐1 (IRE1), an ER‐resident stress‐sensing kinase/endoribonuclease, leads to FMRP phosphorylation and to suppression of macrophage cholesterol efflux and apoptotic cell clearance (efferocytosis). Conversely, FMRP deficiency and pharmacological inhibition of IRE1 kinase activity enhances cholesterol efflux and efferocytosis, reducing atherosclerosis in mice. Our results provide mechanistic insights into how ER stress‐induced IRE1 kinase activity contributes to macrophage cholesterol homeostasis and suggests IRE1 inhibition as a promising new way to counteract atherosclerosis.
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Affiliation(s)
- Zehra Yildirim
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Biology and Genetics, National Nanotechnology Center, Bilkent University, Ankara, Turkey
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Syed M Hamid
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Asli E Dogan
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Biology and Genetics, National Nanotechnology Center, Bilkent University, Ankara, Turkey
| | - Ozlem Tufanli
- Lagone Medical Center, New York University, New York, NY, USA
| | - Sabrina Robichaud
- Department of Biochemistry, Microbiology and Immunology, Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - Christina Emerton
- Department of Biochemistry, Microbiology and Immunology, Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hasan Vatandaslar
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH), Zürich, Switzerland
| | - Fotis Nikolos
- Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yanghong Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Takao Iwawaki
- Department of Life Science, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - Elizabeth Tarling
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Mireille Ouimet
- Department of Biochemistry, Microbiology and Immunology, Heart Institute, University of Ottawa, Ottawa, ON, Canada
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA, USA
| | - Ebru Erbay
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
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10
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Ding Y, Yin R, Zhang S, Xiao Q, Zhao H, Pan X, Zhu X. The Combined Regulation of Long Non-coding RNA and RNA-Binding Proteins in Atherosclerosis. Front Cardiovasc Med 2021; 8:731958. [PMID: 34796209 PMCID: PMC8592911 DOI: 10.3389/fcvm.2021.731958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
Atherosclerosis is a complex disease closely related to the function of endothelial cells (ECs), monocytes/macrophages, and vascular smooth muscle cells (VSMCs). Despite a good understanding of the pathogenesis of atherosclerosis, the underlying molecular mechanisms are still only poorly understood. Therefore, atherosclerosis continues to be an important clinical issue worthy of further research. Recent evidence has shown that long non-coding RNAs (lncRNAs) and RNA-binding proteins (RBPs) can serve as important regulators of cellular function in atherosclerosis. Besides, several studies have shown that lncRNAs are partly dependent on the specific interaction with RBPs to exert their function. This review summarizes the important contributions of lncRNAs and RBPs in atherosclerosis and provides novel and comprehensible interaction models of lncRNAs and RBPs.
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Affiliation(s)
- Yuanyuan Ding
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ruihua Yin
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuai Zhang
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qi Xiao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongqin Zhao
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Pan
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoyan Zhu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
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11
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Kosmas K, Filippakis H, Khabibullin D, Turkiewicz M, Lam HC, Yu J, Kedersha NL, Anderson PJ, Henske EP. TSC2 Interacts with HDLBP/Vigilin and Regulates Stress Granule Formation. Mol Cancer Res 2021; 19:1389-1397. [PMID: 33888601 DOI: 10.1158/1541-7786.mcr-20-1046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/29/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022]
Abstract
Tuberous sclerosis complex (TSC) is caused by mutations of either the TSC1 or TSC2 tumor suppressor gene. TSC causes tumors of the brain, heart, kidney, skin and lymphangioleiomyomatosis (LAM). Here we report that the TSC2 protein physically binds to high-density lipoprotein binding protein (HDLBP), also called vigilin, a core stress granule (SG) protein, and that TSC2 localizes to SGs. SGs contain mRNAs and translation initiation complexes, and regulate gene expression by sequestering specific transcripts, thereby serving a cytoprotective role. TSC2 has never before been shown to localize to SGs and knocking down vigilin impacts SG translocation of TSC2. TSC2-deficient cells showed a striking increase in the number of SGs after thermal shock and arsenite treatment relative to Tsc2-expressing cells. Our findings also show that murine kidney lysates from a model of TSC have increased levels of SG components including G3BP1 and Caprin1. G3BP1 and Caprin are elevated in renal angiomyolipomas (a renal tumor common in patients with TSC) compared with control normal kidney. G3BP1 is also elevated in TSC-associated subependymal giant cell astrocytomas. We found that genetic inhibition of G3BP1 inhibits the proliferation of TSC2-deficient cells in vitro. Finally, in a mouse model of TSC, genetic inhibition of SGs suppresses cell growth, suggesting that targeting SGs may have efficacy in the therapy of TSC. IMPLICATIONS: This study demonstrates that TSC2 physically interacts with HDLBP/vigilin, a component of SGs, that TSC2 localizes to SG and that TSC2-deficient cells have more SGs, suggesting that SGs represent a novel therapeutic target in TSC.
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Affiliation(s)
- Kosmas Kosmas
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Harilaos Filippakis
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Damir Khabibullin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michal Turkiewicz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hilaire C Lam
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jane Yu
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Nancy L Kedersha
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women' Hospital and Harvard Medical School, Boston, Massachusetts
| | - Paul J Anderson
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women' Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elizabeth P Henske
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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12
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Metrnl deficiency decreases blood HDL cholesterol and increases blood triglyceride. Acta Pharmacol Sin 2020; 41:1568-1575. [PMID: 32265491 DOI: 10.1038/s41401-020-0368-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Dyslipidemia is a risk factor for cardiovascular diseases and type 2 diabetes. Several adipokines play important roles in modulation of blood lipids. Metrnl is a recently identified adipokine, and adipose Metrnl participates in regulation of blood triglyceride (TG). In this study, we generated Metrnl global, intestine-specific and liver-specific knockout mice, and explored the effects of Metrnl on serum lipid parameters. Global knockout of Metrnl had no effects on serum lipid parameters under normal chow diet, but increased blood TG by 14%, and decreased total cholesterol (TC) by 16% and high density lipoprotein cholesterol (HDL-C) by 24% under high fat diet. Nevertheless, intestine-specific knockout of Metrnl did not alter the serum lipids parameters under normal chow diet or high fat diet. Notably, liver-specific knockout of Metrnl decreased HDL-C by 24%, TC by 20% and low density lipoprotein cholesterol (LDL-C) by 16% without alterations of blood TG and nonesterified fatty acids (NEFA) under high fat diet. But deficiency of Metrnl in liver did not change VLDL secretion and expression of lipid synthetic and metabolic genes. We conclude that tissue-specific Metrnl controls different components of blood lipids. In addition to modulation of blood TG by adipose Metrnl, blood HDL-C is regulated by liver Metrnl.
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13
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Huang W, Liao CC, Han Y, Lv J, Lei M, Li Y, Lv Q, Dong D, Zhang S, Pan YH, Luo J. Co-activation of Akt, Nrf2, and NF-κB signals under UPR ER in torpid Myotis ricketti bats for survival. Commun Biol 2020; 3:658. [PMID: 33177645 PMCID: PMC7658203 DOI: 10.1038/s42003-020-01378-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022] Open
Abstract
Bats hibernate to survive stressful conditions. Examination of whole cell and mitochondrial proteomes of the liver of Myotis ricketti revealed that torpid bats had endoplasmic reticulum unfolded protein response (UPRER), global reduction in glycolysis, enhancement of lipolysis, and selective amino acid metabolism. Compared to active bats, torpid bats had higher amounts of phosphorylated serine/threonine kinase (p-Akt) and UPRER markers such as PKR-like endoplasmic reticulum kinase (PERK) and activating transcription factor 4 (ATF4). Torpid bats also had lower amounts of the complex of Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-related factor 2 (Nrf2), and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) (p65)/I-κBα. Cellular redistribution of 78 kDa glucose-regulated protein (GRP78) and reduced binding between PERK and GRP78 were also seen in torpid bats. Evidence of such was not observed in fasted, cold-treated, or normal mice. These data indicated that bats activate Akt, Nrf2, and NF-κB via the PERK-ATF4 regulatory axis against endoplasmic reticulum stresses during hibernation.
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Affiliation(s)
- Wenjie Huang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei, 11221, Taiwan
| | - Yijie Han
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junyan Lv
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Ming Lei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangyang Li
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Qingyun Lv
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China
| | - Dong Dong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yi-Husan Pan
- Key Laboratory of Brain Functional Genomics (Ministry of Education and Shanghai), Institute of Brain Functional Genomics, School of Life Sciences and the Collaborative Innovation Center for Brain Science, East China Normal University, Shanghai, 200062, China.
| | - Jian Luo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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Liao HQ, Zhou J, Cao Y, Nie YL, Li MQ, Zhou J. Vigilin interacts with ER-β to protect against palmitic acid-induced granulosa cells apoptosis via inhibiting calcineurin-mediated Drp1 signaling pathway. Steroids 2020; 163:108699. [PMID: 32687845 DOI: 10.1016/j.steroids.2020.108699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/12/2020] [Accepted: 07/11/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hypercholesterolemia is one of the causes of female infertility, and as a common fatty acid in follicular fluid, palmitic acid (PA) level plays a vital role in granule cell which is closely related to the developmental potential of follicle. METHODS The ovarian granulosa cell-like human granulosa (KGN) cell line and the immortalized normal ovarian surface epithelial cell line (IOSE80) were used to verify the effect of PA on cell viability and apoptosis by MTT and flow cytometry assay, respectively. Then mitochondria damage was confirmed by mitochondrial membrane potential, mitochondrial ROS detection assay and western blot in KGN cells. Thorough luciferase reporter assay and RIP-qPCR, the relationship between vigilin and ER-β was investigated. RESULTS In our study, PA induced mitochondrial damage-mediated cell apoptosis of KGN cells was dose-dependently, while PA shown no effects on in IOSE80 cells. Then the role of calcineurin (CnA)-mediated Drp1 signaling pathway on KGN cells was confirmed by treating with Mdivi-1 or FK506T. In addition, the changed level of vigilin and ER-β was observed in cell apoptosis of KGN cells induced by PA. By transfecting vigilin vector or ER-β vector into KGN cells, respectively, vigilin and ER-β were demonstrated to regulate the apoptosis of KGN cells. And vigilin was a binding protein of ER-β mRNA. CONCLUSION Vigilin could interact with ER-β mRNA to promote ER-β expression. And Vigilin/ ER-β relieve the mitochondrial damage and cell apoptosis induced by PA through regulating CnA-mediated Drp1 signaling pathway, which revealed the mechanism and strategy of hypercholesterolemia in female infertility.
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Affiliation(s)
- Hong-Qing Liao
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Jun Zhou
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Yang Cao
- Hunan University of Technology and Business, Changsha 410205, PR China
| | - Yu-Lin Nie
- Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Mei-Qing Li
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China
| | - Jing Zhou
- The Second Affiliated Hospital of South China University, Hengyang 421001, PR China; Hengyang Nanhua-Xinghui Reproductive Health Hospital, Hengyang 421001, PR China.
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15
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Abstract
The emergence of genome-wide analyses to interrogate cellular DNA, RNA, and protein content has revolutionized the study of control networks that mediate cellular homeostasis. mRNA translation represents the last step of genetic flow and primarily defines the proteome. Translational regulation is thus critical for gene expression, in particular under nutrient excess or deficiency. Until recently, it was unclear how the global effects of translational control are orchestrated by nutrient signaling pathways. An emerging concept of translational reprogramming addresses how to maintain the expression of specific proteins during nutrient stress by translation of selective mRNAs. In this review, we describe recent advances in our understanding of translational control principles; nutrient-sensing mechanisms; and their dysregulation in human diseases such as diabetes, cancer, and aging. The mechanistic understanding of translational regulation in response to different nutrient conditions may help identify potential dietary and therapeutic targets to improve human health.
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Affiliation(s)
- Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Robert V. Swanda
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York 14853, USA
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16
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Nikolaou KC, Vatandaslar H, Meyer C, Schmid MW, Tuschl T, Stoffel M. The RNA-Binding Protein A1CF Regulates Hepatic Fructose and Glycerol Metabolism via Alternative RNA Splicing. Cell Rep 2020; 29:283-300.e8. [PMID: 31597092 DOI: 10.1016/j.celrep.2019.08.100] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/09/2019] [Accepted: 08/29/2019] [Indexed: 01/11/2023] Open
Abstract
The regulation of hepatic gene expression has been extensively studied at the transcriptional level; however, the control of metabolism through posttranscriptional gene regulation by RNA-binding proteins in physiological and disease states is less understood. Here, we report a major role for the hormone-sensitive RNA-binding protein (RBP) APOBEC1 complementation factor (A1CF) in the generation of hepatocyte-specific and alternatively spliced transcripts. Among these transcripts are isoforms for the dominant and high-affinity fructose-metabolizing ketohexokinase C and glycerol kinase, two key metabolic enzymes that are linked to hepatic gluconeogenesis and found to be markedly reduced upon hepatic ablation of A1cf. Consequently, mice lacking A1CF exhibit improved glucose tolerance and are protected from fructose-induced hyperglycemia, hepatic steatosis, and development of obesity. Our results identify a previously unreported function of A1CF as a regulator of alternative splicing of a subset of genes influencing hepatic glucose production through fructose and glycerol metabolism.
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Affiliation(s)
- Kostas C Nikolaou
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Hasan Vatandaslar
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Marc W Schmid
- MWSchmid GmbH, Möhrlistrasse 25, 8006 Zurich, Switzerland
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland; Medical Faculty, University of Zurich, 8091 Zurich, Switzerland.
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17
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Lu H, Yuan X, Zhang Y, Han M, Liu S, Han K, Liang P, Cheng J. HCBP6 deficiency exacerbates glucose and lipid metabolism disorders in non-alcoholic fatty liver mice. Biomed Pharmacother 2020; 129:110347. [PMID: 32535386 DOI: 10.1016/j.biopha.2020.110347] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/23/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Non-alcoholic fatty liver disease (NAFLD), which often accompanied by metabolic syndrome, such as obesity, diabetes and dyslipidemia, has become a global health problem. Our previous results show that HCV core protein binding protein 6 (HCBP6) could maintain the triglyceride homeostasis in liver cells. However, the role of HCBP6 in NAFLD and its associated metabolic disorders remains incompletely understood. METHODS Hepatic HCBP6 expression was determined by qRT-PCR, Western blot and immunohistochemistry analysis. HCBP6 knockout (HCBP6-KO) mice were constructed and fed a high-fat diet (HFD) to induce NAFLD. The effects of HCBP6 on glucose and lipid metabolism were measured by HE staining, qRT-PCR, Western blot and GTT. Wild-type and HCBP6-KO mice kept on a HFD were treated with ginsenosides Rh2, and HE staining and GTT were used to study the function of Rh2 in metabolism disorders. RESULTS HCBP6 is reduced in HFD-fed mice. HCBP6 deficiency increased the body weight, aggravated fatty liver and deteriorated lipid homeostasis as well as glucose homeostasis in HFD-induced mouse model of NAFLD. Moreover, HCBP6-KO mice failed to maintain body temperature upon cold challenge. Mechanistically, HCBP6 could regulate lipolysis and fatty acid oxidation via activation of AMKP in vivo. In addition, HCBP6 expression was upregulated by ginsenosides Rh2. Accordingly, ginsenosides Rh2 administrations improved HFD-induced fatty liver and glucose tolerance. CONCLUSIONS These findings indicated that HCBP6 is essential in maintaining lipid and glucose homeostasis and body temperature. HCBP6 augmented by ginsenosides Rh2 may be a promising therapeutic strategy for the treatment of metabolic disorders in NAFLD mice.
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Affiliation(s)
- Hongping Lu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Xiaoxue Yuan
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China.
| | - Yu Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China; Department of Hepatology Division 3, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Ming Han
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Shunai Liu
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Kai Han
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Pu Liang
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China
| | - Jun Cheng
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100015, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100191, China.
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18
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An RNA-centric dissection of host complexes controlling flavivirus infection. Nat Microbiol 2019; 4:2369-2382. [PMID: 31384002 PMCID: PMC6879806 DOI: 10.1038/s41564-019-0518-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/23/2019] [Indexed: 12/26/2022]
Abstract
Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co-opting cellular factors for viral translation and viral genome replication at the endoplasmic reticulum (ER) is a shared replication strategy, despite different clinical outcomes. While the protein products of these viruses have been studied in depth, how the RNA genomes operate inside human cells is poorly understood. Using comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS), we took an RNA-centric viewpoint of flaviviral infection and identified several hundred proteins associated with both DENV and ZIKV genomic RNA in human cells. Genome-scale knockout screens assigned putative functional relevance to the RNA-protein interactions observed by ChIRP-MS. The ER-localized RNA binding proteins vigilin and RRBP1 directly bound viral RNA and each acted at distinct stages in the life cycle of flaviviruses. Thus, this versatile strategy can elucidate features of human biology that control pathogenesis of clinically relevant viruses.
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19
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Xavier MA, Tirloni L, Pinto AF, Diedrich JK, Yates JR, Gonzales S, Farber M, da Silva Vaz I, Termignoni C. Tick Gené’s organ engagement in lipid metabolism revealed by a combined transcriptomic and proteomic approach. Ticks Tick Borne Dis 2019; 10:787-797. [DOI: 10.1016/j.ttbdis.2019.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/27/2019] [Accepted: 03/15/2019] [Indexed: 12/24/2022]
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20
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Liu C, Jiang W, Tian X, Yang P, Xiao L, Li J, Qiu L, Tu H, Tan W. Identification of Vigilin as a Potential Ischemia Biomarker by Brain Slice-Based Systematic Evolution of Ligands by Exponential Enrichment. Anal Chem 2019; 91:6675-6681. [PMID: 30993971 PMCID: PMC6625766 DOI: 10.1021/acs.analchem.9b00609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stroke is one of the leading causes of disability and death among adults worldwide and results in numerous biochemical alterations. However, few efficient biomarkers are clinically available to diagnose stroke because of the limitations of biomarkers and their probes. In this work, we utilized frozen brain slices of middle cerebral artery occlusion (MCAO) in a mouse model of ischemia to select a specific binding aptamer, termed LCW17, by tissue-based SELEX (systematic evolution of ligands by exponential enrichment). LCW17 was enhanced in binding in ischemic brain slices compared to sham control. We identified the binding target of LCW17 as vigilin. Vigilin is increased in ischemia brain slices and exhibits enhanced release from cultured hippocampal neurons after oxygen glucose deprivation in vitro. Taken together, ischemic brain slice-based aptamer selection will enable identification of more probes and potential target molecules for diagnosis and therapy of ischemic stroke. Aptamer LCW17 and vigilin may potentially be applied to define the molecular mechanism underlying ischemic stroke, as well as its diagnosis.
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Affiliation(s)
- Chao Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Wei Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Xibin Tian
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Peng Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Le Xiao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Haijun Tu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
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21
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Kim S, Graham MJ, Lee RG, Yang L, Kim S, Subramanian V, Layne JD, Cai L, Temel RE, Shih D, Lusis AJ, Berliner JA, Lee S. Heparin-binding EGF-like growth factor (HB-EGF) antisense oligonucleotide protected against hyperlipidemia-associated atherosclerosis. Nutr Metab Cardiovasc Dis 2019; 29:306-315. [PMID: 30738642 PMCID: PMC6452438 DOI: 10.1016/j.numecd.2018.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 11/24/2018] [Accepted: 12/27/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND AIMS Heparin-binding EGF-like growth factor (HB-EGF) is a representative EGF family member that interacts with EGFR under diverse stress environment. Previously, we reported that the HB-EGF-targeting using antisense oligonucleotide (ASO) effectively suppressed an aortic aneurysm in the vessel wall and circulatory lipid levels. In this study, we further examined the effects of the HB-EGF ASO administration on the development of hyperlipidemia-associated atherosclerosis using an atherogenic mouse model. METHODS AND RESULTS The male and female LDLR deficient mice under Western diet containing 21% fat and 0.2% cholesterol content were cotreated with control and HB-EGF ASOs for 12 weeks. We observed that the HB-EGF ASO administration effectively downregulated circulatory VLDL- and LDL-associated lipid levels in circulation; concordantly, the HB-EGF targeting effectively suppressed the development of atherosclerosis in the aorta. An EGFR blocker BIBX1382 administration suppressed the hepatic TG secretion rate, suggesting a positive role of the HB-EGF signaling for the hepatic VLDL production. We newly observed that there was a significant improvement of the insulin sensitivity by the HB-EGF ASO administration in a mouse model under the Western diet as demonstrated by the improvement of the glucose and insulin tolerances. CONCLUSION The HB-EGF ASO administration effectively downregulated circulatory lipid levels by suppressing hepatic VLDL production rate, which leads to effective protection against atherosclerosis in the vascular wall.
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Affiliation(s)
- S Kim
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - M J Graham
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, CA, 92010, USA
| | - R G Lee
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, CA, 92010, USA
| | - L Yang
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - S Kim
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - V Subramanian
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA; Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - J D Layne
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - L Cai
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - R E Temel
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA; Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - D Shih
- Department of Medicine-Cardiology, University of California-Los Angeles (UCLA) School of Medicine, Los Angeles, CA, 90095, USA
| | - A J Lusis
- Department of Medicine-Cardiology, University of California-Los Angeles (UCLA) School of Medicine, Los Angeles, CA, 90095, USA; Department of Human Genetics, University of California-Los Angeles (UCLA) School of Medicine, Los Angeles, CA, 90095, USA; Department of Microbiology, Immunology & Molecular Genetics, University of California-Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - J A Berliner
- Department of Pathology and Laboratory Medicine, University of California-Los Angeles (UCLA), Los Angeles, CA, 90095, USA
| | - S Lee
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA; Department of Pharmacology & Nutritional Sciences, University of Kentucky, Lexington, KY, 40536, USA.
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22
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Guevara J, Romo J, Hernandez E, Guevara NV. Identification of Receptor Ligands in Apo B100 Reveals Potential Functional Domains. Protein J 2019; 37:548-571. [PMID: 30259240 DOI: 10.1007/s10930-018-9792-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
LDL, VLDL and other members of the low-density lipoparticles (LLPs) enter cells through a large family of receptors. The actual receptor ligand(s) in apolipoprotein B100, one of the main proteins of LLP, remain(s) unknown. The objective of this study was to identify true receptor ligand(s) in apo B100, a molecule of 4563 residues. Apo B100 contains 33 analogues of Cardin-Weintraub arginine/lysine-based receptor ligand motifs and shares key lysine motifs and sequence similarity with the LDL receptor-associated protein, MESD, and heat shock proteins. Eleven FITC-labeled synthetic peptides of 21-42 residues, with at least one ligand, were tested for binding and internalization using HeLa cells. All peptides bind but display different binding capacities and patterns. Peptides B0013, B0582, B2366, and B2932 mediate endocytosis and appear in distinct sites in the cytoplasm. B0708 and B3181 bind and remain on the cell surface as aggregates/clusters. Peptides B3119 (Site A) and B3347 (Site B), the putative ligands, showed low binding and no cell entry capacity. Apo B100 regions in this study share similarities with related proteins of known function including chaperone proteins and Apo BEC stimulating protein, and not directly related proteins, e.g., the DNA-binding domain of interferon regulatory factors, MSX2-interacting protein, and snake venom Zinc metalloproteinase-disintegrin-like proteins.
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Affiliation(s)
- Juan Guevara
- Biophysics Research Laboratory, Department of Physics and Astronomy, The University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Jamie Romo
- Biophysics Research Laboratory, Department of Physics and Astronomy, The University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Ernesto Hernandez
- Biophysics Research Laboratory, Department of Physics and Astronomy, The University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Natalia Valentinova Guevara
- Biophysics Research Laboratory, Department of Physics and Astronomy, The University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA.
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23
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Wang X, Xin L, Duan Z, Zuo Z, Wang Y, Ren Y, Zhang W, Sun X, Liu X, Ge L, Yang X, Yao Z, Yang J. Global Tudor-SN transgenic mice are protected from obesity-induced hepatic steatosis and insulin resistance. FASEB J 2018; 33:3731-3745. [PMID: 30521378 DOI: 10.1096/fj.201801253rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the current study, we explored the impact of Tudor-staphylococcal nuclease (SN) on obesity induced by a high-fat diet (HFD) in mice, because the functional involvement of Tudor-SN in lipid metabolism in vivo is unknown. HFD-transgenic (Tg) mice exhibited reductions in hepatic steatosis and systemic insulin resistance. There was no difference in hepatic lipid accumulation between chow-fed wild-type (WT) and chow-fed Tg mice; consistently, no difference in activation of the lipogenic pathway was detected. Overactivation of hepatic nuclear sterol regulatory element-binding protein (nSrebp2)-2, the central regulator of cholesterol metabolic proteins, was observed in HFD-Tg livers along with improved cholesterol homeostasis, but no such changes were observed in HFD-WT livers. Consistent results were observed in vitro in α-mouse liver 12 cells treated with palmitate mimicking the HFD state. In addition, global gene analysis indicated that various downstream targets of nSrebp2, were up-regulated in HFD-Tg livers. Moreover, HFD-WT mice displayed islet hypertrophy and suppression of glucose-induced insulin secretion from islets, whereas HFD-Tg mice had normal pancreatic islets. This finding suggests that the improved pancreatic metabolism of HFD-Tg mice is related to the systemic effect of insulin resistance, not to the autonomous influence of pancreatic cells. Tudor-SN is likely to be a key regulator for ameliorating HFD-induced hepatic steatosis and systemic insulin resistance in vivo.-Wang, X., Xin, L., Duan, Z., Zuo, Z., Wang, Y., Ren, Y., Zhang, W., Sun, X., Liu, X., Ge, L., Yang, X., Yao, Z., Yang, J. Global Tudor-SN transgenic mice are protected from obesity-induced hepatic steatosis and insulin resistance.
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Affiliation(s)
- Xinting Wang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lingbiao Xin
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhongchao Duan
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhiyu Zuo
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuan Wang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuanyuan Ren
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Zhang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoming Sun
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xin Liu
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lin Ge
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xi Yang
- Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Immune Microenvironment and Disease, Ministry of Education, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China.,Department of Biochemistry and Molecular Biology, and Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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24
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Woo HH, Lee SC, Stoffer JB, Rush D, Chambers SK. Phenotype of vigilin expressing breast cancer cells binding to the 69 nt 3'UTR element in CSF-1R mRNA. Transl Oncol 2018; 12:106-115. [PMID: 30292064 PMCID: PMC6171096 DOI: 10.1016/j.tranon.2018.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/27/2022] Open
Abstract
Vigilin, a nucleocytoplasmic shuttling protein, post-transcriptionally suppresses proto-oncogene c-fms expression (encoding CSF-1R) in breast cancer by binding to a 69 nt cis-acting 3-UTR element in CSF-1R mRNA. CSF-1R is an important mediator of breast cancer development, metastasis, and survival. We confirm that vigilin decreases in vitro reporter luciferase activity as well as the translation rate of target mRNAs. We further explore the mechanism of suppression of CSF-1R. We show that the 69 nt binding element has profound effects on translation efficiency of CSF-1R mRNA, not seen in the presence of mutation of the element. Also, mutation of the 69 nt element in the CSF-1R mRNA 3′UTR both interferes with direct vigilin binding and obviates effect of vigilin overexpression on translational repression of CSF-1R. We show that stable vigilin binding requires the full length 69 nt CSF-1R element, including the 26 nt pyrimidine-rich core. Furthermore, titration of endogenous vigilin and other proteins which bind the 69 nt element, by exogenously introduced CSF-1R mRNA 3′UTR containing the pyrimidine-rich sequence, increases the adhesion, motility, and invasion of breast cancer cells. This phenotypic effect is not seen when the 69 nt element is deleted. Lastly, we are the first to show that human breast tissues exhibit strong vigilin expression in normal breast epithelium. Our pilot data suggest decreased vigilin protein expression, along with shift from the nucleus to the cytoplasmic location, in the transition to ductal carcinoma in situ.
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Affiliation(s)
- Ho-Hyung Woo
- The University of Arizona Cancer Center, 1515 N Campbell Ave, Tucson, AZ 85724, USA
| | - Sang C Lee
- The University of Arizona Cancer Center, 1515 N Campbell Ave, Tucson, AZ 85724, USA
| | - Jha'nae B Stoffer
- The University of Arizona Cancer Center, 1515 N Campbell Ave, Tucson, AZ 85724, USA
| | - Demaretta Rush
- Department of Pathology, University of Arizona, 1501 N Campbell Ave, Tucson, AZ 85724, USA
| | - Setsuko K Chambers
- The University of Arizona Cancer Center, 1515 N Campbell Ave, Tucson, AZ 85724, USA; Department of Obstetrics and Gynecology, University of Arizona, 1501 N Campbell Ave, Tucson, AZ 85724, USA.
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25
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The RNA-Binding Protein Scp160p Facilitates Aggregation of Many Endogenous Q/N-Rich Proteins. Cell Rep 2018; 24:20-26. [DOI: 10.1016/j.celrep.2018.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 04/18/2018] [Accepted: 06/01/2018] [Indexed: 01/05/2023] Open
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26
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Lampert F, Stafa D, Goga A, Soste MV, Gilberto S, Olieric N, Picotti P, Stoffel M, Peter M. The multi-subunit GID/CTLH E3 ubiquitin ligase promotes cell proliferation and targets the transcription factor Hbp1 for degradation. eLife 2018; 7:35528. [PMID: 29911972 PMCID: PMC6037477 DOI: 10.7554/elife.35528] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 12/17/2022] Open
Abstract
In yeast, the glucose-induced degradation-deficient (GID) E3 ligase selectively degrades superfluous gluconeogenic enzymes. Here, we identified all subunits of the mammalian GID/CTLH complex and provide a comprehensive map of its hierarchical organization and step-wise assembly. Biochemical reconstitution demonstrates that the mammalian complex possesses inherent E3 ubiquitin ligase activity, using Ube2H as its cognate E2. Deletions of multiple GID subunits compromise cell proliferation, and this defect is accompanied by deregulation of critical cell cycle markers such as the retinoblastoma (Rb) tumor suppressor, phospho-Histone H3 and Cyclin A. We identify the negative regulator of pro-proliferative genes Hbp1 as a bonafide GID/CTLH proteolytic substrate. Indeed, Hbp1 accumulates in cells lacking GID/CTLH activity, and Hbp1 physically interacts and is ubiquitinated in vitro by reconstituted GID/CTLH complexes. Our biochemical and cellular analysis thus demonstrates that the GID/CTLH complex prevents cell cycle exit in G1, at least in part by degrading Hbp1.
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Affiliation(s)
| | - Diana Stafa
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Algera Goga
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | | | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
| | - Markus Stoffel
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
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27
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Singh AK, Aryal B, Zhang X, Fan Y, Price NL, Suárez Y, Fernández-Hernando C. Posttranscriptional regulation of lipid metabolism by non-coding RNAs and RNA binding proteins. Semin Cell Dev Biol 2017; 81:129-140. [PMID: 29183708 DOI: 10.1016/j.semcdb.2017.11.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/14/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
Abstract
Alterations in lipoprotein metabolism enhance the risk of cardiometabolic disorders including type-2 diabetes and atherosclerosis, the leading cause of death in Western societies. While the transcriptional regulation of lipid metabolism has been well characterized, recent studies have uncovered the importance of microRNAs (miRNAs), long-non-coding RNAs (lncRNAs) and RNA binding proteins (RBP) in regulating the expression of lipid-related genes at the posttranscriptional level. Work from several groups has identified a number of miRNAs, including miR-33, miR-122 and miR-148a, that play a prominent role in controlling cholesterol homeostasis and lipoprotein metabolism. Importantly, dysregulation of miRNA expression has been associated with dyslipidemia, suggesting that manipulating the expression of these miRNAs could be a useful therapeutic approach to ameliorate cardiovascular disease (CVD). The role of lncRNAs in regulating lipid metabolism has recently emerged and several groups have demonstrated their regulation of lipoprotein metabolism. However, given the high abundance of lncRNAs and the poor-genetic conservation between species, much work will be needed to elucidate the specific role of lncRNAs in controlling lipoprotein metabolism. In this review article, we summarize recent findings in the field and highlight the specific contribution of lncRNAs and RBPs in regulating lipid metabolism.
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Affiliation(s)
- Abhishek K Singh
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA
| | - Binod Aryal
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA
| | - Xinbo Zhang
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA
| | - Yuhua Fan
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA; College of Pharmacy, Harbin Medical University -Daqing, 163000, PR China
| | - Nathan L Price
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA
| | - Yajaira Suárez
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Integrative Cell Signaling and Neurobiology of Metabolism Program, Department of Comparative Medicine, Department of Pathology, Yale University School of Medicine, 10 Amistad St., New Haven, CT 06510, USA.
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28
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Cheng MH, Jansen RP. A jack of all trades: the RNA-binding protein vigilin. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28975734 DOI: 10.1002/wrna.1448] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/21/2017] [Accepted: 08/17/2017] [Indexed: 12/25/2022]
Abstract
The vigilin family of proteins is evolutionarily conserved from yeast to humans and characterized by the proteins' 14 or 15 hnRNP K homology (KH) domains, typically associated with RNA-binding. Vigilin is the largest RNA-binding protein (RBP) in the KH domain-containing family and one of the largest RBP known to date. Since its identification 30 years ago, vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. We provide a brief historic overview of vigilin research and outline the proteins' different functions, focusing on maintenance of genome ploidy, heterochromatin formation, RNA export, as well as regulation of translation, mRNA transport, and mRNA stability. The multitude of associated functions is reflected by the large number of identified interaction partners, ranging from tRNAs, mRNAs, ribosomes and ribosome-associated proteins, to histone methyltransferases and DNA-dependent protein kinases. Most of these partners bind to vigilin's carboxyterminus, and the two most C-terminal KH domains of the protein, KH13 and KH14, represent the main mRNA-binding interface. Since the nuclear functions of vigilins in particular are not conserved, we outline a model for the basal functions of vigilins, as well as those which were acquired during the transition from unicellular organisms to metazoa. WIREs RNA 2017, 8:e1448. doi: 10.1002/wrna.1448 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Matthew Hk Cheng
- International Max Planck Research School, Tuebingen, Germany.,Interfaculty Institute of Biochemistry, Tuebingen, Germany
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29
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Menzies RI, Zhao X, Mullins LJ, Mullins JJ, Cairns C, Wrobel N, Dunbar DR, Bailey MA, Kenyon CJ. Transcription controls growth, cell kinetics and cholesterol supply to sustain ACTH responses. Endocr Connect 2017; 6:446-457. [PMID: 28720595 PMCID: PMC5574282 DOI: 10.1530/ec-17-0092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 01/29/2023]
Abstract
Chronic ACTH exposure is associated with adrenal hypertrophy and steroidogenesis. The underlying molecular processes in mice have been analysed by microarray, histological and immunohistochemical techniques. Synacthen infused for 2 weeks markedly increased adrenal mass and plasma corticosterone levels. Microarray analysis found greater than 2-fold changes in expression of 928 genes (P < 0.001; 397 up, 531 down). These clustered in pathways involved in signalling, sterol/lipid metabolism, cell proliferation/hypertrophy and apoptosis. Signalling genes included some implicated in adrenal adenomas but also upregulated genes associated with cyclic AMP and downregulated genes associated with aldosterone synthesis. Sterol metabolism genes were those promoting cholesterol supply (Scarb1, Sqle, Apoa1) and disposal (Cyp27a1, Cyp7b1). Oil red O staining showed lipid depletion consistent with reduced expression of genes involved in lipid synthesis. Genes involved in steroidogenesis (Star, Cyp11a1, Cyp11b1) were modestly affected (P < 0.05; <1.3-fold). Increased Ki67, Ccna2, Ccnb2 and Tk1 expression complemented immunohistochemical evidence of a 3-fold change in cell proliferation. Growth arrest genes, Cdkn1a and Cdkn1c, which are known to be active in hypertrophied cells, were increased >4-fold and cross-sectional area of fasciculata cells was 2-fold greater. In contrast, genes associated with apoptosis (eg Casp12, Clu,) were downregulated and apoptotic cells (Tunel staining) were fewer (P < 0.001) and more widely distributed throughout the cortex. In summary, long-term steroidogenesis with ACTH excess is sustained by genes controlling cholesterol supply and adrenal mass. ACTH effects on adrenal morphology and genes controlling cell hypertrophy, proliferation and apoptosis suggest the involvement of different cell types and separate molecular pathways.
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Affiliation(s)
- Robert I Menzies
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Xin Zhao
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Linda J Mullins
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - John J Mullins
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Carolynn Cairns
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Nicola Wrobel
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Donald R Dunbar
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Matthew A Bailey
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
| | - Christopher J Kenyon
- The University/BHF Centre for Cardiovascular ScienceUniversity of Edinburgh, The Queen's Medical Research Institute, Edinburgh, UK
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30
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Zabinsky RA, Weum BM, Cui M, Han M. RNA Binding Protein Vigilin Collaborates with miRNAs To Regulate Gene Expression for Caenorhabditis elegans Larval Development. G3 (BETHESDA, MD.) 2017; 7:2511-2518. [PMID: 28576776 PMCID: PMC5555458 DOI: 10.1534/g3.117.043414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/29/2017] [Indexed: 01/16/2023]
Abstract
Extensive studies have suggested that most miRNA functions are executed through complex miRNA-target interaction networks, and such networks function semiredundantly with other regulatory systems to shape gene expression dynamics for proper physiological functions. We found that knocking down vgln-1, which encodes a conserved RNA-binding protein associated with diverse functions, causes severe larval arrest at the early L1 stage in animals with compromised miRISC functions (an ain-2/GW182 mutant). Through an enhancer screen, we identified five specific miRNAs, and miRNA families, that act semiredundantly with VGLN-1 to regulate larval development. By RIP-Seq analysis, we identified mRNAs that are directly bound by VGLN-1, and highly enriched for miRNA binding sites, leading to a hypothesis that VGLN-1 may share common targets with miRNAs to regulate gene expression dynamics for development.
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Affiliation(s)
- Rebecca A Zabinsky
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309
| | - Brett M Weum
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309
| | - Mingxue Cui
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309
| | - Min Han
- Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309
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