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Gajjar G, Huggins HP, Kim ES, Huang W, Bonnet FX, Updike DL, Keiper BD. Two germ granule eIF4E isoforms reside in different mRNPs to hand off C elegans mRNAs from translational repression to activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595216. [PMID: 38826235 PMCID: PMC11142241 DOI: 10.1101/2024.05.24.595216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
We studied the function of translation factor eIF4E isoforms in regulating mRNAs in germ cell granules/condensates. Translational control of mRNAs plays an essential role in germ cell gene regulation. Messenger ribonucleoprotein (mRNP) complexes assemble on mRNAs as they move from the nucleus into perinuclear germ granules to exert both positive and negative post-transcriptional regulation in the cytoplasm. In C. elegans , germ granules are surprisingly dynamic mRNP condensates that remodel during development. Two eIF4E isoforms (called IFE-1 and IFE-3), eIF4E-Interacting Proteins (4EIPs), RBPs, DEAD-box helicases, polyadenylated mRNAs, Argonautes and miRNAs all occupy positions in germ granules. Affinity purification of IFE-1 and IFE-3 allowed mass spectrometry and mRNA-Seq to identify the proteins and mRNAs that populate stable eIF4E mRNPs. We find translationally controlled mRNAs (e.g. pos-1, mex-3, spn-4, etc.) enriched in IFE-3 mRNPs, but excluded from IFE-1 mRNPs. These mRNAs also require IFE-1 for efficient translation. The findings support a model in which oocytes and embryos utilize the two eIF4Es for opposite purposes on critically regulated germline mRNAs. Careful colocalization of the eIF4Es with other germ granule components suggests an architecture in which GLH-1, PGL-1 and the IFEs are stratified to facilitate sequential interactions for mRNAs. Biochemical characterization demonstrates opposing yet cooperative roles for IFE-3 and IFE-1 to hand-off of translationally controlled mRNAs from the repressed to the activated state, respectively. The model involves eIF4E mRNPs shuttling mRNAs through nuclear pore-associated granules/condensates to cytoplasmic ribosomes.
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2
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Kotagama K, McJunkin K. Recent advances in understanding microRNA function and regulation in C. elegans. Semin Cell Dev Biol 2024; 154:4-13. [PMID: 37055330 PMCID: PMC10564972 DOI: 10.1016/j.semcdb.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023]
Abstract
MicroRNAs (miRNAs) were first discovered in C. elegans as essential post-transcriptional regulators of gene expression. Since their initial discovery, miRNAs have been implicated in numerous areas of physiology and disease in all animals examined. In recent years, the C. elegans model continues to contribute important advances to all areas of miRNA research. Technological advances in tissue-specific miRNA profiling and genome editing have driven breakthroughs in understanding biological functions of miRNAs, mechanism of miRNA action, and regulation of miRNAs. In this review, we highlight these new C. elegans findings from the past five to seven years.
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Affiliation(s)
- Kasuen Kotagama
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases Intramural Research Program, Bethesda, MD 20892, USA.
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3
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Nakashima M, Suga N, Ikeda Y, Yoshikawa S, Matsuda S. Circular RNAs, Noncoding RNAs, and N6-methyladenosine Involved in the Development of MAFLD. Noncoding RNA 2024; 10:11. [PMID: 38392966 PMCID: PMC10893449 DOI: 10.3390/ncrna10010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs), including circular RNAs (circRNAs) and N6-methyladenosine (m6A), have been shown to play a critical role in the development of various diseases including obesity and metabolic disorder-associated fatty liver disease (MAFLD). Obesity is a chronic disease caused by excessive fat accumulation in the body, which has recently become more prevalent and is the foremost risk factor for MAFLD. Causes of obesity may involve the interaction of genetic, behavioral, and social factors. m6A RNA methylation might add a novel inspiration for understanding the development of obesity and MAFLD with post-transcriptional regulation of gene expression. In particular, circRNAs, microRNAs (miRNAs), and m6A might be implicated in the progression of MAFLD. Interestingly, m6A modification can modulate the translation, degradation, and other functions of ncRNAs. miRNAs/circRNAs can also modulate m6A modifications by affecting writers, erasers, and readers. In turn, ncRNAs could modulate the expression of m6A regulators in different ways. However, there is limited evidence on how these ncRNAs and m6A interact to affect the promotion of liver diseases. It seems that m6A can occur in DNA, RNA, and proteins that may be associated with several biological properties. This study provides a mechanistic understanding of the association of m6A modification and ncRNAs with liver diseases, especially for MAFLD. Comprehension of the association between m6A modification and ncRNAs may contribute to the development of treatment tactics for MAFLD.
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Affiliation(s)
| | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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4
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Ikeda Y, Morikawa S, Nakashima M, Yoshikawa S, Taniguchi K, Sawamura H, Suga N, Tsuji A, Matsuda S. CircRNAs and RNA-Binding Proteins Involved in the Pathogenesis of Cancers or Central Nervous System Disorders. Noncoding RNA 2023; 9:23. [PMID: 37104005 PMCID: PMC10142617 DOI: 10.3390/ncrna9020023] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Circular RNAs (circRNAs), a newly recognized group of noncoding RNA transcripts, have established widespread attention due to their regulatory role in cell signaling. They are covalently closed noncoding RNAs that form a loop, and are typically generated during the splicing of precursor RNAs. CircRNAs are key post-transcriptional and post-translational regulators of gene expression programs that might influence cellular response and/or function. In particular, circRNAs have been considered to function as sponges of specific miRNA, regulating cellular processes at the post-transcription stage. Accumulating evidence has shown that the aberrant expression of circRNAs could play a key role in the pathogenesis of several diseases. Notably, circRNAs, microRNAs, and several RNA-binding proteins, including the antiproliferative (APRO) family proteins, could be indispensable gene modulators, which might be strongly linked to the occurrence of diseases. In addition, circRNAs have attracted general interest for their stability, abundance in the brain, and their capability to cross the blood-brain barrier. Here, we present the current findings and theragnostic potentials of circRNAs in several diseases. With this, we aim to provide new insights to support the development of novel diagnostic and/or therapeutic strategies for these diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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5
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Ao Q, Wen LL, Yu TH, Ma YZ, Mao XY, Ao TR, Javed R, Ten H, Matsuno A. Sequential expression of miR-221-3p and miR-338-3p in Schwann cells as a therapeutic strategy to promote nerve regeneration and functional recovery. Neural Regen Res 2023; 18:671-682. [DOI: 10.4103/1673-5374.350214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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6
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Donnelly BF, Yang B, Grimme AL, Vieux KF, Liu CY, Zhou L, McJunkin K. The developmentally timed decay of an essential microRNA family is seed-sequence dependent. Cell Rep 2022; 40:111154. [PMID: 35947946 PMCID: PMC9413084 DOI: 10.1016/j.celrep.2022.111154] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 06/04/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNA (miRNA) abundance is tightly controlled by regulation of biogenesis and decay. Here, we show that the mir-35 miRNA family undergoes selective decay at the transition from embryonic to larval development in C. elegans. The seed sequence of the miRNA is necessary and largely sufficient for this regulation. Sequences outside the seed (3' end) regulate mir-35 abundance in the embryo but are not necessary for sharp decay at the transition to larval development. Enzymatic modifications of the miRNA 3' end are neither prevalent nor correlated with changes in decay, suggesting that miRNA 3' end display is not a core feature of this mechanism and further supporting a seed-driven decay model. Our findings demonstrate that seed-sequence-specific decay can selectively and coherently regulate all redundant members of a miRNA seed family, a class of mechanism that has great biological and therapeutic potential for dynamic regulation of a miRNA family's target repertoire.
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Affiliation(s)
- Bridget F Donnelly
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Bing Yang
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Acadia L Grimme
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA; Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Karl-Frédéric Vieux
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Chen-Yu Liu
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Lecong Zhou
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA.
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7
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Guo M, Luo C, Wang Z, Chen S, Morris D, Ruan F, Chen Z, Yang L, Wei X, Wu C, Luo B, Lv Z, Huang J, Zhang D, Yu C, Gao Q, Wang H, Zhang Y, Sun F, Yan W, Tang C. Uncoupling transcription and translation through miRNA-dependent poly(A) length control in haploid male germ cells. Development 2022; 149:275470. [PMID: 35588208 PMCID: PMC9270972 DOI: 10.1242/dev.199573] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/05/2022] [Indexed: 01/31/2023]
Abstract
As one of the post-transcriptional regulatory mechanisms, uncoupling of transcription and translation plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for hours or even days before translation. In addition to oocytes and neurons, developing spermatids display significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoprotein (RNP) granules for translational repression and stabilization. In contrast, re-polyadenylation might allow for translocation of the translationally repressed transcripts from RNP granules to polysomes. Overall, our data suggest that miRNA-dependent poly(A) length control represents a previously unreported mechanism underlying uncoupled translation and transcription in haploid male mouse germ cells.
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Affiliation(s)
- Mei Guo
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Chunhai Luo
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS575, Reno, NV 89557, USA,Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Sheng Chen
- Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA,China Medical University, Department of Laboratory Animal Science, Shenyang 110122, China
| | - Dayton Morris
- Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fengying Ruan
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhichao Chen
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linfeng Yang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiongyi Wei
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China
| | - Chuanwen Wu
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Bei Luo
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhou Lv
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin Huang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Dong Zhang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Cong Yu
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiang Gao
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongqi Wang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Zhang
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
| | - Fei Sun
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, MS575, Reno, NV 89557, USA,Department of Endocrinology and Metabolism, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Authors for correspondence (; ; ; )
| | - Chong Tang
- R&D Department, BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong University, Nantong 226001, Jiangsu, China,Authors for correspondence (; ; ; )
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8
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Hebbar S, Panzade G, Vashisht AA, Wohlschlegel JA, Veksler-Lublinsky I, Zinovyeva AY. Functional identification of microRNA-centered complexes in C. elegans. Sci Rep 2022; 12:7133. [PMID: 35504914 PMCID: PMC9065084 DOI: 10.1038/s41598-022-10771-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/08/2022] [Indexed: 02/02/2023] Open
Abstract
microRNAs (miRNAs) are crucial for normal development and physiology. To identify factors that might coordinate with miRNAs to regulate gene expression, we used 2'O-methylated oligonucleotides to precipitate Caenorhabditis elegans let-7, miR-58, and miR-2 miRNAs and the associated proteins. A total of 211 proteins were identified through mass-spectrometry analysis of miRNA co-precipitates, which included previously identified interactors of key miRNA pathway components. Gene ontology analysis of the identified interactors revealed an enrichment for RNA binding proteins, suggesting that we captured proteins that may be involved in mRNA lifecycle. To determine which miRNA interactors are important for miRNA activity, we used RNAi to deplete putative miRNA co-factors in animals with compromised miRNA activity and looked for alterations of the miRNA mutant phenotypes. Depletion of 25 of 39 tested genes modified the miRNA mutant phenotypes in three sensitized backgrounds. Modulators of miRNA phenotypes ranged from RNA binding proteins RBD-1 and CEY-1 to metabolic factors such as DLST-1 and ECH-5, among others. The observed functional interactions suggest widespread coordination of these proteins with miRNAs to ultimately regulate gene expression. This study provides a foundation for future investigations aimed at deciphering the molecular mechanisms of miRNA-mediated gene regulation.
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Affiliation(s)
- Shilpa Hebbar
- Division of Biology, Kansas State University, Manhattan, 66506, USA
| | - Ganesh Panzade
- Division of Biology, Kansas State University, Manhattan, 66506, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
- Genomics Institute of the Novartis Research Foundation, San Diego, 92121, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, 90095, USA
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Anna Y Zinovyeva
- Division of Biology, Kansas State University, Manhattan, 66506, USA.
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9
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Nsengimana B, Khan FA, Ngowi EE, Zhou X, Jin Y, Jia Y, Wei W, Ji S. Processing body (P-body) and its mediators in cancer. Mol Cell Biochem 2022; 477:1217-1238. [PMID: 35089528 DOI: 10.1007/s11010-022-04359-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
In recent years, processing bodies (P-bodies) formed by liquid-liquid phase separation, have attracted growing scientific attention due to their involvement in numerous cellular activities, including the regulation of mRNAs decay or storage. These cytoplasmic dynamic membraneless granules contain mRNA storage and decay components such as deadenylase and decapping factors. In addition, different mRNA metabolic regulators, including m6A readers and gene-mediated miRNA-silencing, are also associated with such P-bodies. Cancerous cells may profit from these mRNA decay shredders by up-regulating the expression level of oncogenes and down-regulating tumor suppressor genes. The main challenges of cancer treatment are drug resistance, metastasis, and cancer relapse likely associated with cancer stem cells, heterogeneity, and plasticity features of different tumors. The mRNA metabolic regulators based on P-bodies play a great role in cancer development and progression. The dysregulation of P-bodies mediators affects mRNA metabolism. However, less is known about the relationship between P-bodies mediators and cancerous behavior. The current review summarizes the recent studies on P-bodies mediators, their contribution to tumor development, and their potential in the clinical setting, particularly highlighting the P-bodies as potential drug-carriers such as exosomes to anticancer in the future.
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Affiliation(s)
- Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Ebenezeri Erasto Ngowi
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Xuefeng Zhou
- Department of Oncology, Dongtai Affiliated Hospital of Nantong University, Dongtai, 224200, Jiangsu, People's Republic of China
| | - Yu Jin
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Yuting Jia
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Wenqiang Wei
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
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10
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Ikeda Y, Taniguchi K, Nagase N, Tsuji A, Kitagishi Y, Matsuda S. Reactive oxygen species may influence on the crossroads of stemness, senescence, and carcinogenesis in a cell via the roles of APRO family proteins. EXPLORATION OF MEDICINE 2021. [DOI: 10.37349/emed.2021.00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Excessive reactive oxygen species (ROS) may cause oxidative stress which is involved in aging and in the pathogenesis of various human diseases. Whereas unregulated levels of the ROS may be harmful, regulated basal level of ROS are even necessary to support cellular functions as a second messenger for homeostasis under physiological conditions. Therefore, redox medicine could develop as a new therapeutic concept for human health-benefits. Here, we introduce the involvement of ROS on the crossroads of stemness, senescence, and carcinogenesis in a stem cell and cancer cell biology. Amazingly, the anti-proliferative (APRO) family anti-proliferative proteins characterized by immediate early growth responsive genes may also be involved in the crossroads machinery. The biological functions of APRO proteins (APROs) seem to be quite intricate, however, which might be a key modulator of microRNAs (miRNAs). Given the crucial roles of ROS and APROs for pathophysiological functions, upcoming novel therapeutics should include vigilant modulation of the redox state. Next generation of medicine including regenerative medicine and/or cancer therapy will likely comprise strategies for altering the redox environment with the APROs via the modulation of miRNAs as well as with the regulation of ROS of cells in a sustainable manner.
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Affiliation(s)
- Yuka Ikeda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Kurumi Taniguchi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Nozomi Nagase
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Ai Tsuji
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Yasuko Kitagishi
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
| | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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11
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Mayya VK, Flamand MN, Lambert AM, Jafarnejad SM, Wohlschlegel JA, Sonenberg N, Duchaine TF. microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development. Nucleic Acids Res 2021; 49:4803-4815. [PMID: 33758928 PMCID: PMC8136787 DOI: 10.1093/nar/gkab162] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/24/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
microRNA (miRNA)-mediated gene silencing is enacted through the recruitment of effector proteins that direct translational repression or degradation of mRNA targets, but the relative importance of their activities for animal development remains unknown. Our concerted proteomic surveys identified the uncharacterized GYF-domain encoding protein GYF-1 and its direct interaction with IFE-4, the ortholog of the mammalian translation repressor 4EHP, as key miRNA effector proteins in Caenorhabditis elegans. Recruitment of GYF-1 protein to mRNA reporters in vitro or in vivo leads to potent translation repression without affecting the poly(A) tail or impinging on mRNA stability. Loss of gyf-1 is synthetic lethal with hypomorphic alleles of embryonic miR-35-42 and larval (L4) let-7 miRNAs, which is phenocopied through engineered mutations in gyf-1 that abolish interaction with IFE-4. GYF-1/4EHP function is cascade-specific, as loss of gyf-1 had no noticeable impact on the functions of other miRNAs, including lin-4 and lsy-6. Overall, our findings reveal the first direct effector of miRNA-mediated translational repression in C. elegans and its physiological importance for the function of several, but likely not all miRNAs.
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Affiliation(s)
- Vinay K Mayya
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Mathieu N Flamand
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Alice M Lambert
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Seyed Mehdi Jafarnejad
- Patrick G. Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast BT9 7AE UK
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
| | - Thomas F Duchaine
- Goodman Cancer Research Center, McGill University, Montréal H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal H3G 1Y6, Canada
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12
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Zhang W, Wang Q, Feng Y, Chen X, Yang L, Xu M, Wang X, Li W, Niu X, Gao D. MicroRNA-26a Protects the Heart Against Hypertension-Induced Myocardial Fibrosis. J Am Heart Assoc 2020; 9:e017970. [PMID: 32865120 PMCID: PMC7726969 DOI: 10.1161/jaha.120.017970] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Hypertensive myocardial fibrosis (MF) is characterized by excessive deposition of extracellular matrix and cardiac fibroblast proliferation, which can lead to heart failure, malignant arrhythmia, and sudden death. In recent years, with the deepening of research, microRNAs have been found to have an important role in blood pressure control and maintaining normal ventricular structure and function. Methods and Results In this study, we first documented the downregulation of microRNA-26a (miR-26a) in the plasma and myocardium of spontaneously hypertensive rats; more importantly, miR-26a-deficient mice showed MF, whereas overexpression of miR-26a significantly prevented elevated blood pressure and inhibited MF in vivo and angiotensin II-induced fibrogenesis in cardiac fibroblasts by directly targeting connective tissue growth factor and Smad4. miR-26a inhibited cardiac fibroblast proliferation by the enhancer of zeste homolog 2/p21 pathway. Conclusions Our study identified a novel role for miR-26a in blood pressure control and hypertensive MF and provides a possible treatment strategy for miR-26a to alleviate and reverse hypertensive MF.
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Affiliation(s)
- Wenqian Zhang
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Qiaozhu Wang
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Yanjing Feng
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Xuegui Chen
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Lijun Yang
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Min Xu
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Xiaofang Wang
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Weicheng Li
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
| | - Xiaolin Niu
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China.,Department of Cardiology Meishan Brach of the Third Affiliated Hospital Yanan University School of Medical Meishan Sichuan People's Republic of China
| | - Dengfeng Gao
- Department of Cardiology The Second Affiliated Hospital Xi'an Jiaotong University Xi'an Shaanxi People's Republic of China
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13
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Pérez MG, Spiliotis M, Rego N, Macchiaroli N, Kamenetzky L, Holroyd N, Cucher MA, Brehm K, Rosenzvit MC. Deciphering the role of miR-71 in Echinococcus multilocularis early development in vitro. PLoS Negl Trop Dis 2019; 13:e0007932. [PMID: 31881019 PMCID: PMC6957206 DOI: 10.1371/journal.pntd.0007932] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 01/13/2020] [Accepted: 11/17/2019] [Indexed: 01/25/2023] Open
Abstract
Echinococcosis represents a major public health problem worldwide and is considered a neglected disease by the World Health Organization. The etiological agents are Echinococcus tapeworms, which display elaborate developmental traits that imply a complex control of gene expression. MicroRNAs (miRNAs), a class of small regulatory RNAs, are involved in the regulation of many biological processes such as development and metabolism. They act through the repression of messenger RNAs (mRNAs) usually by binding to the 3’ untranslated region (3’UTR). Previously, we described the miRNome of several Echinococcus species and found that miRNAs are highly expressed in all life cycle stages, suggesting an important role in gene expression regulation. However, studying the role of miRNAs in helminth biology remains a challenge. To develop methodology for functional analysis of miRNAs in tapeworms, we performed miRNA knockdown experiments in primary cell cultures of Echinococcus multilocularis, which mimic the development of metacestode vesicles from parasite stem cells in vitro. First, we analysed the miRNA repertoire of E. multilocularis primary cells by small RNA-seq and found that miR-71, a bilaterian miRNA absent in vertebrate hosts, is one of the top five most expressed miRNAs. Using genomic information and bioinformatic algorithms for miRNA binding prediction, we found a high number of potential miR-71 targets in E. multilocularis. Inhibition of miRNAs can be achieved by transfection of antisense oligonucleotides (anti-miRs) that block miRNA function. To this end, we evaluated a variety of chemically modified anti-miRs for miR-71 knockdown. Electroporation of primary cells with 2’-O-methyl modified anti-miR-71 led to significantly reduced miR-71 levels. Transcriptomic analyses showed that several predicted miR-71 targets were up-regulated in anti-miR-treated primary cells, including genes potentially involved in parasite development, host parasite interaction, and several genes of as yet unknown function. Notably, miR-71-silenced primary cell cultures showed a strikingly different phenotype from control cells and did not develop into fully mature metacestodes. These findings indicate an important function of miR-71 in Echinococcus development and provide, for the first time, methodology to functionally study miRNAs in a tapeworm. Echinococcosis, caused by the larval stages of tapeworms of the genus Echinococcus, is a neglected disease that affects millions of people world-wide. These parasites show elaborate developmental features that rely on a complex control of gene expression. microRNAs are small molecules which have been discovered in the last decades and control gene expression in animals, plants and viruses. microRNAs are highly expressed in several tapeworms but their biological function in these parasites is unknown. Assuming that microRNAs will be important for parasite development, we analysed the function of these molecules in Echinococcus multilocularis, employing an in vitro model that mimics the first developmental transitions which occur in the human host. By artificially decreasing the concentration of the highest expressed microRNA, we observed phenotypic alterations and inhibition of development. In addition, we identified possible mRNA molecules targeted by microRNAs and found that some of these are known for being involved in developmental processes in other organisms. This work provides novel methodology to study microRNA function in tapeworms. Furthermore, highly expressed parasite microRNAs that are absent in the host but fulfil an important role in parasite developmental processes can serve as selective drug targets against the underlying diseases.
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Affiliation(s)
- Matías Gastón Pérez
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Markus Spiliotis
- University of Würzburg, Institute for Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
| | - Natalia Rego
- Institut Pasteur de Montevideo, Unidad de Bioinformática, Montevideo, Uruguay
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Marcela Alejandra Cucher
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Klaus Brehm
- University of Würzburg, Institute for Hygiene and Microbiology, Consultant Laboratory for Echinococcosis, Würzburg, Germany
- * E-mail: (KB); (MCR)
| | - Mara Cecilia Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
- * E-mail: (KB); (MCR)
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14
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Meijer HA, Schmidt T, Gillen SL, Langlais C, Jukes-Jones R, de Moor CH, Cain K, Wilczynska A, Bushell M. DEAD-box helicase eIF4A2 inhibits CNOT7 deadenylation activity. Nucleic Acids Res 2019; 47:8224-8238. [PMID: 31180491 PMCID: PMC6736043 DOI: 10.1093/nar/gkz509] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 05/26/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023] Open
Abstract
The CCR4-NOT complex plays an important role in the translational repression and deadenylation of mRNAs. However, little is known about the specific roles of interacting factors. We demonstrate that the DEAD-box helicases eIF4A2 and DDX6 interact directly with the MA3 and MIF domains of CNOT1 and compete for binding. Furthermore, we now show that incorporation of eIF4A2 into the CCR4-NOT complex inhibits CNOT7 deadenylation activity in contrast to DDX6 which enhances CNOT7 activity. Polyadenylation tests (PAT) on endogenous mRNAs determined that eIF4A2 bound mRNAs have longer poly(A) tails than DDX6 bound mRNAs. Immunoprecipitation experiments show that eIF4A2 does not inhibit CNOT7 association with the CCR4-NOT complex but instead inhibits CNOT7 activity. We identified a CCR4-NOT interacting factor, TAB182, that modulates helicase recruitment into the CCR4-NOT complex, potentially affecting the outcome for the targeted mRNA. Together, these data show that the fate of an mRNA is dependent on the specific recruitment of either eIF4A2 or DDX6 to the CCR4-NOT complex which results in different pathways for translational repression and mRNA deadenylation.
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Affiliation(s)
- Hedda A Meijer
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Tobias Schmidt
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Sarah L Gillen
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Claudia Langlais
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Rebekah Jukes-Jones
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Cornelia H de Moor
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kelvin Cain
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Ania Wilczynska
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
| | - Martin Bushell
- Medical Research Council (MRC), Toxicology Unit, University of Cambridge, Hodgkin Building, Leicester LE1 9HN, UK
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15
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Shimo HM, Terassi C, Lima Silva CC, Zanella JDL, Mercaldi GF, Rocco SA, Benedetti CE. Role of the Citrus sinensis RNA deadenylase CsCAF1 in citrus canker resistance. MOLECULAR PLANT PATHOLOGY 2019; 20:1105-1118. [PMID: 31115151 PMCID: PMC6640180 DOI: 10.1111/mpp.12815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Poly(A) tail shortening is a critical step in messenger RNA (mRNA) decay and control of gene expression. The carbon catabolite repressor 4 (CCR4)-associated factor 1 (CAF1) component of the CCR4-NOT deadenylase complex plays an essential role in mRNA deadenylation in most eukaryotes. However, while CAF1 has been extensively investigated in yeast and animals, its role in plants remains largely unknown. Here, we show that the Citrus sinensis CAF1 (CsCAF1) is a magnesium-dependent deadenylase implicated in resistance against the citrus canker bacteria Xanthomonas citri. CsCAF1 interacted with proteins of the CCR4-NOT complex, including CsVIP2, a NOT2 homologue, translin-associated factor X (CsTRAX) and the poly(A)-binding proteins CsPABPN and CsPABPC. CsCAF1 also interacted with PthA4, the main X. citri effector required for citrus canker elicitation. We also present evidence suggesting that PthA4 inhibits CsCAF1 deadenylase activity in vitro and stabilizes the mRNA encoded by the citrus canker susceptibility gene CsLOB1, which is transcriptionally activated by PthA4 during canker formation. Moreover, we show that an inhibitor of CsCAF1 deadenylase activity significantly enhanced canker development, despite causing a reduction in PthA4-dependent CsLOB1 transcription. These results thus link CsCAF1 with canker development and PthA4-dependent transcription in citrus plants.
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Affiliation(s)
- Hugo Massayoshi Shimo
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Carolina Terassi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Caio Cesar Lima Silva
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Silvana Aparecida Rocco
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CEP 13083‐100CampinasSPBrazil
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16
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Rollins JA, Shaffer D, Snow SS, Kapahi P, Rogers AN. Dietary restriction induces posttranscriptional regulation of longevity genes. Life Sci Alliance 2019; 2:2/4/e201800281. [PMID: 31253655 PMCID: PMC6600014 DOI: 10.26508/lsa.201800281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction (DR) increases life span through adaptive changes in gene expression. To understand more about these changes, we analyzed the transcriptome and translatome of Caenorhabditis elegans subjected to DR. Transcription of muscle regulatory and structural genes increased, whereas increased expression of amino acid metabolism and neuropeptide signaling genes was controlled at the level of translation. Evaluation of posttranscriptional regulation identified putative roles for RNA-binding proteins, RNA editing, miRNA, alternative splicing, and nonsense-mediated decay in response to nutrient limitation. Using RNA interference, we discovered several differentially expressed genes that regulate life span. We also found a compensatory role for translational regulation, which offsets dampened expression of a large subset of transcriptionally down-regulated genes. Furthermore, 3' UTR editing and intron retention increase under DR and correlate with diminished translation, whereas trans-spliced genes are refractory to reduced translation efficiency compared with messages with the native 5' UTR. Finally, we find that smg-6 and smg-7, which are genes governing selection and turnover of nonsense-mediated decay targets, are required for increased life span under DR.
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Affiliation(s)
- Jarod A Rollins
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Dan Shaffer
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Santina S Snow
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Aric N Rogers
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
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17
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MiR-35 buffers apoptosis thresholds in the C. elegans germline by antagonizing both MAPK and core apoptosis pathways. Cell Death Differ 2019; 26:2637-2651. [PMID: 30952991 PMCID: PMC7224216 DOI: 10.1038/s41418-019-0325-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
Apoptosis is a genetically programmed cell death process with profound roles in development and disease. MicroRNAs modulate the expression of many proteins and are often deregulated in human diseases, such as cancer. C. elegans germ cells undergo apoptosis in response to genotoxic stress by the combined activities of the core apoptosis and MAPK pathways, but how their signalling thresholds are buffered is an open question. Here we show mir-35–42 miRNA family play a dual role in antagonizing both NDK-1, a positive regulator of MAPK signalling, and the BH3-only pro-apoptotic protein EGL-1 to regulate the magnitude of DNA damage-induced apoptosis in the C. elegans germline. We show that while miR-35 represses EGL-1 by promoting transcript degradation, repression of NDK-1 may be through sequestration of the transcript to inhibit translation. Importantly, dramatic increase in NDK-1 expression was observed in cells about to die. In the absence of miR-35, increased NDK-1 activity enhanced MAPK signalling that lead to significant increases in germ cell death. Our findings demonstrate that NDK-1 acts upstream of (or in parallel to) EGL-1, and that miR-35 targets both egl-1 and ndk-1 to fine-tune cell killing in response to genotoxic stress.
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18
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Duchaine TF, Fabian MR. Mechanistic Insights into MicroRNA-Mediated Gene Silencing. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032771. [PMID: 29959194 DOI: 10.1101/cshperspect.a032771] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) posttranscriptionally regulate gene expression by repressing protein synthesis and exert a broad influence over development, physiology, adaptation, and disease. Over the past two decades, great strides have been made toward elucidating how miRNAs go about shutting down messenger RNA (mRNA) translation and promoting mRNA decay.
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Affiliation(s)
- Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Marc R Fabian
- Department of Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada.,Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
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19
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Mayya VK, Duchaine TF. Ciphers and Executioners: How 3'-Untranslated Regions Determine the Fate of Messenger RNAs. Front Genet 2019; 10:6. [PMID: 30740123 PMCID: PMC6357968 DOI: 10.3389/fgene.2019.00006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022] Open
Abstract
The sequences and structures of 3'-untranslated regions (3'UTRs) of messenger RNAs govern their stability, localization, and expression. 3'UTR regulatory elements are recognized by a wide variety of trans-acting factors that include microRNAs (miRNAs), their associated machinery, and RNA-binding proteins (RBPs). In turn, these factors instigate common mechanistic strategies to execute the regulatory programs encoded by 3'UTRs. Here, we review classes of factors that recognize 3'UTR regulatory elements and the effector machineries they guide toward mRNAs to dictate their expression and fate. We outline illustrative examples of competitive, cooperative, and coordinated interplay such as mRNA localization and localized translation. We further review the recent advances in the study of mRNP granules and phase transition, and their possible significance for the functions of 3'UTRs. Finally, we highlight some of the most recent strategies aimed at deciphering the complexity of the regulatory codes of 3'UTRs, and identify some of the important remaining challenges.
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Affiliation(s)
| | - Thomas F. Duchaine
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, QC, Canada
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20
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Wang X, Chen Q, Yi S, Liu Q, Zhang R, Wang P, Qian T, Li S. The microRNAs let-7 and miR-9 down-regulate the axon-guidance genes Ntn1 and Dcc during peripheral nerve regeneration. J Biol Chem 2019; 294:3489-3500. [PMID: 30626732 DOI: 10.1074/jbc.ra119.007389] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Indexed: 12/15/2022] Open
Abstract
Axon guidance helps growing neural axons to follow precise paths to reach their target locations. It is a critical step for both the formation and regeneration of neuronal circuitry. Netrin-1 (Ntn1) and its receptor, deleted in colorectal carcinoma (Dcc) are essential factors for axon guidance, but their regulation in this process is incompletely understood. In this study, using quantitative real-time RT-PCR (qRT-PCR) and biochemical and reporter gene assays, we found that the Ntn1 and Dcc genes are both robustly up-regulated in the sciatic nerve stump after peripheral nerve injury. Moreover, we found that the microRNA (miR) let-7 directly targets the Ntn1 transcript by binding to its 3'-untranslated region (3'-UTR), represses Ntn1 expression, and reduces the secretion of Ntn1 protein in Schwann cells. We also identified miR-9 as the regulatory miRNA that directly targets Dcc and found that miR-9 down-regulates Dcc expression and suppresses the migration ability of Schwann cells by regulating Dcc abundance. Functional examination in dorsal root ganglion neurons disclosed that let-7 and miR-9 decrease the protein levels of Ntn1 and Dcc in these neurons, respectively, and reduce axon outgrowth. Moreover, we identified a potential regulatory network comprising let-7, miR-9, Ntn1, Dcc, and related molecules, including the RNA-binding protein Lin-28 homolog A (Lin28), SRC proto-oncogene nonreceptor tyrosine kinase (Src), and the transcription factor NF-κB. In summary, our findings reveal that the miRs let-7 and miR-9 are involved in regulating neuron pathfinding and extend our understanding of the regulatory pathways active during peripheral nerve regeneration.
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Affiliation(s)
- Xinghui Wang
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Qianqian Chen
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Sheng Yi
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Qianyan Liu
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Ruirui Zhang
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Pan Wang
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Tianmei Qian
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
| | - Shiying Li
- From the Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nanjing, Jiangsu 226001, China
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21
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Somatic and Germline MicroRNAs Form Distinct Silencing Complexes to Regulate Their Target mRNAs Differently. Dev Cell 2018; 47:239-247.e4. [PMID: 30245155 DOI: 10.1016/j.devcel.2018.08.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 11/23/2022]
Abstract
Animal germ cells possess a specific post-transcriptional regulatory context allowing the storage of maternal transcripts in the oocyte until their translation at a specific point in early development. As key regulators of gene expression, miRNAs repress translation mainly through mRNA destabilization. Thus, germline miRNAs likely use distinct ways to regulate their targets. Here, we use C. elegans to compare miRNA function within germline and somatic tissues. We show that the same miRNA displays tissue-specific gene regulatory mechanisms. While translational repression occurs in both tissues, targeted mRNAs are instead stabilized in the germline. Comparative analyses of miRNA silencing complexes (miRISC) demonstrate that their composition differs from germline to soma. We show that germline miRNA targets preferentially localize to perinuclear regions adjacent to P granules, and their repression is dependent on the core P granule component GLH-1. Together, our findings reveal the existence of different miRISC in animals that affect targeted mRNAs distinctively.
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22
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Wu E, Vashisht AA, Chapat C, Flamand MN, Cohen E, Sarov M, Tabach Y, Sonenberg N, Wohlschlegel J, Duchaine TF. A continuum of mRNP complexes in embryonic microRNA-mediated silencing. Nucleic Acids Res 2018; 45:2081-2098. [PMID: 28204614 PMCID: PMC5389717 DOI: 10.1093/nar/gkw872] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) impinge on the translation and stability of their target mRNAs, and play key roles in development, homeostasis and disease. The gene regulation mechanisms they instigate are largely mediated through the CCR4–NOT deadenylase complex, but the molecular events that occur on target mRNAs are poorly resolved. We observed a broad convergence of interactions of germ granule and P body mRNP components on AIN-1/GW182 and NTL-1/CNOT1 in Caenorhabditis elegans embryos. We show that the miRISC progressively matures on the target mRNA from a scanning form into an effector mRNP particle by sequentially recruiting the CCR4–NOT complex, decapping and decay, or germ granule proteins. Finally, we implicate intrinsically disordered proteins, key components in mRNP architectures, in the embryonic function of lsy-6 miRNA. Our findings define dynamic steps of effector mRNP assembly in miRNA-mediated silencing, and identify a functional continuum between germ granules and P bodies in the C. elegans embryo.
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Affiliation(s)
| | - Ajay A Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Clément Chapat
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - Mathieu N Flamand
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - Emiliano Cohen
- Department of Developmental Biology and Cancer Research, The Institute For Medical Research-Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, The Institute For Medical Research-Israel-Canada, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3G 1Y6 Canada
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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24
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Flamand MN, Gan HH, Mayya VK, Gunsalus KC, Duchaine TF. A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing. Nucleic Acids Res 2017; 45:7212-7225. [PMID: 28482037 PMCID: PMC5499589 DOI: 10.1093/nar/gkx340] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/18/2017] [Indexed: 01/08/2023] Open
Abstract
Although strong evidence supports the importance of their cooperative interactions, microRNA (miRNA)-binding sites are still largely investigated as functionally independent regulatory units. Here, a survey of alternative 3΄UTR isoforms implicates a non-canonical seedless site in cooperative miRNA-mediated silencing. While required for target mRNA deadenylation and silencing, this site is not sufficient on its own to physically recruit miRISC. Instead, it relies on facilitating interactions with a nearby canonical seed-pairing site to recruit the Argonaute complexes. We further show that cooperation between miRNA target sites is necessary for silencing in vivo in the C. elegans embryo, and for the recruitment of the Ccr4-Not effector complex. Using a structural model of cooperating miRISCs, we identified allosteric determinants of cooperative miRNA-mediated silencing that are required for both embryonic and larval miRNA functions. Our results delineate multiple cooperative mechanisms in miRNA-mediated silencing and further support the consideration of target site cooperation as a fundamental characteristic of miRNA function.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Vinay K Mayya
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.,Division of Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6 Canada
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Cao W, Shi P, Ge JJ. miR-21 enhances cardiac fibrotic remodeling and fibroblast proliferation via CADM1/STAT3 pathway. BMC Cardiovasc Disord 2017; 17:88. [PMID: 28335740 PMCID: PMC5364650 DOI: 10.1186/s12872-017-0520-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 03/11/2017] [Indexed: 12/12/2022] Open
Abstract
Background Cardiac fibrosis play a key role in the atrial fibrillation pathogenesis but the underlying potential molecular mechanism is still understood. However, potential mechanisms for miR-21 upregulation and its role in cardiac fibrosis remain unclear. The controls cell proliferation and processes fundamental to disease progression. Methods In this study, immunohistochemistry, real-time RT-PCR, cell transfection, cell cycle, cell proliferation and Western blot were used, respectively. Results Here we have been demonstrated that the tumor suppressor cell adhesion molecule 1 (CADM1) is the potential target of miR-21. Our study revealed that miR-21 regulation of CADM1 expression, which was decreased in cardiac fibroblasts and fibrosis tissue. The cardiac fibroblasts transfected with miR-21 mimic promoted miR-21 overexpression enhanced STAT3 expression and decreased CADM1 expression. Nevertheless, the cardiac fibroblasts transfected with miR-21 inhibitor obtained the opposite expression result. Furthermore, downexpression of miR-21 suppressed cardiac fibroblast proliferation. Conclusions These results suggested that miR-21 overexpression promotes cardiac fibrosis via STAT3 signaling pathway by decrease CADM1 expression, indicating miR-21 as an important signaling molecule for cardiac fibrotic remodeling and AF.
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Affiliation(s)
- Wei Cao
- Department of Cardiology, The first Hospital of Anhui Medical University, Hefei, 230031, China.,Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Peng Shi
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jian-Jun Ge
- Department of Cardiology, The first Hospital of Anhui Medical University, Hefei, 230031, China. .,Department of Cardiology, The first Hospital of Anhui Medical University, Ji-Xi Road, Hefei, Anhui Province, 230032, China.
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