1
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Frédérick PM, Jannot G, Banville I, Simard MJ. Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals. Nucleic Acids Res 2024:gkae272. [PMID: 38613392 DOI: 10.1093/nar/gkae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
MicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex known as miRISC. While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degron system, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loading in vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA function in vivo and provides insights to explain how different small RNAs associate with specific AGO in animals.
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Affiliation(s)
- Pierre-Marc Frédérick
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Guillaume Jannot
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Isabelle Banville
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
| | - Martin J Simard
- Oncology Division, CHU de Québec-Université Laval Research Center, Québec, QC G1R 3S3, Canada
- Université Laval Cancer Research Centre, Québec, QC G1R 3S3, Canada
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2
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Vergani-Junior CA, Moro RDP, Pinto S, De-Souza EA, Camara H, Braga DL, Tonon-da-Silva G, Knittel TL, Ruiz GP, Ludwig RG, Massirer KB, Mair WB, Mori MA. An Intricate Network Involving the Argonaute ALG-1 Modulates Organismal Resistance to Oxidative Stress. Nat Commun 2024; 15:3070. [PMID: 38594249 PMCID: PMC11003958 DOI: 10.1038/s41467-024-47306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/24/2024] [Indexed: 04/11/2024] Open
Abstract
Cellular response to redox imbalance is crucial for organismal health. microRNAs are implicated in stress responses. ALG-1, the C. elegans ortholog of human AGO2, plays an essential role in microRNA processing and function. Here we investigated the mechanisms governing ALG-1 expression in C. elegans and the players controlling lifespan and stress resistance downstream of ALG-1. We show that upregulation of ALG-1 is a shared feature in conditions linked to increased longevity (e.g., germline-deficient glp-1 mutants). ALG-1 knockdown reduces lifespan and oxidative stress resistance, while overexpression enhances survival against pro-oxidant agents but not heat or reductive stress. R02D3.7 represses alg-1 expression, impacting oxidative stress resistance at least in part via ALG-1. microRNAs upregulated in glp-1 mutants (miR-87-3p, miR-230-3p, and miR-235-3p) can target genes in the protein disulfide isomerase pathway and protect against oxidative stress. This study unveils a tightly regulated network involving transcription factors and microRNAs which controls organisms' ability to withstand oxidative stress.
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Affiliation(s)
- Carlos A Vergani-Junior
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Raíssa De P Moro
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Silas Pinto
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Evandro A De-Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Henrique Camara
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Section on Integrative Physiology & Metabolism, Joslin Diabetes Center, Boston, MA, USA
| | - Deisi L Braga
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Thiago L Knittel
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Gabriel P Ruiz
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Raissa G Ludwig
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Katlin B Massirer
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Center of Medicinal Chemistry (CQMED), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - William B Mair
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Program in Genetics and Molecular Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
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3
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Pal A, Vasudevan V, Houle F, Lantin M, Maniates KA, Huberdeau MQ, Abbott AL, Simard MJ. Defining the contribution of microRNA-specific Argonautes with slicer capability in animals. Nucleic Acids Res 2024:gkae173. [PMID: 38477356 DOI: 10.1093/nar/gkae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
microRNAs regulate gene expression through interaction with an Argonaute protein. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicer residues in the canonical microRNA pathway is still unclear in animals. To address this, we created Caenorhabditis elegans strains with mutated slicer residues in the endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the mutation in ALG-1 and ALG-2 catalytic residues affects overall animal fitness and causes phenotypes reminiscent of miRNA defects only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the slicer residues of ALG-1 and ALG-2 contribute differentially to regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the catalytic tetrad of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicer residues of miRNA-specific Argonautes contribute to maintaining levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.
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Affiliation(s)
- Anisha Pal
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Vaishnav Vasudevan
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - François Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Michael Lantin
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Katherine A Maniates
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, USA
| | - Miguel Quévillon Huberdeau
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
| | - Allison L Abbott
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Quebec City, Quebec G1R 3S3, Canada
- Université Laval Cancer Research Centre, Quebec City, Quebec G1R 3S3, Canada
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4
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Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala RM, Yu G, Benner LK, Joshua-Tor L, McJunkin K. Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans. Nucleic Acids Res 2024:gkae170. [PMID: 38471816 DOI: 10.1093/nar/gkae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Many microRNA (miRNA)-guided Argonaute proteins can cleave RNA ('slicing'), even though miRNA-mediated target repression is generally cleavage-independent. Here we use Caenorhabditis elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the catalytic residue mutants, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on catalytic residues for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on catalytic residues for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on catalytic residues. While a few miRNA guide strands are reduced in the mutant background, the basis of this is unclear since changes were not dependent on EBAX-1, an effector of Target-Directed miRNA Degradation (TDMD). Overall, this work defines a role for the catalytic residues of miRNA Argonautes in star strand decay; future work should examine whether this role contributes to the selection pressure to conserve catalytic activity of miRNA Argonautes across the metazoan phylogeny.
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Affiliation(s)
- Kasuen Kotagama
- 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
| | - Leah Braviner
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Bing Yang
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Rima M Sakhawala
- 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
| | - Guoyun Yu
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Lars Kristian Benner
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
| | - Leemor Joshua-Tor
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, NIDDK Intramural Research Program, 50 South Drive, Bethesda, MD 20892, USA
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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6
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Wang S, Sun Y, Yao L, Xing Y, Yang H, Ma Q. The Role of microRNA-23a-3p in the Progression of Human Aging Process by Targeting FOXO3a. Mol Biotechnol 2024; 66:277-287. [PMID: 37087718 PMCID: PMC10803409 DOI: 10.1007/s12033-023-00746-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/02/2023] [Indexed: 04/24/2023]
Abstract
Aging results in deterioration of body functions and, ultimately, death. miRNAs contribute to the regulation of aging. The aim of this study was to explore the contribution of miRNAs to aging and senescence-related changes in gene expression. The expression changes of miRNAs in the blood of people and animal samples collected from different age subjects were examined using Affymetrix miRNA 4.0 microarray and qRT-PCR. MTT assay and flow cytometry were used to examine the effect of miR-23a on cell functions in WI-38 cells. The expression levels of 48 miRNAs, including miR-23a, miR-21, and miR-100, in the blood samples were higher in the middle-aged group than in the young or elderly group. Animal studies further suggested that the expression of miR-23a increased with age. In addition, upregulation of miR-23a dramatically suppressed the cell proliferation and arrested the WI-38 cell cycle in vitro. FOXO3a has been identified as a target gene of miR-23a. MiR-23a downregulated the expression of FOXO3a in WI-38 cells. MiRNAs have different expression levels in different age groups. miR-23a could suppress cell proliferation and arrest the cell cycle in WI-38 cells, which elucidated the mechanism through which miR-23a exerts pivotal role in WI-38 cells by targeting FOXO3a.
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Affiliation(s)
- Shan Wang
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Ying Sun
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Lan Yao
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Yunli Xing
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Huayu Yang
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
| | - Qing Ma
- Department of Geriatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China.
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7
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Pal A, Vasudevan V, Houle F, Lantin M, Maniates KA, Quevillon Huberdeau M, Abbott A, Simard MJ. Defining the contribution of microRNA-specific slicing Argonautes in animals. bioRxiv 2024:2023.01.19.524781. [PMID: 36711744 PMCID: PMC9882343 DOI: 10.1101/2023.01.19.524781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
microRNAs regulate gene expression through interaction with an Argonaute protein family member. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans strains, carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity affects overall animal fitness and causes phenotypes, reminiscent of miRNA defects, only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA-specific Argonautes function to maintain the levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.
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8
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Chen Z, Li C, Huang H, Shi YL, Wang X. Research Progress of Aging-related MicroRNAs. Curr Stem Cell Res Ther 2024; 19:334-350. [PMID: 36892029 DOI: 10.2174/1574888x18666230308111043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 03/10/2023]
Abstract
Senescence refers to the irreversible state in which cells enter cell cycle arrest due to internal or external stimuli. The accumulation of senescent cells can lead to many age-related diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancers. MicroRNAs are short non-coding RNAs that bind to target mRNA to regulate gene expression after transcription and play an important regulatory role in the aging process. From nematodes to humans, a variety of miRNAs have been confirmed to alter and affect the aging process. Studying the regulatory mechanisms of miRNAs in aging can further deepen our understanding of cell and body aging and provide a new perspective for the diagnosis and treatment of aging-related diseases. In this review, we illustrate the current research status of miRNAs in aging and discuss the possible prospects for clinical applications of targeting miRNAs in senile diseases.
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Affiliation(s)
- Zhongyu Chen
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Chenxu Li
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Haitao Huang
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Yi-Ling Shi
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
| | - Xiaobo Wang
- School of Basic Medicine, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of University Cell Biology, Dali, Yunnan, 671000, China
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9
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Chipman LB, Luc S, Nicastro IA, Hulahan JJ, Dann DC, Bodas DM, Pasquinelli AE. Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans. PLoS Genet 2023; 19:e1011055. [PMID: 38011256 PMCID: PMC10703411 DOI: 10.1371/journal.pgen.1011055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 12/07/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by base-pairing to target sequences in messenger RNAs (mRNAs) and recruiting factors that induce translational repression and mRNA decay. In animals, nucleotides 2-8 at the 5' end of the miRNA, called the seed region, are often necessary and sometimes sufficient for functional target interactions. MiRNAs that contain identical seed sequences are grouped into families where individual members have the potential to share targets and act redundantly. A rare exception seemed to be the miR-238/239ab family in Caenorhabditis elegans, as previous work indicated that loss of miR-238 reduced lifespan while deletion of the miR-239ab locus resulted in enhanced longevity and thermal stress resistance. Here, we re-examined these potentially opposing roles using new strains that individually disrupt each miRNA sister. We confirmed that loss of miR-238 is associated with a shortened lifespan but could detect no longevity or stress phenotypes in animals lacking miR-239a or miR-239b, individually or in combination. Additionally, dozens of genes were mis-regulated in miR-238 mutants but almost no gene expression changes were detected in either miR-239a or miR-239b mutants compared to wild type animals. We present evidence that the lack of redundancy between miR-238 and miR-239ab is independent of their sequence differences; miR-239a or miR-239b could substitute for the longevity role of miR-238 when expressed from the miR-238 locus. Altogether, these studies disqualify miR-239ab as negative regulators of aging and demonstrate that expression, not sequence, dictates the specific role of miR-238 in promoting longevity.
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Affiliation(s)
- Laura B. Chipman
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - San Luc
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Ian A. Nicastro
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jesse J. Hulahan
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Delaney C. Dann
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Devavrat M. Bodas
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Amy E. Pasquinelli
- Molecular Biology Department, School of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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10
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Bell AD, Chou HT, Valencia F, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNA interference in Caenorhabditis elegans. G3 (Bethesda) 2023; 13:jkad112. [PMID: 37221008 PMCID: PMC10411595 DOI: 10.1093/g3journal/jkad112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023]
Abstract
Though natural systems harbor genetic and phenotypic variation, research in model organisms is often restricted to a reference strain. Focusing on a reference strain yields a great depth of knowledge but potentially at the cost of breadth of understanding. Furthermore, tools developed in the reference context may introduce bias when applied to other strains, posing challenges to defining the scope of variation within model systems. Here, we evaluate how genetic differences among 5 wild Caenorhabditis elegans strains affect gene expression and its quantification, in general and after induction of the RNA interference (RNAi) response. Across strains, 34% of genes were differentially expressed in the control condition, including 411 genes that were not expressed at all in at least 1 strain; 49 of these were unexpressed in reference strain N2. Reference genome mapping bias caused limited concern: despite hyperdiverse hotspots throughout the genome, 92% of variably expressed genes were robust to mapping issues. The transcriptional response to RNAi was highly strain- and target-gene-specific and did not correlate with RNAi efficiency, as the 2 RNAi-insensitive strains showed more differentially expressed genes following RNAi treatment than the RNAi-sensitive reference strain. We conclude that gene expression, generally and in response to RNAi, differs across C. elegans strains such that the choice of strain may meaningfully influence scientific inferences. Finally, we introduce a resource for querying gene expression variation in this dataset at https://wildworm.biosci.gatech.edu/rnai/.
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Francisco Valencia
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
| | - Annalise B Paaby
- School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Dr NW, EBB Building, Atlanta, GA 30332, USA
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11
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Naidoo D, Brennan R, de Lencastre A. Conservation and Targets of miR-71: A Systematic Review and Meta-Analysis. Noncoding RNA 2023; 9:41. [PMID: 37624033 PMCID: PMC10458147 DOI: 10.3390/ncrna9040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
MicroRNAs (miRNAs) perform a pivotal role in the regulation of gene expression across the animal kingdom. As negative regulators of gene expression, miRNAs have been shown to function in the genetic pathways that control many biological processes and have been implicated in roles in human disease. First identified as an aging-associated gene in C. elegans, miR-71, a miRNA, has a demonstrated capability of regulating processes in numerous different invertebrates, including platyhelminths, mollusks, and insects. In these organisms, miR-71 has been shown to affect a diverse range of pathways, including aging, development, and immune response. However, the exact mechanisms by which miR-71 regulates these pathways are not completely understood. In this paper, we review the identified functions of miR-71 across multiple organisms, including identified gene targets, pathways, and the conditions which affect regulatory action. Additionally, the degree of conservation of miR-71 in the evaluated organisms and the conservation of their predicted binding sites in target 3' UTRs was measured. These studies may provide an insight on the patterns, interactions, and conditions in which miR-71 is able to exert genotypic and phenotypic influence.
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Affiliation(s)
- Devin Naidoo
- Frank H. Netter MD School of Medicine, Quinnipiac University, Hamden, CT 06518, USA
| | - Ryan Brennan
- Frank H. Netter MD School of Medicine, Quinnipiac University, Hamden, CT 06518, USA
| | - Alexandre de Lencastre
- Department of Molecular and Cellular Biology, Quinnipiac University, Hamden, CT 06518, USA
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12
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Cubillas C, Sandoval Del Prado LE, Goldacker S, Fujii C, Pinski AN, Zielke J, Wang D. The alg-1 Gene Is Necessary for Orsay Virus Replication in Caenorhabditis elegans. J Virol 2023; 97:e0006523. [PMID: 37017532 PMCID: PMC10134801 DOI: 10.1128/jvi.00065-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/10/2023] [Indexed: 04/06/2023] Open
Abstract
The establishment of the Orsay virus-Caenorhabditis elegans infection model has enabled the identification of host factors essential for virus infection. Argonautes are RNA interacting proteins evolutionary conserved in the three domains of life that are key components of small RNA pathways. C. elegans encodes 27 argonautes or argonaute-like proteins. Here, we determined that mutation of the argonaute-like gene 1, alg-1, results in a greater than 10,000-fold reduction in Orsay viral RNA levels, which could be rescued by ectopic expression of alg-1. Mutation in ain-1, a known interactor of ALG-1 and component of the RNA-induced silencing complex, also resulted in a significant reduction in Orsay virus levels. Viral RNA replication from an endogenous transgene replicon system was impaired by the lack of ALG-1, suggesting that ALG-1 plays a role during the replication stage of the virus life cycle. Orsay virus RNA levels were unaffected by mutations in the ALG-1 RNase H-like motif that ablate the slicer activity of ALG-1. These findings demonstrate a novel function of ALG-1 in promoting Orsay virus replication in C. elegans. IMPORTANCE All viruses are obligate intracellular parasites that recruit the cellular machinery of the host they infect to support their own proliferation. We used Caenorhabditis elegans and its only known infecting virus, Orsay virus, to identify host proteins relevant for virus infection. We determined that ALG-1, a protein previously known to be important in influencing worm life span and the expression levels of thousands of genes, is required for Orsay virus infection of C. elegans. This is a new function attributed to ALG-1 that was not recognized before. In humans, it has been shown that AGO2, a close relative protein to ALG-1, is essential for hepatitis C virus replication. This demonstrates that through evolution from worms to humans, some proteins have maintained similar functions, and consequently, this suggests that studying virus infection in a simple worm model has the potential to provide novel insights into strategies used by viruses to proliferate.
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Affiliation(s)
- Ciro Cubillas
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Luis Enrique Sandoval Del Prado
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Sydney Goldacker
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Chika Fujii
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Amanda N. Pinski
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jon Zielke
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - David Wang
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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13
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Matai L, Slack FJ. MicroRNAs in Age-Related Proteostasis and Stress Responses. Noncoding RNA 2023; 9:26. [PMID: 37104008 PMCID: PMC10143298 DOI: 10.3390/ncrna9020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
Aging is associated with the accumulation of damaged and misfolded proteins through a decline in the protein homeostasis (proteostasis) machinery, leading to various age-associated protein misfolding diseases such as Huntington's or Parkinson's. The efficiency of cellular stress response pathways also weakens with age, further contributing to the failure to maintain proteostasis. MicroRNAs (miRNAs or miRs) are a class of small, non-coding RNAs (ncRNAs) that bind target messenger RNAs at their 3'UTR, resulting in the post-transcriptional repression of gene expression. From the discovery of aging roles for lin-4 in C. elegans, the role of numerous miRNAs in controlling the aging process has been uncovered in different organisms. Recent studies have also shown that miRNAs regulate different components of proteostasis machinery as well as cellular response pathways to proteotoxic stress, some of which are very important during aging or in age-related pathologies. Here, we present a review of these findings, highlighting the role of individual miRNAs in age-associated protein folding and degradation across different organisms. We also broadly summarize the relationships between miRNAs and organelle-specific stress response pathways during aging and in various age-associated diseases.
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Affiliation(s)
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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14
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Bell AD, Chou HT, Paaby AB. Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans. bioRxiv 2023:2023.03.24.533964. [PMID: 36993640 PMCID: PMC10055391 DOI: 10.1101/2023.03.24.533964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A universal feature of living systems is that natural variation in genotype underpins variation in phenotype. Yet, research in model organisms is often constrained to a single genetic background, the reference strain. Further, genomic studies that do evaluate wild strains typically rely on the reference strain genome for read alignment, leading to the possibility of biased inferences based on incomplete or inaccurate mapping; the extent of reference bias can be difficult to quantify. As an intermediary between genome and organismal traits, gene expression is well positioned to describe natural variability across genotypes generally and in the context of environmental responses, which can represent complex adaptive phenotypes. C. elegans sits at the forefront of investigation into small-RNA gene regulatory mechanisms, or RNA interference (RNAi), and wild strains exhibit natural variation in RNAi competency following environmental triggers. Here, we examine how genetic differences among five wild strains affect the C. elegans transcriptome in general and after inducing RNAi responses to two germline target genes. Approximately 34% of genes were differentially expressed across strains; 411 genes were not expressed at all in at least one strain despite robust expression in others, including 49 genes not expressed in reference strain N2. Despite the presence of hyper-diverse hotspots throughout the C. elegans genome, reference mapping bias was of limited concern: over 92% of variably expressed genes were robust to mapping issues. Overall, the transcriptional response to RNAi was strongly strain-specific and highly specific to the target gene, and the laboratory strain N2 was not representative of the other strains. Moreover, the transcriptional response to RNAi was not correlated with RNAi phenotypic penetrance; the two germline RNAi incompetent strains exhibited substantial differential gene expression following RNAi treatment, indicating an RNAi response despite failure to reduce expression of the target gene. We conclude that gene expression, both generally and in response to RNAi, differs across C. elegans strains such that choice of strain may meaningfully influence scientific conclusions. To provide a public, easily accessible resource for querying gene expression variation in this dataset, we introduce an interactive website at https://wildworm.biosci.gatech.edu/rnai/ .
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Affiliation(s)
- Avery Davis Bell
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Han Ting Chou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
| | - Annalise B. Paaby
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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15
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Quévillon Huberdeau M, Shah VN, Nahar S, Neumeier J, Houle F, Bruckmann A, Gypas F, Nakanishi K, Großhans H, Meister G, Simard MJ. A specific type of Argonaute phosphorylation regulates binding to microRNAs during C. elegans development. Cell Rep 2022; 41:111822. [PMID: 36516777 PMCID: PMC10436268 DOI: 10.1016/j.celrep.2022.111822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/22/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Argonaute proteins are at the core of the microRNA-mediated gene silencing pathway essential for animals. In C. elegans, the microRNA-specific Argonautes ALG-1 and ALG-2 regulate multiple processes required for proper animal developmental timing and viability. Here we identified a phosphorylation site on ALG-1 that modulates microRNA association. Mutating ALG-1 serine 642 into a phospho-mimicking residue impairs microRNA binding and causes embryonic lethality and post-embryonic phenotypes that are consistent with alteration of microRNA functions. Monitoring microRNA levels in alg-1 phosphorylation mutant animals shows that microRNA passenger strands increase in abundance but are not preferentially loaded into ALG-1, indicating that the miRNA binding defects could lead to microRNA duplex accumulation. Our genetic and biochemical experiments support protein kinase A (PKA) KIN-1 as the putative kinase that phosphorylates ALG-1 serine 642. Our data indicate that PKA triggers ALG-1 phosphorylation to regulate its microRNA association during C. elegans development.
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Affiliation(s)
- Miguel Quévillon Huberdeau
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Vivek Nilesh Shah
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Smita Nahar
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - François Houle
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Foivos Gypas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, Columbus, OH 43210, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4056 Basel, Switzerland
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Martin J Simard
- CHU de Québec-Université Laval Research Center (Oncology Division), Québec City, QC G1R 3S3, Canada; Université Laval Cancer Research Centre, Québec City, QC G1R 3S3, Canada.
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16
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Elder CR, Pasquinelli AE. New Roles for MicroRNAs in Old Worms. Front Aging 2022; 3:871226. [PMID: 35821862 PMCID: PMC9261348 DOI: 10.3389/fragi.2022.871226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/09/2022] [Indexed: 11/30/2022]
Abstract
The use of Caenorhabditis elegans as a model organism in aging research has been integral to our understanding of genes and pathways involved in this process. Several well-conserved signaling pathways that respond to insulin signaling, diet, and assaults to proteostasis have defined roles in controlling lifespan. New evidence shows that microRNAs (miRNAs) play prominent roles in regulating these pathways. In some cases, key aging-related genes have been established as direct targets of specific miRNAs. However, the precise functions of other miRNAs and their protein cofactors in promoting or antagonizing longevity still need to be determined. Here, we highlight recently uncovered roles of miRNAs in common aging pathways, as well as new techniques for the ongoing discovery of miRNA functions in aging C. elegans.
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17
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Francisco S, Martinho V, Ferreira M, Reis A, Moura G, Soares AR, Santos MAS. The Role of MicroRNAs in Proteostasis Decline and Protein Aggregation during Brain and Skeletal Muscle Aging. Int J Mol Sci 2022; 23:ijms23063232. [PMID: 35328652 PMCID: PMC8955204 DOI: 10.3390/ijms23063232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 01/14/2023] Open
Abstract
Aging can be defined as the progressive deterioration of cellular, tissue, and organismal function over time. Alterations in protein homeostasis, also known as proteostasis, are a hallmark of aging that lead to proteome imbalances and protein aggregation, phenomena that also occur in age-related diseases. Among the various proteostasis regulators, microRNAs (miRNAs) have been reported to play important roles in the post-transcriptional control of genes involved in maintaining proteostasis during the lifespan in several organismal tissues. In this review, we consolidate recently published reports that demonstrate how miRNAs regulate fundamental proteostasis-related processes relevant to tissue aging, with emphasis on the two most studied tissues, brain tissue and skeletal muscle. We also explore an emerging perspective on the role of miRNA regulatory networks in age-related protein aggregation, a known hallmark of aging and age-related diseases, to elucidate potential miRNA candidates for anti-aging diagnostic and therapeutic targets.
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Affiliation(s)
- Stephany Francisco
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Vera Martinho
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Margarida Ferreira
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Andreia Reis
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Gabriela Moura
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
| | - Ana Raquel Soares
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
- Correspondence: (A.R.S.); (M.A.S.S.)
| | - Manuel A. S. Santos
- Institute of Biomedicine—iBiMED, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal; (S.F.); (V.M.); (M.F.); (A.R.); (G.M.)
- Multidisciplinary Institute of Aging, MIA-Portugal, Faculty of Medicine, University of Coimbra, Rua Largo 2, 3º, 3000-370 Coimbra, Portugal
- Correspondence: (A.R.S.); (M.A.S.S.)
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18
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Finger F, Ottens F, Hoppe T. The Argonaute Proteins ALG-1 and ALG-2 Are Linked to Stress Resistance and Proteostasis. MicroPubl Biol 2021; 2021. [PMID: 34723149 PMCID: PMC8553546 DOI: 10.17912/micropub.biology.000457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 09/12/2021] [Indexed: 11/06/2022]
Abstract
The conserved Argonaute-family members ALG-1 and ALG-2 are known to regulate processing and maturation of microRNAs to target mRNAs for degradation or translational inhibition (Bouasker and Simard 2012; Meister 2013). Consequently, depletion of alg-1 and alg-2 results in multiple phenotypes. Our data describe a role of microRNA-regulation in stress resistance and proteostasis with special emphasis on ubiquitin-dependent degradation pathways, such as ubiquitin fusion degradation (UFD) and endoplasmic reticulum (ER)-associated protein degradation (ERAD).
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Affiliation(s)
- Fabian Finger
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.,Novo Nordisk Foundation Center for Basic Metabolic Research, DK-2200 Copenhagen N, Denmark
| | - Franziska Ottens
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, 50931 Cologne, Germany
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19
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Pagliuso DC, Bodas DM, Pasquinelli AE. Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009734. [PMID: 34351906 PMCID: PMC8370650 DOI: 10.1371/journal.pgen.1009734] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/17/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
The heat shock response (HSR) is a highly conserved cellular process that promotes survival during stress. A hallmark of the HSR is the rapid induction of heat shock proteins (HSPs), such as HSP-70, by transcriptional activation. Once the stress is alleviated, HSPs return to near basal levels through incompletely understood mechanisms. Here, we show that the microRNA pathway acts during heat shock recovery in Caenorhabditis elegans. Depletion of the miRNA Argonaute, Argonaute Like Gene 1 (ALG-1), after an episode of heat shock resulted in decreased survival and perdurance of high hsp-70 levels. We present evidence that regulation of hsp-70 is dependent on miR-85 and sequences in the hsp-70 3’UTR that contain target sites for this miRNA. Regulation of hsp-70 by the miRNA pathway was found to be particularly important during recovery from HS, as animals that lacked miR-85 or its target sites in the hsp-70 3’UTR overexpressed HSP-70 and exhibited reduced viability. In summary, our findings show that down-regulation of hsp-70 by miR-85 after HS promotes survival, highlighting a previously unappreciated role for the miRNA pathway during recovery from stress. In the natural world, organisms constantly face stressful conditions such as oxidative stress, pathogen infection, starvation and heat stress. While many studies have focused on the cellular response to stress, less is known about how gene expression re-sets after the stress has been ameliorated. Here, we show that the microRNA pathway plays a critical role during the recovery phase after an episode of heat shock in the nematode, Caenorhabditis elegans. Elevated temperatures induce high expression of heat shock proteins (HSPs), including HSP-70, that provide protection from the damaging effects of high heat. We found that restoration of basal levels of HSP-70 after heat shock depends on Argonaute Like Gene 1 and miR-85. Moreover, loss of miRNA-mediated repression of HSP-70 results in compromised survival following heat shock. Our study draws attention to the recovery phase of the heat shock response and highlights an important role for the microRNA pathway in re-establishing gene expression programs needed for organismal viability post stress.
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Affiliation(s)
- Delaney C. Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Devavrat M. Bodas
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Amy E. Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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20
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Brosnan CA, Palmer AJ, Zuryn S. Cell-type-specific profiling of loaded miRNAs from Caenorhabditis elegans reveals spatial and temporal flexibility in Argonaute loading. Nat Commun 2021; 12:2194. [PMID: 33850152 PMCID: PMC8044110 DOI: 10.1038/s41467-021-22503-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/18/2021] [Indexed: 12/13/2022] Open
Abstract
Multicellularity has coincided with the evolution of microRNAs (miRNAs), small regulatory RNAs that are integrated into cellular differentiation and homeostatic gene-regulatory networks. However, the regulatory mechanisms underpinning miRNA activity have remained largely obscured because of the precise, and thus difficult to access, cellular contexts under which they operate. To resolve these, we have generated a genome-wide map of active miRNAs in Caenorhabditis elegans by revealing cell-type-specific patterns of miRNAs loaded into Argonaute (AGO) silencing complexes. Epitope-labelled AGO proteins were selectively expressed and immunoprecipitated from three distinct tissue types and associated miRNAs sequenced. In addition to providing information on biological function, we define adaptable miRNA:AGO interactions with single-cell-type and AGO-specific resolution. We demonstrate spatial and temporal dynamicism, flexibility of miRNA loading, and suggest miRNA regulatory mechanisms via AGO selectivity in different tissues and during ageing. Additionally, we resolve widespread changes in AGO-regulated gene expression by analysing translatomes specifically in neurons.
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Affiliation(s)
- Christopher A Brosnan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia.
| | - Alexander J Palmer
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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21
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Furtado GV, Yang J, Wu D, Papagiannopoulos CI, Terpstra HM, Kuiper EFE, Krauss S, Zhu WG, Kampinga HH, Bergink S. FOXO1 controls protein synthesis and transcript abundance of mutant polyglutamine proteins, preventing protein aggregation. Hum Mol Genet 2021; 30:996-1005. [PMID: 33822053 PMCID: PMC8170844 DOI: 10.1093/hmg/ddab095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/03/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022] Open
Abstract
FOXO1, a transcription factor downstream of the insulin/insulin like growth factor axis, has been linked to protein degradation. Elevated expression of FOXO orthologs can also prevent the aggregation of cytosine adenine guanine (CAG)-repeat disease causing polyglutamine (polyQ) proteins but whether FOXO1 targets mutant proteins for degradation is unclear. Here, we show that increased expression of FOXO1 prevents toxic polyQ aggregation in human cells while reducing FOXO1 levels has the opposite effect and accelerates it. Although FOXO1 indeed stimulates autophagy, its effect on polyQ aggregation is independent of autophagy, ubiquitin-proteasome system (UPS) mediated protein degradation and is not due to a change in mutant polyQ protein turnover. Instead, FOXO1 specifically downregulates protein synthesis rates from expanded pathogenic CAG repeat transcripts. FOXO1 orchestrates a change in the composition of proteins that occupy mutant expanded CAG transcripts, including the recruitment of IGF2BP3. This mRNA binding protein enables a FOXO1 driven decrease in pathogenic expanded CAG transcript- and protein levels, thereby reducing the initiation of amyloidogenesis. Our data thus demonstrate that FOXO1 not only preserves protein homeostasis at multiple levels, but also reduces the accumulation of aberrant RNA species that may co-contribute to the toxicity in CAG-repeat diseases.
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Affiliation(s)
- Gabriel Vasata Furtado
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Jing Yang
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Di Wu
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Christos I Papagiannopoulos
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Hanna M Terpstra
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - E F Elsiena Kuiper
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Sybille Krauss
- Faculty IV: School of Science and Technology, Institute of Biology, Human Biology / Neurobiology, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Nanshan District, 1066 Xueyuan Avenue, Shenzhen 508055, China
| | - Harm H Kampinga
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
| | - Steven Bergink
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen 9713 AV, The Netherlands
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22
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Ruediger C, Karimzadegan S, Lin S, Shapira M. miR-71 mediates age-dependent opposing contributions of the stress-activated kinase KGB-1 in Caenorhabditis elegans. Genetics 2021; 218:6182682. [PMID: 33755114 PMCID: PMC8619845 DOI: 10.1093/genetics/iyab049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Studying the evolutionary processes that shaped aging offers a path for understanding the causes of aging. The antagonistic pleiotropy theory for the evolution of aging proposes that the inverse correlation between age and natural selection strength allows positive selection of gene variants with early-life beneficial contributions to fitness despite detrimental late-life consequences. However, mechanistic understanding of how this principle manifests in aging is still lacking. We previously identified antagonistic pleiotropy in the function of the Caenorhabditis elegans JNK homolog KGB-1, which provided stress protection in developing larvae, but sensitized adults to stress and shortened their lifespan. To a large extent, KGB-1's contributions depended on age-dependent and opposing regulation of the stress-protective transcription factor DAF-16, but the underlying mechanisms remained unknown. Here, we describe a role for the microRNA miR-71 in mediating effects of KGB-1 on DAF-16 and downstream phenotypes. Fluorescent imaging along with genetic and survival analyses revealed age-dependent regulation of mir-71 expression by KGB-1-upregulation in larvae, but downregulation in adults-and showed that mir-71 was required both for late-life effects of KGB-1 (infection sensitivity and shortened lifespan), as well as for early life resistance to cadmium. While mir-71 disruption did not compromise development under protein-folding stress (known to depend on KGB-1), disruption of the argonaute gene alg-1, a central component of the microRNA machinery, did. These results suggest that microRNAs play a role in mediating age-dependent antagonistic contributions of KGB-1 to survival, with mir-71 playing a central role and additional microRNAs potentially contributing redundantly.
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Affiliation(s)
- Cyrus Ruediger
- Department of Molecular and Cellular Biology, University of California
Berkeley, Berkeley, CA 94720, USA
| | - Siavash Karimzadegan
- Department of Integrative Biology, University of California
Berkeley, Berkeley, CA 94720, USA
| | - Sonya Lin
- Department of Integrative Biology, University of California
Berkeley, Berkeley, CA 94720, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California
Berkeley, Berkeley, CA 94720, USA,Corresponding author: Department of Integrative Biology,
University of California Berkeley, Room 5190, 3060 Valley Life Sciences Bldg, Berkeley, CA
94720-3140, USA.
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23
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Proshkina E, Yushkova E, Koval L, Zemskaya N, Shchegoleva E, Solovev I, Yakovleva D, Pakshina N, Ulyasheva N, Shaposhnikov M, Moskalev A. Tissue-Specific Knockdown of Genes of the Argonaute Family Modulates Lifespan and Radioresistance in Drosophila Melanogaster. Int J Mol Sci 2021; 22:2396. [PMID: 33673647 PMCID: PMC7957547 DOI: 10.3390/ijms22052396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Small RNAs are essential to coordinate many cellular processes, including the regulation of gene expression patterns, the prevention of genomic instability, and the suppression of the mutagenic transposon activity. These processes determine the aging, longevity, and sensitivity of cells and an organism to stress factors (particularly, ionizing radiation). The biogenesis and activity of small RNAs are provided by proteins of the Argonaute family. These proteins participate in the processing of small RNA precursors and the formation of an RNA-induced silencing complex. However, the role of Argonaute proteins in regulating lifespan and radioresistance remains poorly explored. We studied the effect of knockdown of Argonaute genes (AGO1, AGO2, AGO3, piwi) in various tissues on the Drosophila melanogaster lifespan and survival after the γ-irradiation at a dose of 700 Gy. In most cases, these parameters are reduced or did not change significantly in flies with tissue-specific RNA interference. Surprisingly, piwi knockdown in both the fat body and the nervous system causes a lifespan increase. But changes in radioresistance depend on the tissue in which the gene was knocked out. In addition, analysis of changes in retrotransposon levels and expression of stress response genes allow us to determine associated molecular mechanisms.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Liubov Koval
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Nadezhda Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Evgeniya Shchegoleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Ilya Solovev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Daria Yakovleva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prosp., 167001 Syktyvkar, Russia
| | - Natalya Pakshina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Natalia Ulyasheva
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya St., 167982 Syktyvkar, Russia; (E.P.); (E.Y.); (L.K.); (N.Z.); (E.S.); (I.S.); (D.Y.); (N.P.); (N.U.); (M.S.)
- Laboratory of Post-Genomic Research, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia
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24
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Le HH, Wrobel CJ, Cohen SM, Yu J, Park H, Helf MJ, Curtis BJ, Kruempel JC, Rodrigues PR, Hu PJ, Sternberg PW, Schroeder FC. Modular metabolite assembly in Caenorhabditis elegans depends on carboxylesterases and formation of lysosome-related organelles. eLife 2020; 9:61886. [PMID: 33063667 PMCID: PMC7641594 DOI: 10.7554/elife.61886] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Signaling molecules derived from attachment of diverse metabolic building blocks to ascarosides play a central role in the life history of C. elegans and other nematodes; however, many aspects of their biogenesis remain unclear. Using comparative metabolomics, we show that a pathway mediating formation of intestinal lysosome-related organelles (LROs) is required for biosynthesis of most modular ascarosides as well as previously undescribed modular glucosides. Similar to modular ascarosides, the modular glucosides are derived from highly selective assembly of moieties from nucleoside, amino acid, neurotransmitter, and lipid metabolism, suggesting that modular glucosides, like the ascarosides, may serve signaling functions. We further show that carboxylesterases that localize to intestinal organelles are required for the assembly of both modular ascarosides and glucosides via ester and amide linkages. Further exploration of LRO function and carboxylesterase homologs in C. elegans and other animals may reveal additional new compound families and signaling paradigms.
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Affiliation(s)
- Henry H Le
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Chester Jj Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Sarah M Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Jingfang Yu
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Joseph C Kruempel
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, United States
| | - Pedro Reis Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Patrick J Hu
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
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25
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Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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26
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Proshkina E, Solovev I, Koval L, Moskalev A. The critical impacts of small RNA biogenesis proteins on aging, longevity and age-related diseases. Ageing Res Rev 2020; 62:101087. [PMID: 32497728 DOI: 10.1016/j.arr.2020.101087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
Small RNAs and enzymes that provide their biogenesis and functioning are involved in the organism development and coordination of biological processes, including metabolism, maintaining genome integrity, immune and stress responses. In this review, we focused on the role of small RNA biogenesis proteins in determining the aging and longevity of animals and human. A number of studies have revealed that changes in expression profiles of key enzymes, in particular proteins of the Drosha, Dicer and Argonaute families, are associated with the aging process, as well as with some age-related diseases and progeroid syndromes. Down-regulation of small RNA biogenesis proteins leads to global alterations in the expression of regulatory RNAs, disruption of key molecular, cellular and systemic processes, which leads to a lifespan shortening. In contrast, overexpression of Dicer prolongs lifespan and improves cellular defense. Additionally, the role of small RNA biogenesis proteins in the pathogenesis of age-related diseases, including cancer, inflammaging, neurodegeneration, cardiovascular, metabolic and immune disorders, has been conclusively evidenced. Recent advances in biomedicine allow using these proteins as diagnostic and prognostic biomarkers and therapeutic targets.
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27
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Möller S, Saul N, Cohen AA, Köhling R, Sender S, Murua Escobar H, Junghanss C, Cirulli F, Berry A, Antal P, Adler P, Vilo J, Boiani M, Jansen L, Repsilber D, Grabe HJ, Struckmann S, Barrantes I, Hamed M, Wouters B, Schoofs L, Luyten W, Fuellen G. Healthspan pathway maps in C. elegans and humans highlight transcription, proliferation/biosynthesis and lipids. Aging (Albany NY) 2020; 12:12534-81. [PMID: 32634117 DOI: 10.18632/aging.103514] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022]
Abstract
The molecular basis of aging and of aging-associated diseases is being unraveled at an increasing pace. An extended healthspan, and not merely an extension of lifespan, has become the aim of medical practice. Here, we define health based on the absence of diseases and dysfunctions. Based on an extensive review of the literature, in particular for humans and C. elegans, we compile a list of features of health and of the genes associated with them. These genes may or may not be associated with survival/lifespan. In turn, survival/lifespan genes that are not known to be directly associated with health are not considered. Clusters of these genes based on molecular interaction data give rise to maps of healthspan pathways for humans and for C. elegans. Overlaying healthspan-related gene expression data onto the healthspan pathway maps, we observe the downregulation of (pro-inflammatory) Notch signaling in humans and of proliferation in C. elegans. We identify transcription, proliferation/biosynthesis and lipids as a common theme on the annotation level, and proliferation-related kinases on the gene/protein level. Our literature-based data corpus, including visualization, should be seen as a pilot investigation of the molecular underpinnings of health in two different species. Web address: http://pathways.h2020awe.eu.
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28
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Braga DL, Mousovich-Neto F, Tonon-da-Silva G, Salgueiro WG, Mori MA. Epigenetic changes during ageing and their underlying mechanisms. Biogerontology 2020; 21:423-443. [PMID: 32356238 DOI: 10.1007/s10522-020-09874-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/20/2020] [Indexed: 12/12/2022]
Abstract
As life expectancy increases worldwide, ageing and age-related diseases arise as a major issue for societies around the globe. Understanding the biological mechanisms underlying the ageing process is thus instrumental for the development of efficient interventions aimed to prevent and treat age-related conditions. Current knowledge in the biogerontology field points to epigenetics as a critical component of the ageing process, not only by serving as a bona-fide marker of biological age but also by controlling and conferring inheritability to cellular and organismal ageing. This is reflected by a myriad of evidences demonstrating the relationship between DNA methylation, histone modifications, chromatin remodeling and small non-coding RNAs and several age-related phenotypes. Given the reversibility of epigenetic alterations, epigenetic reprogramming may also be envisioned as a potential approach to treat age-related disorders. Here we review how different types of epigenetic mechanisms are involved in the ageing process. In addition, we highlight how interventions modulate epigenetics and thus promote health- and lifespan.
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Affiliation(s)
- Deisi L Braga
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Felippe Mousovich-Neto
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
| | - Guilherme Tonon-da-Silva
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Willian G Salgueiro
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil
- Program in Genetics and Molecular Biology, University of Campinas, Campinas, São Paulo, 13083-862, Brazil
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, University of Campinas, Rua Monteiro Lobato, 255, Campinas, São Paulo, 13083-862, Brazil.
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, São Paulo, 13083-862, Brazil.
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29
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Cohen-Berkman M, Dudkevich R, Ben-Hamo S, Fishman A, Salzberg Y, Waldman Ben-Asher H, Lamm AT, Henis-Korenblit S. Endogenous siRNAs promote proteostasis and longevity in germline-less Caenorhabditis elegans. eLife 2020; 9:e50896. [PMID: 32213289 PMCID: PMC7136021 DOI: 10.7554/elife.50896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
How lifespan and the rate of aging are set is a key problem in biology. Small RNAs are conserved molecules that impact diverse biological processes through the control of gene expression. However, in contrast to miRNAs, the role of endo-siRNAs in aging remains unexplored. Here, by combining deep sequencing and genomic and genetic approaches in Caenorhabditis elegans, we reveal an unprecedented role for endo-siRNA molecules in the maintenance of proteostasis and lifespan extension in germline-less animals. Furthermore, we identify an endo-siRNA-regulated tyrosine phosphatase, which limits the longevity of germline-less animals by restricting the activity of the heat shock transcription factor HSF-1. Altogether, our findings point to endo-siRNAs as a link between germline removal and the HSF-1 proteostasis and longevity-promoting somatic pathway. This establishes a role for endo siRNAs in the aging process and identifies downstream genes and physiological processes that are regulated by the endo siRNAs to affect longevity.
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Affiliation(s)
- Moran Cohen-Berkman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Reut Dudkevich
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Shani Ben-Hamo
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Alla Fishman
- Faculty of Biology, Technion-Israel Institute of Technology, Technion CityHaifaIsrael
| | - Yehuda Salzberg
- Department of Neurobiology, Weizmann Institute of ScienceRehovotIsrael
| | | | - Ayelet T Lamm
- Faculty of Biology, Technion-Israel Institute of Technology, Technion CityHaifaIsrael
| | - Sivan Henis-Korenblit
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
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30
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Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res 2019; 47:9829-9841. [PMID: 31396626 PMCID: PMC6765114 DOI: 10.1093/nar/gkz693] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023] Open
Abstract
Elevated temperatures activate a heat shock response (HSR) to protect cells from the pathological effects of protein mis-folding, cellular mis-organization, organelle dysfunction and altered membrane fluidity. This response includes activation of the conserved transcription factor heat shock factor 1 (HSF-1), which binds heat shock elements (HSEs) in the promoters of genes induced by heat shock (HS). The upregulation of protein-coding genes (PCGs), such as heat shock proteins and cytoskeletal regulators, is critical for cellular survival during elevated temperatures. While the transcriptional response of PCGs to HS has been comprehensively analyzed in a variety of organisms, the effect of this stress on the expression of non-coding RNAs (ncRNAs) has not been systematically examined. Here we show that in Caenorhabditis elegans HS induces up- and downregulation of specific ncRNAs from multiple classes, including miRNA, piRNA, lincRNA, pseudogene and repeat elements. Moreover, some ncRNA genes appear to be direct targets of the HSR, as they contain HSF-1 bound HSEs in their promoters and their expression is regulated by this factor during HS. These results demonstrate that multiple ncRNA genes respond to HS, some as direct HSF-1 targets, providing new candidates that may contribute to organismal survival during this stress.
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Affiliation(s)
- William P Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Delaney C Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jacob M Garrigues
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Jerry S Chen
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Antti P Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093-0349, USA
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31
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Doll MA, Soltanmohammadi N, Schumacher B. ALG-2/AGO-Dependent mir-35 Family Regulates DNA Damage-Induced Apoptosis Through MPK-1/ERK MAPK Signaling Downstream of the Core Apoptotic Machinery in Caenorhabditis elegans. Genetics 2019; 213:173-194. [PMID: 31296532 PMCID: PMC6727803 DOI: 10.1534/genetics.119.302458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) associate with argonaute (AGO) proteins to post-transcriptionally modulate the expression of genes involved in various cellular processes. Herein, we show that loss of the Caenorhabditis elegans AGO gene alg-2 results in rapid and significantly increased germ cell apoptosis in response to DNA damage inflicted by ionizing radiation (IR). We demonstrate that the abnormal apoptosis phenotype in alg-2 mutant animals can be explained by reduced expression of mir-35 miRNA family members. We show that the increased apoptosis levels in IR-treated alg-2 or mir-35 family mutants depend on a transient hyperactivation of the C. elegans ERK1/2 MAPK ortholog MPK-1 in dying germ cells. Unexpectedly, MPK-1 phosphorylation occurs downstream of caspase activation and depends at least in part on a functional cell corpse-engulfment machinery. Therefore, we propose a refined mechanism, in which an initial proapoptotic stimulus by the core apoptotic machinery initiates the engulfment process, which in turn activates MAPK signaling to facilitate the demise of genomically compromised germ cells.
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Affiliation(s)
- Markus Alexander Doll
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, 50931, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
| | - Najmeh Soltanmohammadi
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, 50931, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, 50931, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
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32
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Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally repress translation or induce mRNA degradation of target transcripts through sequence-specific binding. miRNAs target hundreds of transcripts to regulate diverse biological pathways and processes, including aging. Many microRNAs are differentially expressed during aging, generating interest in their use as aging biomarkers and roles as regulators of the aging process. In the invertebrates Caenorhabditis elegans and Drosophila, a number of miRNAs have been found to both positive and negatively modulate longevity through canonical aging pathways. Recent studies have also shown that miRNAs regulate age-associated processes and pathologies in a diverse array of mammalian tissues, including brain, heart, bone, and muscle. The review will present an overview of these studies, highlighting the role of individual miRNAs as biomarkers of aging and regulators of longevity and tissue-specific aging processes.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, USA.
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Abstract
Non-coding RNAs (ncRNAs) comprise various RNA species, including small ncRNAs and long ncRNAs (lncRNAs). ncRNAs regulate various cellular processes, including transcription and translation of target messenger RNAs. Recent studies also indicate that ncRNAs affect organismal aging and conversely aging influences ncRNA levels. In this review, we discuss our current understanding of the roles of ncRNAs in aging and longevity, focusing on recent advances using the roundworm Caenorhabditis elegans. Expression of various ncRNAs, including microRNA (miRNA), tRNA-derived small RNA (tsRNA), ribosomal RNA (rRNA), PIWI-interacting RNA (piRNA), circular RNA (circRNA), and lncRNA, is altered during aging in C. elegans. Genetic modulation of specific ncRNAs affects longevity and aging rates by modulating established aging-regulating protein factors. Because many aging-regulating mechanisms in C. elegans are evolutionarily conserved, these studies will provide key information regarding how ncRNAs modulate aging and lifespan in complex organisms, including mammals.
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Affiliation(s)
- Sieun S. Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141,
Korea
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Affiliation(s)
- Kristen C. Brown
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado, United States of America
| | - Taiowa A. Montgomery
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
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