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Wang XF, Yu CQ, You ZH, Wang Y, Huang L, Qiao Y, Wang L, Li ZW. BEROLECMI: a novel prediction method to infer circRNA-miRNA interaction from the role definition of molecular attributes and biological networks. BMC Bioinformatics 2024; 25:264. [PMID: 39127625 DOI: 10.1186/s12859-024-05891-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Circular RNA (CircRNA)-microRNA (miRNA) interaction (CMI) is an important model for the regulation of biological processes by non-coding RNA (ncRNA), which provides a new perspective for the study of human complex diseases. However, the existing CMI prediction models mainly rely on the nearest neighbor structure in the biological network, ignoring the molecular network topology, so it is difficult to improve the prediction performance. In this paper, we proposed a new CMI prediction method, BEROLECMI, which uses molecular sequence attributes, molecular self-similarity, and biological network topology to define the specific role feature representation for molecules to infer the new CMI. BEROLECMI effectively makes up for the lack of network topology in the CMI prediction model and achieves the highest prediction performance in three commonly used data sets. In the case study, 14 of the 15 pairs of unknown CMIs were correctly predicted.
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Affiliation(s)
- Xin-Fei Wang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chang-Qing Yu
- School of Information Engineering, Xijing University, Xi'an, China.
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
- School of Artificial Intelligence, Jilin University, Changchun, China.
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yan Qiao
- College of Agriculture and Forestry, Longdong University, Qingyang, China
| | - Lei Wang
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
- Guangxi Academy of Sciences, Nanning, China
| | - Zheng-Wei Li
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
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2
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Ow MC, Nishiguchi MA, Dar AR, Butcher RA, Hall SE. RNAi-dependent expression of sperm genes in ADL chemosensory neurons is required for olfactory responses in Caenorhabditis elegans. Front Mol Biosci 2024; 11:1396587. [PMID: 39055986 PMCID: PMC11269235 DOI: 10.3389/fmolb.2024.1396587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent differentially expressed genes. Surprisingly, 214 of the ADL DE genes are considered "germline-expressed", including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.
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Affiliation(s)
- Maria C. Ow
- Biology Department, Syracuse University, Syracuse, NY, United States
| | | | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Sarah E. Hall
- Biology Department, Syracuse University, Syracuse, NY, United States
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3
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Jang D, Kim CJ, Shin BH, Lim DH. The Biological Roles of microRNAs in Drosophila Development. INSECTS 2024; 15:491. [PMID: 39057224 PMCID: PMC11277110 DOI: 10.3390/insects15070491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024]
Abstract
Drosophila is a well-established insect model system for studying various physiological phenomena and developmental processes, with a focus on gene regulation. Drosophila development is controlled by programmed regulatory mechanisms specific to individual tissues. When key developmental processes are shared among various insects, the associated regulatory networks are believed to be conserved across insects. Thus, studies of developmental regulation in Drosophila have substantially contributed to our understanding of insect development. Over the past two decades, studies on microRNAs (miRNAs) in Drosophila have revealed their crucial regulatory roles in various developmental processes. This review focuses on the biological roles of miRNAs in specific tissues and processes associated with Drosophila development. Additionally, as a future direction, we discuss sequencing technologies that can analyze the interactions between miRNAs and their target genes, with the aim of enhancing miRNA studies in Drosophila development.
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Affiliation(s)
| | | | | | - Do-Hwan Lim
- School of Systems Biomedical Science, Soongsil University, Seoul 06978, Republic of Korea; (D.J.); (C.J.K.); (B.H.S.)
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4
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Frédérick PM, Jannot G, Banville I, Simard M. Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals. Nucleic Acids Res 2024; 52:6253-6268. [PMID: 38613392 PMCID: PMC11194074 DOI: 10.1093/nar/gkae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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5
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Cheng H, Xu L, Jia C. Characterization of double-stranded RNA and its silencing efficiency for insects using hybrid deep-learning framework. Brief Funct Genomics 2024:elae027. [PMID: 38912767 DOI: 10.1093/bfgp/elae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/24/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
RNA interference (RNAi) technology is widely used in the biological prevention and control of terrestrial insects. One of the main factors with the application of RNAi in insects is the difference in RNAi efficiency, which may vary not only in different insects, but also in different genes of the same insect, and even in different double-stranded RNAs (dsRNAs) of the same gene. This work focuses on the last question and establishes a bioinformatics software that can help researchers screen for the most efficient dsRNA targeting target genes. Among insects, the red flour beetle (Tribolium castaneum) is known to be one of the most sensitive to RNAi. From iBeetle-Base, we extracted 12 027 efficient dsRNA sequences with a lethality rate of ≥20% or with experimentation-induced phenotypic changes and processed these data to correspond to specific silence efficiency. Based on the first complied novel benchmark dataset, we specifically designed a deep neural network to identify and characterize efficient dsRNA for RNAi in insects. The dna2vec word embedding model was trained to extract distributed feature representations, and three powerful modules, namely convolutional neural network, bidirectional long short-term memory network, and self-attention mechanism, were integrated to form our predictor model to characterize the extracted dsRNAs and their silencing efficiencies for T. castaneum. Our model dsRNAPredictor showed reliable performance in multiple independent tests based on different species, including both T. castaneum and Aedes aegypti. This indicates that dsRNAPredictor can facilitate prescreening for designing high-efficiency dsRNA targeting target genes of insects in advance.
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Affiliation(s)
- Han Cheng
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
| | - Liping Xu
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
| | - Cangzhi Jia
- Mathematics Department of the School of Science, Dalian Maritime University, Dalian 116026, China
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6
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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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7
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Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B. A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1280-1291. [PMID: 38489006 DOI: 10.1007/s11427-023-2466-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 03/17/2024]
Abstract
Lariat RNA is concomitantly produced by excised intron during RNA splicing, which is usually debranched by DBR1, an RNA debranching enzyme. However, increasing evidence showed that some lariat RNA could escape debranching. Little is known about how and why these lariat RNAs could be retained. By comparing the atlas of lariat RNAs between the non-dividing cell (mature pollen) and three actively dividing tissues (young shoot apex, young seeds, and young roots), we identified hundreds to thousands of lariat RNA naturally retained in each tissue, and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen. Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-mRNA could be retained in one tissue while degraded in the other tissues. By deciphering lariat RNA sequences, we identified an AG-rich (RAAAAVAAAR) motif and a UC-rich (UCUCUYUCUC) motif for pollen-specific and the other three tissues-retained lariat RNAs, respectively. Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants. Biologically, hundreds of lariat RNAs harbored miRNA binding sites, and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of miRNA target genes. Collectively, our results uncover that selective retention of lariat RNA is an actively regulatory process, and provide new insights into understanding how lariat RNA metabolism may impact miRNA activity.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yixiao Fang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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8
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Pal A, Vasudevan V, Houle F, Lantin M, Maniates K, Huberdeau MQ, Abbott A, Simard M. Defining the contribution of microRNA-specific Argonautes with slicer capability in animals. Nucleic Acids Res 2024; 52:5002-5015. [PMID: 38477356 PMCID: PMC11109967 DOI: 10.1093/nar/gkae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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9
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Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala R, 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; 52:4985-5001. [PMID: 38471816 PMCID: PMC11109956 DOI: 10.1093/nar/gkae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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10
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Montgomery BE, Knittel TL, Reed KJ, Chong MC, Isolehto IJ, Cafferty ER, Smith MJ, Sprister RA, Magelky CN, Scherman H, Ketting RF, Montgomery TA. Regulation of Microprocessor assembly and localization via Pasha's WW domain in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590772. [PMID: 38712061 PMCID: PMC11071396 DOI: 10.1101/2024.04.23.590772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Primary microRNA (pri-miRNA) transcripts are processed by the Microprocessor, a protein complex that includes the ribonuclease Drosha and its RNA binding partner DGCR8/Pasha. We developed a live, whole animal, fluorescence-based sensor that reliably monitors pri-miRNA processing with high sensitivity in C. elegans. Through a forward genetic selection for alleles that desilence the sensor, we identified a mutation in the conserved G residue adjacent to the namesake W residue of Pasha's WW domain. Using genome editing we also mutated the W residue and reveal that both the G and W residue are required for dimerization of Pasha and proper assembly of the Microprocessor. Surprisingly, we find that the WW domain also facilitates nuclear localization of Pasha, which in turn promotes nuclear import or retention of Drosha. Furthermore, depletion of Pasha or Drosha causes both components of the Microprocessor to mislocalize to the cytoplasm. Thus, Pasha and Drosha mutually regulate each other's spatial expression in C. elegans.
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Affiliation(s)
| | - Thiago L. Knittel
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kailee J. Reed
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Madeleine C. Chong
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Ida J. Isolehto
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
- International PhD Program on Gene Regulation, Epigenetics and Genome Stability, Mainz, Germany
| | - Erin R. Cafferty
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Margaret J. Smith
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Reese A. Sprister
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Colin N. Magelky
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Hataichanok Scherman
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Rene F. Ketting
- Biology of Non-coding RNA group, Institute of Molecular Biology, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Mainz, Germany
| | - Taiowa A. Montgomery
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523, USA
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11
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Drury RE, Camara S, Chelysheva I, Bibi S, Sanders K, Felle S, Emary K, Phillips D, Voysey M, Ferreira DM, Klenerman P, Gilbert SC, Lambe T, Pollard AJ, O'Connor D. Multi-omics analysis reveals COVID-19 vaccine induced attenuation of inflammatory responses during breakthrough disease. Nat Commun 2024; 15:3402. [PMID: 38649734 PMCID: PMC11035709 DOI: 10.1038/s41467-024-47463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
The immune mechanisms mediating COVID-19 vaccine attenuation of COVID-19 remain undescribed. We conducted comprehensive analyses detailing immune responses to SARS-CoV-2 virus in blood post-vaccination with ChAdOx1 nCoV-19 or a placebo. Samples from randomised placebo-controlled trials (NCT04324606 and NCT04400838) were taken at baseline, onset of COVID-19-like symptoms, and 7 days later, confirming COVID-19 using nucleic amplification test (NAAT test) via real-time PCR (RT-PCR). Serum cytokines were measured with multiplexed immunoassays. The transcriptome was analysed with long, short and small RNA sequencing. We found attenuation of RNA inflammatory signatures in ChAdOx1 nCoV-19 compared with placebo vaccinees and reduced levels of serum proteins associated with COVID-19 severity. KREMEN1, a putative alternative SARS-CoV-2 receptor, was downregulated in placebo compared with ChAdOx1 nCoV-19 vaccinees. Vaccination ameliorates reductions in cell counts across leukocyte populations and platelets noted at COVID-19 onset, without inducing potentially deleterious Th2-skewed immune responses. Multi-omics integration links a global reduction in miRNA expression at COVID-19 onset to increased pro-inflammatory responses at the mRNA level. This study reveals insights into the role of COVID-19 vaccines in mitigating disease severity by abrogating pro-inflammatory responses associated with severe COVID-19, affirming vaccine-mediated benefit in breakthrough infection, and highlighting the importance of clinically relevant endpoints in vaccine evaluation.
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Affiliation(s)
- Ruth E Drury
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Susana Camara
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Sanders
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Salle Felle
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Katherine Emary
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel Phillips
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniela M Ferreira
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Dept. of Clinical Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute, University of Oxford, Oxford, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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12
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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] [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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13
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Lui A, Do T, Alzayat O, Yu N, Phyu S, Santuya HJ, Liang B, Kailash V, Liu D, Inslicht SS, Shahlaie K, Liu D. Tumor Suppressor MicroRNAs in Clinical and Preclinical Trials for Neurological Disorders. Pharmaceuticals (Basel) 2024; 17:426. [PMID: 38675388 PMCID: PMC11054060 DOI: 10.3390/ph17040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Cancers and neurological disorders are two major types of diseases in humans. We developed the concept called the "Aberrant Cell Cycle Disease (ACCD)" due to the accumulating evidence that shows that two different diseases share the common mechanism of aberrant cell cycle re-entry. The aberrant cell cycle re-entry is manifested as kinase/oncoprotein activation and tumor suppressor (TS) inactivation, which are associated with both tumor growth in cancers and neuronal death in neurological disorders. Therefore, some cancer therapies (e.g., kinase/oncogene inhibition and TS elevation) can be leveraged for neurological treatments. MicroRNA (miR/miRNA) provides a new style of drug-target binding. For example, a single tumor suppressor miRNA (TS-miR/miRNA) can bind to and decrease tens of target kinases/oncogenes, producing much more robust efficacy to block cell cycle re-entry than inhibiting a single kinase/oncogene. In this review, we summarize the miRNAs that are altered in both cancers and neurological disorders, with an emphasis on miRNA drugs that have entered into clinical trials for neurological treatment.
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Affiliation(s)
- Austin Lui
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Timothy Do
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Omar Alzayat
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Nina Yu
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Su Phyu
- Department of Neurological Surgery, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Hillary Joy Santuya
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Benjamin Liang
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Vidur Kailash
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Dewey Liu
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
| | - Sabra S. Inslicht
- Department of Psychiatry and Behavioral Sciences, University of California at San Francisco, San Francisco, CA 94143, USA
- San Francisco VA Health Care System, San Francisco, CA 94121, USA
| | - Kiarash Shahlaie
- Department of Neurological Surgery, University of California at Davis, Davis, CA 95616, USA
| | - DaZhi Liu
- Department of Neurology, University of California at Davis, Davis, CA 95616, USA; (A.L.); (V.K.)
- Mirnova Therapeutics Inc., Davis, CA 95618, USA
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14
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Baek SC, Kim B, Jang H, Kim K, Park IS, Min DH, Kim VN. Structural atlas of human primary microRNAs generated by SHAPE-MaP. Mol Cell 2024; 84:1158-1172.e6. [PMID: 38447581 DOI: 10.1016/j.molcel.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3' bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.
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Affiliation(s)
- S Chan Baek
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Boseon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Harim Jang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea
| | - Il-Soo Park
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Dal-Hee Min
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, South Korea; School of Biological Science, Seoul National University, Seoul 08826, South Korea.
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15
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Hynes C, Kakumani PK. Regulatory role of RNA-binding proteins in microRNA biogenesis. Front Mol Biosci 2024; 11:1374843. [PMID: 38567098 PMCID: PMC10985210 DOI: 10.3389/fmolb.2024.1374843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that silence gene expression through their interaction with complementary sequences in the 3' untranslated regions (UTR) of target mRNAs. miRNAs undergo a series of steps during their processing and maturation, which are tightly regulated to fine-tune their abundance and ability to function in post-transcriptional gene silencing. miRNA biogenesis typically involves core catalytic proteins, namely, Drosha and Dicer, and several other RNA-binding proteins (RBPs) that recognize and interact with miRNA precursors and/or their intermediates, and mature miRNAs along with their interacting proteins. The series of RNA-protein and protein-protein interactions are critical to maintaining miRNA expression levels and their function, underlying a variety of cellular processes. Throughout this article, we review RBPs that play a role in miRNA biogenesis and focus on their association with components of the miRNA pathway with functional consequences in the processing and generation of mature miRNAs.
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Affiliation(s)
| | - Pavan Kumar Kakumani
- Department of Biochemistry, Memorial University of Newfoundland, St. John’s, NL, Canada
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16
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Akkaya-Ulum YZ, Sen B, Akbaba TH, Balci-Peynircioglu B. InflammamiRs in focus: Delivery strategies and therapeutic approaches. FASEB J 2024; 38:e23528. [PMID: 38441434 DOI: 10.1096/fj.202302028r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/22/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
microRNAs (miRNAs) are small non-protein-coding RNAs which are essential regulators of host genome expression at the post-transcriptional level. There is evidence of dysregulated miRNA expression patterns in a wide variety of diseases, such as autoimmune and inflammatory conditions. These miRNAs have been termed "inflammamiRs." When working with miRNAs, the method followed, the approach to treat or diagnosis, and the selected biological material are very crucial. Demonstration of the role of miRNAs in particular disease phenotypes facilitates their evaluation as potential and effective therapeutic tools. A growing number of reports suggest the significant utility of miRNAs and other small RNA drugs in clinical medicine. Most miRNAs seem promising therapeutic options, but some features associated with miRNA therapy like off-target effect, effective dosage, or differential delivery methods, mainly caused by the short target's sequence, make miRNA therapies challenging. In this review, we aim to discuss some of the inflammamiRs in diseases associated with inflammatory pathways and the challenge of identifying the most potent therapeutic candidates and provide a perspective on achieving safe and targeted delivery of miRNA therapeutics. We also discuss the status of inflammamiRs in clinical trials.
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Affiliation(s)
- Yeliz Z Akkaya-Ulum
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Basak Sen
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Tayfun Hilmi Akbaba
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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17
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Roka Pun H, Karp X. An RNAi screen for conserved kinases that enhance microRNA activity after dauer in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkae007. [PMID: 38226857 PMCID: PMC10917497 DOI: 10.1093/g3journal/jkae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/17/2023] [Accepted: 01/05/2024] [Indexed: 01/17/2024]
Abstract
Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes posttranscriptionally through the activity of the microRNA-induced silencing complex. Argonaute is the core microRNA-induced silencing complex protein that binds to both the microRNA and to other microRNA-induced silencing complex proteins. The 2 major microRNA Argonautes in the Caenorhabditis elegans soma are ALG-1 and ALG-2, which function partially redundantly. Loss of alg-1 [alg-1(0)] causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent if alg-1(0) animals undergo a diapause stage called dauer. Levels of the relevant microRNAs are not higher during or after dauer, suggesting that activity of the microRNA-induced silencing complex may be enhanced in this context. To identify genes that are required for alg-1(0) mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating microRNA-induced silencing complex activity. We found RNAi knockdown of 4 kinase-encoding genes, air-2, bub-1, chk-1, and nekl-3, caused vulval defects and reiterative phenotypes in alg-1(0) mutants after dauer, and that these defects were more penetrant in an alg-1(0) background than in wild type. Our results implicate these kinases as potential regulators of microRNA-induced silencing complex activity during postdauer development in C. elegans.
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Affiliation(s)
- Himal Roka Pun
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Xantha Karp
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
- Biochemistry, Cell and Molecular Biology Program, Central Michigan University, Mount Pleasant, MI 48859, USA
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18
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Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated human AGO1 mutations in Caenorhabditis elegans Argonaute alg-1. Proc Natl Acad Sci U S A 2024; 121:e2308255121. [PMID: 38412125 DOI: 10.1073/pnas.2308255121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/30/2023] [Indexed: 02/29/2024] Open
Abstract
MicroRNAs (miRNA) associate with Argonaute (AGO) proteins and repress gene expression by base pairing to sequences in the 3' untranslated regions of target genes. De novo coding variants in the human AGO genes AGO1 and AGO2 cause neurodevelopmental disorders (NDD) with intellectual disability, referred to as Argonaute syndromes. Most of the altered amino acids are conserved between the miRNA-associated AGO in Homo sapiens and Caenorhabditis elegans, suggesting that the human mutations could disrupt conserved functions in miRNA biogenesis or activity. We genetically modeled four human AGO1 mutations in C. elegans by introducing identical mutations into the C. elegans AGO1 homologous gene, alg-1. These alg-1 NDD mutations cause phenotypes in C. elegans indicative of disrupted miRNA processing, miRISC (miRNA silencing complex) formation, and/or target repression. We show that the alg-1 NDD mutations are antimorphic, causing developmental and molecular phenotypes stronger than those of alg-1 null mutants, likely by sequestrating functional miRISC components into non-functional complexes. The alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles, accompanied by perturbation of downstream gene expression, including altered translational efficiency and/or messenger RNA abundance. The perturbed genes include those with human orthologs whose dysfunction is associated with NDD. These cross-clade genetic studies illuminate fundamental AGO functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Ye Duan
- Program of Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Li Li
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | | | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch 67 400, France
| | - Anna Zinovyeva
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Victor Ambros
- Program of Molecular Medicine, UMass Chan Medical School, Worcester, MA 01605
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19
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Hiers NM, Li T, Traugot CM, Xie M. Target-directed microRNA degradation: Mechanisms, significance, and functional implications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1832. [PMID: 38448799 PMCID: PMC11098282 DOI: 10.1002/wrna.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 03/08/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a fundamental role in enabling miRNA-mediated target repression, a post-transcriptional gene regulatory mechanism preserved across metazoans. Loss of certain animal miRNA genes can lead to developmental abnormalities, disease, and various degrees of embryonic lethality. These short RNAs normally guide Argonaute (AGO) proteins to target RNAs, which are in turn translationally repressed and destabilized, silencing the target to fine-tune gene expression and maintain cellular homeostasis. Delineating miRNA-mediated target decay has been thoroughly examined in thousands of studies, yet despite these exhaustive studies, comparatively less is known about how and why miRNAs are directed for decay. Several key observations over the years have noted instances of rapid miRNA turnover, suggesting endogenous means for animals to induce miRNA degradation. Recently, it was revealed that certain targets, so-called target-directed miRNA degradation (TDMD) triggers, can "trigger" miRNA decay through inducing proteolysis of AGO and thereby the bound miRNA. This process is mediated in animals via the ZSWIM8 ubiquitin ligase complex, which is recruited to AGO during engagement with triggers. Since its discovery, several studies have identified that ZSWIM8 and TDMD are indispensable for proper animal development. Given the rapid expansion of this field of study, here, we summarize the key findings that have led to and followed the discovery of ZSWIM8-dependent TDMD. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Conner M Traugot
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, College of Medicine, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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20
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Kotagama K, McJunkin K. Recent advances in understanding microRNA function and regulation in C. elegans. Semin Cell Dev Biol 2024; 154:4-13. [PMID: 37055330 PMCID: PMC10564972 DOI: 10.1016/j.semcdb.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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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21
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Chowdhury S, Sais D, Donnelly S, Tran N. The knowns and unknowns of helminth-host miRNA cross-kingdom communication. Trends Parasitol 2024; 40:176-191. [PMID: 38151361 DOI: 10.1016/j.pt.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that oversee gene modulation. They are integral to cellular functions and can migrate between species, leading to cross-kingdom gene suppression. Recent breakthroughs in helminth genome studies have sparked curiosity about helminth RNA regulators and their ability to regulate genes across species. Growing data indicate that helminth miRNAs have a significant impact on the host's immune system. Specific miRNAs from helminth parasites can merge with the host's miRNA system, implying that parasites could exploit their host's regulatory machinery and function. This review highlights the role of cross-kingdom helminth-derived miRNAs in the interplay between host and parasite, exploring potential routes for their uptake, processing, and consequences in host interaction.
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Affiliation(s)
- Sumaiya Chowdhury
- The School of Life Sciences, University of Technology, Sydney, Australia; School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Dayna Sais
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia
| | - Sheila Donnelly
- The School of Life Sciences, University of Technology, Sydney, Australia.
| | - Nham Tran
- School of Biomedical Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, Ultimo, NSW, Australia.
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22
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Guo LX, Wang L, You ZH, Yu CQ, Hu ML, Zhao BW, Li Y. Biolinguistic graph fusion model for circRNA-miRNA association prediction. Brief Bioinform 2024; 25:bbae058. [PMID: 38426324 PMCID: PMC10939421 DOI: 10.1093/bib/bbae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/19/2024] [Accepted: 01/27/2024] [Indexed: 03/02/2024] Open
Abstract
Emerging clinical evidence suggests that sophisticated associations with circular ribonucleic acids (RNAs) (circRNAs) and microRNAs (miRNAs) are a critical regulatory factor of various pathological processes and play a critical role in most intricate human diseases. Nonetheless, the above correlations via wet experiments are error-prone and labor-intensive, and the underlying novel circRNA-miRNA association (CMA) has been validated by numerous existing computational methods that rely only on single correlation data. Considering the inadequacy of existing machine learning models, we propose a new model named BGF-CMAP, which combines the gradient boosting decision tree with natural language processing and graph embedding methods to infer associations between circRNAs and miRNAs. Specifically, BGF-CMAP extracts sequence attribute features and interaction behavior features by Word2vec and two homogeneous graph embedding algorithms, large-scale information network embedding and graph factorization, respectively. Multitudinous comprehensive experimental analysis revealed that BGF-CMAP successfully predicted the complex relationship between circRNAs and miRNAs with an accuracy of 82.90% and an area under receiver operating characteristic of 0.9075. Furthermore, 23 of the top 30 miRNA-associated circRNAs of the studies on data were confirmed in relevant experiences, showing that the BGF-CMAP model is superior to others. BGF-CMAP can serve as a helpful model to provide a scientific theoretical basis for the study of CMA prediction.
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Affiliation(s)
- Lu-Xiang Guo
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 221116, China
| | - Lei Wang
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, 221116, China
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi’an, 710129, China
| | - Chang-Qing Yu
- College of Information Engineering, Xijing University, Xi’an 710123, China
| | - Meng-Lei Hu
- School of Medicine, Peking University, Beijing, 100091, China
| | - Bo-Wei Zhao
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China
| | - Yang Li
- School of Computer Science and Information Engineering, Hefei University of Technology, Hefei 230601, China
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23
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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24
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Kotagama K, Grimme AL, Braviner L, Yang B, Sakhawala RM, Yu G, Benner LK, Joshua-Tor L, McJunkin K. The catalytic activity of microRNA Argonautes plays a modest role in microRNA star strand destabilization in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.19.524782. [PMID: 36711716 PMCID: PMC9882359 DOI: 10.1101/2023.01.19.524782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many Argonaute proteins can cleave RNA ("slicing") as part of the microRNA-induced silencing complex (miRISC), even though miRNA-mediated target repression is generally independent of target cleavage. Here we use genome editing in C. elegans to examine the role of miRNA-guided slicing in organismal development. In contrast to previous work, slicing-inactivating mutations did not interfere with normal development when introduced by CRISPR. We find that unwinding and decay of miRNA star strands is weakly defective in the absence of slicing, with the largest effect observed in embryos. Argonaute-Like Gene 2 (ALG-2) is more dependent on slicing for unwinding than ALG-1. The miRNAs that displayed the greatest (albeit minor) dependence on slicing for unwinding tend to form stable duplexes with their star strand, and in some cases, lowering duplex stability alleviates dependence on slicing. Gene expression changes were consistent with negligible to moderate loss of function for miRNA guides whose star strand was upregulated, suggesting a reduced proportion of mature miRISC in slicing mutants. 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, a factor in the Target-Directed miRNA Degradation (TDMD) pathway. Overall, this work defines a role for miRNA Argonaute slicing in star strand decay; future work should examine whether this role could have contributed 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
- Current address: Johns Hopkins University Department of Biology, 3400 N. Charles Street, Baltimore, MD 21218, 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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25
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Chen Y, Liu F, Chen X, Li W, Li K, Cai H, Wang S, Wang H, Xu K, Zhang C, Ye S, Shen Y, Mou T, Cai S, Zhou J, Yu J. microRNA-622 upregulates cell cycle process by targeting FOLR2 to promote CRC proliferation. BMC Cancer 2024; 24:26. [PMID: 38166756 PMCID: PMC10763126 DOI: 10.1186/s12885-023-11766-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Epigenetic alterations contribute greatly to the development and progression of colorectal cancer, and effect of aberrant miR-622 expression is still controversial. This study aimed to discover miR-622 regulation in CRC proliferation. METHODS miR-622 expression and prognosis were analyzed in clinical CRC samples from Nanfang Hospital. miR-622 regulation on cell cycle and tumor proliferation was discovered, and FOLR2 was screened as functional target of miR-622 using bioinformatics analysis, which was validated via dual luciferase assay and gain-of-function and loss-of-function experiments both in vitro and in vivo. RESULTS miR-622 overexpression in CRC indicated unfavorable prognosis and it regulated cell cycle to promote tumor growth both in vitro and in vivo. FOLR2 is a specific, functional target of miR-622, which negatively correlates with signature genes in cell cycle process to promote CRC proliferation. CONCLUSIONS miR-622 upregulates cell cycle process by targeting FOLR2 to promote CRC proliferation, proposing a novel mechanism and treatment target in CRC epigenetic regulation of miR-622.
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Affiliation(s)
- Yuehong Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Feng Liu
- Department of Colorectal and Anal Surgery Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, 510515, China
| | - Xinhua Chen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wenyi Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Kejun Li
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Hailang Cai
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shunyi Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Honglei Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ke Xu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Chenxi Zhang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shengzhi Ye
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yunhao Shen
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Tingyu Mou
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shumin Cai
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Critical Care Medicine, The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Jianwei Zhou
- Department of Medical Imaging Center, Nanfang Hospital, Southern Medical University, No. 1838, Guangzhou Avenue North, Guangzhou, 510515, China.
| | - Jiang Yu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Precision Medicine for Gastrointestinal Tumor, The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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26
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Freen-van Heeren JJ. Posttranscriptional Events Orchestrate Immune Homeostasis of CD8 + T Cells. Methods Mol Biol 2024; 2782:65-80. [PMID: 38622392 DOI: 10.1007/978-1-0716-3754-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Maintaining immune homeostasis is instrumental for host health. Immune cells, such as T cells, are instrumental for the eradication of pathogenic bacteria, fungi and viruses. Furthermore, T cells also play a major role in the fight against cancer. Through the formation of immunological memory, a pool of antigen-experienced T cells remains in the body to rapidly protect the host upon reinfection or retransformation. In order to perform their protective function, T cells produce cytolytic molecules, such as granzymes and perforin, and cytokines such as interferon γ and tumor necrosis factor α. Recently, it has become evident that posttranscriptional regulatory events dictate the kinetics and magnitude of cytokine production by murine and human CD8+ T cells. Here, the recent literature regarding the role posttranscriptional regulation plays in maintaining immune homeostasis of antigen-experienced CD8+ T cells is reviewed.
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27
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Verbeeren J, Teixeira J, Garcia SMDA. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism. PLoS Genet 2023; 19:e1011109. [PMID: 38134228 PMCID: PMC10773944 DOI: 10.1371/journal.pgen.1011109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/08/2024] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The Muscleblind-like (MBNL) family is a highly conserved set of RNA-binding proteins (RBPs) that regulate RNA metabolism during the differentiation of various animal tissues. Functional insufficiency of MBNL affects muscle and central nervous system development, and contributes to the myotonic dystrophies (DM), a set of incurable multisystemic disorders. Studies on the regulation of MBNL genes are essential to provide insight into the gene regulatory networks controlled by MBNL proteins and to understand how dysregulation within these networks causes disease. In this study, we demonstrate the evolutionary conservation of an autoregulatory mechanism that governs the function of MBNL proteins by generating two distinct protein isoform types through alternative splicing. Our aim was to further our understanding of the regulatory principles that underlie this conserved feedback loop in a whole-organismal context, and to address the biological significance of the respective isoforms. Using an alternative splicing reporter, our studies show that, during development of the Caenorhabditis elegans central nervous system, the orthologous mbl-1 gene shifts production from long protein isoforms that localize to the nucleus to short isoforms that also localize to the cytoplasm. Using isoform-specific CRISPR/Cas9-generated strains, we showed that expression of short MBL-1 protein isoforms is required for healthy neuromuscular function and neurodevelopment, while expression of long MBL-1 protein isoforms is dispensable, emphasizing a key role for cytoplasmic functionalities of the MBL-1 protein. Furthermore, RNA-seq and lifespan analyses indicated that short MBL-1 isoforms are crucial regulators of miRNA expression and, in consequence, required for normal lifespan. In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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28
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Shah VN, Neumeier J, Huberdeau MQ, Zeitler DM, Bruckmann A, Meister G, Simard MJ. Casein kinase 1 and 2 phosphorylate Argonaute proteins to regulate miRNA-mediated gene silencing. EMBO Rep 2023; 24:e57250. [PMID: 37712432 PMCID: PMC10626430 DOI: 10.15252/embr.202357250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
MicroRNAs (miRNAs) together with Argonaute (AGO) proteins form the core of the RNA-induced silencing complex (RISC) to regulate gene expression of their target RNAs post-transcriptionally. Argonaute proteins are subjected to intensive regulation via various post-translational modifications that can affect their stability, silencing efficacy and specificity for targeted gene regulation. We report here that in Caenorhabditis elegans, two conserved serine/threonine kinases - casein kinase 1 alpha 1 (CK1A1) and casein kinase 2 (CK2) - regulate a highly conserved phosphorylation cluster of 4 Serine residues (S988:S998) on the miRNA-specific AGO protein ALG-1. We show that CK1A1 phosphorylates ALG-1 at sites S992 and S995, while CK2 phosphorylates ALG-1 at sites S988 and S998. Furthermore, we demonstrate that phospho-mimicking mutants of the entire S988:S998 cluster rescue the various developmental defects observed upon depleting CK1A1 and CK2. In humans, we show that CK1A1 also acts as a priming kinase of this cluster on AGO2. Altogether, our data suggest that phosphorylation of AGO within the cluster by CK1A1 and CK2 is required for efficient miRISC-target RNA binding and silencing.
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Affiliation(s)
- Vivek Nilesh Shah
- CHU de Québec‐Université Laval Research Center (Oncology Division)Quebec CityQuebecCanada
- Université Laval Cancer Research CentreQuebec CityQuebecCanada
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA BiologyUniversity of RegensburgRegensburgGermany
| | - Miguel Quévillon Huberdeau
- CHU de Québec‐Université Laval Research Center (Oncology Division)Quebec CityQuebecCanada
- Université Laval Cancer Research CentreQuebec CityQuebecCanada
| | - Daniela M Zeitler
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA BiologyUniversity of RegensburgRegensburgGermany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA BiologyUniversity of RegensburgRegensburgGermany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA BiologyUniversity of RegensburgRegensburgGermany
| | - Martin J Simard
- CHU de Québec‐Université Laval Research Center (Oncology Division)Quebec CityQuebecCanada
- Université Laval Cancer Research CentreQuebec CityQuebecCanada
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29
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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30
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Worner K, Liu Q, Maschhoff KR, Hu W. Identification of RNA-binding proteins' direct effects on gene expression via the degradation tag system. RNA (NEW YORK, N.Y.) 2023; 29:1453-1457. [PMID: 37414463 PMCID: PMC10578468 DOI: 10.1261/rna.079669.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/22/2023] [Indexed: 07/08/2023]
Abstract
RNA-binding proteins (RBPs) are critical regulators of gene expression. An RBP typically binds to multiple mRNAs and modulates their expression. Although loss-of-function experiments on an RBP can infer how it regulates a specific target mRNA, the results are confounded by potential secondary effects due to the attenuation of all other interactions of the target RBP. For example, regarding the interaction between Trim71, an evolutionarily conserved RBP, and Ago2 mRNA, although Trim71 binds to Ago2 mRNA and overexpression of Trim71 represses Ago2 mRNA translation, it is puzzling that AGO2 protein levels are not altered in the Trim71 knockdown/knockout cells. To address this, we adapted the dTAG (degradation tag) system for determining the direct effects of the endogenous Trim71. Specifically, we knocked in the dTAG to the Trim71 locus, enabling inducible rapid Trim71 protein degradation. We observed that following the induction of Trim71 degradation, Ago2 protein levels first increased, confirming the Trim71-mediated repression, and then returned to the original levels after 24 h post-induction, revealing that the secondary effects from the Trim71 knockdown/knockout counteracted its direct effects on Ago2 mRNA. These results highlight a caveat in interpreting the results from loss-of-function studies on RBPs and provide a method to determine the primary effect(s) of RBPs on their target mRNAs.
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Affiliation(s)
- Kailey Worner
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Katharine R Maschhoff
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
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31
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Hasiuk M, Dölz M, Marone R, Jeker LT. Leveraging microRNAs for cellular therapy. Immunol Lett 2023; 262:27-35. [PMID: 37660892 DOI: 10.1016/j.imlet.2023.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Owing to Karl Landsteiner's discovery of blood groups, blood transfusions became safe cellular therapies in the early 1900s. Since then, cellular therapy made great advances from transfusions with unmodified cells to today's commercially available chimeric antigen receptor (CAR) T cells requiring complex manufacturing. Modern cellular therapy products can be improved using basic knowledge of cell biology and molecular genetics. Emerging genome engineering tools are becoming ever more versatile and precise and thus catalyze rapid progress towards programmable therapeutic cells that compute input and respond with defined output. Despite a large body of literature describing important functions of non-coding RNAs including microRNAs (miRNAs), the vast majority of cell engineering efforts focuses on proteins. However, miRNAs form an important layer of posttranscriptional regulation of gene expression. Here, we highlight examples of how miRNAs can successfully be incorporated into engineered cellular therapies.
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Affiliation(s)
- Marko Hasiuk
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Marianne Dölz
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland; Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland.
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32
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Burgon PG, Weldrick JJ, Talab OMSA, Nadeer M, Nomikos M, Megeney LA. Regulatory Mechanisms That Guide the Fetal to Postnatal Transition of Cardiomyocytes. Cells 2023; 12:2324. [PMID: 37759546 PMCID: PMC10528641 DOI: 10.3390/cells12182324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Heart disease remains a global leading cause of death and disability, necessitating a comprehensive understanding of the heart's development, repair, and dysfunction. This review surveys recent discoveries that explore the developmental transition of proliferative fetal cardiomyocytes into hypertrophic postnatal cardiomyocytes, a process yet to be well-defined. This transition is key to the heart's growth and has promising therapeutic potential, particularly for congenital or acquired heart damage, such as myocardial infarctions. Although significant progress has been made, much work is needed to unravel the complex interplay of signaling pathways that regulate cardiomyocyte proliferation and hypertrophy. This review provides a detailed perspective for future research directions aimed at the potential therapeutic harnessing of the perinatal heart transitions.
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Affiliation(s)
- Patrick G. Burgon
- Department of Chemistry and Earth Sciences, College of Arts and Sciences, Qatar University, Doha P.O. Box 2713, Qatar
| | - Jonathan J. Weldrick
- Department of Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.J.W.); (L.A.M.)
| | | | - Muhammad Nadeer
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (O.M.S.A.T.)
| | - Michail Nomikos
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (O.M.S.A.T.)
| | - Lynn A. Megeney
- Department of Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (J.J.W.); (L.A.M.)
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
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33
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Li WA, Efendizade A, Ding Y. The role of microRNA in neuronal inflammation and survival in the post ischemic brain: a review. Neurol Res 2023; 45:1-9. [PMID: 28552032 DOI: 10.1080/01616412.2017.1327505] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/15/2017] [Indexed: 12/21/2022]
Abstract
Each year, more than 790 000 people in the United States suffer from a stroke. Although progress has been made in diagnosis and treatment of ischemic stroke (IS), new therapeutic interventions to protect the brain during an ischemic insult is highly needed. MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression post-transcriptionally. Growing evidence suggests that miRNAs have a profound impact on ischemic stroke progression and are potential targets of novel treatments. Notably, inflammatory pathways play an important role in the pathogenesis of ischemic stroke and its pathophysiologic progression. Experimental and clinical studies have illustrated that inflammatory molecular events collaboratively contribute to neuronal and glial cell survival, edema formation and regression, and vascular integrity. In the present review, we examine recent discoveries regarding miRNAs and their roles in post-ischemic stroke neuropathogenesis.
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Affiliation(s)
- William A Li
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
| | - Aslan Efendizade
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
| | - Yuchuan Ding
- Department of Neurosurgery, Wayne State University School of Medicine , Detroit, MI, USA
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Abbas Syed R, Davey MG, Richard V, Miller N, Kerin MJ. Biological Implications of MicroRNAs as Regulators and Biomarkers of Therapeutic Toxicities in Breast Cancer. Int J Mol Sci 2023; 24:12694. [PMID: 37628874 PMCID: PMC10454054 DOI: 10.3390/ijms241612694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/29/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Contemporary breast cancer management includes surgical resection combined with a multimodal approach, including chemotherapy, radiotherapy, endocrine therapy, and targeted therapies. Breast cancer treatment is now personalised in accordance with disease and host factors, which has translated to enhanced outcomes for the vast majority of patients. Unfortunately, the treatment of the disease involves patients developing treatment-induced toxicities, with cardiovascular and metabolic side effects having negative implications for long-term quality-of-life metrics. MicroRNAs (miRNAs) are a class of small non-coding ribonucleic acids that are 17 to 25 nucleotides in length, which have utility in modifying genetic expression by working at a post-transcriptional cellular level. miRNAs have involvement in modulating breast cancer development, which is well described, with these biomarkers acting as important regulators of disease, as well as potential diagnostic and therapeutic biomarkers. This review focuses on highlighting the role of miRNAs as regulators and biomarkers of disease, particularly in breast cancer management, with a specific mention of the potential value of miRNAs in predicting treatment-related cardiovascular toxicity.
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Affiliation(s)
- Raza Abbas Syed
- Discipline of Surgery, Lambe Institute for Translational Research, University of Galway, H91 YR71 Galway, Ireland; (M.G.D.)
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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, MD.) 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] [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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Sharma S, Sett S, Das T, Prasad A, Prasad M. Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107852. [PMID: 37356385 DOI: 10.1016/j.plaphy.2023.107852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/06/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.
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Affiliation(s)
| | - Susmita Sett
- National Institute of Plant Genome Research, New Delhi, India.
| | - Tuhin Das
- National Institute of Plant Genome Research, New Delhi, India.
| | - Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India.
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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Chen T, Yuan H, Qiao H, Jiang S, Zhang W, Xiong Y, Fu H, Jin S. Mn-XRN1 Has an Inhibitory Effect on Ovarian Reproduction in Macrobrachium nipponense. Genes (Basel) 2023; 14:1454. [PMID: 37510358 PMCID: PMC10380074 DOI: 10.3390/genes14071454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
XRN1 is an exoribonuclease that degrades mRNA in the cytoplasm along the 5'-3' direction. A previous study indicated that it may be involved in the reproduction of Macrobrachium nipponense. Quantitative real-time PCR was used to detect the spatiotemporal expression pattern of Mn-XRN1. At the tissue level, Mn-XRN1 was significantly expressed in the ovary. During development, Mn-XRN1 was significantly expressed at the CS stage of the embryo, on the 10th day post-larval and in the O2 stage of ovarian reproduction. The in situ hybridization results showed the location of Mn-XRN1 in the ovary. The expression of Mn-VASA was significantly increased after in vivo injection of Mn-XRN1 dsRNA. This suggests that Mn-XRN1 negatively regulates the expression of Mn-VASA. Furthermore, we counted the number of M. nipponense at various stages of ovarian reproduction on different days after RNAi. The results showed that ovarian development was significantly accelerated. In general, the results of the present study indicate that Mn-XRN1 has an inhibitory effect on the ovarian maturation of M. nipponense. The inhibitory effect might be through negative regulation of Mn-VASA.
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Affiliation(s)
- Tianyong Chen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Huwei Yuan
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Hui Qiao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Sufei Jiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Wenyi Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Yiwei Xiong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongtuo Fu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Shubo Jin
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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Gao K, Li X, Ni J, Wu B, Guo J, Zhang R, Wu G. Non-coding RNAs in enzalutamide resistance of castration-resistant prostate cancer. Cancer Lett 2023; 566:216247. [PMID: 37263338 DOI: 10.1016/j.canlet.2023.216247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
Enzalutamide (Enz) is a next-generation androgen receptor (AR) antagonist used to treat castration-resistant prostate cancer (CRPC). Unfortunately, the relapsing nature of CRPC results in the development of Enz resistance in many patients. Non-coding RNAs (ncRNAs) are RNA molecules that do not encode proteins, which include microRNAs (miRNA), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and other ncRNAs with known and unknown functions. Recently, dysregulation of ncRNAs in CRPC, particularly their regulatory function in drug resistance, has attracted more and more attention. Herein, we introduce the roles of dysregulation of different ncRNAs subclasses in the development of CRPC progression and Enz resistance. Recently determined mechanisms of Enz resistance are discussed, focusing mainly on the role of AR-splice variant-7 (AR-V7), mutations, circRNAs and lncRNAs that act as miRNA sponges. Also, the contributions of epithelial-mesenchymal transition and glucose metabolism to Enz resistance are discussed. We summarize the different mechanisms of miRNAs, lncRNAs, and circRNAs in the progression of CRPC and Enz resistance, and highlight the prospect of future therapeutic strategies against Enz resistance.
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MESH Headings
- Male
- Humans
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/therapeutic use
- RNA, Circular/genetics
- Drug Resistance, Neoplasm/genetics
- Neoplasm Recurrence, Local
- Nitriles
- Androgen Receptor Antagonists/therapeutic use
- MicroRNAs/genetics
- MicroRNAs/therapeutic use
- Cell Line, Tumor
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Affiliation(s)
- Ke Gao
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China; The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Xiaoshun Li
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Jianxin Ni
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Bin Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Jiaheng Guo
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China; The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Rui Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China; The State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Guojun Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
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Jarallah SJ, Aldossary AM, Tawfik EA, Altamimi RM, Alsharif WK, Alzahrani NM, As Sobeai HM, Qamar W, Alfahad AJ, Alshabibi MA, Alqahtani SH, Alshehri AA, Almughem FA. GL67 lipid-based liposomal formulation for efficient siRNA delivery into human lung cancer cells. Saudi Pharm J 2023; 31:1139-1148. [PMID: 37273265 PMCID: PMC10236467 DOI: 10.1016/j.jsps.2023.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/14/2023] [Indexed: 06/06/2023] Open
Abstract
The efficient delivery of small interfering RNA (siRNA) to the targeted cells significantly affects the regulation of the overexpressed proteins involved in the progression of several genetic diseases. SiRNA molecules in naked form suffer from low internalization across the cell membrane, high susceptibility to degradation by nuclease enzyme and low stability, which hinder their efficacy. Therefore, there is an urge to develop a delivery system that can protect siRNA from degradation and facilitate their uptake across the cell membrane. In this study, the cationic lipid (GL67) was exploited, in addition to DC-Chol and DOPE lipids, to design an efficient liposomal nanocarrier for siRNA delivery. The physiochemical characterizations demonstrated that the molar ratio of 3:1 has proper particle size measurements from 144 nm to 332 nm and zeta potential of -9 mV to 47 mV that depends on the ratio of the GL67 in the liposomal formulation. Gel retardation assay exhibited that increasing the percentage of GL67 in the formulations has a good impact on the encapsulation efficiency compared to DC-Chol. The optimal formulations of the 3:1 M ratio also showed high metabolic activity against A549 cells following a 24 h cell exposure. Flow cytometry findings showed that the highest GL67 lipid ratio (100 % GL67 and 0 % DC-Chol) had the highest percentage of cellular uptake. The lipoplex nanocarriers based on GL67 lipid could potentially influence treating genetic diseases owing to the high internalization efficiency and safety profile.
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Affiliation(s)
- Somayah J. Jarallah
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Ahmad M. Aldossary
- Wellness and Preventative Medicine Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Essam A. Tawfik
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Reem M. Altamimi
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Wijdan K. Alsharif
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Nouf M. Alzahrani
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Homood M. As Sobeai
- Pharmacology and Toxicology Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Wajhul Qamar
- Pharmacology and Toxicology Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed J. Alfahad
- Bioengineering Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Manal A. Alshabibi
- Healthy Aging Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Sarah H. Alqahtani
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Abdullah A. Alshehri
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Fahad A. Almughem
- Advanced Diagnostics and Therapeutics Institute, Health Sector, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
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40
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Munkhzul C, Lee JM, Kim B, Nguyen TTM, Ginting RP, Jeong D, Kim YK, Lee MW, Lee M. H19X-encoded microRNAs induced by IL-4 in adipocyte precursors regulate proliferation to facilitate differentiation. Biol Direct 2023; 18:32. [PMID: 37322541 PMCID: PMC10273709 DOI: 10.1186/s13062-023-00388-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
Adipose tissue, an organ critical for systemic energy homeostasis, is influenced by type 2 immunity in its development and function. The type 2 cytokine interleukin (IL)-4 induces the proliferation of bipotential adipocyte precursors (APs) in white fat tissue and primes these cells for differentiation into beige adipocytes, which are specialized for thermogenesis. However, the underlying mechanisms have not yet been comprehensively examined. Here, we identified six microRNA (miRNA) genes upregulated upon IL-4 stimulation in APs, miR-322, miR-503, miR-351, miR-542, miR-450a, and miR-450b; these are encoded in the H19X locus of the genome. Their expression is positively regulated by the transcription factor Klf4, whose expression also increases upon IL-4 stimulation. These miRNAs shared a large set of target genes, of which 381 genes were downregulated in mRNA expression upon IL-4 stimulation and enriched in Wnt signaling pathways. Two genes with downregulated expression, Ccnd1 and Fzd6, were repressed by H19X-encoded miRNAs. Additionally, the Wnt signaling activator LiCl downregulated the expression of this group of miRNAs in APs, indicating that Wnt signaling-related genes and these miRNAs form a double-negative feedback regulatory loop. This miRNA/Wnt feedback regulation modulated the elevated proliferation of APs induced by IL-4 stimulation and contributed to priming them for beige adipocyte differentiation. Moreover, the aberrant expression of these miRNAs attenuates the differentiation of APs into beige adipocytes. Collectively, our results suggest that H19X-encoded miRNAs facilitate the transition of APs from proliferation to differentiation in the IL-4-mediated regulation.
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Affiliation(s)
- Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Ji-Min Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Boseon Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Thi Thanh My Nguyen
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Rehna Paula Ginting
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Dahee Jeong
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Hwasun, 58128, Korea
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea.
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea.
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan, 31151, Korea.
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, 31151, Korea.
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Wang W, Zhang F, Guo K, Xu J, Zhao P, Xia Q. CRISPR/Cas9-mediated gene editing of the let-7 seed sequence improves silk yield in the silkworm, Bombyx mori. Int J Biol Macromol 2023:124793. [PMID: 37182624 DOI: 10.1016/j.ijbiomac.2023.124793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023]
Abstract
Body size and silk protein synthesis ability are two crucial aspects of artificial selection in silkworm breeding; however, the role of genes in both pathways remains unknown. To determine whether let-7 microRNA could regulate larval development and silk gland growth simultaneously, we designed a guide RNA to edit let-7 using the CRISPR/Cas9 system. The indels predominantly appeared in the let-7 seed region, and the vast majority of the mutations were small-fragment deletions. Loss of let-7 function prolonged the fifth larval period, and substantially increased body weight during the wandering stage, but it resulted in developmental arrest during the pupal-moth transition. let-7 systemic knock down promoted silk gland growth and increased silk yield by >50 %, with efficiency significantly higher than in tissue-specific edited individuals. Hormone signaling and cell cycle pathway genes were activated in different patterns in the body and silk gland, implying that let-7 may regulate different target genes to play role in tissue growth. In summary, we first report that conditional knock down let-7 promoting the simultaneous growth of body and silk gland, greatly improve silk yield in the silkworm.
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Affiliation(s)
- Wei Wang
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, PR China; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, PR China
| | - Fan Zhang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China
| | - Kaiyu Guo
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, PR China; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, PR China
| | - Jiahui Xu
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, PR China
| | - Ping Zhao
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, PR China; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, PR China
| | - Qingyou Xia
- Biological Science Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, 400715 Chongqing, PR China; State Key Laboratory of Resource Insects, Southwest University, Chongqing 400715, PR China; Key Laboratory for Germplasm Creation in Upper Reaches of the Yangtze River, Ministry of Agriculture and Rural Affairs, 400715 Chongqing, PR China.
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Jarva T, Zhang J, Flynt A. MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539760. [PMID: 37214880 PMCID: PMC10197562 DOI: 10.1101/2023.05.07.539760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
RNA interference (RNAi) is mediated by small (20-30 nucleotide) RNAs that are produced by complex processing pathways. In animals, three main classes are recognized: microRNAs (miRNAs), small-interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs). Understanding of small RNA pathways has benefited from genetic models where key enzymatic events were identified that lead to stereotypical positioning of small RNAs relative to precursor transcripts. Increasingly there is interest in using RNAi in non-model systems due to ease of generating synthetic small RNA precursors for research and biotechnology. Unfortunately, small RNAs are often rapidly evolving, requiring investigation of a species' endogenous small RNAs prior to deploying an RNAi approach. This can be accomplished through small non-coding RNA sequencing followed by applying various computational tools; however, the complexity and separately maintained packages lead to significant challenges for annotating global small RNA populations. To address this need, we developed a simple and efficient R package (MiSiPi-Rna) which can be used to characterize pre-selected loci with plots and statistics, aiding researchers understanding RNAi biology specific to their target species. Additionally, MiSiPi-Rna pioneers several computational approaches to identifying Dicer processing to assist annotation of miRNA and siRNA.
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43
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Son S, Kim B, Yang J, Kim VN. Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing. Genes Dev 2023; 37:383-397. [PMID: 37236670 PMCID: PMC10270192 DOI: 10.1101/gad.350275.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/24/2023] [Indexed: 05/28/2023]
Abstract
DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well documented, the contribution of N-terminal proline-rich disordered domain (PRD) remains elusive. Here we show that the PRD promotes the processing of miRNA hairpins located within introns. We identified a DROSHA isoform (p140) lacking the PRD, which is produced by proteolytic cleavage. Small RNA sequencing revealed that p140 is significantly impaired in the maturation of intronic miRNAs. Consistently, our minigene constructs demonstrated that PRD enhances the processing of intronic hairpins, but not those in exons. Splice site mutations did not affect the PRD's enhancing effect on intronic constructs, suggesting that the PRD acts independently of splicing reaction by interacting with sequences residing within introns. The N-terminal regions from zebrafish and Xenopus DROSHA can replace the human counterpart, indicating functional conservation despite poor sequence alignment. Moreover, we found that rapidly evolving intronic miRNAs are generally more dependent on PRD than conserved ones, suggesting a role of PRD in miRNA evolution. Our study reveals a new layer of miRNA regulation mediated by a low-complexity disordered domain that senses the genomic contexts of miRNA loci.
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Affiliation(s)
- Soomin Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Baekgyu Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea;
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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Quesnelle DC, Bendena WG, Chin-Sang ID. A Compilation of the Diverse miRNA Functions in Caenorhabditis elegans and Drosophila melanogaster Development. Int J Mol Sci 2023; 24:ijms24086963. [PMID: 37108126 PMCID: PMC10139094 DOI: 10.3390/ijms24086963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs are critical regulators of post-transcriptional gene expression in a wide range of taxa, including invertebrates, mammals, and plants. Since their discovery in the nematode, Caenorhabditis elegans, miRNA research has exploded, and they are being identified in almost every facet of development. Invertebrate model organisms, particularly C. elegans, and Drosophila melanogaster, are ideal systems for studying miRNA function, and the roles of many miRNAs are known in these animals. In this review, we compiled the functions of many of the miRNAs that are involved in the development of these invertebrate model species. We examine how gene regulation by miRNAs shapes both embryonic and larval development and show that, although many different aspects of development are regulated, several trends are apparent in the nature of their regulation.
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Affiliation(s)
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ian D Chin-Sang
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
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Duan Y, Li L, Panzade GP, Piton A, Zinovyeva A, Ambros V. Modeling neurodevelopmental disorder-associated hAGO1 mutations in C. elegans Argonaute ALG-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535748. [PMID: 37066388 PMCID: PMC10104039 DOI: 10.1101/2023.04.06.535748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
MicroRNAs (miRNA) are endogenous non-coding RNAs important for post-transcriptional regulation of gene expression. miRNAs associate with Argonaute proteins to bind to the 3' UTR of target genes and confer target repression. Recently, multiple de novo coding variants in the human Argonaute gene AGO1 ( hAGO1 ) have been reported to cause a neurodevelopmental disorder (NDD) with intellectual disability (ID). Most of the altered amino acids are conserved between the miRNA-associated Argonautes in H. sapiens and C. elegans , suggesting the hAGO1 mutations could disrupt evolutionarily conserved functions in the miRNA pathway. To investigate how the hAGO1 mutations may affect miRNA biogenesis and/or functions, we genetically modeled four of the hAGO1 de novo variants (referred to as NDD mutations) by introducing the identical mutations to the C. elegans hAGO1 homolog, alg-1 . This array of mutations caused distinct effects on C. elegans miRNA functions, miRNA populations, and downstream gene expression, indicative of profound alterations in aspects of miRNA processing and miRISC formation and/or activity. Specifically, we found that the alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles both in terms of overall abundances and association with mutant ALG-1. We also observed allele-specific profiles of gene expression with altered translational efficiency and/or mRNA abundance. The sets of perturbed genes include human homologs whose dysfunction is known to cause NDD. We anticipate that these cross-clade genetic studies may advance the understanding of fundamental Argonaute functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.
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Tan S, Wu W, Ge X, Zhang Y, Han J, Guo X, Zhou L, Yang H. A novel strategy to attenuate porcine reproductive and respiratory syndrome virus by inhibiting viral replication in the target pulmonary alveolar macrophages via hematopoietic-specific miR-142. ONE HEALTH ADVANCES 2023; 1:3. [PMID: 37521530 PMCID: PMC10060136 DOI: 10.1186/s44280-023-00002-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 08/01/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important pathogen for the global pork industry. Although modified live virus (MLV) vaccines are commonly used for PRRSV prevention and control, they still carry a risk of infecting the host and replicating in target cells, thereby increasing the likehood of virus recombination and reversion to virulence. In this study, we inserted the target sequence of miR-142 into the nsp2 hypervariable region of PRRSV to inhibit viral replication in its host cells of pigs, with the aim of achieving virus attenuation. The chimeric virus RvJX-miR-142t was successfully rescued and retained its growth characteristics in MARC-145 cells. Furthermore, it did not replicate in MARC-145 cells transfected with miRNA-142 mimic. We also observed limited replication ability of RvJX-miR-142t in pulmonary alveolar macrophages, which are the main cell types that PRRSV infects. Our animal inoculation study showed that pigs infected with RvJX-miR-142t displayed less severe clinical symptoms, lower viremia titers, lighter lung lesions, and significantly lower mortality rates during the first 7 days post-inoculation, in comparison to pigs infected with the backbone virus RvJXwn. We detected a partially deletion of the miR-142 target sequence in the RvJX-miR-142t genome at 14 dpi. It is highly possible that the reversion of viral virulence observed in the later timepoints of our animal experiment was caused by that. Our study provided a new strategy for attenuating PRRSV and confirmed its effectiveness. However, further studies are necessary to increase the stability of this virus under host selection pressure.
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Affiliation(s)
- Shaoyuan Tan
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Weixin Wu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xinna Ge
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yongning Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jun Han
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xin Guo
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hanchun Yang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Gao Y, Zhu Y, Sun Q, Chen D. Argonaute-dependent ribosome-associated protein quality control. Trends Cell Biol 2023; 33:260-272. [PMID: 35981909 DOI: 10.1016/j.tcb.2022.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Ribosome-associated protein quality control (RQC) is a protein surveillance mechanism that eliminates defective nascent polypeptides. The E3 ubiquitin ligase, Ltn1, is a key regulator of RQC that targets substrates for ubiquitination. Argonaute proteins (AGOs) are central players in miRNA-mediated gene silencing and have recently been shown to also regulate RQC by facilitating Ltn1. Therefore, AGOs directly coordinate post-transcriptional gene silencing and RQC, ensuring efficient gene silencing. We summarize the principles of RQC and the functions of AGOs in miRNA-mediated gene silencing, and discuss how AGOs associate with the endoplasmic reticulum (ER) to assist Ltn1 in controlling RQC. We highlight that RQC not only eliminates defective nascent polypeptides but also removes unwanted protein products when AGOs participate.
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Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China.
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Nguyen TL, Nguyen TD, Ngo MK, Nguyen TA. Dissection of the Caenorhabditis elegans Microprocessor. Nucleic Acids Res 2023; 51:1512-1527. [PMID: 36598924 PMCID: PMC9976908 DOI: 10.1093/nar/gkac1170] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 01/05/2023] Open
Abstract
Microprocessor (MP) is a complex involved in initiating the biogenesis of microRNAs (miRNAs) by cleaving primary microRNAs (pri-miRNAs). miRNAs are small single-stranded RNAs that play a key role in the post-transcriptional regulation of gene expression. Thus, understanding the molecular mechanism of MP is critical for interpreting the roles of miRNAs in normal cellular processes and during the onset of various diseases. MP comprises a ribonuclease enzyme, DROSHA, and a dimeric RNA-binding protein, which is called DGCR8 in humans and Pasha in Caenorhabditis elegans. DROSHA cleaves stem-loop structures located within pri-miRNAs to generate pre-miRNAs. Although the molecular mechanism of human MP (hMP; hDROSHA-DGCR8) is well understood, that of Caenorhabditis elegans MP (cMP; cDrosha-Pasha) is still largely unknown. Here, we reveal the molecular mechanism of cMP and show that it is distinct from that of hMP. We demonstrate that cDrosha and Pasha measure ∼16 and ∼25 bp along a pri-miRNA stem, respectively, and they work together to determine the site of cMP cleavage in pri-miRNAs. We also demonstrate the molecular basis for their substrate measurement. Thus, our findings reveal a previously unknown molecular mechanism of cMP; demonstrate the differences between the mechanisms of hMP and cMP; and provide a foundation for revealing the mechanisms regulating miRNA expression in different animal species.
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Affiliation(s)
- Thuy Linh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Trung Duc Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Minh Khoa Ngo
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science & Technology, Hong Kong, China
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Yang M, Zhang Y, Li M, Liu X, Darvishi M. The various role of microRNAs in breast cancer angiogenesis, with a special focus on novel miRNA-based delivery strategies. Cancer Cell Int 2023; 23:24. [PMID: 36765409 PMCID: PMC9912632 DOI: 10.1186/s12935-022-02837-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 02/12/2023] Open
Abstract
After skin malignancy, breast cancer is the most widely recognized cancer detected in women in the United States. Breast cancer (BCa) can happen in all kinds of people, but it's much more common in women. One in four cases of cancer and one in six deaths due to cancer are related to breast cancer. Angiogenesis is an essential factor in the growth of tumors and metastases in various malignancies. An expanded level of angiogenesis is related to diminished endurance in BCa patients. This function assumes a fundamental part inside the human body, from the beginning phases of life to dangerous malignancy. Various factors, referred to as angiogenic factors, work to make a new capillary. Expanding proof demonstrates that angiogenesis is managed by microRNAs (miRNAs), which are small non-coding RNA with 19-25 nucleotides. MiRNA is a post-transcriptional regulator of gene expression that controls many critical biological processes. Endothelial miRNAs, referred to as angiomiRs, are probably concerned with tumor improvement and angiogenesis via regulation of pro-and anti-angiogenic factors. In this article, we reviewed therapeutic functions of miRNAs in BCa angiogenesis, several novel delivery carriers for miRNA-based therapeutics, as well as CRISPR/Cas9 as a targeted therapy in breast cancer.
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Affiliation(s)
- Min Yang
- College of Traditional Chinese Medicine, Jilin Agricultural Science and Technology University, Jilin, 132101 China
| | - Ying Zhang
- College of Traditional Chinese Medicine, Jilin Agricultural Science and Technology University, Jilin, 132101 China
| | - Min Li
- College of Traditional Chinese Medicine, Jilin Agricultural Science and Technology University, Jilin, 132101 China
| | - Xinglong Liu
- College of Traditional Chinese Medicine, Jilin Agricultural Science and Technology University, Jilin, 132101 China
| | - Mohammad Darvishi
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
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