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Pamula MC, Lehmann R. How germ granules promote germ cell fate. Nat Rev Genet 2024:10.1038/s41576-024-00744-8. [PMID: 38890558 DOI: 10.1038/s41576-024-00744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Germ cells are the only cells in the body capable of giving rise to a new organism, and this totipotency hinges on their ability to assemble membraneless germ granules. These specialized RNA and protein complexes are hallmarks of germ cells throughout their life cycle: as embryonic germ granules in late oocytes and zygotes, Balbiani bodies in immature oocytes, and nuage in maturing gametes. Decades of developmental, genetic and biochemical studies have identified protein and RNA constituents unique to germ granules and have implicated these in germ cell identity, genome integrity and gamete differentiation. Now, emerging research is defining germ granules as biomolecular condensates that achieve high molecular concentrations by phase separation, and it is assigning distinct roles to germ granules during different stages of germline development. This organization of the germ cell cytoplasm into cellular subcompartments seems to be critical not only for the flawless continuity through the germline life cycle within the developing organism but also for the success of the next generation.
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Affiliation(s)
| | - Ruth Lehmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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3
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Luo Y, He P, Kanrar N, Fejes Toth K, Aravin AA. Maternally inherited siRNAs initiate piRNA cluster formation. Mol Cell 2023; 83:3835-3851.e7. [PMID: 37875112 PMCID: PMC10846595 DOI: 10.1016/j.molcel.2023.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/08/2023] [Accepted: 09/26/2023] [Indexed: 10/26/2023]
Abstract
PIWI-interacting RNAs (piRNAs) guide transposable element repression in animal germ lines. In Drosophila, piRNAs are produced from heterochromatic loci, called piRNA clusters, which act as information repositories about genome invaders. piRNA generation by dual-strand clusters depends on the chromatin-bound Rhino-Deadlock-Cutoff (RDC) complex, which is deposited on clusters guided by piRNAs, forming a positive feedback loop in which piRNAs promote their own biogenesis. However, how piRNA clusters are formed before cognate piRNAs are present remains unknown. Here, we report spontaneous de novo piRNA cluster formation from repetitive transgenic sequences. Cluster formation occurs over several generations and requires continuous trans-generational maternal transmission of small RNAs. We discovered that maternally supplied small interfering RNAs (siRNAs) trigger de novo cluster activation in progeny. In contrast, siRNAs are dispensable for cluster function after its establishment. These results reveal an unexpected interplay between the siRNA and piRNA pathways and suggest a mechanism for de novo piRNA cluster formation triggered by siRNAs.
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Affiliation(s)
- Yicheng Luo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peng He
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nivedita Kanrar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katalin Fejes Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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4
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Ninova M, Holmes H, Lomenick B, Fejes Tóth K, Aravin AA. Pervasive SUMOylation of heterochromatin and piRNA pathway proteins. CELL GENOMICS 2023; 3:100329. [PMID: 37492097 PMCID: PMC10363806 DOI: 10.1016/j.xgen.2023.100329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 07/27/2023]
Abstract
Genome regulation involves complex protein interactions that are often mediated through post-translational modifications (PTMs). SUMOylation-modification by the small ubiquitin-like modifier (SUMO)-has been implicated in numerous essential processes in eukaryotes. In Drosophila, SUMO is required for viability and fertility, with its depletion from ovaries leading to heterochromatin loss and ectopic transposon and gene activation. Here, we developed a proteomics-based strategy to uncover the Drosophila ovarian "SUMOylome," which revealed that SUMOylation is widespread among proteins involved in heterochromatin regulation and different aspects of the Piwi-interacting small RNA (piRNA) pathway that represses transposons. Furthermore, we show that SUMOylation of several piRNA pathway proteins occurs in a Piwi-dependent manner. Together, these data highlight broad implications of protein SUMOylation in epigenetic regulation and indicate novel roles of this modification in the cellular defense against genomic parasites. Finally, this work provides a resource for the study of SUMOylation in other biological contexts in the Drosophila model.
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Affiliation(s)
- Maria Ninova
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Hannah Holmes
- Department of Biochemistry, University of California Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA 92521, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory of the Beckman Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
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5
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Pathania AS. Crosstalk between Noncoding RNAs and the Epigenetics Machinery in Pediatric Tumors and Their Microenvironment. Cancers (Basel) 2023; 15:2833. [PMID: 37345170 DOI: 10.3390/cancers15102833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
According to the World Health Organization, every year, an estimated 400,000+ new cancer cases affect children under the age of 20 worldwide. Unlike adult cancers, pediatric cancers develop very early in life due to alterations in signaling pathways that regulate embryonic development, and environmental factors do not contribute much to cancer development. The highly organized complex microenvironment controlled by synchronized gene expression patterns plays an essential role in the embryonic stages of development. Dysregulated development can lead to tumor initiation and growth. The low mutational burden in pediatric tumors suggests the predominant role of epigenetic changes in driving the cancer phenotype. However, one more upstream layer of regulation driven by ncRNAs regulates gene expression and signaling pathways involved in the development. Deregulation of ncRNAs can alter the epigenetic machinery of a cell, affecting the transcription and translation profiles of gene regulatory networks required for cellular proliferation and differentiation during embryonic development. Therefore, it is essential to understand the role of ncRNAs in pediatric tumor development to accelerate translational research to discover new treatments for childhood cancers. This review focuses on the role of ncRNA in regulating the epigenetics of pediatric tumors and their tumor microenvironment, the impact of their deregulation on driving pediatric tumor progress, and their potential as effective therapeutic targets.
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Affiliation(s)
- Anup S Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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6
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Yao Y, Li Y, Zhu X, Zhao C, Yang L, Huang X, Wang L. The emerging role of the piRNA/PIWI complex in respiratory tract diseases. Respir Res 2023; 24:76. [PMID: 36915129 PMCID: PMC10010017 DOI: 10.1186/s12931-023-02367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
PIWI-interacting RNA (piRNA) is a class of recently discovered small non-coding RNA molecules with a length of 18-33 nt that interacts with the PIWI protein to form the piRNA/PIWI complex. The PIWI family is a subfamily of Argonaute (AGO) proteins that also contain the AGO family which bind to microRNA (miRNA). Recently studies indicate that piRNAs are not specific to in the mammalian germline, they are also expressed in a tissue-specific manner in a variety of human tissues and participated in various of diseases, such as cardiovascular, neurological, and urinary tract diseases, and are especially prevalent in malignant tumors in these systems. However, the functions and abnormal expression of piRNAs in respiratory tract diseases and their underlying mechanisms remain incompletely understood. In this review, we discuss current studies summarizing the biogenetic processes, functions, and emerging roles of piRNAs in respiratory tract diseases, providing a reference value for future piRNA research.
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Affiliation(s)
- Yizhu Yao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yaozhe Li
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Xiayan Zhu
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Chengguang Zhao
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.,School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lehe Yang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Xiaoying Huang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Liangxing Wang
- Division of Pulmonary Medicine, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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7
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Nguyen TTM, Munkhzul C, Kim J, Kyoung Y, Vianney M, Shin S, Ju S, Pham-Bui HA, Kim J, Kim JS, Lee M. In vivo profiling of the Zucchini proximal proteome in the Drosophila ovary. Development 2023; 150:286990. [PMID: 36762624 DOI: 10.1242/dev.201220] [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: 08/23/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs that play a conserved role in genome defense. The piRNA processing pathway is dependent on the sequestration of RNA precursors and protein factors in specific subcellular compartments. Therefore, a highly resolved spatial proteomics approach can help identify the local interactions and elucidate the unknown aspects of piRNA biogenesis. Herein, we performed TurboID proximity labeling to investigate the interactome of Zucchini (Zuc), a key factor of piRNA biogenesis in germline cells and somatic follicle cells of the Drosophila ovary. Quantitative mass spectrometry analysis of biotinylated proteins defined the Zuc-proximal proteome, including the well-known partners of Zuc. Many of these were enriched in the outer mitochondrial membrane (OMM), where Zuc was specifically localized. The proximal proteome of Zuc showed a distinct set of proteins compared with that of Tom20, a representative OMM protein, indicating that chaperone function-related and endomembrane system/vesicle transport proteins are previously unreported interacting partners of Zuc. The functional relevance of several candidates in piRNA biogenesis was validated by derepression of transposable elements after knockdown. Our results present potential Zuc-interacting proteins, suggesting unrecognized biological processes.
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Affiliation(s)
- Thi Thanh My Nguyen
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Choijamts Munkhzul
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeonju Kyoung
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Michele Vianney
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seonmin Ju
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hoang-Anh Pham-Bui
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan 31151, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, 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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8
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Horjales S, Li Calzi M, Francia ME, Cayota A, Garcia-Silva MR. piRNA pathway evolution beyond gonad context: Perspectives from apicomplexa and trypanosomatids. Front Genet 2023; 14:1129194. [PMID: 36816026 PMCID: PMC9935688 DOI: 10.3389/fgene.2023.1129194] [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: 12/21/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
piRNAs function as genome defense mechanisms against transposable elements insertions within germ line cells. Recent studies have unraveled that piRNA pathways are not limited to germ cells as initially reckoned, but are instead also found in non-gonadal somatic contexts. Moreover, these pathways have also been reported in bacteria, mollusks and arthropods, associated with safeguard of genomes against transposable elements, regulation of gene expression and with direct consequences in axon regeneration and memory formation. In this Perspective we draw attention to early branching parasitic protozoa, whose genome preservation is an essential function as in late eukaryotes. However, little is known about the defense mechanisms of these genomes. We and others have described the presence of putative PIWI-related machinery members in protozoan parasites. We have described the presence of a PIWI-like protein in Trypanosoma cruzi, bound to small non-coding RNAs (sRNAs) as cargo of secreted extracellular vesicles relevant in intercellular communication and host infection. Herein, we put forward the presence of members related to Argonaute pathways in both Trypanosoma cruzi and Toxoplasma gondii. The presence of PIWI-like machinery in Trypansomatids and Apicomplexa, respectively, could be evidence of an ancestral piRNA machinery that evolved to become more sophisticated and complex in multicellular eukaryotes. We propose a model in which ancient PIWI proteins were expressed broadly and had functions independent of germline maintenance. A better understanding of current and ancestral PIWI/piRNAs will be relevant to better understand key mechanisms of genome integrity conservation during cell cycle progression and modulation of host defense mechanisms by protozoan parasites.
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Affiliation(s)
- S. Horjales
- Apicomplexa Biology Laboratory, Institute Pasteur Montevideo, Montevideo, Uruguay
| | - M Li Calzi
- Functional Genomics Laboratory, Institute Pasteur Montevideo, Montevideo, Uruguay
| | - M. E. Francia
- Apicomplexa Biology Laboratory, Institute Pasteur Montevideo, Montevideo, Uruguay
- Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - A. Cayota
- Functional Genomics Laboratory, Institute Pasteur Montevideo, Montevideo, Uruguay
- Departmento Basico de Medicina, Facultad de Medicina, Hospital de Clinicas, Universidad de la República, Montevideo, Uruguay
| | - M. R. Garcia-Silva
- Functional Genomics Laboratory, Institute Pasteur Montevideo, Montevideo, Uruguay
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9
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Paramanantham A, Asfiya R, Das S, McCully G, Srivastava A. Extracellular Vesicle (EVs) Associated Non-Coding RNAs in Lung Cancer and Therapeutics. Int J Mol Sci 2022; 23:13637. [PMID: 36362424 PMCID: PMC9655370 DOI: 10.3390/ijms232113637] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/26/2022] [Indexed: 08/13/2023] Open
Abstract
Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area of scientific investigation. Enhanced knowledge about the disease will lead to the development of potent therapeutic interventions. Extracellular vesicles (EVs) are membrane-bound heterogeneous populations of cellular entities that are abundantly produced by all cells in the human body, including the tumor cells. A defined class of EVs called small Extracellular Vesicles (sEVs or exosomes) carries key biomolecules such as RNA, DNA, Proteins and Lipids. Exosomes, therefore, mediate physiological activities and intracellular communication between various cells, including constituent cells of the tumor microenvironment, namely stromal cells, immunological cells, and tumor cells. In recent years, a surge in studying tumor-associated non-coding RNAs (ncRNAs) has been observed. Subsequently, studies have also reported that exosomes abundantly carry different species of ncRNAs and these exosomal ncRNAs are functionally involved in cancer initiation and progression. Here, we discuss the function of exosomal ncRNAs, such as miRNAs and long non-coding RNAs, in the pathophysiology of lung tumors. Further, the future application of exosomal-ncRNAs in clinics as biomarkers and therapeutic targets in lung cancer is also discussed due to the multifaceted influence of exosomes on cellular physiology.
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Affiliation(s)
- Anjugam Paramanantham
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Rahmat Asfiya
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Siddharth Das
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Grace McCully
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Akhil Srivastava
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65212, USA
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10
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Galton R, Fejes-Toth K, Bronner ME. Co-option of the piRNA pathway to regulate neural crest specification. SCIENCE ADVANCES 2022; 8:eabn1441. [PMID: 35947657 PMCID: PMC9365273 DOI: 10.1126/sciadv.abn1441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/24/2022] [Indexed: 05/26/2023]
Abstract
Across Metazoa, Piwi proteins play a critical role in protecting the germline genome through piRNA-mediated repression of transposable elements. In vertebrates, activity of Piwi proteins and the piRNA pathway was thought to be gonad specific. Our results reveal the expression of Piwil1 in a vertebrate somatic cell type, the neural crest. Piwil1 is expressed at low levels throughout the chicken neural tube, peaking in neural crest cells just before the specification event that enables epithelial-to-mesenchymal transition (EMT) and migration into the periphery. Loss of Piwil1 impedes neural crest specification and emigration. Small RNA sequencing reveals somatic piRNAs with sequence signatures of an active ping-pong loop. RNA-seq and functional experiments identify the transposon-derived gene ERNI as Piwil1's target in the neural crest. ERNI, in turn, suppresses Sox2 to precisely control the timing of neural crest specification and EMT. Our data provide mechanistic insight into a novel function of the piRNA pathway as a regulator of somatic development in a vertebrate species.
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Affiliation(s)
| | - Katalin Fejes-Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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11
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Bornelöv S, Czech B, Hannon GJ. An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs. Nat Commun 2022; 13:2118. [PMID: 35440552 PMCID: PMC9018710 DOI: 10.1038/s41467-022-29787-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/03/2022] [Indexed: 11/10/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs required to recognize and silence transposable elements. The 5' ends of mature piRNAs are defined through cleavage of long precursor transcripts, primarily by Zucchini (Zuc). Zuc-dependent cleavage typically occurs immediately upstream of a uridine. However, Zuc lacks sequence preference in vitro, pointing towards additional unknown specificity factors. Here, we examine murine piRNAs and reveal a strong and specific enrichment of three sequences (UAA, UAG, UGA)-corresponding to stop codons-at piRNA 5' ends. Stop codon sequences are also enriched immediately after piRNA processing intermediates, reflecting their Zuc-dependent tail-to-head arrangement. Further analyses reveal that a Zuc in vivo cleavage preference at four sequences (UAA, UAG, UGA, UAC) promotes 5' end stop codons. This observation is conserved across mammals and possibly further. Our work provides new insights into Zuc-dependent cleavage and may point to a previously unrecognized connection between piRNA biogenesis and the translational machinery.
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Affiliation(s)
- Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
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12
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Haase AD. An introduction to PIWI-interacting RNAs (piRNAs) in the context of metazoan small RNA silencing pathways. RNA Biol 2022; 19:1094-1102. [PMID: 36217279 PMCID: PMC9559041 DOI: 10.1080/15476286.2022.2132359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022] Open
Abstract
PIWI proteins and their associated PIWI-interacting RNAs (piRNAs) constitute a small RNA-based adaptive immune system that restricts the deleterious activity of mobile genetic elements to protect genome integrity. Self/nonself discrimination is at the very core of successful defence and relies on complementary base-pairing in RNA-guided immunity. How the millions of piRNA sequences faithfully discriminate between self and nonself and how they adapt to novel genomic invaders remain key outstanding questions in genome biology. This review aims to introduce principles of piRNA silencing in the context of metazoan small RNA pathways. A distinct feature of piRNAs is their origin from single-stranded instead of double-stranded RNA precursors, and piRNAs require a unique set of processing factors. Novel nucleases, helicases and RNA binding proteins have been identified in piRNA biology, and while we are starting to understand some mechanisms of piRNA biogenesis and function, this diverse and prolific class of small RNAs remains full of surprises.
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Affiliation(s)
- Astrid D. Haase
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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13
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Genzor P, Konstantinidou P, Stoyko D, Manzourolajdad A, Marlin Andrews C, Elchert AR, Stathopoulos C, Haase AD. Cellular abundance shapes function in piRNA-guided genome defense. Genome Res 2021; 31:2058-2068. [PMID: 34667116 PMCID: PMC8559710 DOI: 10.1101/gr.275478.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/09/2021] [Indexed: 12/21/2022]
Abstract
Defense against genome invaders universally relies on RNA-guided immunity. Prokaryotic CRISPR-Cas and eukaryotic RNA interference pathways recognize targets by complementary base-pairing, which places the sequences of their guide RNAs at the center of self/nonself discrimination. Here, we explore the sequence space of PIWI-interacting RNAs (piRNAs), the genome defense of animals, and establish functional priority among individual sequences. Our results reveal that only the topmost abundant piRNAs are commonly present in every cell, whereas rare sequences generate cell-to-cell diversity in flies and mice. We identify a skewed distribution of sequence abundance as a hallmark of piRNA populations and show that quantitative differences of more than a 1000-fold are established by conserved mechanisms of biogenesis. Finally, our genomics analyses and direct reporter assays reveal that abundance determines function in piRNA-guided genome defense. Taken together, we identify an effective sequence space and untangle two classes of piRNAs that differ in complexity and function. The first class represents the topmost abundant sequences and drives silencing of genomic parasites. The second class sparsely covers an enormous sequence space. These rare piRNAs cannot function in every cell, every individual, or every generation but create diversity with potential for adaptation in the ongoing arms race with genome invaders.
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Affiliation(s)
- Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Parthena Konstantinidou
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Daniel Stoyko
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Amirhossein Manzourolajdad
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Celine Marlin Andrews
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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14
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Qian L, Xie H, Zhang L, Zhao Q, Lü J, Yu Z. Piwi-Interacting RNAs: A New Class of Regulator in Human Breast Cancer. Front Oncol 2021; 11:695077. [PMID: 34295823 PMCID: PMC8290475 DOI: 10.3389/fonc.2021.695077] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/15/2021] [Indexed: 01/17/2023] Open
Abstract
P-element-induced wimpy testis (Piwi)-interacting RNAs (piRNAs) are a class of germline-enriched small non-coding RNA that associate with Piwi family proteins and mostly induce transposon silencing and epigenetic regulation. Emerging evidence indicated the aberrant expression of Piwil proteins and associated piRNAs in multiple types of human cancer including breast cancer. Although the majority of piRNAs in breast cancer remains unclear of the function mainly due to the variety of regulatory mechanisms, the potential of piRNAs serving as biomarkers for cancer diagnosis and prognosis or therapeutic targets for cancer treatment has been demonstrated by in vitro and in vivo studies. Herein we summarized the research progress of oncogenic or tumor suppressing piRNAs and their regulatory mechanisms in regulating human breast cancer, including piR-021285, piR-823, piR-932, piR-36712, piR-016658, piR-016975 and piR-4987. The challenges and perspectives of piRNAs in the field of human cancer were discussed.
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Affiliation(s)
- Lu Qian
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Jinzhou Medical University, School of Basic Medical Sciences, Jinzhou, China
| | - Heying Xie
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Jinzhou Medical University, School of Basic Medical Sciences, Jinzhou, China
| | - Libo Zhang
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qian Zhao
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinhui Lü
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zuoren Yu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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15
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Ohtani H, Iwasaki YW. Rewiring of chromatin state and gene expression by transposable elements. Dev Growth Differ 2021; 63:262-273. [DOI: 10.1111/dgd.12735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 01/18/2023]
Affiliation(s)
- Hitoshi Ohtani
- Laboratory of Genome and Epigenome Dynamics Department of Animal Sciences Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Yuka W. Iwasaki
- Department of Molecular Biology Keio University School of Medicine Tokyo Japan
- Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO) Saitama Japan
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16
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Ishizu H, Kinoshita T, Hirakata S, Komatsuzaki C, Siomi MC. Distinct and Collaborative Functions of Yb and Armitage in Transposon-Targeting piRNA Biogenesis. Cell Rep 2020; 27:1822-1835.e8. [PMID: 31067466 DOI: 10.1016/j.celrep.2019.04.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 03/18/2019] [Accepted: 04/03/2019] [Indexed: 11/27/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) repress transposons to maintain germline genome integrity. Previous studies showed that artificial tethering of Armitage (Armi) to reporter RNAs induced piRNA biogenesis. However, the lack of female sterile (1) Yb (Yb) in Drosophila ovarian somatic cells (OSCs) impaired the production of transposon-targeting piRNAs, even in the presence of Armi. Here, we show that the specific interaction of Armi with RNA transcripts of the flamenco piRNA cluster, the primary source of transposon-targeting piRNAs in OSCs, is strictly regulated by Yb. The lack of Yb allowed Armi to bind RNAs promiscuously, leading to the production of piRNAs unrelated to transposon silencing. The ATP hydrolysis-defective mutants of Armi failed to unwind RNAs and were retained on them, abolishing piRNA production. These findings shed light on distinct and collaborative requirements of Yb and Armi in transposon-targeting piRNA biogenesis. We also provide evidence supporting the direct involvement of Armi but not Yb in Zucchini-dependent piRNA phasing.
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Affiliation(s)
- Hirotsugu Ishizu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Tatsuki Kinoshita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shigeki Hirakata
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Chihiro Komatsuzaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.
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17
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Sun YH, Zhu J, Xie LH, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci EP, Weng Z, Li XZ. Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Nat Cell Biol 2020; 22:200-212. [PMID: 32015435 PMCID: PMC8041231 DOI: 10.1038/s41556-019-0457-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs essential for fertility. In adult mouse testes, most piRNAs are derived from long single-stranded RNAs lacking annotated open reading frames (ORFs). The mechanisms underlying how piRNA sequences are defined during the cleavages of piRNA precursors remain elusive. Here, we show that 80S ribosomes translate the 5'-proximal short ORFs (uORFs) of piRNA precursors. The MOV10L1/Armitage RNA helicase then facilitates the translocation of ribosomes into the uORF downstream regions (UDRs). The ribosome-bound UDRs are targeted by piRNA processing machinery, with the processed ribosome-protected regions becoming piRNAs. The dual modes of interaction between ribosomes and piRNA precursors underlie the distinct piRNA biogenesis requirements at uORFs and UDRs. Ribosomes also mediate piRNA processing in roosters and green lizards, implying that this mechanism is evolutionarily conserved in amniotes. Our results uncover a function for ribosomes on non-coding regions of RNAs and reveal the mechanisms underlying how piRNAs are defined.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Jiang Zhu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Li Huitong Xie
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Ziwei Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Rajyalakshmi Meduri
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Xiaopeng Zhu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Emiliano P Ricci
- Université de Lyon, ENSL, UCBL, INSERM, CNRS, LBMC, Lyon, France
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA. .,Department of Urology, University of Rochester Medical Center, Rochester, NY, USA.
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18
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SATO K, SIOMI MC. The piRNA pathway in Drosophila ovarian germ and somatic cells. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:32-42. [PMID: 31932527 PMCID: PMC6974405 DOI: 10.2183/pjab.96.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
RNA silencing refers to gene silencing pathways mediated by small non-coding RNAs, including microRNAs. Piwi-interacting RNAs (piRNAs) constitute the largest class of small non-coding RNAs in animal gonads, which repress transposons to protect the germline genome from the selfish invasion of transposons. Deterioration of the system causes DNA damage, leading to severe defects in gametogenesis and infertility. Studies using Drosophila ovaries show that piRNAs originate from specific genomic loci, termed piRNA clusters, and that in piRNA biogenesis, cluster transcripts are processed into mature piRNAs via three distinct pathways: initiator or responder for ping-pong piRNAs and trailing for phased piRNAs. piRNAs then assemble with PIWI members of the Argonaute family of proteins to form piRNA-induced RNA silencing complexes (piRISCs), the core engine of the piRNA-mediated silencing pathway. Upon piRISC assembly, the PIWI member, Piwi, is translocated to the nucleus and represses transposons co-transcriptionally by inducing local heterochromatin formation at target transposon loci.
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Affiliation(s)
- Kaoru SATO
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mikiko C. SIOMI
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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19
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Ninova M, Chen YCA, Godneeva B, Rogers AK, Luo Y, Fejes Tóth K, Aravin AA. Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing. Mol Cell 2019; 77:556-570.e6. [PMID: 31901446 DOI: 10.1016/j.molcel.2019.11.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023]
Abstract
Regulation of transcription is the main mechanism responsible for precise control of gene expression. Whereas the majority of transcriptional regulation is mediated by DNA-binding transcription factors that bind to regulatory gene regions, an elegant alternative strategy employs small RNA guides, Piwi-interacting RNAs (piRNAs) to identify targets of transcriptional repression. Here, we show that in Drosophila the small ubiquitin-like protein SUMO and the SUMO E3 ligase Su(var)2-10 are required for piRNA-guided deposition of repressive chromatin marks and transcriptional silencing of piRNA targets. Su(var)2-10 links the piRNA-guided target recognition complex to the silencing effector by binding the piRNA/Piwi complex and inducing SUMO-dependent recruitment of the SetDB1/Wde histone methyltransferase effector. We propose that in Drosophila, the nuclear piRNA pathway has co-opted a conserved mechanism of SUMO-dependent recruitment of the SetDB1/Wde chromatin modifier to confer repression of genomic parasites.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Yung-Chia Ariel Chen
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Baira Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Alicia K Rogers
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Yicheng Luo
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA.
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20
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Pandey RR, Homolka D, Olotu O, Sachidanandam R, Kotaja N, Pillai RS. Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12. Cell Rep 2019; 24:3423-3432.e4. [PMID: 30257204 DOI: 10.1016/j.celrep.2018.08.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 08/06/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Abstract
PIWI proteins and their associated small RNAs, called PIWI-interacting RNAs (piRNAs), restrict transposon activity in animal gonads to ensure fertility. Distinct biogenesis pathways load piRNAs into the PIWI proteins MILI and MIWI2 in the mouse male embryonic germline. While most MILI piRNAs are derived via a slicer-independent pathway, MILI slicing loads MIWI2 with a series of phased piRNAs. Tudor domain-containing 12 (TDRD12) and its interaction partner Exonuclease domain-containing 1 (EXD1) are required for loading MIWI2, but only Tdrd12 is essential for fertility, leaving us with no explanation for the physiological role of Exd1. Using an artificial piRNA precursor, we demonstrate that MILI-triggered piRNA biogenesis is greatly reduced in the Exd1 mutant. The situation deteriorates in the sensitized Exd1 mutant (Exd1-/-;Tdrd12+/-), where diminished MIWI2 piRNA levels de-repress LINE1 retrotransposons, leading to infertility. Thus, EXD1 enhances MIWI2 piRNA biogenesis via a functional interaction with TDRD12.
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Affiliation(s)
- Radha Raman Pandey
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
| | - David Homolka
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Opeyemi Olotu
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Noora Kotaja
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Ramesh S Pillai
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland.
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21
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Mino T, Iwai N, Endo M, Inoue K, Akaki K, Hia F, Uehata T, Emura T, Hidaka K, Suzuki Y, Standley DM, Okada-Hatakeyama M, Ohno S, Sugiyama H, Yamashita A, Takeuchi O. Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs. Nucleic Acids Res 2019; 47:8838-8859. [PMID: 31329944 PMCID: PMC7145602 DOI: 10.1093/nar/gkz628] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 01/14/2023] Open
Abstract
Regnase-1-mediated mRNA decay (RMD), in which inflammatory mRNAs harboring specific stem–loop structures are degraded, is a critical part of proper immune homeostasis. Prior to initial translation, Regnase-1 associates with target stem–loops but does not carry out endoribonucleolytic cleavage. Single molecule imaging revealed that UPF1 is required to first unwind the stem–loops, thus licensing Regnase-1 to proceed with RNA degradation. Following translation, Regnase-1 physically associates with UPF1 using two distinct points of interaction: The Regnase-1 RNase domain binds to SMG1-phosphorylated residue T28 in UPF1; in addition, an intrinsically disordered segment in Regnase-1 binds to the UPF1 RecA domain, enhancing the helicase activity of UPF1. The SMG1-UPF1–Regnase-1 axis targets pioneer rounds of translation and is critical for rapid resolution of inflammation through restriction of the number of proteins translated by a given mRNA. Furthermore, small-molecule inhibition of SMG1 prevents RNA unwinding in dendritic cells, allowing post-transcriptional control of innate immune responses.
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Affiliation(s)
- Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kentaro Inoue
- Department of Computer Science and Systems Engineering, Faculty of Engineering, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Kotaro Akaki
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yutaka Suzuki
- Laboratory of Functional Genomics, Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Daron M Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0871, Japan
| | - Mariko Okada-Hatakeyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shigeo Ohno
- Department of Molecular Biology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akio Yamashita
- Department of Molecular Biology, Yokohama City University School of Medicine, Kanagawa 236-0004, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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22
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Assembly and Function of Gonad-Specific Non-Membranous Organelles in Drosophila piRNA Biogenesis. Noncoding RNA 2019; 5:ncrna5040052. [PMID: 31698692 PMCID: PMC6958439 DOI: 10.3390/ncrna5040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, the piRNA pathway is indispensable for the continuation of animal life. piRNA-mediated transposon silencing occurs in both the nucleus and cytoplasm while piRNA biogenesis is a solely cytoplasmic event. piRNA production requires a number of proteins, the majority of which localize to non-membranous organelles that specifically appear in the gonads. Other piRNA factors are localized on outer mitochondrial membranes. In situ RNA hybridization experiments show that piRNA precursors are compartmentalized into other non-membranous organelles. In this review, we summarize recent findings about the function of these organelles in the Drosophila piRNA pathway by focusing on their assembly and function.
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23
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Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 2019; 20:89-108. [PMID: 30446728 DOI: 10.1038/s41576-018-0073-3] [Citation(s) in RCA: 666] [Impact Index Per Article: 133.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.
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Affiliation(s)
- Deniz M Ozata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ansgar Zoch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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24
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Dennis C, Brasset E, Vaury C. flam piRNA precursors channel from the nucleus to the cytoplasm in a temporally regulated manner along Drosophila oogenesis. Mob DNA 2019; 10:28. [PMID: 31312260 PMCID: PMC6612187 DOI: 10.1186/s13100-019-0170-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023] Open
Abstract
Background PIWI-interacting RNAs (piRNAs) are the effectors of transposable element silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from long RNA precursors presumably processed within cytoplasmic Yb-bodies. Results Here we show that the nucleo-cytoplasmic traffic of piRNA precursors encoded by the flamenco locus is subjected to a spatio-temporal regulation. Precursor RNAs first gather in a single nuclear focus, Dot COM, close to the nuclear periphery, and transit through the membrane before being delivered to the cytoplasmic Yb-bodies. Early in oogenesis, flamenco transcripts are rapidly transferred to the cytoplasm making their initial nuclear gathering in Dot COM too transient to be visualized. As oogenesis proceeds, the cytoplasmic delivery steadily decreases concomitantly with the decrease in the protein levels of Armi and Yb, two components of the Yb-bodies. Both events lead to a reduction of Yb-body assembly in late stages of oogenesis, which likely results in a drop in piRNA production. Conclusion Our findings show a spatio-temporal regulation of the piRNA biogenesis in the follicle cells of Drosophila ovaries, that involves coordinated control of both piRNA precursors and components of the piRNA processing machinery. This newly unveiled regulation establishes another level of complexity in the production of piRNAs and suggests a stage-dependent involvement of the piRNA biogenesis in the mechanism of transposable elements silencing along oogenesis. Electronic supplementary material The online version of this article (10.1186/s13100-019-0170-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cynthia Dennis
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
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25
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Munafò M, Manelli V, Falconio FA, Sawle A, Kneuss E, Eastwood EL, Seah JWE, Czech B, Hannon GJ. Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery. Genes Dev 2019; 33:844-856. [PMID: 31123065 PMCID: PMC6601507 DOI: 10.1101/gad.325662.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/16/2019] [Indexed: 11/28/2022]
Abstract
The Piwi-interacting RNA (piRNA) pathway is a small RNA-based immune system that silences mobile genetic elements in animal germlines. piRNA biogenesis requires a specialized machinery that converts long single-stranded precursors into small RNAs of ∼25-nucleotides in length. This process involves factors that operate in two different subcellular compartments: the nuage/Yb body and mitochondria. How these two sites communicate to achieve accurate substrate selection and efficient processing remains unclear. Here, we investigate a previously uncharacterized piRNA biogenesis factor, Daedalus (Daed), that is located on the outer mitochondrial membrane. Daed is essential for Zucchini-mediated piRNA production and the correct localization of the indispensable piRNA biogenesis factor Armitage (Armi). We found that Gasz and Daed interact with each other and likely provide a mitochondrial "anchoring platform" to ensure that Armi is held in place, proximal to Zucchini, during piRNA processing. Our data suggest that Armi initially identifies piRNA precursors in nuage/Yb bodies in a manner that depends on Piwi and then moves to mitochondria to present precursors to the mitochondrial biogenesis machinery. These results represent a significant step in understanding a critical aspect of transposon silencing; namely, how RNAs are chosen to instruct the piRNA machinery in the nature of its silencing targets.
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Affiliation(s)
- Marzia Munafò
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Vera Manelli
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Federica A Falconio
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Ashley Sawle
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Jun Wen Eugene Seah
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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26
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Kolliopoulou A, Santos D, Taning CNT, Wynant N, Vanden Broeck J, Smagghe G, Swevers L. PIWI pathway against viruses in insects. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1555. [PMID: 31183996 DOI: 10.1002/wrna.1555] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are an animal-specific class of small non-coding RNAs that are generated via a biogenesis pathway distinct from small interfering RNAs (siRNAs) and microRNAs (miRNAs). There are variations in piRNA biogenesis that depend on several factors, such as the cell type (germline or soma), the organism, and the purpose for which they are being produced, such as transposon-targeting, viral-targeting, or gene-derived piRNAs. Interestingly, the genes involved in the PIWI/piRNA pathway are more rapidly evolving compared with other RNA interference (RNAi) genes. In this review, the role of the piRNA pathway in the antiviral response is reviewed based on recent findings in insect models such as Drosophila, mosquitoes, midges and the silkworm, Bombyx mori. We extensively discuss the special features that characterize host-virus piRNA responses with respect to the proteins and the genes involved, the viral piRNAs' sequence characteristics, the target strand orientation biases as well as the viral piRNA target hotspots across the viral genomes. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms of Action Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Dulce Santos
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Clauvis Nji Tizi Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Niels Wynant
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction Research Group, Animal Physiology and Neurobiology Division, Department of Biology, KU Leuven, Leuven, Belgium
| | - Guy Smagghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", Athens, Greece
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27
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Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Mol Cell 2019; 74:982-995.e6. [PMID: 31076285 DOI: 10.1016/j.molcel.2019.04.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022]
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in Drosophila ovaries, ensuring female fertility. Two coupled pathways generate germline piRNAs: the ping-pong cycle, in which the PIWI proteins Aubergine and Ago3 increase the abundance of pre-existing piRNAs, and the phased piRNA pathway, which generates strings of tail-to-head piRNAs, one after another. Proteins acting in the ping-pong cycle localize to nuage, whereas phased piRNA production requires Zucchini, an endonuclease on the mitochondrial surface. Here, we report that Armitage (Armi), an RNA-binding ATPase localized to both nuage and mitochondria, links the ping-pong cycle to the phased piRNA pathway. Mutations that block phased piRNA production deplete Armi from nuage. Armi ATPase mutants cannot support phased piRNA production and inappropriately bind mRNA instead of piRNA precursors. We propose that Armi shuttles between nuage and mitochondria, feeding precursor piRNAs generated by Ago3 cleavage into the Zucchini-dependent production of Aubergine- and Piwi-bound piRNAs on the mitochondrial surface.
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Affiliation(s)
- Daniel Tianfang Ge
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Wei Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cindy Tipping
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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28
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Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun 2019; 10:828. [PMID: 30783109 PMCID: PMC6381166 DOI: 10.1038/s41467-019-08803-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are at the center of a small RNA-based immune system that defends genomes against the deleterious action of mobile genetic elements (transposons). PiRNAs are highly variable in sequence with extensive targeting potential. Their diversity is restricted by their preference to start with a Uridine (U) at the 5' most position (1U-bias), a bias that remains poorly understood. Here we uncover that the 1U-bias of Piwi-piRNAs is established by consecutive discrimination against all nucleotides but U, first during piRNA biogenesis and then upon interaction with Piwi's specificity loop. Sequence preferences during piRNA processing also restrict U across the piRNA body with the potential to directly impact target recognition. Overall, the uncovered signatures could modulate specificity and efficacy of piRNA-mediated transposon restriction, and provide a substrate for purifying selection in the ongoing arms race between genomes and their mobile parasites.
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Affiliation(s)
- Chad B Stein
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sanga Mitra
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jonathan J Ipsaro
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leif Benner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sushil Sobti
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun Su
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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29
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Chang TH, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore PD. Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster. Mol Cell 2019; 73:291-303.e6. [PMID: 30527661 PMCID: PMC6551610 DOI: 10.1016/j.molcel.2018.10.038] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/05/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022]
Abstract
In Drosophila, 23-30 nt long PIWI-interacting RNAs (piRNAs) direct the protein Piwi to silence germline transposon transcription. Most germline piRNAs derive from dual-strand piRNA clusters, heterochromatic transposon graveyards that are transcribed from both genomic strands. These piRNA sources are marked by the heterochromatin protein 1 homolog Rhino (Rhi), which facilitates their promoter-independent transcription, suppresses splicing, and inhibits transcriptional termination. Here, we report that the protein Maelstrom (Mael) represses canonical, promoter-dependent transcription in dual-strand clusters, allowing Rhi to initiate piRNA precursor transcription. Mael also represses promoter-dependent transcription at sites outside clusters. At some loci, Mael repression requires the piRNA pathway, while at others, piRNAs play no role. We propose that by repressing canonical transcription of individual transposon mRNAs, Mael helps Rhi drive non-canonical transcription of piRNA precursors without generating mRNAs encoding transposon proteins.
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MESH Headings
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Transposable Elements
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/enzymology
- Drosophila melanogaster/genetics
- Gene Expression Regulation
- Promoter Regions, Genetic
- Protein Binding
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Small Interfering/biosynthesis
- RNA, Small Interfering/genetics
- Transcription, Genetic
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Timothy H Chang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Eugenio Mattei
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, Worcester, MA, USA.
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30
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Czech B, Munafò M, Ciabrelli F, Eastwood EL, Fabry MH, Kneuss E, Hannon GJ. piRNA-Guided Genome Defense: From Biogenesis to Silencing. Annu Rev Genet 2018; 52:131-157. [PMID: 30476449 PMCID: PMC10784713 DOI: 10.1146/annurev-genet-120417-031441] [Citation(s) in RCA: 303] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) and their associated PIWI clade Argonaute proteins constitute the core of the piRNA pathway. In gonadal cells, this conserved pathway is crucial for genome defense, and its main function is to silence transposable elements. This is achieved through posttranscriptional and transcriptional gene silencing. Precursors that give rise to piRNAs require specialized transcription and transport machineries because piRNA biogenesis is a cytoplasmic process. The ping-pong cycle, a posttranscriptional silencing mechanism, combines the cleavage-dependent silencing of transposon RNAs with piRNA production. PIWI proteins also function in the nucleus, where they scan for nascent target transcripts with sequence complementarity, instructing transcriptional silencing and deposition of repressive chromatin marks at transposon loci. Although studies have revealed numerous factors that participate in each branch of the piRNA pathway, the precise molecular roles of these factors often remain unclear. In this review, we summarize our current understanding of the mechanisms involved in piRNA biogenesis and function.
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Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Filippo Ciabrelli
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Martin H Fabry
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom; ,
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31
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A novel miRNA, miR-13664, targets CpCYP314A1 to regulate deltamethrin resistance in Culex pipiens pallens. Parasitology 2018; 146:197-205. [PMID: 29966536 DOI: 10.1017/s0031182018001002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Extensive insecticide use has led to the resistance of mosquitoes to these insecticides, posing a major barrier to mosquito control. Previous Solexa high-throughput sequencing of Culex pipiens pallens in the laboratory has revealed that the abundance of a novel microRNA (miRNA), miR-13664, was higher in a deltamethrin-sensitive (DS) strain than a deltamethrin-resistant (DR) strain. Real-time quantitative PCR revealed that the miR-13664 transcript level was lower in the DR strain than in the DS strain. MiR-13664 oversupply in the DR strain increased the susceptibility of these mosquitoes to deltamethrin, whereas inhibition of miR-13664 made the DS strain more resistant to deltamethrin. Results of bioinformatic analysis, quantitative reverse-transcriptase polymerase chain reaction, luciferase assay and miR mimic/inhibitor microinjection revealed CpCYP314A1 to be a target of miR-13664. In addition, downregulation of CpCYP314A1 expression in the DR strain reduced the resistance of mosquitoes to deltamethrin. Taken together, our results indicate that miR-13664 could regulate deltamethrin resistance by interacting with CpCYP314A1, providing new insights into mosquito resistance mechanisms.
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32
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Huang X, Fejes Tóth K, Aravin AA. piRNA Biogenesis in Drosophila melanogaster. Trends Genet 2017; 33:882-894. [PMID: 28964526 DOI: 10.1016/j.tig.2017.09.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense system that protects the genome integrity of the animal germline from deleterious transposable elements. Targets of silencing are recognized by small noncoding piRNAs that are processed from long precursor molecules. Although piRNAs and other classes of small noncoding RNAs, such as miRNAs and small interfering (si)RNAs, interact with members of the same family of Argonaute (Ago) proteins and their function in target repression is similar, the biogenesis of piRNAs differs from those of the other two small RNAs. Recently, many aspects of piRNA biogenesis have been revealed in Drosophila melanogaster. In this review, we elaborate on piRNA biogenesis in Drosophila somatic and germline cells. We focus on the mechanisms by which piRNA precursor transcription is regulated and highlight recent work that has advanced our understanding of piRNA precursor processing to mature piRNAs. We finish by discussing current models to the still unresolved question of how piRNA precursors are selected and channeled into the processing machinery.
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Affiliation(s)
- Xiawei Huang
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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