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Li B, Wang K, Cheng W, Fang B, Li YH, Yang SM, Zhang MH, Wang YH, Wang K. Recent advances of PIWI-interacting RNA in cardiovascular diseases. Clin Transl Med 2024; 14:e1770. [PMID: 39083321 PMCID: PMC11290350 DOI: 10.1002/ctm2.1770] [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: 02/04/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The relationship between noncoding RNAs (ncRNAs) and human diseases has been a hot topic of research, but the study of ncRNAs in cardiovascular diseases (CVDs) is still in its infancy. PIWI-interacting RNA (piRNA), a small ncRNA that binds to the PIWI protein to maintain genome stability by silencing transposons, was widely studied in germ lines and stem cells. In recent years, piRNA has been shown to be involved in key events of multiple CVDs through various epigenetic modifications, revealing the potential value of piRNA as a new biomarker or therapeutic target. CONCLUSION This review explores origin, degradation, function, mechanism and important role of piRNA in CVDs, and the promising therapeutic targets of piRNA were summarized. This review provide a new strategy for the treatment of CVDs and lay a theoretical foundation for future research. KEY POINTS piRNA can be used as a potential therapeutic target and biomaker in CVDs. piRNA influences apoptosis, inflammation and angiogenesis by regulating epigenetic modificaions. Critical knowledge gaps remain in the unifying piRNA nomenclature and PIWI-independent function.
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Affiliation(s)
- Bo Li
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Kai Wang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Wei Cheng
- Department of Cardiovascular SurgeryBeijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Bo Fang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Ying Hui Li
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Su Min Yang
- Department of Cardiovascular SurgeryThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Mei Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
| | - Yun Hong Wang
- Hypertension CenterBeijing Anzhen HospitalCapital Medical UniversityBeijingChina
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
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2
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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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3
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Lau NC, Macias VM. Transposon and Transgene Tribulations in Mosquitoes: A Perspective of piRNA Proportions. DNA 2024; 4:104-128. [PMID: 39076684 PMCID: PMC11286205 DOI: 10.3390/dna4020006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Mosquitoes, like Drosophila, are dipterans, the order of "true flies" characterized by a single set of two wings. Drosophila are prime model organisms for biomedical research, while mosquito researchers struggle to establish robust molecular biology in these that are arguably the most dangerous vectors of human pathogens. Both insects utilize the RNA interference (RNAi) pathway to generate small RNAs to silence transposons and viruses, yet details are emerging that several RNAi features are unique to each insect family, such as how culicine mosquitoes have evolved extreme genomic feature differences connected to their unique RNAi features. A major technical difference in the molecular genetic studies of these insects is that generating stable transgenic animals are routine in Drosophila but still variable in stability in mosquitoes, despite genomic DNA-editing advances. By comparing and contrasting the differences in the RNAi pathways of Drosophila and mosquitoes, in this review we propose a hypothesis that transgene DNAs are possibly more intensely targeted by mosquito RNAi pathways and chromatin regulatory pathways than in Drosophila. We review the latest findings on mosquito RNAi pathways, which are still much less well understood than in Drosophila, and we speculate that deeper study into how mosquitoes modulate transposons and viruses with Piwi-interacting RNAs (piRNAs) will yield clues to improving transgene DNA expression stability in transgenic mosquitoes.
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Affiliation(s)
- Nelson C. Lau
- Department of Biochemistry and Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- Genome Science Institute and National Emerging Infectious Disease Laboratory, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
| | - Vanessa M. Macias
- Department of Biology, University of North Texas, Denton, TX 76205, USA
- Advanced Environmental Research Institute, University of North Texas, Denton, TX 76205, USA
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4
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Sharma S, Fazal FM. Localization of RNAs to the mitochondria-mechanisms and functions. RNA (NEW YORK, N.Y.) 2024; 30:597-608. [PMID: 38448244 PMCID: PMC11098466 DOI: 10.1261/rna.079999.124] [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: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
The mammalian mitochondrial proteome comprises over 1000 proteins, with the majority translated from nuclear-encoded messenger RNAs (mRNAs). Mounting evidence suggests many of these mRNAs are localized to the outer mitochondrial membrane (OMM) in a pre- or cotranslational state. Upon reaching the mitochondrial surface, these mRNAs are locally translated to produce proteins that are cotranslationally imported into mitochondria. Here, we summarize various mechanisms cells use to localize RNAs, including transfer RNAs (tRNAs), to the OMM and recent technological advancements in the field to study these processes. While most early studies in the field were carried out in yeast, recent studies reveal RNA localization to the OMM and their regulation in higher organisms. Various factors regulate this localization process, including RNA sequence elements, RNA-binding proteins (RBPs), cytoskeletal motors, and translation machinery. In this review, we also highlight the role of RNA structures and modifications in mitochondrial RNA localization and discuss how these features can alter the binding properties of RNAs. Finally, in addition to RNAs related to mitochondrial function, RNAs involved in other cellular processes can also localize to the OMM, including those implicated in the innate immune response and piRNA biogenesis. As impairment of messenger RNA (mRNA) localization and regulation compromise mitochondrial function, future studies will undoubtedly expand our understanding of how RNAs localize to the OMM and investigate the consequences of their mislocalization in disorders, particularly neurodegenerative diseases, muscular dystrophies, and cancers.
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Affiliation(s)
- Surbhi Sharma
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
| | - Furqan M Fazal
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA
- Therapeutic Innovation Center (THINC), Baylor College of Medicine, Houston, Texas 77030, USA
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5
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Izumi N, Shoji K, Negishi L, Tomari Y. The dual role of Spn-E in supporting heterotypic ping-pong piRNA amplification in silkworms. EMBO Rep 2024; 25:2239-2257. [PMID: 38632376 PMCID: PMC11094040 DOI: 10.1038/s44319-024-00137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers the biogenesis of new piRNAs from the cleaved RNA fragments. This process, known as the ping-pong cycle, is mediated by the two PIWI proteins, Siwi and BmAgo3, in silkworms. However, the detailed molecular mechanism of the ping-pong cycle remains largely unclear. Here, we show that Spindle-E (Spn-E), a putative ATP-dependent RNA helicase, is essential for BmAgo3-dependent production of Siwi-bound piRNAs in the ping-pong cycle and that this function of Spn-E requires its ATPase activity. Moreover, Spn-E acts to suppress homotypic Siwi-Siwi ping-pong, but this function of Spn-E is independent of its ATPase activity. These results highlight the dual role of Spn-E in facilitating proper heterotypic ping-pong in silkworms.
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Affiliation(s)
- Natsuko Izumi
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Keisuke Shoji
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei-shi, Tokyo, 184-8588, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0032, Japan.
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6
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Ho S, Theurkauf W, Rice N. piRNA-Guided Transposon Silencing and Response to Stress in Drosophila Germline. Viruses 2024; 16:714. [PMID: 38793595 PMCID: PMC11125864 DOI: 10.3390/v16050714] [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: 03/28/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
Transposons are integral genome constituents that can be domesticated for host functions, but they also represent a significant threat to genome stability. Transposon silencing is especially critical in the germline, which is dedicated to transmitting inherited genetic material. The small Piwi-interacting RNAs (piRNAs) have a deeply conserved function in transposon silencing in the germline. piRNA biogenesis and function are particularly well understood in Drosophila melanogaster, but some fundamental mechanisms remain elusive and there is growing evidence that the pathway is regulated in response to genotoxic and environmental stress. Here, we review transposon regulation by piRNAs and the piRNA pathway regulation in response to stress, focusing on the Drosophila female germline.
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Affiliation(s)
- Samantha Ho
- Program in Molecular Medicine, University Campus, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA;
| | | | - Nicholas Rice
- Program in Molecular Medicine, University Campus, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA;
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7
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Allikka Parambil S, Li D, Zelko M, Poulet A, van Wolfswinkel J. piRNA generation is associated with the pioneer round of translation in stem cells. Nucleic Acids Res 2024; 52:2590-2608. [PMID: 38142432 PMCID: PMC10954484 DOI: 10.1093/nar/gkad1212] [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: 04/13/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023] Open
Abstract
Much insight has been gained on how stem cells maintain genomic integrity, but less attention has been paid to how they maintain their transcriptome. Here, we report that the PIWI protein SMEDWI-1 plays a role in the filtering of dysfunctional transcripts from the transcriptome of planarian stem cells. SMEDWI-1 accomplishes this through association with the ribosomes during the pioneer round of translation, and processing of poorly translated transcripts into piRNAs. This results in the removal of such transcripts from the cytoplasmic pool and at the same time creates a dynamic pool of small RNAs for post-transcriptional surveillance through the piRNA pathway. Loss of SMEDWI-1 results in elevated levels of several non-coding transcripts, including rRNAs, snRNAs and pseudogene mRNAs, while reducing levels of several coding transcripts. In the absence of SMEDWI-1, stem cell colonies are delayed in their expansion and a higher fraction of descendants exit the stem cell state, indicating that this transcriptomic sanitation mediated by SMEDWI-1 is essential to maintain stem cell health. This study presents a new model for the function of PIWI proteins in stem cell maintenance, that complements their role in transposon repression, and proposes a new biogenesis pathway for piRNAs in stem cells.
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Affiliation(s)
- Sudheesh Allikka Parambil
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Danyan Li
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Michael Zelko
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Axel Poulet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
| | - Josien C van Wolfswinkel
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06511, USA
- Center for RNA science and medicine, Yale School of Medicine, New Haven. CT 06511, USA
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8
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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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9
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Venkei ZG, Gainetdinov I, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, Yamashita YM. A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Nat Cell Biol 2023; 25:1495-1505. [PMID: 37723298 PMCID: PMC10567549 DOI: 10.1038/s41556-023-01227-4] [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: 09/26/2022] [Accepted: 08/09/2023] [Indexed: 09/20/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) direct PIWI proteins to silence complementary targets such as transposons. In Drosophila and other species with a maternally specified germline, piRNAs deposited in the egg initiate piRNA biogenesis in the progeny. However, Y chromosome loci cannot participate in such a chain of intergenerational inheritance. How then can the biogenesis of Y-linked piRNAs be initiated? Here, using Suppressor of Stellate (Su(Ste)), a Y-linked Drosophila melanogaster piRNA locus as a model, we show that Su(Ste) piRNAs are made in the early male germline via 5'-to-3' phased piRNA biogenesis initiated by maternally deposited 1360/Hoppel transposon piRNAs. Notably, deposition of Su(Ste) piRNAs from XXY mothers obviates the need for phased piRNA biogenesis in sons. Together, our study uncovers a developmentally programmed, intergenerational mechanism that allows fly mothers to protect their sons using a Y-linked piRNA locus.
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Affiliation(s)
- Zsolt G Venkei
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Ayca Bagci
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Charlotte P Choi
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peiwei Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chiraag Balsara
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Troy W Whitfield
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George W Bell
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Whitehead Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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10
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Lv X, Xiao W, Lai Y, Zhang Z, Zhang H, Qiu C, Hou L, Chen Q, Wang D, Gao Y, Song Y, Shui X, Chen Q, Qin R, Liang S, Zeng W, Shi A, Li J, Wu L. The non-redundant functions of PIWI family proteins in gametogenesis in golden hamsters. Nat Commun 2023; 14:5267. [PMID: 37644029 PMCID: PMC10465502 DOI: 10.1038/s41467-023-40650-x] [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: 12/18/2022] [Accepted: 08/07/2023] [Indexed: 08/31/2023] Open
Abstract
The piRNA pathway is essential for female fertility in golden hamsters and likely humans, but not in mice. However, the role of individual PIWIs in mammalian reproduction remains poorly understood outside of mice. Here, we describe the expression profiles, subcellular localization, and knockout-associated reproductive defects for all four PIWIs in golden hamsters. In female golden hamsters, PIWIL1 and PIWIL3 are highly expressed throughout oogenesis and early embryogenesis, while knockout of PIWIL1 leads to sterility, and PIWIL3 deficiency results in subfertility with lagging zygotic development. PIWIL1 can partially compensate for TE silencing in PIWIL3 knockout females, but not vice versa. PIWIL1 and PIWIL4 are the predominant PIWIs expressed in adult and postnatal testes, respectively, while PIWIL2 is present at both stages. Loss of any PIWI expressed in testes leads to sterility and severe but distinct spermatogenesis disorders. These findings illustrate the non-redundant regulatory functions of PIWI-piRNAs in gametogenesis and early embryogenesis in golden hamsters, facilitating study of their role in human fertility.
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Affiliation(s)
- Xiaolong Lv
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wen Xiao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yana Lai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhaozhen Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongdao Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chen Qiu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Li Hou
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qin Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Duanduan Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yun Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yuanyuan Song
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xinjia Shui
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qinghua Chen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ruixin Qin
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Shuang Liang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Wentao Zeng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Aimin Shi
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Jianmin Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Laboratory Animal Center, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
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11
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Du Z, Shi K, Brown JS, He T, Wu WS, Zhang Y, Lee HC, Zhang D. Condensate cooperativity underlies transgenerational gene silencing. Cell Rep 2023; 42:112859. [PMID: 37505984 PMCID: PMC10540246 DOI: 10.1016/j.celrep.2023.112859] [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: 02/07/2023] [Revised: 05/26/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Biomolecular condensates have been shown to interact in vivo, yet it is unclear whether these interactions are functionally meaningful. Here, we demonstrate that cooperativity between two distinct condensates-germ granules and P bodies-is required for transgenerational gene silencing in C. elegans. We find that P bodies form a coating around perinuclear germ granules and that P body components CGH-1/DDX6 and CAR-1/LSM14 are required for germ granules to organize into sub-compartments and concentrate small RNA silencing factors. Functionally, while the P body mutant cgh-1 is competent to initially trigger gene silencing, it is unable to propagate the silencing to subsequent generations. Mechanistically, we trace this loss of transgenerational silencing to defects in amplifying secondary small RNAs and the stability of WAGO-4 Argonaute, both known carriers of gene silencing memories. Together, these data reveal that cooperation between condensates results in an emergent capability of germ cells to establish heritable memory.
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Affiliation(s)
- Zhenzhen Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430032, China
| | - Kun Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430032, China
| | - Jordan S Brown
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Tao He
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430032, China
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430032, China.
| | - Heng-Chi Lee
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
| | - Donglei Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430032, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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12
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Ho S, Rice NP, Yu T, Weng Z, Theurkauf WE. Aub, Vasa and Armi localization to phase separated nuage is dispensable for piRNA biogenesis and transposon silencing in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.549160. [PMID: 37546958 PMCID: PMC10402007 DOI: 10.1101/2023.07.25.549160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
From nematodes to placental mammals, key components of the germline transposon silencing piRNAs pathway localize to phase separated perinuclear granules. In Drosophila, the PIWI protein Aub, DEAD box protein Vasa and helicase Armi localize to nuage granules and are required for ping-pong piRNA amplification and phased piRNA processing. Drosophila piRNA mutants lead to genome instability and Chk2 kinase DNA damage signaling. By systematically analyzing piRNA pathway organization, small RNA production, and long RNA expression in single piRNA mutants and corresponding chk2/mnk double mutants, we show that Chk2 activation disrupts nuage localization of Aub and Vasa, and that the HP1 homolog Rhino, which drives piRNA precursor transcription, is required for Aub, Vasa, and Armi localization to nuage. However, these studies also show that ping-pong amplification and phased piRNA biogenesis are independent of nuage localization of Vasa, Aub and Armi. Dispersed cytoplasmic proteins thus appear to mediate these essential piRNA pathway functions.
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Affiliation(s)
- Samantha Ho
- Program in Molecular Medicine, UMass Chan Medical School, Worcester MA
| | - Nicholas P Rice
- Program in Molecular Medicine, UMass Chan Medical School, Worcester MA
| | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester MA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester MA
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13
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Iki T, Kawaguchi S, Kai T. miRNA/siRNA-directed pathway to produce noncoding piRNAs from endogenous protein-coding regions ensures Drosophila spermatogenesis. SCIENCE ADVANCES 2023; 9:eadh0397. [PMID: 37467338 PMCID: PMC10355832 DOI: 10.1126/sciadv.adh0397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
PIWI-interacting RNA (piRNA) pathways control transposable elements (TEs) and endogenous genes, playing important roles in animal gamete formation. However, the underlying piRNA biogenesis mechanisms remain elusive. Here, we show that endogenous protein coding sequences (CDSs), which are normally used for translation, serve as origins of noncoding piRNA biogenesis in Drosophila melanogaster testes. The product, namely, CDS-piRNAs, formed silencing complexes with Aubergine (Aub) in germ cells. Proximity proteome and functional analyses show that CDS-piRNAs and cluster/TE-piRNAs are distinct species occupying Aub, the former loading selectively relies on chaperone Cyclophilin 40. Moreover, Argonaute 2 (Ago2) and Dicer-2 activities were found critical for CDS-piRNA production. We provide evidence that Ago2-bound short interfering RNAs (siRNAs) and microRNAs (miRNAs) specify precursors to be processed into piRNAs. We further demonstrate that Aub is crucial in spermatid differentiation, regulating chromatins through mRNA cleavage. Collectively, our data illustrate a unique strategy used by male germ line, expanding piRNA repertoire for silencing of endogenous genes during spermatogenesis.
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Affiliation(s)
| | - Shinichi Kawaguchi
- Laboratory of Germline Biology, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka1-3, Suita, Osaka, Japan
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14
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Saquib M, Agnihotri P, Biswas S. Interrelated grid of non-coding RNA: An important aspect in Rheumatoid Arthritis pathogenesis. Mol Biol Rep 2023:10.1007/s11033-023-08543-w. [PMID: 37294467 DOI: 10.1007/s11033-023-08543-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
Inflammation and autoimmunity are the root cause of rheumatoid arthritis, a destructive disease of joints. Multiple biomolecules are involved in the pathogenesis of RA and are related to various events of molecular biology. RNA is a versatile biomolecule, playing numerous roles at structural, functional, and regulatory stages to maintain cellular homeostasis. The involvement of RNA (coding/non-coding) in disease development and progression has left a wide whole to fill with newer approaches. Non-coding RNAs belong to the housekeeping and regulatory categories and both have their specific roles, and their alteration causes specific implications in disease pathogenesis. Housekeeping RNAs, rRNA, tRNA and regulatory RNA, micro-RNA, circular RNA, piRNA and long non-coding RNA were found to be important regulators of inflammation. They work at the pre-and post-transcriptional levels and were found to be more intriguing to study their regulatory impact on disease pathogenesis. The review addresses a question on how the non-coding RNA gets involved in early RA pathogenesis and can be utilized to know their targets to understand the disease better and make way towards the unresolved mystery of RA development.
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Affiliation(s)
- Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Integrative and Functional Biology Department CSIR- Institute of Genomics & Integrative Biology, Mall Road, Delhi, 110 007, India.
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15
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The epigenetic regulatory mechanism of PIWI/piRNAs in human cancers. Mol Cancer 2023; 22:45. [PMID: 36882835 PMCID: PMC9990219 DOI: 10.1186/s12943-023-01749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
PIWI proteins have a strong correlation with PIWI-interacting RNAs (piRNAs), which are significant in development and reproduction of organisms. Recently, emerging evidences have indicated that apart from the reproductive function, PIWI/piRNAs with abnormal expression, also involve greatly in varieties of human cancers. Moreover, human PIWI proteins are usually expressed only in germ cells and hardly in somatic cells, so the abnormal expression of PIWI proteins in different types of cancer offer a promising opportunity for precision medicine. In this review, we discussed current researches about the biogenesis of piRNA, its epigenetic regulatory mechanisms in human cancers, such as N6-methyladenosine (m6A) methylation, histone modifications, DNA methylation and RNA interference, providing novel insights into the markers for clinical diagnosis, treatment and prognosis in human cancers.
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16
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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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17
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Santos D, Feng M, Kolliopoulou A, Taning CNT, Sun J, Swevers L. What Are the Functional Roles of Piwi Proteins and piRNAs in Insects? INSECTS 2023; 14:insects14020187. [PMID: 36835756 PMCID: PMC9962485 DOI: 10.3390/insects14020187] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 06/01/2023]
Abstract
Research on Piwi proteins and piRNAs in insects has focused on three experimental models: oogenesis and spermatogenesis in Drosophila melanogaster, the antiviral response in Aedes mosquitoes and the molecular analysis of primary and secondary piRNA biogenesis in Bombyx mori-derived BmN4 cells. Significant unique and complementary information has been acquired and has led to a greater appreciation of the complexity of piRNA biogenesis and Piwi protein function. Studies performed in other insect species are emerging and promise to add to the current state of the art on the roles of piRNAs and Piwi proteins. Although the primary role of the piRNA pathway is genome defense against transposons, particularly in the germline, recent findings also indicate an expansion of its functions. In this review, an extensive overview is presented of the knowledge of the piRNA pathway that so far has accumulated in insects. Following a presentation of the three major models, data from other insects were also discussed. Finally, the mechanisms for the expansion of the function of the piRNA pathway from transposon control to gene regulation were considered.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Anna Kolliopoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
| | - Clauvis N. T. Taning
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences & Applications, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, 15341 Athens, Greece
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18
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Wang X, Ramat A, Simonelig M, Liu MF. Emerging roles and functional mechanisms of PIWI-interacting RNAs. Nat Rev Mol Cell Biol 2023; 24:123-141. [PMID: 36104626 DOI: 10.1038/s41580-022-00528-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 02/02/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with proteins of the PIWI clade of the Argonaute family. First identified in animal germ line cells, piRNAs have essential roles in germ line development. The first function of PIWI-piRNA complexes to be described was the silencing of transposable elements, which is crucial for maintaining the integrity of the germ line genome. Later studies provided new insights into the functions of PIWI-piRNA complexes by demonstrating that they regulate protein-coding genes. Recent studies of piRNA biology, including in new model organisms such as golden hamsters, have deepened our understanding of both piRNA biogenesis and piRNA function. In this Review, we discuss the most recent advances in our understanding of piRNA biogenesis, the molecular mechanisms of piRNA function and the emerging roles of piRNAs in germ line development mainly in flies and mice, and in infertility, cancer and neurological diseases in humans.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Anne Ramat
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Martine Simonelig
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China. .,Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. .,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.
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19
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Izumi N, Shoji K, Kiuchi T, Katsuma S, Tomari Y. The two Gtsf paralogs in silkworms orthogonally activate their partner PIWI proteins for target cleavage. RNA (NEW YORK, N.Y.) 2022; 29:rna.079380.122. [PMID: 36319089 PMCID: PMC9808576 DOI: 10.1261/rna.079380.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a protection mechanism against transposons in animal germ cells. Most PIWI proteins possess piRNA-guided endonuclease activity, which is critical for silencing transposons and producing new piRNAs. Gametocyte-specific factor 1 (Gtsf1), an evolutionarily conserved zinc finger protein, promotes catalysis by PIWI proteins. Many animals have multiple Gtsf1 paralogs; however, their respective roles in the piRNA pathway are not fully understood. Here, we dissected the roles of Gtsf1 and its paralog Gtsf1-like (Gtsf1L) in the silkworm piRNA pathway. We found that Gtsf1 and Gtsf1L preferentially bind the two silkworm PIWI paralogs, Siwi and BmAgo3, respectively, and facilitate the endonuclease activity of each PIWI protein. This orthogonal activation effect was further supported by specific reduction of BmAgo3-bound Masculinizer piRNA and Siwi-bound Feminizer piRNA, the unique piRNA pair required for silkworm feminization, upon depletion of Gtsf1 and Gtsf1L, respectively. Our results indicate that the two Gtsf paralogs in silkworms activate their respective PIWI partners, thereby facilitating the amplification of piRNAs.
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20
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GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance. Nat Commun 2022; 13:5306. [PMID: 36085149 PMCID: PMC9463143 DOI: 10.1038/s41467-022-32880-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
piRNAs function as guardians of the genome by silencing non-self nucleic acids and transposable elements in animals. Many piRNA factors are enriched in perinuclear germ granules, but whether their localization is required for piRNA biogenesis or function is not known. Here we show that GLH/VASA helicase mutants exhibit defects in forming perinuclear condensates containing PIWI and other small RNA cofactors. These mutant animals produce largely normal levels of piRNA but are defective in triggering piRNA silencing. Strikingly, while many piRNA targets are activated in GLH mutants, we observe that hundreds of endogenous genes are aberrantly silenced by piRNAs. This defect in self versus non-self recognition is also observed in other mutants where perinuclear germ granules are disrupted. Together, our results argue that perinuclear germ granules function critically to promote the fidelity of piRNA-based transcriptome surveillance in C. elegans and preserve self versus non-self distinction. Phase separated, membrane-less germ granules preserve fertility and cellular function in animal germ cells. Here the authors show that loss of germ granules impacts piRNA pathway fidelity in the recognition of self and non-self nucleic acids.
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21
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Yang S, Zhang X, Li X, Yin X, Teng L, Ji G, Li H. Evolutionary and Expression Analysis of MOV10 and MOV10L1 Reveals Their Origin, Duplication and Divergence. Int J Mol Sci 2022; 23:ijms23147523. [PMID: 35886872 PMCID: PMC9319325 DOI: 10.3390/ijms23147523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
MOV10 and MOV10L1 both encode ATP-dependent RNA helicases. In mammals, MOV10 and MOV10L1 participate in various kinds of biological contexts, such as defense of RNA virus invasion, neuron system, germ cell and early development. However, mov10 and mov10l1 in zebrafish are obscure and the evolutionary relationships of mov10 among different species remain unclear. In this study, we found MOV10 and MOV10L1 had some variations despite they possessed the conserved feature of RNA helicase, however, they may originate from a single ancestor although they shared limited homology. A single MOV10L1 gene existed among all species, while MOV10 gene experienced lineage-specific intra-chromosomal gene duplication in several species. Interestingly, the mov10 gene expanded to three in zebrafish, which originating from a duplication by whole genome specific duplication of teleost lineage followed by a specific intra-chromosome tandem duplication. The mov10 and mov10l1 showed distinct expression profiles in early stages, however, in adult zebrafish, three mov10 genes exhibited similar diverse expression patterns in almost all tissues. We also demonstrated mov10 genes were upregulated upon virus challenge, highlighting they had redundant conserved roles in virus infection. These results provide valuable data for the evolution of MOV10 and MOV10L1 and they are important to the further functional exploration.
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Affiliation(s)
- Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xiangmin Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xianpeng Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Xiu Yin
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
| | - Lei Teng
- School of Basic Medicine, Qingdao University, Qingdao 266071, China;
| | - Guangdong Ji
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
- Correspondence: (G.J.); (H.L.); Tel.: +86-0532-82032092 (H.L.)
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; (S.Y.); (X.Z.); (X.L.); (X.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266003, China
- Correspondence: (G.J.); (H.L.); Tel.: +86-0532-82032092 (H.L.)
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22
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Hearn J, Little TJ. Daphnia magna egg piRNA cluster expression profiles change as mothers age. BMC Genomics 2022; 23:429. [PMID: 35672706 PMCID: PMC9175491 DOI: 10.1186/s12864-022-08660-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND PiRNAs prevent transposable elements wreaking havoc on the germline genome. Changes in piRNA expression over the lifetime of an individual may impact on ageing through continued suppression, or release, of transposable element expression. We identified piRNA producing clusters in the genome of Daphnia magna by a combination of bioinformatic methods, and then contrasted their expression between parthenogenetically produced eggs representing maternally-deposited germline piRNAs of young (having their 1st clutch) and old (having their 5th clutch) mothers. Results from eggs were compared to cluster expression in three generations of adults. RESULTS As for other arthropods, D. magna encodes long uni-directionally transcribed non-coding RNAs consisting of fragmented transposable elements which account for most piRNAs expressed. Egg tissues showed extensive differences between clutches from young mothers and those from old mothers, with 578 and 686 piRNA clusters upregulated, respectively. Most log fold-change differences for significant clusters were modest, however. When considering only highly expressed clusters, there was a bias towards 1st clutch eggs at 41 upregulated versus eight clusters in the eggs from older mothers. F0 generation differences between young and old mothers were fewer than eggs, as 179 clusters were up-regulated in young versus 170 old mothers. This dropped to 31 versus 22 piRNA clusters when comparing adults in the F1 generation, and no differences were detected in the F3 generation. Inter-generational losses of differential piRNA cluster were similar to that observed for D. magna micro-RNA expression. CONCLUSIONS Little overlap in differentially expressed clusters was found between adults containing mixed somatic and germline (ovary) tissues and germ-line representing eggs. A cluster encompassing a Tudor domain containing gene important in the piRNA pathway was upregulated in the eggs from old mothers. We hypothesise that regulation of this gene could form part of a feedback loop that reduces piRNA pathway activity explaining the reduced number of highly-expressed clusters in eggs from old mothers.
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Affiliation(s)
- Jack Hearn
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Tom J. Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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23
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Mahabady MK, Mirzaei S, Saebfar H, Gholami MH, Zabolian A, Hushmandi K, Hashemi F, Tajik F, Hashemi M, Kumar AP, Aref AR, Zarrabi A, Khan H, Hamblin MR, Nuri Ertas Y, Samarghandian S. Noncoding RNAs and their therapeutics in paclitaxel chemotherapy: Mechanisms of initiation, progression, and drug sensitivity. J Cell Physiol 2022; 237:2309-2344. [PMID: 35437787 DOI: 10.1002/jcp.30751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022]
Abstract
The identification of agents that can reverse drug resistance in cancer chemotherapy, and enhance the overall efficacy is of great interest. Paclitaxel (PTX) belongs to taxane family that exerts an antitumor effect by stabilizing microtubules and inhibiting cell cycle progression. However, PTX resistance often develops in tumors due to the overexpression of drug transporters and tumor-promoting pathways. Noncoding RNAs (ncRNAs) are modulators of many processes in cancer cells, such as apoptosis, migration, differentiation, and angiogenesis. In the present study, we summarize the effects of ncRNAs on PTX chemotherapy. MicroRNAs (miRNAs) can have opposite effects on PTX resistance (stimulation or inhibition) via influencing YES1, SK2, MRP1, and STAT3. Moreover, miRNAs modulate the growth and migration rates of tumor cells in regulating PTX efficacy. PIWI-interacting RNAs, small interfering RNAs, and short-hairpin RNAs are other members of ncRNAs regulating PTX sensitivity of cancer cells. Long noncoding RNAs (LncRNAs) are similar to miRNAs and can modulate PTX resistance/sensitivity by their influence on miRNAs and drug efflux transport. The cytotoxicity of PTX against tumor cells can also be affected by circular RNAs (circRNAs) and limitation is that oncogenic circRNAs have been emphasized and experiments should also focus on onco-suppressor circRNAs.
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Affiliation(s)
- Mahmood K Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Hamidreza Saebfar
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad H Gholami
- Faculty of Veterinary Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Amirhossein Zabolian
- Resident of Orthopedics, Department of Orthopedics, School of Medicine, 5th Azar Hospital, Golestan University of Medical Sciences, Golestan, Iran
| | - Kiavash Hushmandi
- Division of Epidemiology, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Farid Hashemi
- Department of Comparative Biosciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Tajik
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alan P Kumar
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pharmacology, Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amir R Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Xsphera Biosciences Inc, Boston, Massachusetts, USA
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer, Istanbul, Turkey
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
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24
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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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25
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Ouyang JPT, Seydoux G. Nuage condensates: accelerators or circuit breakers for sRNA silencing pathways? RNA (NEW YORK, N.Y.) 2022; 28:58-66. [PMID: 34772788 PMCID: PMC8675287 DOI: 10.1261/rna.079003.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nuage are RNA-rich condensates that assemble around the nuclei of developing germ cells. Many proteins required for the biogenesis and function of silencing small RNAs (sRNAs) enrich in nuage, and it is often assumed that nuage is the cellular site where sRNAs are synthesized and encounter target transcripts for silencing. Using C. elegans as a model, we examine the complex multicondensate architecture of nuage and review evidence for compartmentalization of silencing pathways. We consider the possibility that nuage condensates balance the activity of competing sRNA pathways and serve to limit, rather than enhance, sRNA amplification to protect transcripts from dangerous runaway silencing.
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Affiliation(s)
- John Paul Tsu Ouyang
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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26
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Zhang J, Zhang W, Liu Y, Pi M, Jiang Y, Ainiwaer A, Mao S, Chen H, Ran Y, Sun S, Li W, Yao X, Chang Z, Yan Y. Emerging roles and potential application of PIWI-interacting RNA in urological tumors. Front Endocrinol (Lausanne) 2022; 13:1054216. [PMID: 36733811 PMCID: PMC9887041 DOI: 10.3389/fendo.2022.1054216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The piRNA (PIWI-interacting RNA) is P-Element induced wimpy testis (PIWI)-interacting RNA which is a small molecule, non-coding RNA with a length of 24-32nt. It was originally found in germ cells and is considered a regulator of germ cell function. It can interact with PIWI protein, a member of the Argonaute family, and play a role in the regulation of gene transcription and epigenetic silencing of transposable factors in the nucleus. More and more studies have shown that piRNAs are abnormally expressed in a variety of cancer tissues and patient fluids, and may become diagnostic tools, therapeutic targets, staging markers, and prognostic evaluation tools for cancer. This article reviews the recent research on piRNA and summarizes the structural characteristics, production mechanism, applications, and its role in urological tumors, to provide a reference value for piRNA to regulate urological tumors.
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Affiliation(s)
- Jingcheng Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Wentao Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yuchao Liu
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Man Pi
- Department of Pathology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yufeng Jiang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Ailiyaer Ainiwaer
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Shiyu Mao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Haotian Chen
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yuefei Ran
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Shuwen Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Li
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
| | - Yang Yan
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
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27
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Ito N, Takahashi T, Shiiba I, Nagashima S, Inatome R, Yanagi S. MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51. J Biochem 2021; 171:529-541. [PMID: 34964862 DOI: 10.1093/jb/mvab153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/19/2021] [Indexed: 11/12/2022] Open
Abstract
The transfer of phospholipids from the endoplasmic reticulum to mitochondria via the mitochondria-endoplasmic reticulum (ER) contact site (MERCS) is essential for maintaining mitochondrial function and integrity. Here, we identified RMDN3/PTPIP51, possessing phosphatidic acid (PA)-transfer activity, as a neighboring protein of the mitochondrial E3 ubiquitin ligase MITOL/MARCH5 by proximity-dependent biotin labeling using APEX2. We found that MITOL interacts with and ubiquitinates RMDN3. Mutational analysis identified lysine residue 89 in RMDN3 as a site of ubiquitination by MITOL. Loss of MITOL or the substitution of lysine 89 to arginine in RMDN3 significantly reduced the PA-binding activity of RMDN3, suggesting that MITOL regulates the transport of PA to mitochondria by activating RMDN3. Our findings imply that ubiquitin signaling regulates phospholipid transport at the MERCS.
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Affiliation(s)
- Naoki Ito
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Takara Takahashi
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Isshin Shiiba
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.,Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shun Nagashima
- Laboratory of Regenerative Medicine, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Ryoko Inatome
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
| | - Shigeru Yanagi
- Laboratory of Molecular Biochemistry, Department of Life Science, Faculty of Science, Gakushuin University, Toshima, Tokyo 171-8588, Japan
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28
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Xu C, Cao Y, Bao J. Building RNA-protein germ granules: insights from the multifaceted functions of DEAD-box helicase Vasa/Ddx4 in germline development. Cell Mol Life Sci 2021; 79:4. [PMID: 34921622 PMCID: PMC11072811 DOI: 10.1007/s00018-021-04069-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023]
Abstract
The segregation and maintenance of a dedicated germline in multicellular organisms is essential for species propagation in the sexually reproducing metazoan kingdom. The germline is distinct from somatic cells in that it is ultimately dedicated to acquiring the "totipotency" and to regenerating the offspring after fertilization. The most striking feature of germ cells lies in the presence of characteristic membraneless germ granules that have recently proven to behave like liquid droplets resulting from liquid-liquid phase separation (LLPS). Vasa/Ddx4, a faithful DEAD-box family germline marker highly conserved across metazoan species, harbors canonical DEAD-box motifs and typical intrinsically disordered sequences at both the N-terminus and C-terminus. This feature enables it to serve as a primary driving force behind germ granule formation and helicase-mediated RNA metabolism (e.g., piRNA biogenesis). Genetic ablation of Vasa/Ddx4 or the catalytic-dead mutations abolishing its helicase activity led to sexually dimorphic germline defects resulting in either male or female sterility among diverse species. While recent efforts have discovered pivotal functions of Vasa/Ddx4 in somatic cells, especially in multipotent stem cells, we herein summarize the helicase-dependent and -independent functions of Vasa/Ddx4 in the germline, and discuss recent findings of Vasa/Ddx4-mediated phase separation, germ granule formation and piRNA-dependent retrotransposon control essential for germline development.
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Affiliation(s)
- Caoling Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Yuzhu Cao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China
| | - Jianqiang Bao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Anhui, China.
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29
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Gainetdinov I, Colpan C, Cecchini K, Arif A, Jouravleva K, Albosta P, Vega-Badillo J, Lee Y, Özata DM, Zamore PD. Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability. Mol Cell 2021; 81:4826-4842.e8. [PMID: 34626567 DOI: 10.1016/j.molcel.2021.09.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) silence transposons, fight viral infections, and regulate gene expression. piRNA biogenesis concludes with 3' terminal trimming and 2'-O-methylation. Both trimming and methylation influence piRNA stability. Our biochemical data show that multiple mechanisms destabilize unmethylated mouse piRNAs, depending on whether the piRNA 5' or 3' sequence is complementary to a trigger RNA. Unlike target-directed degradation of microRNAs, complementarity-dependent destabilization of piRNAs in mice and flies is blocked by 3' terminal 2'-O-methylation and does not require base pairing to both the piRNA seed and the 3' sequence. In flies, 2'-O-methylation also protects small interfering RNAs (siRNAs) from complementarity-dependent destruction. By contrast, pre-piRNA trimming protects mouse piRNAs from a degradation pathway unaffected by trigger complementarity. In testis lysate and in vivo, internal or 3' terminal uridine- or guanine-rich tracts accelerate pre-piRNA decay. Loss of both trimming and 2'-O-methylation causes the mouse piRNA pathway to collapse, demonstrating that these modifications collaborate to stabilize piRNAs.
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Affiliation(s)
- Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Cansu Colpan
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Katharine Cecchini
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Amena Arif
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Karina Jouravleva
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Paul Albosta
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Joel Vega-Badillo
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Yongjin Lee
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, 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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30
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Bestetti I, Barbieri C, Sironi A, Specchia V, Yatsenko SA, De Donno MD, Caslini C, Gentilini D, Crippa M, Larizza L, Marozzi A, Rajkovic A, Toniolo D, Bozzetti MP, Finelli P. Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency. Hum Reprod 2021; 36:2975-2991. [PMID: 34480478 PMCID: PMC8523209 DOI: 10.1093/humrep/deab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/29/2021] [Indexed: 11/25/2022] Open
Abstract
STUDY QUESTION Can a targeted whole exome sequencing (WES) on a cohort of women showing a primary ovarian insufficiency (POI) phenotype at a young age, combined with a study of copy number variations, identify variants in candidate genes confirming their deleterious effect on ovarian function? SUMMARY ANSWER This integrated approach has proved effective in identifying novel candidate genes unveiling mechanisms involved in POI pathogenesis. WHAT IS KNOWN ALREADY POI, a condition occurring in 1% of women under 40 years of age, affects women’s fertility leading to a premature loss of ovarian reserve. The genetic causes of POI are highly heterogeneous and several determinants contributing to its prominent oligogenic inheritance pattern still need to be elucidated. STUDY DESIGN, SIZE, DURATION WES screening for pathogenic variants of 41 Italian women with non-syndromic primary and early secondary amenorrhoea occurring before age 25 was replicated on another 60 POI patients, including 35 French and 25 American women, to reveal statistically significant shared variants. PARTICIPANTS/MATERIALS, SETTING, METHODS The Italian POI patients’ DNA were processed by targeted WES including 542 RefSeq genes expressed or functioning during distinct reproductive or ovarian processes (e.g. DNA repair, meiosis, oocyte maturation, folliculogenesis and menopause). Extremely rare variants were filtered and selected by means of a Fisher Exact test using several publicly available datasets. A case-control Burden test was applied to highlight the most significant genes using two ad-hoc control female cohorts. To support the obtained data, the identified genes were screened on a novel cohort of 60 Caucasian POI patients and the same case-control analysis was carried out. Comparative analysis of the human identified genes was performed on mouse and Drosophila melanogaster by analysing the orthologous genes in their ovarian phenotype, and two of the selected genes were fruit fly modelled to explore their role in fertility. MAIN RESULTS AND THE ROLE OF CHANCE The filtering steps applied to search for extremely rare pathogenic variants in the Italian cohort revealed 64 validated single-nucleotide variants/Indels in 59 genes in 30 out of 41 screened women. Burden test analysis highlighted 13 ovarian genes as being the most enriched and significant. To validate these findings, filtering steps and Burden analysis on the second cohort of Caucasian patients yielded 11 significantly enriched genes. Among them, AFP, DMRT3, MOV10, FYN and MYC were significant in both patient cohorts and hence were considered strong candidates for POI. Mouse and Drosophila comparative analysis evaluated a conserved role through the evolution of several candidates, and functional studies using a Drosophila model, when applicable, supported the conserved role of the MOV10 armitage and DMRT3 dmrt93B orthologues in female fertility. LARGE SCALE DATA The datasets for the Italian cohort generated during the current study are publicly available at ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/): accession numbers SCV001364312 to SCV001364375. LIMITATIONS, REASONS FOR CAUTION This is a targeted WES analysis hunting variants in candidate genes previously identified by different genomic approaches. For most of the investigated sporadic cases, we could not track the parental inheritance, due to unavailability of the parents’ DNA samples; in addition, we might have overlooked additional rare variants in novel candidate POI genes extracted from the exome data. On the contrary, we might have considered some inherited variants whose clinical significance is uncertain and might not be causative for the patients’ phenotype. Additionally, as regards the Drosophila model, it will be extremely important in the future to have more mutants or RNAi strains available for each candidate gene in order to validate their role in POI pathogenesis. WIDER IMPLICATIONS OF THE FINDINGS The genomic, statistical, comparative and functional approaches integrated in our study convincingly support the extremely heterogeneous oligogenic nature of POI, and confirm the maintenance across the evolution of some key genes safeguarding fertility and successful reproduction. Two principal classes of genes were identified: (i) genes primarily involved in meiosis, namely in synaptonemal complex formation, asymmetric division and oocyte maturation and (ii) genes safeguarding cell maintenance (piRNA and DNA repair pathways). STUDY FUNDING/COMPETING INTEREST(S) This work was supported by Italian Ministry of Health grants ‘Ricerca Corrente’ (08C621_2016 and 08C924_2019) provided to IRCCS Istituto Auxologico Italiano, and by ‘Piano Sostegno alla Ricerca’ (PSR2020_FINELLI_LINEA_B) provided by the University of Milan; M.P.B. was supported by Telethon-Italy (grant number GG14181). There are no conflicts of interest.
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Affiliation(s)
- I Bestetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - C Barbieri
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milan, Italy
| | - A Sironi
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - V Specchia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - S A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M D De Donno
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - C Caslini
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - D Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Bioinformatics and Statistical Genomics Unit, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - M Crippa
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - L Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - A Marozzi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
| | - A Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San, Francisco, San Francisco, CA, USA.,Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - D Toniolo
- Division of Genetics and Cell Biology, San Raffaele Research Institute and Vita Salute University, Milan, Italy
| | - M P Bozzetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - P Finelli
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, Milan, Italy
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31
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Su JF, Concilla A, Zhang DZ, Zhao F, Shen FF, Zhang H, Zhou FY. PIWI-interacting RNAs: Mitochondria-based biogenesis and functions in cancer. Genes Dis 2021; 8:603-622. [PMID: 34291132 PMCID: PMC8278532 DOI: 10.1016/j.gendis.2020.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/27/2020] [Indexed: 12/29/2022] Open
Abstract
PIWI-interacting RNA (piRNAs), once thought to be mainly functioning in germlines, are now known to play an essential role in somatic and cancerous tissues. Ping-pong cycle initiation and mitochondria-based phased production constitute the core of the piRNA biogenesis and these two processes are well conserved in mammals, including humans. By being involved in DNA methylation, histone marker deposition, mRNA degradation, and protein modification, piRNAs also contribute to carcinogenesis partly due to oncogenic stress-induced piRNA dysregulation. Also, piRNAs play important roles in cancer stemness, drug resistance, and tumor immunology. Results from liquid biopsy analysis of piRNA can be used in both cancer diagnoses and cancer prognoses. A combination of targeting piRNA with other therapeutic strategies could be groundbreaking cancer treatment.
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Affiliation(s)
- Jing-Fen Su
- Anyang Key Laboratory for Esophageal Cancer Research, Anyang Cancer Hospital, The Forth Affiliated Hospital of Henan University of Science and Technology, Anyang, Henan Province, 455000, PR China
| | - Anthony Concilla
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA 19131, USA
| | - Dian-zheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA 19131, USA
| | - Fang Zhao
- Anyang Key Laboratory for Esophageal Cancer Research, Anyang Cancer Hospital, The Forth Affiliated Hospital of Henan University of Science and Technology, Anyang, Henan Province, 455000, PR China
| | - Fang-Fang Shen
- Key Laboratory for Tumor Translational Medicine, The Third Affiliated Hospital, Xinxiang Medical University, Xinxiang, Henan Province, 453000, PR China
| | - Hao Zhang
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, Guangdong Province, 510630, PR China
| | - Fu-You Zhou
- Anyang Key Laboratory for Esophageal Cancer Research, Anyang Cancer Hospital, The Forth Affiliated Hospital of Henan University of Science and Technology, Anyang, Henan Province, 455000, PR China
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32
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Onishi R, Yamanaka S, Siomi MC. piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: new insights and biodiversity. EMBO Rep 2021; 22:e53062. [PMID: 34347367 PMCID: PMC8490990 DOI: 10.15252/embr.202153062] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The PIWI‐interacting RNA (piRNA) pathway acts as a self‐defense mechanism against transposons to maintain germline genome integrity. Failures in the piRNA pathway cause DNA damage in the germline genome, disturbing inheritance of “correct” genetic information by the next generations and leading to infertility. piRNAs execute transposon repression in two ways: degrading their RNA transcripts and compacting the genomic loci via heterochromatinization. The former event is mechanistically similar to siRNA‐mediated RNA cleavage that occurs in the cytoplasm and has been investigated in many species including nematodes, fruit flies, and mammals. The latter event seems to be mechanistically parallel to siRNA‐centered kinetochore assembly and subsequent chromosome segregation, which has so far been studied particularly in fission yeast. Despite the interspecies conservations, the overall schemes of the nuclear events show clear biodiversity across species. In this review, we summarize the recent progress regarding piRNA‐mediated transcriptional silencing in Drosophila and discuss the biodiversity by comparing it with the equivalent piRNA‐mediated system in mice and the siRNA‐mediated system in fission yeast.
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Affiliation(s)
- Ryo Onishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Soichiro Yamanaka
- 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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33
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Chung PY, Shoji K, Izumi N, Tomari Y. Dynamic subcellular compartmentalization ensures fidelity of piRNA biogenesis in silkworms. EMBO Rep 2021; 22:e51342. [PMID: 33973704 DOI: 10.15252/embr.202051342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 11/09/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) guide PIWI proteins to silence transposable elements and safeguard fertility in germ cells. Many protein factors required for piRNA biogenesis localize to perinuclear ribonucleoprotein (RNP) condensates named nuage, where target silencing and piRNA amplification are thought to occur. In mice, some of the piRNA factors are found in discrete cytoplasmic foci called processing bodies (P-bodies). However, the dynamics and biological significance of such compartmentalization of the piRNA pathway remain unclear. Here, by analyzing the subcellular localization of functional mutants of piRNA factors, we show that piRNA factors are actively compartmentalized into nuage and P-bodies in silkworm cells. Proper demixing of nuage and P-bodies requires target cleavage by the PIWI protein Siwi and ATP hydrolysis by the DEAD-box helicase BmVasa, disruption of which leads to promiscuous overproduction of piRNAs deriving from non-transposable elements. Our study highlights a role of dynamic subcellular compartmentalization in ensuring the fidelity of piRNA biogenesis.
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Affiliation(s)
- Pui Yuen Chung
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Keisuke Shoji
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Natsuko Izumi
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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34
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Specchia V, Bozzetti MP. The Role of HSP90 in Preserving the Integrity of Genomes Against Transposons Is Evolutionarily Conserved. Cells 2021; 10:cells10051096. [PMID: 34064379 PMCID: PMC8147803 DOI: 10.3390/cells10051096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/31/2022] Open
Abstract
The HSP90 protein is a molecular chaperone intensively studied for its role in numerous cellular processes both under physiological and stress conditions. This protein acts on a wide range of substrates with a well-established role in cancer and neurological disorders. In this review, we focused on the involvement of HSP90 in the silencing of transposable elements and in the genomic integrity maintenance. The common feature of transposable elements is the potential jumping in new genomic positions, causing chromosome structure rearrangements, gene mutations, and influencing gene expression levels. The role of HSP90 in the control of these elements is evolutionarily conserved and opens new perspectives in the HSP90-related mechanisms underlying human disorders. Here, we discuss the hypothesis that its role in the piRNA pathway regulating transposons may be implicated in the onset of neurological diseases.
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35
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Munafò M, Lawless VR, Passera A, MacMillan S, Bornelöv S, Haussmann IU, Soller M, Hannon GJ, Czech B. Channel nuclear pore complex subunits are required for transposon silencing in Drosophila. eLife 2021; 10:e66321. [PMID: 33856346 PMCID: PMC8133776 DOI: 10.7554/elife.66321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
The nuclear pore complex (NPC) is the principal gateway between nucleus and cytoplasm that enables exchange of macromolecular cargo. Composed of multiple copies of ~30 different nucleoporins (Nups), the NPC acts as a selective portal, interacting with factors which individually license passage of specific cargo classes. Here we show that two Nups of the inner channel, Nup54 and Nup58, are essential for transposon silencing via the PIWI-interacting RNA (piRNA) pathway in the Drosophila ovary. In ovarian follicle cells, loss of Nup54 and Nup58 results in compromised piRNA biogenesis exclusively from the flamenco locus, whereas knockdowns of other NPC subunits have widespread consequences. This provides evidence that some Nups can acquire specialised roles in tissue-specific contexts. Our findings consolidate the idea that the NPC has functions beyond simply constituting a barrier to nuclear/cytoplasmic exchange as genomic loci subjected to strong selective pressure can exploit NPC subunits to facilitate their expression.
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Affiliation(s)
- Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Victoria R Lawless
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Alessandro Passera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Serena MacMillan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Irmgard U Haussmann
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City UniversityBirminghamUnited Kingdom
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of BirminghamBirminghamUnited Kingdom
- Birmingham Center for Genome Biology, University of BirminghamBirminghamUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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36
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Ramat A, Simonelig M. Functions of PIWI Proteins in Gene Regulation: New Arrows Added to the piRNA Quiver. Trends Genet 2021; 37:188-200. [DOI: 10.1016/j.tig.2020.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
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37
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Abstract
With the length of about 26-31 nt, PIWI-interacting RNA (piRNA) is a small non-coding RNA (ncRNA) that interacts with PIWI proteins to form the piRNA silencing complex (piRISC). PIWI is a subfamily of Argonaute, and piRNA must bind to PIWI to exert its regulatory role. Current studies indicated that piRNA and PIWI are significantly abnormally expressed in gastric, breast, kidney, colon, and lung cancers, and are involved in the initiation, progression, and metastasis of cancers, which may be the potential diagnostic tools, prognostic markers, and therapeutic targets for cancers. By reviewing piRNA recent studies, this research summarized the mechanism of piRNA generation and the functions of piRNA/PIWI in gastric, breast, kidney, colon, and lung cancers, providing a reference value for further piRNA research.
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38
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Mao K, Breen P, Ruvkun G. Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response. PLoS Biol 2020; 18:e3000996. [PMID: 33264285 PMCID: PMC7735679 DOI: 10.1371/journal.pbio.3000996] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/14/2020] [Accepted: 11/09/2020] [Indexed: 12/27/2022] Open
Abstract
RNA interference (RNAi) is an antiviral pathway common to many eukaryotes that detects and cleaves foreign nucleic acids. In mammals, mitochondrially localized proteins such as mitochondrial antiviral signaling (MAVS), retinoic acid-inducible gene I (RIG-I), and melanoma differentiation-associated protein 5 (MDA5) mediate antiviral responses. Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. The induction of RNAi also requires the conserved RNA decapping enzyme EOL-1/DXO. The transcriptional induction of eol-1 requires DRH-1 as well as the mitochondrial unfolded protein response (UPRmt). Upon mitochondrial dysfunction, EOL-1 is concentrated into foci that depend on the transcription of mitochondrial RNAs that may form double-stranded RNA (dsRNA), as has been observed in mammalian antiviral responses. Enhanced RNAi triggered by mitochondrial dysfunction is necessary for the increase in longevity that is induced by mitochondrial dysfunction. Surveillance of mitochondrial dysfunction in the nematode Caenorhabditis elegans triggers the activation of an RNA interference pathway to mediate antiviral defense, in a manner homologous to the mammalian RIG-I helicase viral response pathway.
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Affiliation(s)
- Kai Mao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Breen
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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39
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Chen K, Yu Y, Yang D, Yang X, Tang L, Liu Y, Luo X, R. Walter J, Liu Z, Xu J, Huang Y. Gtsf1 is essential for proper female sex determination and transposon silencing in the silkworm, Bombyx mori. PLoS Genet 2020; 16:e1009194. [PMID: 33137136 PMCID: PMC7660909 DOI: 10.1371/journal.pgen.1009194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/12/2020] [Accepted: 10/14/2020] [Indexed: 01/15/2023] Open
Abstract
Sex determination pathways are astoundingly diverse in insects. For instance, the silk moth Bombyx mori uniquely use various components of the piRNA pathway to produce the Fem signal for specification of the female fate. In this study, we identified BmGTSF1 as a novel piRNA factor which participates in B. mori sex determination. We found that BmGtsf1 has a distinct expression pattern compared to Drosophila and mouse. CRISPR/Cas9 induced mutation in BmGtsf1 resulted in partial sex reversal in genotypically female animals by shifting expression of the downstream targets BmMasc and Bmdsx to the male pattern. As levels of Fem piRNAs were substantially reduced in female mutants, we concluded that BmGtsf1 plays a critical role in the biogenesis of the feminizing signal. We also demonstrated that BmGTSF1 physically interacted with BmSIWI, a protein previously reported to be involved in female sex determination, indicating BmGTSF1 function as the cofactor of BmSIWI. BmGtsf1 mutation resulted in piRNA pathway dysregulation, including piRNA biogenesis defects and transposon derepression, suggesting BmGtsf1 is also a piRNA factor in the silkworm. Furthermore, we found that BmGtsf1 mutation leads to gametogenesis defects in both male and female. Our data suggested that BmGtsf1 is a new component involved in the sex determination pathway in B. mori. Sex determination is a fundamentally important process in most sexually reproducing metazoan. Nevertheless, the underlying mechanisms of sex determination are highly diverse. In B. mori, piRNAs derived from the W-chromosome-linked Fem precursor serve as the primary female determining signal. However, we still know little about the initiation of B. mori sex determination and its relationship with piRNA pathway. Here, we provided evidence that BmGTSF1 is a novel piRNA factor which is indispensable for B.mori female sex determination. Mutations in BmGtsf1 resulted in dysregulation of the piRNA pathway and caused partial female-male sex reversal. We also detected dramatic diminution of Fem piRNA in female mutant, indicating BmGTSF1 regulates B. mori sex determination via piRNA pathway. More importantly, we showed that BmGTSF1 interacted with BmSIWI, which protein had been reported to be involved in piRNA pathway and sex determination in B. mori, supporting the conclusion that BmGTSF1 is a novel factor for piRNA pathway and sex determination.
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Affiliation(s)
- Kai Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Yu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Dehong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xu Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Linmeng Tang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yujia Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xingyu Luo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - James R. Walter
- Department of Ecology and Evolutionary Biology, University of Kansas, NV, United States of America
| | - Zulian Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (JX); (YH)
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (JX); (YH)
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40
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Gamez S, Srivastav S, Akbari OS, Lau NC. Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways. Cells 2020; 9:E2180. [PMID: 32992598 PMCID: PMC7601171 DOI: 10.3390/cells9102180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Satyam Srivastav
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA;
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Nelson C. Lau
- Department of Biochemistry and Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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41
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Pippadpally S, Venkatesh T. Deciphering piRNA biogenesis through cytoplasmic granules, mitochondria and exosomes. Arch Biochem Biophys 2020; 695:108597. [PMID: 32976825 DOI: 10.1016/j.abb.2020.108597] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 12/31/2022]
Abstract
RNA systems biology is marked by a myriad of cellular processes mediated by small and long non-coding RNAs. Small non-coding RNAs include siRNAs (small interfering RNAs), miRNAs (microRNAs), tRFs(tRNA derived fragments), and piRNAs (PIWI-interacting RNAs). piRNAs are vital for the maintenance of the germ-line integrity and repress the transposons either transcriptionally or post-transcriptionally. Studies based on model organisms have shown that defects in the piRNA pathway exhibit impaired gametogenesis and loss of fertility. piRNA biogenesis is marked by transcription of precursor molecules and their subsequent processing in the cytoplasm to generate mature piRNAs. Their biogenesis is unique and complex, which involves non-canonical transcription and self-amplification mechanisms such as the ping-pong cycle. piRNA biogenesis is different in somatic and germ cells and involves the role of cytoplasmic granules in addition to mitochondria. In this review, we discuss the biogenesis and maturation of piRNAs in various cytoplasmic granules such as Yb and nuage bodies. Also, we review the role of P bodies, stress granules, and P granules, and membrane-bound compartments such as mitochondria and exosomes in piRNA biogenesis.
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Affiliation(s)
- Srikanth Pippadpally
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, 671316, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, 671316, India.
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42
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Ding D, Chen C. Zucchini: the key ingredient to unveil piRNA precursor processing†. Biol Reprod 2020; 103:452-454. [PMID: 32524138 DOI: 10.1093/biolre/ioaa090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
- Deqiang Ding
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, Michigan, USA.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
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43
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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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44
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Wang L, Barbash DA, Kelleher ES. Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity. PLoS Genet 2020; 16:e1008861. [PMID: 32525870 PMCID: PMC7310878 DOI: 10.1371/journal.pgen.1008861] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 06/23/2020] [Accepted: 05/14/2020] [Indexed: 02/05/2023] Open
Abstract
In metazoan germlines, the piRNA pathway acts as a genomic immune system, employing small RNA-mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). Expression of genomic TEs is proposed to initiate self regulation by increasing the production of repressive piRNAs, thereby “adapting” piRNA-mediated control to the most active TE families. Surprisingly, however, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, evolve rapidly and adaptively in animals. If TE silencing is ensured through piRNA biogenesis, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences between Drosophila melanogaster and D. simulans alleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. In contrast to piRNA-mediated transcriptional regulators examined in previous studies, these three proteins have cytoplasmic functions in piRNA maturation and post-transcriptional silencing. Across all three proteins we observed interspecific divergence in the regulation of only a handful of TE families, which were more robustly silenced by the heterospecific piRNA pathway protein. This unexpected result suggests that unlike transcriptional regulators, positive selection has not acted on cytoplasmic piRNA effector proteins to enhance their function in TE repression. Rather, TEs may evolve to “escape” silencing by host proteins. We further discovered that D. simulans alleles of aub and armi exhibit enhanced off-target effects on host transcripts in a D. melanogaster background, as well as modest reductions in the efficiency of piRNA biogenesis, suggesting that promiscuous binding of D. simulans Aub and Armi proteins to host transcripts reduces their participation in piRNA production. Avoidance of genomic auto-immunity may therefore be a critical target of selection. Our observations suggest that piRNA effector proteins are subject to an evolutionary trade-off between defending the host genome from the harmful effect of TEs while also minimizing collateral damage to host genes. Transposable elements are mobile fragments of selfish DNA that burden host genomes with deleterious mutations and incite genome instability. Host cells employ a specialized small-RNA mediated silencing pathway, the piRNA pathway, to act as a genomic immune system suppressing the mobilization of TEs. Changes in genomic TE content are met with rapid changes in the piRNA pool, thereby maintaining host control over transposition. However, piRNA pathway proteins—which enact piRNA biogenesis and silence target TEs—also evolve adaptively. To isolate forces that underlie this adaptive evolution, we examined functional divergence between two Drosophila species for three adaptively evolving piRNA pathway proteins. To our surprise, we found very few differences in TE regulation, suggesting that evolution has not generally acted to enhance control of TE parasites. Rather, we discovered interspecific differences in the regulation of host mRNAs for two proteins, which suggested that proteins evolve to avoid off-target silencing of host transcripts. We propose that the avoidance of such “genomic autoimmunity” is an important and underappreciated force driving the adaptive evolution of piRNA proteins.
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Affiliation(s)
- Luyang Wang
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Daniel A. Barbash
- Dept. Molecular Biology & Genetics, Cornell University, Ithaca, New York, United States of America
| | - Erin S. Kelleher
- Dept. Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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Cacchione S, Cenci G, Raffa GD. Silence at the End: How Drosophila Regulates Expression and Transposition of Telomeric Retroelements. J Mol Biol 2020; 432:4305-4321. [PMID: 32512004 DOI: 10.1016/j.jmb.2020.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 01/26/2023]
Abstract
The maintenance of chromosome ends in Drosophila is an exceptional phenomenon because it relies on the transposition of specialized retrotransposons rather than on the activity of the enzyme telomerase that maintains telomeres in almost every other eukaryotic species. Sequential transpositions of Het-A, TART, and TAHRE (HTT) onto chromosome ends produce long head-to-tail arrays that are reminiscent to the long arrays of short repeats produced by telomerase in other organisms. Coordinating the activation and silencing of the HTT array with the recruitment of telomere capping proteins favors proper telomere function. However, how this coordination is achieved is not well understood. Like other Drosophila retrotransposons, telomeric elements are regulated by the piRNA pathway. Remarkably, HTT arrays are both source of piRNA and targets of gene silencing thus making the regulation of Drosophila telomeric transposons a unique event among eukaryotes. Herein we will review the genetic and molecular mechanisms underlying the regulation of HTT transcription and transposition and will discuss the possibility of a crosstalk between piRNA-mediated regulation, telomeric chromatin establishment, and telomere protection.
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Affiliation(s)
- Stefano Cacchione
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy.
| | - Giovanni Cenci
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy; Fondazione Cenci Bolognetti, Istituto Pasteur, Rome, Italy.
| | - Grazia Daniela Raffa
- Department of Biology and Biotechnology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy.
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Fonseca Cabral G, Azevedo dos Santos Pinheiro J, Vidal AF, Santos S, Ribeiro-dos-Santos Â. piRNAs in Gastric Cancer: A New Approach Towards Translational Research. Int J Mol Sci 2020; 21:ijms21062126. [PMID: 32204558 PMCID: PMC7139476 DOI: 10.3390/ijms21062126] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Gastric cancer is currently the third leading cause of cancer-related deaths worldwide, usually diagnosed at late stages. The development of new biomarkers to improve its prevention and patient management is critical for disease control. piRNAs are small regulatory RNAs important for gene silencing mechanisms, mainly associated with the silencing of transposable elements. piRNA pathways may also be involved in gene regulation and the deregulation of piRNAs may be an important factor in carcinogenic processes. Thus, several studies suggest piRNAs as potential cancer biomarkers. Translational studies suggest that piRNAs may regulate key genes and pathways associated with gastric cancer progression, though there is no functional annotation in piRNA databases. The impacts of genetic variants in piRNA genes and their influence in gastric cancer development remains elusive, highlighting the gap in piRNA regulatory mechanisms knowledge. Here, we discuss the current state of understanding of piRNA-mediated regulation and piRNA functions and suggest that genetic alterations in piRNA genes may affect their functionality, thus, it may be associated with gastric carcinogenesis. Conclusions: In the era of precision medicine, investigations about genetic and epigenetic mechanisms are essential to further comprehend gastric carcinogenesis and the role of piRNAs as potential biomarkers for translational research.
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Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Amanda Ferreira Vidal
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
- Correspondence: ; Tel.: +55-091-3201-7843
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Yamashiro H, Negishi M, Kinoshita T, Ishizu H, Ohtani H, Siomi MC. Armitage determines Piwi-piRISC processing from precursor formation and quality control to inter-organelle translocation. EMBO Rep 2020; 21:e48769. [PMID: 31833223 PMCID: PMC7001504 DOI: 10.15252/embr.201948769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 01/06/2023] Open
Abstract
Piwi and piRNA form the piRNA-induced silencing complex (piRISC) to repress transposons. In the current model, Armitage (Armi) brings the Piwi-piRISC precursor (pre-piRISC) to mitochondria, where Zucchini-dependent piRISC maturation occurs. Here, we show that Armi is necessary for Piwi-pre-piRISC formation at Yb bodies and that Armi triggers the exit of Piwi-pre-piRISC from Yb bodies and the translocation to mitochondria. Piwi-pre-piRISC resist leaving Yb bodies until Armi binds Piwi-pre-piRISC through the piRNA precursors. The lack of the Armi N-terminus also blocks the Piwi-pre-piRISC exit from Yb bodies. Thus, Armi determines Piwi-piRISC processing, in a multilayered manner, from precursor formation and quality control to inter-organelle translocation for maturation.
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Affiliation(s)
- Haruna Yamashiro
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Mayu Negishi
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Tatsuki Kinoshita
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
| | - Hirotsugu Ishizu
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
| | - Hitoshi Ohtani
- Department of Molecular BiologyKeio University School of MedicineTokyoJapan
- Present address:
Van Andel Research InstituteGrand RapidsMIUSA
| | - Mikiko C Siomi
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoTokyoJapan
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Zucchini consensus motifs determine the mechanism of pre-piRNA production. Nature 2020; 578:311-316. [PMID: 31996847 DOI: 10.1038/s41586-020-1966-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022]
Abstract
PIWI-interacting RNAs (piRNAs) of between approximately 24 and 31 nucleotides in length guide PIWI proteins to silence transposons in animal gonads, thereby ensuring fertility1. In the biogenesis of piRNAs, PIWI proteins are first loaded with 5'-monophosphorylated RNA fragments called pre-pre-piRNAs, which then undergo endonucleolytic cleavage to produce pre-piRNAs1,2. Subsequently, the 3'-ends of pre-piRNAs are trimmed by the exonuclease Trimmer (PNLDC1 in mouse)3-6 and 2'-O-methylated by the methyltransferase Hen1 (HENMT1 in mouse)7-9, generating mature piRNAs. It is assumed that the endonuclease Zucchini (MitoPLD in mouse) is a major enzyme catalysing the cleavage of pre-pre-piRNAs into pre-piRNAs10-13. However, direct evidence for this model is lacking, and how pre-piRNAs are generated remains unclear. Here, to analyse pre-piRNA production, we established a Trimmer-knockout silkworm cell line and derived a cell-free system that faithfully recapitulates Zucchini-mediated cleavage of PIWI-loaded pre-pre-piRNAs. We found that pre-piRNAs are generated by parallel Zucchini-dependent and -independent mechanisms. Cleavage by Zucchini occurs at previously unrecognized consensus motifs on pre-pre-piRNAs, requires the RNA helicase Armitage, and is accompanied by 2'-O-methylation of pre-piRNAs. By contrast, slicing of pre-pre-piRNAs with weak Zucchini motifs is achieved by downstream complementary piRNAs, producing pre-piRNAs without 2'-O-methylation. Regardless of the endonucleolytic mechanism, pre-piRNAs are matured by Trimmer and Hen1. Our findings highlight multiplexed processing of piRNA precursors that supports robust and flexible piRNA biogenesis.
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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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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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