1
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Shaker FH, Sanad EF, Elghazaly H, Hsia SM, Hamdy NM. piR-823 tale as emerging cancer-hallmark molecular marker in different cancer types: a step-toward ncRNA-precision. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03308-z. [PMID: 39102033 DOI: 10.1007/s00210-024-03308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
PIWI-interacting RNAs (piRNAs) have received a lot of attention for their functions in cancer research. This class of short non-coding RNAs (ncRNA) has roles in genomic stability, chromatin remodeling, messenger RNA (mRNA) integrity, and genome structure. We summarized the mechanisms underlying the biogenesis and regulatory molecular functions of piRNAs. Among all piRNAs studied in cancer, this review offers a comprehensive analysis of the emerging roles of piR-823 in various types of cancer, including colorectal, gastric, liver, breast, and renal cancers, as well as multiple myeloma. piR-823 has emerged as a crucial modulator of various cancer hallmarks through regulating multiple pathways. In the current review, we analyzed several databases and conducted an extensive literature search to explore the influence of piR-823 in carcinogenesis in addition to describing the potential application of piR-823 as prognostic and diagnostic markers as well as the therapeutic potential toward ncRNA precision.
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Affiliation(s)
- Fatma H Shaker
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Eman F Sanad
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Hesham Elghazaly
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Shih-Min Hsia
- School of Food and Safety, Nutrition Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 110301, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 110301, Taiwan
| | - Nadia M Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt.
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2
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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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3
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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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4
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Ma X, Niu X, Huang S, Li S, Ran X, Wang J, Dai X. The piRNAs present in the developing testes of Chinese indigenous Xiang pigs. Theriogenology 2022; 189:92-106. [PMID: 35738035 DOI: 10.1016/j.theriogenology.2022.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/21/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
The piRNA pathway plays an essential role in defense against transposable elements in the germline tissues of animals and contributes to post-transcriptional regulation of genes. Xiang pigs present an earlier sexual maturation compared with most European pig breeds, but the role that the piRNA pathway plays in the development of Xiang pigs is currently not understood. In this study, we sequenced and analyzed piRNAs expressed in the testes of Xiang pigs at four different ages, and identified endogenous piRNAs which were highly abundant at each time point. The lengths of the identified piRNAs ranged from 24 to 34 nucleotides (nt), with the most abundant length being 29 nt. Additionally, there was a strong bias for uracil at the first position, a slight bias for adenine at position 10 and frequent 5'-10 nt complementary sequences, suggesting that ping-pong-mediated silencing is present in the Xiang pig germline. We observed that the piRNA composition changed from TE-associated piRNAs in two- and three-month-old testes to predominantly gene-derived and intergenic piRNAs in six- and twelve-month-old testes, with a gradual increase in the expression level of piRNAs over the course of testis development. And more than half of piRNA reads mapped to just a few of 473 predicted piRNA clusters. Additionally, we found that several genes were highly enriched by piRNA reads, including CYP19A1, PRMT8, SUZ12, WWOX, SGSM1 and MIF. The functions of these genes are primarily associated with steroidogenesis and histone modification. Changes in piRNA composition and widespread expression patterns during spermatid development indicate that these small ncRNAs may be responsible not only for transposon suppression but also for post-transcriptional regulation of several protein-coding genes essential for normal spermatogenesis.
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Affiliation(s)
- Xinrui Ma
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Shihui Huang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Sheng Li
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xueqin Ran
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Jiafu Wang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xinlan Dai
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
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5
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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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6
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Joosten J, Overheul GJ, Van Rij RP, Miesen P. Endogenous piRNA-guided slicing triggers responder and trailer piRNA production from viral RNA in Aedes aegypti mosquitoes. Nucleic Acids Res 2021; 49:8886-8899. [PMID: 34331446 PMCID: PMC8421150 DOI: 10.1093/nar/gkab640] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
In the germline of animals, PIWI interacting (pi)RNAs protect the genome against the detrimental effects of transposon mobilization. In Drosophila, piRNA-mediated cleavage of transposon RNA triggers the production of responder piRNAs via ping-pong amplification. Responder piRNA 3' end formation by the nuclease Zucchini is coupled to the production of downstream trailer piRNAs, expanding the repertoire of transposon piRNA sequences. In Aedes aegypti mosquitoes, piRNAs are generated from viral RNA, yet, it is unknown how viral piRNA 3' ends are formed and whether viral RNA cleavage gives rise to trailer piRNA production. Here we report that in Ae. aegypti, virus- and transposon-derived piRNAs have sharp 3' ends, and are biased for downstream uridine residues, features reminiscent of Zucchini cleavage of precursor piRNAs in Drosophila. We designed a reporter system to study viral piRNA 3' end formation and found that targeting viral RNA by abundant endogenous piRNAs triggers the production of responder and trailer piRNAs. Using this reporter, we identified the Ae. aegypti orthologs of Zucchini and Nibbler, two nucleases involved in piRNA 3' end formation. Our results furthermore suggest that autonomous piRNA production from viral RNA can be triggered and expanded by an initial cleavage event guided by genome-encoded piRNAs.
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Affiliation(s)
- Joep Joosten
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, P.O. Box 9101, 6500 HB, The Netherlands
| | - Gijs J Overheul
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, P.O. Box 9101, 6500 HB, The Netherlands
| | - Ronald P Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, P.O. Box 9101, 6500 HB, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, P.O. Box 9101, 6500 HB, The Netherlands
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7
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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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8
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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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9
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Shin E, Jin H, Suh D, Luo Y, Ha H, Kim TH, Hahn Y, Hyun S, Lee K, Bae J. An alternative miRISC targets a cancer-associated coding sequence mutation in FOXL2. EMBO J 2020; 39:e104719. [PMID: 33215742 PMCID: PMC7737606 DOI: 10.15252/embj.2020104719|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent evidence suggests that animal microRNAs (miRNAs) can target coding sequences (CDSs); however, the pathophysiological importance of such targeting remains unknown. Here, we show that a somatic heterozygous missense mutation (c.402C>G; p.C134W) in FOXL2, a feature shared by virtually all adult-type granulosa cell tumors (AGCTs), introduces a target site for miR-1236, which causes haploinsufficiency of the tumor-suppressor FOXL2. This miR-1236-mediated selective degradation of the variant FOXL2 mRNA is preferentially conducted by a distinct miRNA-loaded RNA-induced silencing complex (miRISC) directed by the Argonaute3 (AGO3) and DHX9 proteins. In both patients and a mouse model of AGCT, abundance of the inversely regulated variant FOXL2 with miR-1236 levels is highly correlated with malignant features of AGCT. Our study provides a molecular basis for understanding the conserved FOXL2 CDS mutation-mediated etiology of AGCT, revealing the existence of a previously unidentified mechanism of miRNA-targeting disease-associated mutations in the CDS by forming a non-canonical miRISC.
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Affiliation(s)
| | - Hanyong Jin
- Department of Life ScienceChung‐Ang UniversitySeoulKorea
| | - Dae‐Shik Suh
- Department of Obstetrics and GynecologyAsan Medical CenterUniversity of Ulsan College of MedicineSeoulKorea
| | - Yongyang Luo
- School of PharmacyChung‐Ang UniversitySeoulKorea
| | - Hye‐Jeong Ha
- School of PharmacyChung‐Ang UniversitySeoulKorea
| | - Tae Heon Kim
- Department of PathologyBundang CHA HospitalCHA UniversitySeongnamKorea
| | - Yoonsoo Hahn
- Department of Life ScienceChung‐Ang UniversitySeoulKorea
| | - Seogang Hyun
- Department of Life ScienceChung‐Ang UniversitySeoulKorea
| | - Kangseok Lee
- Department of Life ScienceChung‐Ang UniversitySeoulKorea
| | - Jeehyeon Bae
- School of PharmacyChung‐Ang UniversitySeoulKorea
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10
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Shin E, Jin H, Suh DS, Luo Y, Ha HJ, Kim TH, Hahn Y, Hyun S, Lee K, Bae J. An alternative miRISC targets a cancer-associated coding sequence mutation in FOXL2. EMBO J 2020; 39:e104719. [PMID: 33215742 PMCID: PMC7737606 DOI: 10.15252/embj.2020104719] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 08/28/2020] [Accepted: 09/06/2020] [Indexed: 12/16/2022] Open
Abstract
Recent evidence suggests that animal microRNAs (miRNAs) can target coding sequences (CDSs); however, the pathophysiological importance of such targeting remains unknown. Here, we show that a somatic heterozygous missense mutation (c.402C>G; p.C134W) in FOXL2, a feature shared by virtually all adult-type granulosa cell tumors (AGCTs), introduces a target site for miR-1236, which causes haploinsufficiency of the tumor-suppressor FOXL2. This miR-1236-mediated selective degradation of the variant FOXL2 mRNA is preferentially conducted by a distinct miRNA-loaded RNA-induced silencing complex (miRISC) directed by the Argonaute3 (AGO3) and DHX9 proteins. In both patients and a mouse model of AGCT, abundance of the inversely regulated variant FOXL2 with miR-1236 levels is highly correlated with malignant features of AGCT. Our study provides a molecular basis for understanding the conserved FOXL2 CDS mutation-mediated etiology of AGCT, revealing the existence of a previously unidentified mechanism of miRNA-targeting disease-associated mutations in the CDS by forming a non-canonical miRISC.
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Affiliation(s)
| | - Hanyong Jin
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Dae-Shik Suh
- Department of Obstetrics and Gynecology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yongyang Luo
- School of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Hye-Jeong Ha
- School of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Tae Heon Kim
- Department of Pathology, Bundang CHA Hospital, CHA University, Seongnam, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seogang Hyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Jeehyeon Bae
- School of Pharmacy, Chung-Ang University, Seoul, Korea
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11
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Greenhalgh R, Dermauw W, Glas JJ, Rombauts S, Wybouw N, Thomas J, Alba JM, Pritham EJ, Legarrea S, Feyereisen R, Van de Peer Y, Van Leeuwen T, Clark RM, Kant MR. Genome streamlining in a minute herbivore that manipulates its host plant. eLife 2020; 9:56689. [PMID: 33095158 PMCID: PMC7738191 DOI: 10.7554/elife.56689] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, United States
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris J Glas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Juan M Alba
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Saioa Legarrea
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Richard M Clark
- School of Biological Sciences, University of Utah, Salt Lake City, United States.,Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, United States
| | - Merijn R Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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12
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Sukthaworn S, Panyim S, Udomkit A. Homologues of Piwi control transposable elements and development of male germline in Penaeus monodon. Comp Biochem Physiol A Mol Integr Physiol 2020; 250:110807. [PMID: 32971288 DOI: 10.1016/j.cbpa.2020.110807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
PIWI belongs to the Argonaute protein family, which is a major protein component in RNA silencing pathway. Piwi proteins play roles in the control of transposons and germline development. They have been widely studied in vertebrates and flies, while very little is known in crustacean so far. We have previously identified and characterized a cDNA encoding Piwi protein (PmPiwi1) in the black tiger shrimp Penaeus monodon. In this study, a cDNA encoding another Piwi protein namely PmPiwi2 was identified by rapid amplification of cDNA ends (RACEs). PmPiwi2 was expressed solely in shrimp testis and ovary, indicating its potential role in germ cell development. Similar to PmPiwi1, PmPiwi2 also plays a part in the control of transposons as PmPiwi2-knockdown shrimp showed a significant increase in the expression of gypsy2 retrotransposon and mariner element in the testis. In addition, a reduction of sperm numbers in the spermatophore of PmPiwi2-knockdown shrimp suggests that PmPiwi2 is required for spermatogenesis similar to PmPiwi1. This study further demonstrated that apoptotic cell death was strongly detected in spermatogonia and spermatocyte cells of both PmPiwi-knockdown shrimp and thus, could be the cause of reduced sperm count. Investigation of sperm morphology showed a remarkably high proportion of abnormal sperms in the spermatophore of the PmPiwi1-knockdown shrimp, while PmPiwi2-knockdown shrimp had comparable percentage of abnormal sperms to the control shrimp. Consistently, the expression of KIFC1, a gene that is necessary for spermiogenesis was significantly reduced upon PmPiwi1 silencing, but not in the PmPiwi2-knockdown shrimp. Our results suggested that while both PmPiwis are required for the development of spermatid, only PmPiwi1 is possibly involved in the final stage of sperm maturation.
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Affiliation(s)
- Suchitraporn Sukthaworn
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand
| | - Sakol Panyim
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand; Department of Biochemistry, Faculty of Sciences, Mahidol University, Rama VI Road, Phayathai, Bangkok 10400, Thailand
| | - Apinunt Udomkit
- Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom 73170, Thailand.
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13
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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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14
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Abstract
Liver cancer is one of the most common and deadly cancers in the world. In recent years, non-coding RNA has been a hot topic in liver cancer research. piRNAs (PIWI-interacting RNAs) are a new type of small non-coding RNA, which are formed by the PIWI proteins interacting with RNA. The latest research shows that piRNA and PIWI proteins are abnormally expressed in various cancers, including pancreatic, colorectal, breast, etc. piRNA plays an important regulatory role in liver cancer. In this review, we discuss the biological function of piRNAs and new progress in the development of liver cancer, and new targets and ideas for piRNA and PIWI proteins in the diagnosis and treatment of liver cancer.
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Affiliation(s)
- Jiamin Xu
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Xi Yang
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Qing Zhou
- Department of Critical Care Medicine, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Jing Zhuang
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Shuwen Han
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
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15
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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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16
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Abstract
Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
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17
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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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18
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Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 2019; 20:89-108. [PMID: 30446728 DOI: 10.1038/s41576-018-0073-3] [Citation(s) in RCA: 641] [Impact Index Per Article: 128.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.
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Affiliation(s)
- Deniz M Ozata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ansgar Zoch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
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19
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Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Mol Cell 2019; 74:982-995.e6. [PMID: 31076285 DOI: 10.1016/j.molcel.2019.04.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022]
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in Drosophila ovaries, ensuring female fertility. Two coupled pathways generate germline piRNAs: the ping-pong cycle, in which the PIWI proteins Aubergine and Ago3 increase the abundance of pre-existing piRNAs, and the phased piRNA pathway, which generates strings of tail-to-head piRNAs, one after another. Proteins acting in the ping-pong cycle localize to nuage, whereas phased piRNA production requires Zucchini, an endonuclease on the mitochondrial surface. Here, we report that Armitage (Armi), an RNA-binding ATPase localized to both nuage and mitochondria, links the ping-pong cycle to the phased piRNA pathway. Mutations that block phased piRNA production deplete Armi from nuage. Armi ATPase mutants cannot support phased piRNA production and inappropriately bind mRNA instead of piRNA precursors. We propose that Armi shuttles between nuage and mitochondria, feeding precursor piRNAs generated by Ago3 cleavage into the Zucchini-dependent production of Aubergine- and Piwi-bound piRNAs on the mitochondrial surface.
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Affiliation(s)
- Daniel Tianfang Ge
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Wei Wang
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Cindy Tipping
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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20
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Erwin AA, Blumenstiel JP. Aging in the Drosophila ovary: contrasting changes in the expression of the piRNA machinery and mitochondria but no global release of transposable elements. BMC Genomics 2019; 20:305. [PMID: 31014230 PMCID: PMC6480902 DOI: 10.1186/s12864-019-5668-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/08/2019] [Indexed: 01/06/2023] Open
Abstract
Background Evolutionary theory indicates that the dynamics of aging in the soma and reproductive tissues may be distinct. This difference arises from the fact that only the germline lineage establishes future generations. In the soma, changes in the landscape of heterochromatin have been proposed to have an important role in aging. This is because redistribution of heterochromatin during aging has been linked to the derepression of transposable elements and an overall loss of somatic gene regulation. A role for changes in the chromatin landscape in the aging of reproductive tissues is less well established. Whether or not epigenetic factors, such as heterochromatin marks, are perturbed in aging reproductive tissues is of interest because, in special cases, epigenetic variation may be heritable. Using mRNA sequencing data from late-stage egg chambers in Drosophila melanogaster, we characterized the landscape of altered gene and transposable element expression in aged reproductive tissues. This allowed us to test the hypothesis that reproductive tissues may differ from somatic tissues in their response to aging. Results We show that age-related expression changes in late-stage egg chambers tend to occur in genes residing in heterochromatin, particularly on the largely heterochromatic 4th chromosome. However, these expression differences are seen as both decreases and increases during aging, inconsistent with a general loss of heterochromatic silencing. We also identify an increase in expression of the piRNA machinery, suggesting an age-related increased investment in the maintenance of genome stability. We further identify a strong age-related reduction in the expression of mitochondrial transcripts. However, we find no evidence for global TE derepression in reproductive tissues. Rather, the observed effects of aging on TEs are primarily strain and family specific. Conclusions These results identify unique responses in somatic versus reproductive tissue with regards to aging. As in somatic tissues, female reproductive tissues show reduced expression of mitochondrial genes. In contrast, the piRNA machinery shows increased expression during aging. Overall, these results also indicate that global loss of TE control observed in other studies may be unique to the soma and sensitive to genetic background and TE family. Electronic supplementary material The online version of this article (10.1186/s12864-019-5668-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra A Erwin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
| | - Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA.
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21
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Sukthaworn S, Panyim S, Udomkit A. Functional characterization of a cDNA encoding Piwi protein in Penaeus monodon and its potential roles in controlling transposon expression and spermatogenesis. Comp Biochem Physiol A Mol Integr Physiol 2019; 229:60-68. [DOI: 10.1016/j.cbpa.2018.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/22/2023]
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22
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Cheng Y, Chen D. Fruit fly research in China. J Genet Genomics 2018; 45:583-592. [PMID: 30455037 DOI: 10.1016/j.jgg.2018.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/21/2018] [Accepted: 09/29/2018] [Indexed: 11/19/2022]
Abstract
Served as a model organism over a century, fruit fly has significantly pushed forward the development of global scientific research, including in China. The high similarity in genomic features between fruit fly and human enables this tiny insect to benefit the biomedical studies of human diseases. In the past decades, Chinese biologists have used fruit fly to make numerous achievements on understanding the fundamental questions in many diverse areas of biology. Here, we review some of the recent fruit fly studies in China, and mainly focus on those studies in the fields of stem cell biology, cancer therapy and regeneration medicine, neurological disorders and epigenetics.
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Affiliation(s)
- Ying Cheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahua Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Subcellular Specialization and Organelle Behavior in Germ Cells. Genetics 2018; 208:19-51. [PMID: 29301947 DOI: 10.1534/genetics.117.300184] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 08/17/2017] [Indexed: 11/18/2022] Open
Abstract
Gametes, eggs and sperm, are the highly specialized cell types on which the development of new life solely depends. Although all cells share essential organelles, such as the ER (endoplasmic reticulum), Golgi, mitochondria, and centrosomes, germ cells display unique regulation and behavior of organelles during gametogenesis. These germ cell-specific functions of organelles serve critical roles in successful gamete production. In this chapter, I will review the behaviors and roles of organelles during germ cell differentiation.
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24
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Dattani A, Sridhar D, Aziz Aboobaker A. Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation. Semin Cell Dev Biol 2018; 87:79-94. [PMID: 29694837 DOI: 10.1016/j.semcdb.2018.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
Abstract
Planarian flatworms possess pluripotent stem cells (neoblasts) that are able to differentiate into all cell types that constitute the adult body plan. Consequently, planarians possess remarkable regenerative capabilities. Transcriptomic studies have revealed that gene expression is coordinated to maintain neoblast pluripotency, and ensure correct lineage specification during differentiation. But as yet they have not revealed how this regulation of expression is controlled. In this review, we propose that planarians represent a unique and effective system to study the epigenetic regulation of these processes in an in vivo context. We consolidate evidence suggesting that although DNA methylation is likely present in some flatworm lineages, it does not regulate neoblast function in Schmidtea mediterranea. A number of phenotypic studies have documented the role of histone modification and chromatin remodelling complexes in regulating distinct neoblast processes, and we focus on four important examples of planarian epigenetic regulators: Nucleosome Remodeling Deacetylase (NuRD) complex, Polycomb Repressive Complex (PRC), the SET1/MLL methyltransferases, and the nuclear PIWI/piRNA complex. Given the recent advent of ChIP-seq in planarians, we propose future avenues of research that will identify the genomic targets of these complexes allowing for a clearer picture of how neoblast processes are coordinated at the epigenetic level. These insights into neoblast biology may be directly relevant to mammalian stem cells and disease. The unique biology of planarians will also allow us to investigate how extracellular signals feed into epigenetic regulatory networks to govern concerted neoblast responses during regenerative polarity, tissue patterning, and remodelling.
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Affiliation(s)
- Anish Dattani
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
| | - Divya Sridhar
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
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25
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Hameed MS, Wang Z, Vasseur L, Yang G. Molecular Characterization and the Function of Argonaute3 in RNAi Pathway of Plutella xylostella. Int J Mol Sci 2018; 19:ijms19041249. [PMID: 29677157 PMCID: PMC5979473 DOI: 10.3390/ijms19041249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 01/30/2023] Open
Abstract
Argonaute (Ago) protein family plays a key role in the RNA interference (RNAi) process in different insects including Lepidopteran. However, the role of Ago proteins in the RNAi pathway of Plutella xylostella is still unknown. We cloned an Argonaute3 gene in P. xylostella (PxAgo3) with the complete coding sequence of 2832 bp. The encoded protein had 935 amino acids with an expected molecular weight of 108.9 kDa and an isoelectric point of 9.29. It contained a PAZ (PIWI/Argonaute/Zwile) domain and PIWI (P-element-induced whimpy testes) domain. PxAgo3 was classified into the Piwi subfamily of Ago proteins with a high similarity of 93.0% with Bombyx mori Ago3 (BmAgo3). The suppression of PxAgo3 by dsPxAgo3 was observed 3 h after treatment and was maintained until 24 h. Knockdown of PxAgo3 decreased the suppression level of PxActin by dsPxActin in P. xylostella cells, while overexpression of PxAgo3 increased the RNAi efficiency. Our results suggest that PxAgo3 play a key role in the double stranded RNA (dsRNA)-regulated RNAi pathway in P. xylostella.
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Affiliation(s)
- Muhammad Salman Hameed
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China.
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
| | - Zhengbing Wang
- Key Laboratory of Natural Pesticides and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou 510642, China.
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, St. Catharines, ON L2S 3A1, Canada.
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou 350002, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou 350002, China.
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou 350002, China.
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Rewired RNAi-mediated genome surveillance in house dust mites. PLoS Genet 2018; 14:e1007183. [PMID: 29377900 PMCID: PMC5805368 DOI: 10.1371/journal.pgen.1007183] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 02/08/2018] [Accepted: 01/03/2018] [Indexed: 11/19/2022] Open
Abstract
House dust mites are common pests with an unusual evolutionary history, being descendants of a parasitic ancestor. Transition to parasitism is frequently accompanied by genome rearrangements, possibly to accommodate the genetic change needed to access new ecology. Transposable element (TE) activity is a source of genomic instability that can trigger large-scale genomic alterations. Eukaryotes have multiple transposon control mechanisms, one of which is RNA interference (RNAi). Investigation of the dust mite genome failed to identify a major RNAi pathway: the Piwi-associated RNA (piRNA) pathway, which has been replaced by a novel small-interfering RNA (siRNA)-like pathway. Co-opting of piRNA function by dust mite siRNAs is extensive, including establishment of TE control master loci that produce siRNAs. Interestingly, other members of the Acari have piRNAs indicating loss of this mechanism in dust mites is a recent event. Flux of RNAi-mediated control of TEs highlights the unusual arc of dust mite evolution. Investigation of small RNA populations in dust mites revealed absence of the piwi-associated RNA (piRNA) pathway. Apart from several nematode and platyhelminths lineages, piRNAs are an essential component of animal genome surveillance, actively targeting and silencing transposable elements. In dust mites, expansion of Dicer produced small-interfering RNA (siRNA) biology compensates for loss of piRNAs. The dramatic difference we find in dust mites is likely a consequence of their evolutionary history, which is marked by descent from a parasite to the current free-living form. Our study highlights a correlation between perturbation of transposon surveillance and shifts in ecology.
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Yamashiro H, Siomi MC. PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond. Chem Rev 2017; 118:4404-4421. [PMID: 29281264 DOI: 10.1021/acs.chemrev.7b00393] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing. However, the uniqueness of this piRNA pathway has emerged through intensive genetic, biochemical, bioinformatic, and structural investigations. Here, we review the studies that elucidated the piRNA pathway, mainly in Drosophila, by describing both historical and recent progress. Studies in other species that have made important contributions to the field are also described.
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Affiliation(s)
- Haruna Yamashiro
- 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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Rogers AK, Situ K, Perkins EM, Toth KF. Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery. Genes Dev 2017; 31:1858-1869. [PMID: 29021243 PMCID: PMC5695087 DOI: 10.1101/gad.303214.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/13/2017] [Indexed: 11/24/2022]
Abstract
Here, Rogers et al. investigated how piRNA precursors are selected and channeled into the endonuclease Zucchini (Zuc)-dependent processing pathway in Drosophila germ cells. They engineered a modular system that can induce primary piRNA biogenesis at an arbitrary locus even in the absence of native piRNA precursors. They also established a subcellular compartmentalization as a key factor in RNA processing. The piRNA pathway represses transposable elements in the gonads and thereby plays a vital role in protecting the integrity of germline genomes of animals. Mature piRNAs are processed from longer transcripts, piRNA precursors (pre-piRNAs). In Drosophila, processing of pre-piRNAs is initiated by piRNA-guided Slicer cleavage or the endonuclease Zucchini (Zuc). As Zuc does not have any sequence or structure preferences in vitro, it is not known how piRNA precursors are selected and channeled into the Zuc-dependent processing pathway. We show that a heterologous RNA that lacks complementary piRNAs is processed into piRNAs upon recruitment of several piRNA pathway factors. This processing requires Zuc and the helicase Armitage (Armi). Aubergine (Aub), Argonaute 3 (Ago3), and components of the nuclear RDC complex, which are required for normal piRNA biogenesis in germ cells, are dispensable. Our approach allows discrimination of proteins involved in the transcription and export of piRNA precursors from components required for the cytoplasmic processing steps. piRNA processing correlates with localization of the substrate RNA to nuage, a distinct membraneless cytoplasmic compartment, which surrounds the nucleus of germ cells, suggesting that sequestration of RNA to this subcellular compartment is both necessary and sufficient for selecting piRNA biogenesis substrates.
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Affiliation(s)
- Alicia K Rogers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Kathy Situ
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Edward M Perkins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Katalin Fejes Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Molecular characterization of mitochondrial Zucchini and its relation to nuage-piRNA pathway components in Bombyx mori ovary-derived BmN4 cells. Biochem Biophys Res Commun 2017; 493:971-978. [PMID: 28942151 DOI: 10.1016/j.bbrc.2017.09.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 11/23/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs that associate with PIWI subfamily proteins, which play an important role in transposon silencing in animal germ cell. The piRNAs biogenesis is divided into two major pathways: primary and secondary, and both pathways are independent of double-stranded RNA-processing enzyme Dicer, which processes the single-stranded RNA transcripts in microRNA (miRNA) and siRNA (small interfering RNA) pathway. Primary piRNAs are processed from long non-coding RNA precursors transcribed from piRNA clusters. Zucchini (Zuc), a mitochondrial phospholipase D (PLD) superfamily protein is conserved among the animals and involved in piRNA biogenesis. Recent studies showed that the Zucchini is an endoribonuclease essential for primary piRNA maturation and production of phased piRNA in secondary piRNA biogenesis of drosophila germ cell. Based on these reports, here we identified and studied the silkworm Zucchini (BmZuc) at subcellular level in ovary-derived BmN4 cell. The silkworm Zuc specifically expressed in germ-related tissues and localized on mitochondria and partially co-localized with perinuclear nuage-piRNA pathway components and nuage marker protein BmVasa. Molecular dissection analyses revealed that the conserved mitochondrial localization sequence, RGV motif, PLDc 2 domain and HKD motif are important for the BmZuc mitochondrial localization. Moreover, the knockdown analyses showed that the piRNA pathway components are independent on BmZuc for their nuage localization, whereas BmZuc depend on piRNA pathway components for the proper localization. Our data provides vital information on mitochondrial BmZuc and its relationship to "nuage" in ovary-derived BmN4 cell.
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Pandey RR, Homolka D, Chen KM, Sachidanandam R, Fauvarque MO, Pillai RS. Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries. PLoS Genet 2017; 13:e1006956. [PMID: 28827804 PMCID: PMC5578672 DOI: 10.1371/journal.pgen.1006956] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/31/2017] [Accepted: 08/04/2017] [Indexed: 01/25/2023] Open
Abstract
Small RNAs called PIWI -interacting RNAs (piRNAs) are essential for transposon control and fertility in animals. Primary processing is the small RNA biogenesis pathway that uses long single-stranded RNA precursors to generate millions of individual piRNAs, but the molecular mechanisms that identify a transcript as a precursor are poorly understood. Here we demonstrate that artificial tethering of the piRNA biogenesis factor, Armi, to a transcript is sufficient to direct it into primary processing in Drosophila ovaries and in an ovarian cell culture model. In the fly ovarian somatic follicle cells, the transcript becomes cleaved in a stepwise manner, with a 5'→3' directionality, liberating U1-containing ~24 nt piRNAs that are loaded into Piwi. Although uridines are preferred for generation of piRNA 5' ends, processing takes place even in their absence, albeit at a lower efficiency. We show that recombinant Armi has 5'→3' helicase activity, and mutations that abolish this activity also reduce piRNA processing in vivo. Another somatic piRNA pathway factor Yb, an interactor of Armi, is also able to trigger piRNA biogenesis when tethered to a transcript. Tethering-mediated primary piRNA biogenesis is also functional in the fly ovarian germline and loads all the three PIWI proteins present in this environment. Our study finds a broad correlation between piRNA processing and localization of the tethered factors to the cytoplasmic perinuclear ribonucleoprotein granules called germline nuage or somatic Yb bodies. We conclude that transcripts bound by Armi and Yb are identified as piRNA precursors, resulting in localization to cytoplasmic processing granules and their subsequent engagement by the resident piRNA biogenesis machinery.
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Affiliation(s)
- Radha Raman Pandey
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - David Homolka
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Kuan-Ming Chen
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, New York, New York, United States of America
| | - Marie-Odile Fauvarque
- Biosciences and Biotechnology Institute of Grenoble (BIG), CEA-DRF-BIG-BGE, INSERM U1038, Univ. Grenoble Alpes, Grenoble, France
| | - Ramesh S. Pillai
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
- * E-mail:
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31
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Characterization of Armitage and Yb containing granules and their relationship to nuage in ovary-derived cultured silkworm cell. Biochem Biophys Res Commun 2017; 490:134-140. [PMID: 28595904 DOI: 10.1016/j.bbrc.2017.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/03/2017] [Indexed: 11/20/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are a class of endogenous small non-coding RNAs, which are mostly 24-32 nucleotides in length and interact specifically with PIWI subfamily of argonaute proteins. Despite the significant research progress in germ line piRNA pathway, its role in somatic cell is not well known. In Drosophila ovarian somatic cell, maturation of primary piRNA and its loading onto Piwi occurs at perinuclear Yb body. The Armitage (Armi) and Yb proteins are the major components of Yb body and specially expressed in ovarian somatic cell. Based on the reports, here we studied the BmArmi and BmYb in Bombyx mori ovary-derived BmN4 cells expressing BmVasa. In this study, we show that BmArmi and BmYb co-localized with BmVasa at nuage. The helicase domains of BmArmi and BmYb are important for nuage localization. Moreover, RNAi of piRNA components reveal that BmArmi depend on BmAgo3 for nuage localization, and BmArmi and BmYb form cytoplasmic granules independently in the absence of BmVasa. Our results provide evidence that the BmArmi and BmYb coexist with BmVasa and play an important role in perinuclear nuage granules formation in ovary-derived BmN4 cell.
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32
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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33
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Liu T, Wang Q, Li W, Mao F, Yue S, Liu S, Liu X, Xiao S, Xia L. Gcn5 determines the fate of
Drosophila
germline stem cells through degradation of Cyclin A. FASEB J 2017; 31:2185-2194. [DOI: 10.1096/fj.201601217r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/23/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Tianqi Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Qi Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Wenqing Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Feiyu Mao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Shanshan Yue
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Sun Liu
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Xiaona Liu
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Shan Xiao
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
| | - Laixin Xia
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouChina
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34
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piRNA pathway is not required for antiviral defense in Drosophila melanogaster. Proc Natl Acad Sci U S A 2016; 113:E4218-27. [PMID: 27357659 DOI: 10.1073/pnas.1607952113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Since its discovery, RNA interference has been identified as involved in many different cellular processes, and as a natural antiviral response in plants, nematodes, and insects. In insects, the small interfering RNA (siRNA) pathway is the major antiviral response. In recent years, the Piwi-interacting RNA (piRNA) pathway also has been implicated in antiviral defense in mosquitoes infected with arboviruses. Using Drosophila melanogaster and an array of viruses that infect the fruit fly acutely or persistently or are vertically transmitted through the germ line, we investigated in detail the extent to which the piRNA pathway contributes to antiviral defense in adult flies. Following virus infection, the survival and viral titers of Piwi, Aubergine, Argonaute-3, and Zucchini mutant flies were similar to those of wild type flies. Using next-generation sequencing of small RNAs from wild type and siRNA mutant flies, we showed that no viral-derived piRNAs were produced in fruit flies during different types of viral infection. Our study provides the first evidence, to our knowledge, that the piRNA pathway does not play a major role in antiviral defense in adult Drosophila and demonstrates that viral-derived piRNA production depends on the biology of the host-virus combination rather than being part of a general antiviral process in insects.
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35
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Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA. Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. Mol Cell 2016; 59:564-75. [PMID: 26295961 DOI: 10.1016/j.molcel.2015.07.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/26/2015] [Accepted: 07/20/2015] [Indexed: 02/08/2023]
Abstract
In Drosophila, two Piwi proteins, Aubergine (Aub) and Argonaute-3 (Ago3), localize to perinuclear "nuage" granules and use guide piRNAs to target and destroy transposable element transcripts. We find that Aub and Ago3 are recruited to nuage by two different mechanisms. Aub requires a piRNA guide for nuage recruitment, indicating that its localization depends on recognition of RNA targets. Ago3 is recruited to nuage independently of a piRNA cargo and relies on interaction with Krimper, a stable component of nuage that is able to aggregate in the absence of other nuage proteins. We show that Krimper interacts directly with Aub and Ago3 to coordinate the assembly of the ping-pong piRNA processing (4P) complex. Symmetrical dimethylated arginines are required for Aub to interact with Krimper, but they are dispensable for Ago3 to bind Krimper. Our study reveals a multi-step process responsible for the assembly and function of nuage complexes in piRNA-guided transposon repression.
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Affiliation(s)
- Alexandre Webster
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sisi Li
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Junho K Hur
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Malte Wachsmuth
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin S Bois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Edward M Perkins
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10021 USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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36
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Multiple Roles for Egalitarian in Polarization of the Drosophila Egg Chamber. Genetics 2016; 203:415-32. [PMID: 27017624 DOI: 10.1534/genetics.115.184622] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/20/2016] [Indexed: 01/08/2023] Open
Abstract
The Drosophila egg chamber provides a useful model for examining mechanisms by which cell fates are specified and maintained in the context of a complex tissue. The egg chamber is also an excellent model for understanding the mechanism by which cytoskeletal filaments are organized and the critical interplay between cytoskeletal organization, polarity establishment, and cell fate specification. Previous work has shown that Egalitarian (Egl) is required for specification and maintenance of oocyte fate. Mutants in egl either completely fail to specify an oocyte, or if specified, the oocyte eventually reverts back to nurse cell fate. Due to this very early role for Egl in egg chamber maturation, it is unclear whether later stages of egg chamber development also require Egl function. In this report, we have depleted Egl at specific stages of egg chamber development. We demonstrate that in early-stage egg chambers, Egl has an additional role in organization of oocyte microtubules. In the absence of Egl function, oocyte microtubules completely fail to reorganize. As such, the localization of microtubule motors and their cargo is disrupted. In addition, Egl also appears to function in regulating the translation of critical polarity determining messenger RNAs (mRNAs). Finally, we demonstrate that in midstage egg chambers, Egl does not appear to be required for microtubule organization, but rather for the correct spatial localization of oskar, bicoid, and gurken mRNAs.
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37
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piRNA biogenesis in the germline: From transcription of piRNA genomic sources to piRNA maturation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:82-92. [DOI: 10.1016/j.bbagrm.2015.09.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/25/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
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38
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Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, Zamore PD. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell 2015; 59:819-30. [PMID: 26340424 DOI: 10.1016/j.molcel.2015.08.007] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/08/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
In Drosophila ovarian germ cells, PIWI-interacting RNAs (piRNAs) direct Aubergine and Argonaute3 to cleave transposon transcripts and instruct Piwi to repress transposon transcription, thereby safeguarding the germline genome. Here, we report that RNA cleavage by Argonaute3 initiates production of most Piwi-bound piRNAs. We find that the cardinal function of Argonaute3, whose piRNA guides predominantly correspond to sense transposon sequences, is to produce antisense piRNAs that direct transcriptional silencing by Piwi, rather than to make piRNAs that guide post-transcriptional silencing by Aubergine. We also find that the Tudor domain protein Qin prevents Aubergine's cleavage products from becoming Piwi-bound piRNAs, ensuring that antisense piRNAs guide Piwi. Although Argonaute3 slicing is required to efficiently trigger phased piRNA production, an alternative, slicing-independent pathway suffices to generate Piwi-bound piRNAs that repress transcription of a subset of transposon families. This alternative pathway may help flies silence newly acquired transposons for which they lack extensively complementary piRNAs.
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Affiliation(s)
- Wei Wang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Cindy Tipping
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Daniel Tianfang Ge
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhao Zhang
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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39
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Lempradl A, Pospisilik JA, Penninger JM. Exploring the emerging complexity in transcriptional regulation of energy homeostasis. Nat Rev Genet 2015; 16:665-81. [PMID: 26460345 DOI: 10.1038/nrg3941] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Obesity and its associated diseases are expected to affect more than 1 billion people by the year 2030. These figures have sparked intensive research into the molecular control of food intake, nutrient distribution, storage and metabolism--processes that are collectively termed energy homeostasis. Recent decades have also seen dramatic developments in our understanding of gene regulation at the signalling, chromatin and post-transcriptional levels. The seemingly exponential growth in this complexity now poses a major challenge for translational researchers in need of simplified but accurate paradigms for clinical use. In this Review, we consider the current understanding of transcriptional control of energy homeostasis, including both transcriptional and epigenetic regulators, and crosstalk between pathways. We also provide insights into emerging developments and challenges in this field.
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Affiliation(s)
- Adelheid Lempradl
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - J Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohr-Gasse 3, 1030 Vienna, Austria
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40
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Sato K, Iwasaki Y, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi M, Siomi H. Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline. Mol Cell 2015. [DOI: 10.1016/j.molcel.2015.06.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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41
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Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res 2015; 43:e109. [PMID: 26007652 PMCID: PMC4632877 DOI: 10.1093/nar/gkv537] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/10/2015] [Indexed: 12/19/2022] Open
Abstract
Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
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Affiliation(s)
- Min-Te Chou
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chiung-Po Hsiao
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
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N6-methyladenine DNA modification in Drosophila. Cell 2015; 161:893-906. [PMID: 25936838 DOI: 10.1016/j.cell.2015.04.018] [Citation(s) in RCA: 428] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/25/2015] [Accepted: 03/25/2015] [Indexed: 12/20/2022]
Abstract
DNA N(6)-methyladenine (6mA) modification is commonly found in microbial genomes and plays important functions in regulating numerous biological processes in bacteria. However, whether 6mA occurs and what its potential roles are in higher-eukaryote cells remain unknown. Here, we show that 6mA is present in Drosophila genome and that the 6mA modification is dynamic and is regulated by the Drosophila Tet homolog, DNA 6mA demethylase (DMAD), during embryogenesis. Importantly, our biochemical assays demonstrate that DMAD directly catalyzes 6mA demethylation in vitro. Further genetic and sequencing analyses reveal that DMAD is essential for development and that DMAD removes 6mA primarily from transposon regions, which correlates with transposon suppression in Drosophila ovary. Collectively, we uncover a DNA modification in Drosophila and describe a potential role of the DMAD-6mA regulatory axis in controlling development in higher eukaryotes.
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Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Mol Cell 2014; 56:708-16. [PMID: 25453759 DOI: 10.1016/j.molcel.2014.10.016] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/03/2014] [Accepted: 10/16/2014] [Indexed: 11/25/2022]
Abstract
PIWI-interacting RNAs (piRNAs) silence transposons in animal germ cells. PIWI proteins bind and amplify piRNAs via the "Ping-Pong" pathway. Because PIWI proteins cleave RNAs between target nucleotides t10 and t11-the nucleotides paired to piRNA guide positions g10 and g11-the first ten nucleotides of piRNAs participating in the Ping-Pong amplification cycle are complementary. Drosophila piRNAs bound to the PIWI protein Aubergine typically begin with uridine (1U), while piRNAs bound to Argonaute3, which are produced by Ping-Pong amplification, often have adenine at position 10 (10A). The Ping-Pong model proposes that the 10A is a consequence of 1U. We find that 10A is not caused by 1U. Instead, fly Aubergine as well as its homologs, Siwi in silkmoth and MILI in mice, have an intrinsic preference for adenine at the t1 position of their target RNAs; during Ping-Pong amplification, this t1A subsequently becomes the g10A of a piRNA bound to Argonaute3.
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Affiliation(s)
- Wei Wang
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mayu Yoshikawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Natsuko Izumi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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