101
|
PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis. Cell Rep 2015; 12:418-28. [DOI: 10.1016/j.celrep.2015.06.030] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/12/2015] [Accepted: 06/05/2015] [Indexed: 01/14/2023] Open
|
102
|
Lim AK, Knowles BB. Controlling Endogenous Retroviruses and Their Chimeric Transcripts During Natural Reprogramming in the Oocyte. J Infect Dis 2015; 212 Suppl 1:S47-51. [DOI: 10.1093/infdis/jiu567] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
103
|
Milani L, Ghiselli F. Mitochondrial activity in gametes and transmission of viable mtDNA. Biol Direct 2015; 10:22. [PMID: 25981894 PMCID: PMC4435915 DOI: 10.1186/s13062-015-0057-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 04/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The retention of a genome in mitochondria (mtDNA) has several consequences, among which the problem of ensuring a faithful transmission of its genetic information through generations despite the accumulation of oxidative damage by reactive oxygen species (ROS) predicted by the free radical theory of ageing. A division of labour between male and female germ line mitochondria was proposed: since mtDNA is maternally inherited, female gametes would prevent damages by repressing oxidative phosphorylation, thus being quiescent genetic templates. We assessed mitochondrial activity in gametes of an unusual biological system (doubly uniparental inheritance of mitochondria, DUI), in which also sperm mtDNA is transmitted to the progeny, thus having to overcome the problem of maintaining genetic information viability while producing ATP for swimming. RESULTS Ultrastructural analysis shows no difference in the conformation of mitochondrial cristae in male and female mature gametes, while mitochondria in immature oocytes exhibit a simpler internal structure. Our data on transcriptional activity in germ line mitochondria show variability between sexes and different developmental stages, but we do not find evidence for transcriptional quiescence of mitochondria. Our observations on mitochondrial membrane potential are consistent with mitochondria being active in both male and female gametes. CONCLUSIONS Our findings and the literature we discussed may be consistent with the hypothesis that template mitochondria are not functionally silenced, on the contrary their activity might be fundamental for the inheritance mechanism. We think that during gametogenesis, fertilization and embryo development, mitochondria undergo selection for different traits (e.g. replication, membrane potential), increasing the probability of the transmission of functional organelles. In these phases of life cycle, the great reduction in mtDNA copy number per organelle/cell and the stochastic segregation of mtDNA variants would greatly improve the efficiency of selection. When a higher mtDNA copy number per organelle/cell is present, selection on mtDNA deleterious mutants is less effective, due to the buffering effect of wild-type variants. In our opinion, a combination of drift and selection on germ line mtDNA population, might be responsible for the maintenance of viable mitochondrial genetic information through generations, and a mitochondrial activity would be necessary for the selective process.
Collapse
Affiliation(s)
- Liliana Milani
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Università di Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Fabrizio Ghiselli
- Dipartimento di Scienze Biologiche, Geologiche ed Ambientali, Università di Bologna, Via Selmi 3, 40126, Bologna, Italy.
| |
Collapse
|
104
|
Chen KM, Campbell E, Pandey RR, Yang Z, McCarthy AA, Pillai RS. Metazoan Maelstrom is an RNA-binding protein that has evolved from an ancient nuclease active in protists. RNA (NEW YORK, N.Y.) 2015; 21:833-839. [PMID: 25778731 PMCID: PMC4408791 DOI: 10.1261/rna.049437.114] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/26/2015] [Indexed: 06/04/2023]
Abstract
Piwi-interacting RNAs (piRNAs) guide Piwi argonautes to their transposon targets for silencing. The highly conserved protein Maelstrom is linked to both piRNA biogenesis and effector roles in this pathway. One defining feature of Maelstrom is the predicted MAEL domain of unknown molecular function. Here, we present the first crystal structure of the MAEL domain from Bombyx Maelstrom, which reveals a nuclease fold. The overall architecture resembles that found in Mg(2+)- or Mn(2+)-dependent DEDD nucleases, but a clear distinguishing feature is the presence of a structural Zn(2+) ion coordinated by the conserved ECHC residues. Strikingly, metazoan Maelstrom orthologs across the animal kingdom lack the catalytic DEDD residues, and as we show for Bombyx Maelstrom are inactive as nucleases. However, a MAEL domain-containing protein from amoeba having both sequence motifs (DEDD and ECHC) is robustly active as an exoribonuclease. Finally, we show that the MAEL domain of Bombyx Maelstrom displays a strong affinity for single-stranded RNAs. Our studies suggest that the ancient MAEL nuclease domain evolved to function as an RNA-binding module in metazoan Maelstrom.
Collapse
Affiliation(s)
- Kuan-Ming Chen
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| | - Edgar Campbell
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| | - Radha Raman Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| | - Zhaolin Yang
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 38042 Grenoble Cedex 9, France
| |
Collapse
|
105
|
Bozzetti MP, Specchia V, Cattenoz PB, Laneve P, Geusa A, Sahin HB, Di Tommaso S, Friscini A, Massari S, Diebold C, Giangrande A. The Drosophila fragile X mental retardation protein participates in the piRNA pathway. J Cell Sci 2015; 128:2070-84. [PMID: 25908854 DOI: 10.1242/jcs.161810] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022] Open
Abstract
RNA metabolism controls multiple biological processes, and a specific class of small RNAs, called piRNAs, act as genome guardians by silencing the expression of transposons and repetitive sequences in the gonads. Defects in the piRNA pathway affect genome integrity and fertility. The possible implications in physiopathological mechanisms of human diseases have made the piRNA pathway the object of intense investigation, and recent work suggests that there is a role for this pathway in somatic processes including synaptic plasticity. The RNA-binding fragile X mental retardation protein (FMRP, also known as FMR1) controls translation and its loss triggers the most frequent syndromic form of mental retardation as well as gonadal defects in humans. Here, we demonstrate for the first time that germline, as well as somatic expression, of Drosophila Fmr1 (denoted dFmr1), the Drosophila ortholog of FMRP, are necessary in a pathway mediated by piRNAs. Moreover, dFmr1 interacts genetically and biochemically with Aubergine, an Argonaute protein and a key player in this pathway. Our data provide novel perspectives for understanding the phenotypes observed in Fragile X patients and support the view that piRNAs might be at work in the nervous system.
Collapse
Affiliation(s)
- Maria Pia Bozzetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Valeria Specchia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Pierre B Cattenoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Pietro Laneve
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Annamaria Geusa
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - H Bahar Sahin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Silvia Di Tommaso
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Antonella Friscini
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Serafina Massari
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali (DiSTeBA) - University of Salento, 73100 Lecce, Italy
| | - Celine Diebold
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| | - Angela Giangrande
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France Université de Strasbourg, Illkirch, France
| |
Collapse
|
106
|
Gvozdev VA, Stolyarenko AD, Klenov MS. Functions of piRNAs and the Piwi protein in Drosophila. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
107
|
Matsumoto N, Sato K, Nishimasu H, Namba Y, Miyakubi K, Dohmae N, Ishitani R, Siomi H, Siomi MC, Nureki O. Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom. Cell Rep 2015; 11:366-75. [PMID: 25865890 DOI: 10.1016/j.celrep.2015.03.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/19/2015] [Accepted: 03/10/2015] [Indexed: 01/09/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) protect the genome from transposons in animal gonads. Maelstrom (Mael) is an evolutionarily conserved protein, composed of a high-mobility group (HMG) domain and a MAEL domain, and is essential for piRNA-mediated transcriptional transposon silencing in various species, such as Drosophila and mice. However, its structure and biochemical function have remained elusive. Here, we report the crystal structure of the MAEL domain from Drosophila melanogaster Mael, at 1.6 Å resolution. The structure reveals that the MAEL domain has an RNase H-like fold but lacks canonical catalytic residues conserved among RNase H-like superfamily nucleases. Our biochemical analyses reveal that the MAEL domain exhibits single-stranded RNA (ssRNA)-specific endonuclease activity. Our cell-based analyses further indicate that ssRNA cleavage activity appears dispensable for piRNA-mediated transcriptional transposon silencing in Drosophila. Our findings provide clues toward understanding the multiple roles of Mael in the piRNA pathway.
Collapse
Affiliation(s)
- Naoki Matsumoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan; JST, PRESTO, Tokyo 113-0032, Japan
| | - Yurika Namba
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kana Miyakubi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Team and CREST/JST, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan.
| |
Collapse
|
108
|
Sato K, Siomi MC. Functional and structural insights into the piRNA factor Maelstrom. FEBS Lett 2015; 589:1688-93. [DOI: 10.1016/j.febslet.2015.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/19/2015] [Indexed: 10/23/2022]
|
109
|
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small RNAs that are 24-31 nucleotides in length. They associate with PIWI proteins, which constitute a germline-specific subclade of the Argonaute family, to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. In addition to having a role in transposon silencing, piRNAs in diverse organisms function in the regulation of cellular genes. In some cases, piRNAs have shown transgenerational inheritance to pass on the memory of "self" and "nonself," suggesting a contribution to various cellular processes over generations. Many piRNA factors have been identified; however, both the molecular mechanisms leading to the production of mature piRNAs and the effector phases of gene silencing are still enigmatic. Here, we summarize the current state of our knowledge on the biogenesis of piRNA, its biological functions, and the underlying mechanisms.
Collapse
Affiliation(s)
- Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | | | | |
Collapse
|
110
|
Nishida K, Iwasaki Y, Murota Y, Nagao A, Mannen T, Kato Y, Siomi H, Siomi M. Respective Functions of Two Distinct Siwi Complexes Assembled during PIWI-Interacting RNA Biogenesis in Bombyx Germ Cells. Cell Rep 2015; 10:193-203. [DOI: 10.1016/j.celrep.2014.12.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 11/24/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022] Open
|
111
|
Small RNAs: Their Possible Roles in Reproductive Failure. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 868:49-79. [PMID: 26178845 DOI: 10.1007/978-3-319-18881-2_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Posttranscriptional gene regulation is a regulatory mechanism which occurs "above the genome" and confers different phenotypes and functions within a cell. Transcript and protein abundance above the level of transcription can be regulated via noncoding ribonucleic acid (ncRNA) molecules, which potentially play substantial roles in the regulation of reproductive function. MicroRNA (miRNA), endogenous small interfering RNA (endo-siRNA), and PIWI-interacting RNA (piRNA) are three primary classes of small ncRNA. Similarities and distinctions between their biogenesis and in the interacting protein machinery that facilitate their function distinguish these three classes. Characterization of the expression and importance of the critical components for the biogenesis of each class in different tissues contributes a clearer understanding of their contributions in specific reproductive tissues and their ability to influence fertility in both males and females. This chapter discusses the expression and potential roles of miRNA, endo-siRNA, and piRNA in the regulation of reproductive function. Additionally, this chapter elaborates on investigations aimed to address and characterize specific mechanisms through which miRNA may influence infertility and the use of miRNA as biomarkers associated with several reproductive calamities such as defective spermatogenesis in males, polycystic ovarian failure, endometriosis and obesity, and chemical-induced subfertility.
Collapse
|
112
|
Théron E, Dennis C, Brasset E, Vaury C. Distinct features of the piRNA pathway in somatic and germ cells: from piRNA cluster transcription to piRNA processing and amplification. Mob DNA 2014; 5:28. [PMID: 25525472 PMCID: PMC4269861 DOI: 10.1186/s13100-014-0028-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are major components of genomes. Their mobilization may affect genomic expression and be a threat to genetic stability. This is why they have to be tightly regulated by a dedicated system. In the reproductive tissues of a large range of organisms, they are repressed by a subclass of small interfering RNAs called piRNAs (PIWI interacting RNAs). In Drosophila melanogaster, piRNAs are produced both in the ovarian germline cells and in their surrounding somatic cells. Accumulating evidence suggests that germinal and somatic piRNA pathways are far more different than previously thought. Here we review the current knowledge on piRNA production in both these cell types, and explore their similarities and differences.
Collapse
Affiliation(s)
- Emmanuelle Théron
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Cynthia Dennis
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Emilie Brasset
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Chantal Vaury
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| |
Collapse
|
113
|
Nosov GA, Kibanov MV, Olenina LV. Dynamic properties of a germinal granule piNG-body in the testes of Drosophila melanogaster. Mol Biol 2014. [DOI: 10.1134/s0026893314050112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
114
|
Patil VS, Anand A, Chakrabarti A, Kai T. The Tudor domain protein Tapas, a homolog of the vertebrate Tdrd7, functions in the piRNA pathway to regulate retrotransposons in germline of Drosophila melanogaster. BMC Biol 2014; 12:61. [PMID: 25287931 PMCID: PMC4210518 DOI: 10.1186/s12915-014-0061-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/25/2014] [Indexed: 01/21/2023] Open
Abstract
Background Piwi-interacting RNAs (piRNAs) are a special class of small RNAs that provide defense against transposable elements in animal germline cells. In Drosophila, germline piRNAs are thought to be processed at a unique perinuclear structure, the nuage, that houses piRNA pathway proteins including the Piwi clade of Argonaute family proteins, along with several Tudor domain proteins, RNA helicases and nucleases. We previously demonstrated that Tudor domain protein Tejas (Tej), an ortholog of vertebrate Tdrd5, is an important component of the piRNA pathway. Results In the current study, we identified the paralog of the Drosophila tej gene, tapas (tap), which is an ortholog of vertebrate Tdrd7. Like Tej, Tap is localized at the nuage. Alone, tap loss leads to a mild increase in transposon expression and decrease in piRNAs targeting transposons expressed in the germline. The tap gene genetically interacts with other piRNA pathway genes and we also show that Tap physically interacts with piRNA pathway components, such as Piwi family proteins Aubergine and Argonaute3 and the RNA helicases Spindle-E and Vasa. Together with tej, tap is required for survival of germline cells during early stages and for polarity formation. We further observed that loss of tej and tap together results in more severe defects in the piRNA pathway in germline cells compared to single mutants: the double-mutant ovaries exhibit mis-localization of piRNA pathway components and significantly greater reduction of piRNAs against transposons predominantly expressed in germline compared to single mutants. The single or double mutants did not have any reduction in piRNAs mapping to transposons predominantly expressed in gonadal somatic cells or those derived from unidirectional clusters such as flamenco. Consistently, the loss of both tej and tap function resulted in mis-localization of Piwi in germline cells, whereas Piwi remained localized to the nucleus in somatic cells. Conclusions Our observations suggest that tej and tap work together for germline maintenance. tej and tap also function in a synergistic manner to maintain examined piRNA components at the perinuclear nuage and for piRNA production in Drosophila germline cells. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0061-9) contains supplementary material, which is available to authorized users.
Collapse
|
115
|
Huang H, Li Y, Szulwach KE, Zhang G, Jin P, Chen D. AGO3 Slicer activity regulates mitochondria-nuage localization of Armitage and piRNA amplification. ACTA ACUST UNITED AC 2014; 206:217-30. [PMID: 25049272 PMCID: PMC4107788 DOI: 10.1083/jcb.201401002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The endonuclease AGO3 and mitochondria-associated protein Zucchini together control the dynamic subcellular localization of Armitage between mitochondria and germline granules to regulate secondary piRNA amplification. In Drosophila melanogaster the reciprocal “Ping-Pong” cycle of PIWI-interacting RNA (piRNA)–directed RNA cleavage catalyzed by the endonuclease (or “Slicer”) activities of the PIWI proteins Aubergine (Aub) and Argonaute3 (AGO3) has been proposed to expand the secondary piRNA population. However, the role of AGO3/Aub Slicer activity in piRNA amplification remains to be explored. We show that AGO3 Slicer activity is essential for piRNA amplification and that AGO3 inhibits the homotypic Aub:Aub Ping-Pong process in a Slicer-independent manner. We also find that expression of an AGO3 Slicer mutant causes ectopic accumulation of Armitage, a key component in the primary piRNA pathway, in the Drosophila melanogaster germline granules known as nuage. AGO3 also coexists and interacts with Armitage in the mitochondrial fraction. Furthermore, AGO3 acts in conjunction with the mitochondria-associated protein Zucchini to control the dynamic subcellular localization of Armitage between mitochondria and nuage in a Slicer-dependent fashion. Collectively, our findings uncover a new mechanism that couples mitochondria with nuage to regulate secondary piRNA amplification.
Collapse
Affiliation(s)
- Haidong Huang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Keith E Szulwach
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Guoqiang Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Dahua Chen
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| |
Collapse
|
116
|
The DExH box helicase domain of spindle-E is necessary for retrotransposon silencing and axial patterning during Drosophila oogenesis. G3-GENES GENOMES GENETICS 2014; 4:2247-57. [PMID: 25239103 PMCID: PMC4232550 DOI: 10.1534/g3.114.014332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transposable selfish genetic elements have the potential to cause debilitating mutations as they replicate and reinsert within the genome. Therefore, it is critical to keep the cellular levels of these elements low. This is especially true in the germline where these mutations could affect the viability of the next generation. A class of small noncoding RNAs, the Piwi-associated RNAs, is responsible for silencing transposable elements in the germline of most organisms. Several proteins have been identified as playing essential roles in piRNA generation and transposon silencing. However, for the most part their function in piRNA generation is currently unknown. One of these proteins is the Drosophila melanogaster DExH box/Tudor domain protein Spindle-E, whose activity is necessary for the generation of most germline piRNAs. In this study we molecularly and phenotypically characterized 14 previously identified spindle-E alleles. Of the alleles that express detectable Spindle-E protein, we found that five had mutations in the DExH box domain. Additionally, we found that processes that depend on piRNA function, including Aubergine localization, Dynein motor movement, and retrotransposon silencing, were severely disrupted in alleles with DExH box domain mutations. The phenotype of many of these alleles is as severe as the strongest spindle-E phenotype, whereas alleles with mutations in other regions of Spindle-E did not affect these processes as much. From these data we conclude that the DExH box domain of Spindle-E is necessary for its function in the piRNA pathway and retrotransposon silencing.
Collapse
|
117
|
Abstract
Precursors for most Piwi-interacting RNAs (piRNAs) are indistinguishable from other RNA polymerase II-transcribed long noncoding RNAs. So, it is currently unclear how they are recognized as substrates by the piRNA processing machinery that resides in cytoplasmic granules called nuage. In this issue, Castaneda et al (2014) reveal a role for the nuage component and nucleo-cytoplasmic shuttling protein Maelstrom in mouse piRNA biogenesis.
Collapse
Affiliation(s)
- Radha Raman Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France Unit for Virus Host Cell Interactions, University Grenoble Alpes-EMBL-CNRS, Grenoble, France
| |
Collapse
|
118
|
Chambeyron S, Seitz H. Insect small non-coding RNA involved in epigenetic regulations. CURRENT OPINION IN INSECT SCIENCE 2014; 1:1-9. [PMID: 32846724 DOI: 10.1016/j.cois.2014.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 05/01/2014] [Accepted: 05/01/2014] [Indexed: 06/11/2023]
Abstract
Small regulatory RNAs can not only guide post-transcriptional repression of target genes, but some of them can also direct heterochromatin formation of specific genomic loci. Here we review the published literature on small RNA-guided epigenetic regulation in insects. The recent development of novel analytical technologies (deep sequencing and RNAi screens) has led to the identification of some of the factors involved in these processes, as well as their molecular mechanism and subcellular localization. Other findings uncovered an additional mode of epigenetic control, where maternally inherited small RNAs can affect phenotypes in a stable, transgenerational manner. The evolutive history of small RNA effector proteins in insects suggests that these two modes of regulation are variably conserved among species.
Collapse
Affiliation(s)
- Séverine Chambeyron
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Hervé Seitz
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique (CNRS), UPR 1142, 141, rue de la Cardonille, 34396 Montpellier Cedex 5, France.
| |
Collapse
|
119
|
Ku HY, Lin H. PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. Natl Sci Rev 2014; 1:205-218. [PMID: 25512877 DOI: 10.1093/nsr/nwu014] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a complex class of small non-coding RNAs that are mostly 24-32 nucleotides in length and composed of at least hundreds of thousands of species that specifically interact with the PIWI protein subfamily of the ARGONAUTE family. Recent studies revealed that PIWI proteins interact with a number of proteins, especially the TUDOR-domain-containing proteins, to regulate piRNA biogenesis and regulatory function. Current research also provides evidence that PIWI proteins and piRNAs are not only crucial for transposon silencing in the germline, but also mediate novel mechanisms of epigenetic programming, DNA rearrangements, mRNA turnover, and translational control both in the germline and in the soma. These new discoveries begin to reveal an exciting new dimension of gene regulation in the cell.
Collapse
Affiliation(s)
- Hsueh-Yen Ku
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| |
Collapse
|
120
|
van Wolfswinkel JC. Piwi and Potency: PIWI Proteins in Animal Stem Cells and Regeneration. Integr Comp Biol 2014; 54:700-13. [DOI: 10.1093/icb/icu084] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
121
|
Chak LL, Okamura K. Argonaute-dependent small RNAs derived from single-stranded, non-structured precursors. Front Genet 2014; 5:172. [PMID: 24959173 PMCID: PMC4050365 DOI: 10.3389/fgene.2014.00172] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/22/2014] [Indexed: 12/31/2022] Open
Abstract
A general feature of Argonaute-dependent small RNAs is their base-paired precursor structures, and precursor duplex structures are often required for confident annotation of miRNA genes. However, this rule has been broken by discoveries of functional small RNA species whose precursors lack a predictable double-stranded (ds-) RNA structure, arguing that duplex structures are not prerequisite for small RNA loading to Argonautes. The biological significance of single-stranded (ss-) RNA loading has been recognized particularly in systems where active small RNA amplification mechanisms are involved, because even a small amount of RNA molecules can trigger the production of abundant RNA species leading to profound biological effects. However, even in the absence of small RNA amplification mechanisms, recent studies have demonstrated that potent gene silencing can be achieved using chemically modified synthetic ssRNAs that are resistant to RNases in mice. Therefore, such ssRNA-mediated gene regulation may have broader roles than previously recognized, and the findings have opened the door for further research to optimize the design of ss-siRNAs toward future pharmaceutical and biomedical applications of gene silencing technologies. In this review, we will summarize studies about endogenous ssRNA species that are bound by Argonaute proteins and how ssRNA precursors are recognized by various small RNA pathways.
Collapse
Affiliation(s)
- Li-Ling Chak
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore Singapore, Singapore ; School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| |
Collapse
|
122
|
Simmons MJ, Meeks MW, Jessen E, Becker JR, Buschette JT, Thorp MW. Genetic interactions between P elements involved in piRNA-mediated repression of hybrid dysgenesis in Drosophila melanogaster. G3 (BETHESDA, MD.) 2014; 4:1417-27. [PMID: 24902606 PMCID: PMC4132173 DOI: 10.1534/g3.114.011221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 05/31/2014] [Indexed: 11/24/2022]
Abstract
Previous studies have shown that telomeric P elements inserted at the left end of the X chromosome are anchors of the P cytotype, the maternally inherited state that regulates P-element activity in the germ line of Drosophila melanogaster. This regulation is mediated by small RNAs that associate with the Piwi family of proteins (piRNAs). We extend the analysis of cytotype regulation by studying new combinations of telomeric and nontelomeric P elements (TPs and non-TPs). TPs interact with each other to enhance cytotype regulation. This synergism involves a strictly maternal effect, called presetting, which is apparently mediated by piRNAs transmitted through the egg. Presetting by a maternal TP can elicit regulation by an inactive paternally inherited TP, possibly by stimulating its production of primary piRNAs. When one TP has come from a stock heterozygous for a mutation in the aubergine, piwi, or Suppressor of variegation 205 genes, the synergism between two TPs is impaired. TPs also interact with non-TPs to enhance cytotype regulation, even though the non-TPs lack regulatory ability on their own. Non-TPs are not susceptible to presetting by a TP, nor is a TP susceptible to presetting by a non-TP. The synergism between TPs and non-TPs is stronger when the TP was inherited maternally. This synergism may be due to the accumulation of secondary piRNAs created by ping-pong cycling between primary piRNAs from the TPs and mRNAs from the non-TPs. Maternal transmission of P-element piRNAs plays an important role in the maintenance of strong cytotype regulation over generations.
Collapse
Affiliation(s)
- Michael J Simmons
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Marshall W Meeks
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Erik Jessen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Jordan R Becker
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Jared T Buschette
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Michael W Thorp
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| |
Collapse
|
123
|
Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Couté Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS. RNA clamping by Vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 2014; 157:1698-711. [PMID: 24910301 DOI: 10.1016/j.cell.2014.05.018] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/28/2014] [Accepted: 05/15/2014] [Indexed: 01/25/2023]
Abstract
Germline-specific Piwi-interacting RNAs (piRNAs) protect animal genomes against transposons and are essential for fertility. piRNAs targeting active transposons are amplified by the ping-pong cycle, which couples Piwi endonucleolytic slicing of target RNAs to biogenesis of new piRNAs. Here, we describe the identification of a transient Amplifier complex that mediates biogenesis of secondary piRNAs in insect cells. Amplifier is nucleated by the DEAD box RNA helicase Vasa and contains the two Piwi proteins participating in the ping-pong loop, the Tudor protein Qin/Kumo and antisense piRNA guides. These components assemble on the surface of Vasa's helicase domain, which functions as an RNA clamp to anchor Amplifier onto transposon transcripts. We show that ATP-dependent RNP remodeling by Vasa facilitates transfer of 5' sliced piRNA precursors between ping-pong partners, and loss of this activity causes sterility in Drosophila. Our results reveal the molecular basis for the small RNA amplification that confers adaptive immunity against transposons.
Collapse
Affiliation(s)
- Jordi Xiol
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Pietro Spinelli
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Maike A Laussmann
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - David Homolka
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Zhaolin Yang
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Elisa Cora
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Yohann Couté
- Laboratoire Biologie à Grande Echelle, IRTSV, CEA, 38054 Grenoble, France
| | - Simon Conn
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Jan Kadlec
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, New York, NY 10029, USA
| | - Marko Kaksonen
- Cell Biology and Biophysics Unit, EMBL, 69117 Heidelberg, Germany
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France
| | - Anne Ephrussi
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042, France.
| |
Collapse
|
124
|
Malki S, van der Heijden GW, O'Donnell KA, Martin SL, Bortvin A. A role for retrotransposon LINE-1 in fetal oocyte attrition in mice. Dev Cell 2014; 29:521-533. [PMID: 24882376 DOI: 10.1016/j.devcel.2014.04.027] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/31/2014] [Accepted: 04/23/2014] [Indexed: 11/24/2022]
Abstract
Fetal oocyte attrition (FOA) is a conserved but poorly understood process of elimination of more than two-thirds of meiotic prophase I (MPI) oocytes before birth. We now implicate retrotransposons LINE-1 (L1), activated during epigenetic reprogramming of the embryonic germline, in FOA in mice. We show that wild-type fetal oocytes possess differential nuclear levels of L1ORF1p, an L1-encoded protein essential for L1 ribonucleoprotein particle (L1RNP) formation and L1 retrotransposition. We demonstrate that experimental elevation of L1 expression correlates with increased MPI defects, FOA, oocyte aneuploidy, and embryonic lethality. Conversely, reverse transcriptase (RT) inhibitor AZT has a profound effect on the FOA dynamics and meiotic recombination, and it implicates an RT-dependent trigger in oocyte elimination in early MPI. We propose that FOA serves to select oocytes with limited L1 activity that are therefore best suited for the next generation.
Collapse
Affiliation(s)
- Safia Malki
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | | | - Kathryn A O'Donnell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| |
Collapse
|
125
|
Basquin D, Spierer A, Begeot F, Koryakov DE, Todeschini AL, Ronsseray S, Vieira C, Spierer P, Delattre M. The Drosophila Su(var)3-7 gene is required for oogenesis and female fertility, genetically interacts with piwi and aubergine, but impacts only weakly transposon silencing. PLoS One 2014; 9:e96802. [PMID: 24820312 PMCID: PMC4018442 DOI: 10.1371/journal.pone.0096802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/11/2014] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin is made of repetitive sequences, mainly transposable elements (TEs), the regulation of which is critical for genome stability. We have analyzed the role of the heterochromatin-associated Su(var)3-7 protein in Drosophila ovaries. We present evidences that Su(var)3-7 is required for correct oogenesis and female fertility. It accumulates in heterochromatic domains of ovarian germline and somatic cells nuclei, where it co-localizes with HP1. Homozygous mutant females display ovaries with frequent degenerating egg-chambers. Absence of Su(var)3-7 in embryos leads to defects in meiosis and first mitotic divisions due to chromatin fragmentation or chromosome loss, showing that Su(var)3-7 is required for genome integrity. Females homozygous for Su(var)3-7 mutations strongly impair repression of P-transposable element induced gonadal dysgenesis but have minor effects on other TEs. Su(var)3-7 mutations reduce piRNA cluster transcription and slightly impact ovarian piRNA production. However, this modest piRNA reduction does not correlate with transposon de-silencing, suggesting that the moderate effect of Su(var)3-7 on some TE repression is not linked to piRNA production. Strikingly, Su(var)3-7 genetically interacts with the piwi and aubergine genes, key components of the piRNA pathway, by strongly impacting female fertility without impairing transposon silencing. These results lead us to propose that the interaction between Su(var)3-7 and piwi or aubergine controls important developmental processes independently of transposon silencing.
Collapse
Affiliation(s)
- Denis Basquin
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Anne Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Flora Begeot
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Anne-Laure Todeschini
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, Paris, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon1, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Pierre Spierer
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Marion Delattre
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| |
Collapse
|
126
|
Hirose T, Mishima Y, Tomari Y. Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Rep 2014; 15:489-507. [PMID: 24731943 PMCID: PMC4210095 DOI: 10.1002/embr.201338390] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 12/26/2022] Open
Abstract
Although recent transcriptome analyses have uncovered numerous non-coding RNAs (ncRNAs), their functions remain largely unknown. ncRNAs assemble with proteins and operate as ribonucleoprotein (RNP) machineries, formation of which is thought to be determined by specific fundamental elements embedded in the primary RNA transcripts. Knowledge about the relationships between RNA elements, RNP machinery, and molecular and physiological functions is critical for understanding the diverse roles of ncRNAs and may eventually allow their systematic classification or "taxonomy." In this review, we catalog and discuss representative small and long non-coding RNA classes, focusing on their currently known (and unknown) RNA elements and RNP machineries.
Collapse
Affiliation(s)
- Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido UniversitySapporo, Hokkaido, Japan
| | - Yuichiro Mishima
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| |
Collapse
|
127
|
Olovnikov IA, Kalmykova AI. piRNA clusters as a main source of small RNAs in the animal germline. BIOCHEMISTRY (MOSCOW) 2014; 78:572-84. [PMID: 23980884 DOI: 10.1134/s0006297913060035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PIWI subfamily Argonaute proteins and small RNAs bound to them (PIWI interacting RNA, piRNA) control mobilization of transposable elements (TE) in the animal germline. piRNAs are generated by distinct genomic regions termed piRNA clusters. piRNA clusters are often extensive loci enriched in damaged fragments of TEs. New TE integration into piRNA clusters causes production of TE-specific piRNAs and repression of cognate sequences. piRNAs are thought to be generated from long single-stranded precursors encoded by piRNA clusters. Special chromatin structures might be essential to distinguish these genomic loci as a source for piRNAs. In this review, we present recent findings on the structural organization of piRNA clusters and piRNA biogenesis in Drosophila and other organisms, which are important for understanding a key epigenetic mechanism that provides defense against TE expansion.
Collapse
Affiliation(s)
- I A Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| | | |
Collapse
|
128
|
Bortvin A. PIWI-interacting RNAs (piRNAs) - a mouse testis perspective. BIOCHEMISTRY (MOSCOW) 2014; 78:592-602. [PMID: 23980886 DOI: 10.1134/s0006297913060059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past decade, PIWI-interacting RNAs (piRNAs) have emerged as the most intriguing class of small RNAs. Almost every aspect of piRNA biology defies established rules of the RNA interference world while the scope of piRNA functional potential spans from transcriptional gene silencing to genome defense to transgenerational epigenetic phenomena. This review will focus on the genomic origins, biogenesis, and function of piRNAs in the mouse testis - an exceptionally robust experimental system amenable to genetic, cell-biological, molecular, and biochemical studies. Aided and frequently guided by knowledge obtained in insect, worm, and fish germ cells, mouse spermatogenesis has emerged as the primary model in understanding the role of this conserved pathway in mammals.
Collapse
Affiliation(s)
- A Bortvin
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA.
| |
Collapse
|
129
|
Abstract
The integrity of the germline genome must be maintained to achieve successive generations of a species, because germline cells are the only source for transmitting genetic information to the next generation. Accordingly, the germline has acquired a system dedicated to protecting the genome from 'injuries' caused by harmful selfish nucleic acid elements, such as TEs (transposable elements). Accumulating evidence shows that a germline-specific subclass of small non-coding RNAs, piRNAs (piwi-interacting RNAs), are necessary for silencing TEs to protect the genome in germline cells. To silence TEs post-transcriptionally and/or transcriptionally, mature piRNAs are loaded on to germline-specific Argonaute proteins, or PIWI proteins, to form the piRISC (piRNA-induced silencing complex). The present chapter will highlight insights into the molecular mechanisms underlying piRISC-mediated silencing and piRNA biogenesis, and discuss a possible link with tumorigenesis, particularly in Drosophila.
Collapse
|
130
|
Shirayama M, Stanney W, Gu W, Seth M, Mello CC. The Vasa Homolog RDE-12 engages target mRNA and multiple argonaute proteins to promote RNAi in C. elegans. Curr Biol 2014; 24:845-51. [PMID: 24684931 DOI: 10.1016/j.cub.2014.03.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 02/27/2014] [Accepted: 03/04/2014] [Indexed: 12/12/2022]
Abstract
Argonaute (AGO) proteins are key nuclease effectors of RNAi. Although purified AGOs can mediate a single round of target RNA cleavage in vitro, accessory factors are required for small interfering RNA (siRNA) loading and to achieve multiple-target turnover. To identify AGO cofactors, we immunoprecipitated the C. elegans AGO WAGO-1, which engages amplified small RNAs during RNAi. These studies identified a robust association between WAGO-1 and a conserved Vasa ATPase-related protein RDE-12. rde-12 mutants are deficient in RNAi, including viral suppression, and fail to produce amplified secondary siRNAs and certain endogenous siRNAs (endo-siRNAs). RDE-12 colocalizes with WAGO-1 in germline P granules and in cytoplasmic and perinuclear foci in somatic cells. These findings and our genetic studies suggest that RDE-12 is first recruited to target mRNA by upstream AGOs (RDE-1 and ERGO-1), where it promotes small RNA amplification and/or WAGO-1 loading. Downstream of these events, RDE-12 forms an RNase-resistant (target mRNA-independent) complex with WAGO-1 and may thus have additional functions in target mRNA surveillance and silencing.
Collapse
Affiliation(s)
- Masaki Shirayama
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - William Stanney
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Weifeng Gu
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Meetu Seth
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Craig C Mello
- Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
131
|
Tatsuke T, Zhu L, Li Z, Mitsunobu H, Yoshimura K, Mon H, Lee JM, Kusakabe T. Roles of Piwi proteins in transcriptional regulation mediated by HP1s in cultured silkworm cells. PLoS One 2014; 9:e92313. [PMID: 24637637 PMCID: PMC3956929 DOI: 10.1371/journal.pone.0092313] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/21/2014] [Indexed: 11/18/2022] Open
Abstract
Piwi proteins are part of a superfamily of Argonaute proteins, which are one of the core components of the RNA silencing pathway in many eukaryotes. Piwi proteins are thought to repress the transposon expression both transcriptionally and post-transcriptionally. Recently, Drosophila melanogaster Piwi was recently reported to associate with chromatin and to interact directly with the Heterochromatin Protein 1 (HP1a). However, similar interactions have not been reported in other higher eukaryotes. Here we show that silkworm Piwi proteins interact with HP1s in the nucleus. The silkworm, Bombyx mori, has two Piwi proteins, Ago3 and Siwi, and two typical HP1 proteins, HP1a and HP1b. We found that HP1a plays an important role in the interaction between Ago3/Siwi and HP1b in the ovary-derived BmN4 cell line. We also found that Ago3/Siwi regulates the transcription in an HP1-dependent manner. These results suggest that silkworm Piwi proteins function as a chromatin regulator in collaboration with HP1a and HP1b.
Collapse
Affiliation(s)
- Tsuneyuki Tatsuke
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Li Zhu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Zhiqing Li
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Hitoshi Mitsunobu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kaito Yoshimura
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Hiroaki Mon
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Jae Man Lee
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Takahiro Kusakabe
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
- * E-mail:
| |
Collapse
|
132
|
|
133
|
Minakhina S, Changela N, Steward R. Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery. Development 2014; 141:259-68. [PMID: 24381196 DOI: 10.1242/dev.101410] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The maintenance of stem cells is central to generating diverse cell populations in many tissues throughout the life of an animal. Elucidating the mechanisms involved in how stem cells are formed and maintained is crucial to understanding both normal developmental processes and the growth of many cancers. Previously, we showed that Zfrp8/PDCD2 is essential for the maintenance of Drosophila hematopoietic stem cells. Here, we show that Zfrp8/PDCD2 is also required in both germline and follicle stem cells in the Drosophila ovary. Expression of human PDCD2 fully rescues the Zfrp8 phenotype, underlining the functional conservation of Zfrp8/PDCD2. The piRNA pathway is essential in early oogenesis, and we find that nuclear localization of Zfrp8 in germline stem cells and their offspring is regulated by some piRNA pathway genes. We also show that Zfrp8 forms a complex with the piRNA pathway protein Maelstrom and controls the accumulation of Maelstrom in the nuage. Furthermore, Zfrp8 regulates the activity of specific transposable elements also controlled by Maelstrom and Piwi. Our results suggest that Zfrp8/PDCD2 is not an integral member of the piRNA pathway, but has an overlapping function, possibly competing with Maelstrom and Piwi.
Collapse
Affiliation(s)
- Svetlana Minakhina
- Rutgers University, Department of Molecular Biology, Waksman Institute, Cancer Institute of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | | |
Collapse
|
134
|
How might flukes and tapeworms maintain genome integrity without a canonical piRNA pathway? Trends Parasitol 2014; 30:123-9. [PMID: 24485046 DOI: 10.1016/j.pt.2014.01.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/29/2013] [Accepted: 01/06/2014] [Indexed: 12/31/2022]
Abstract
Surveillance by RNA interference is central to controlling the mobilization of transposable elements (TEs). In stem cells, Piwi argonaute (Ago) proteins and associated proteins repress mobilization of TEs to maintain genome integrity. This defense mechanism targeting TEs is termed the Piwi-interacting RNA (piRNA) pathway. In this opinion article, we draw attention to the situation that the genomes of cestodes and trematodes have lost the piwi and vasa genes that are hallmark characters of the germline multipotency program. This absence of Piwi-like Agos and Vasa helicases prompts the question: how does the germline of these flatworms withstand mobilization of TEs? Here, we present an interpretation of mechanisms likely to defend the germline integrity of parasitic flatworms.
Collapse
|
135
|
Clark JP, Lau NC. Piwi Proteins and piRNAs step onto the systems biology stage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:159-97. [PMID: 25201106 PMCID: PMC4248790 DOI: 10.1007/978-1-4939-1221-6_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animal germ cells are totipotent because they maintain a highly unique and specialized epigenetic state for its genome. To accomplish this, germ cells express a rich repertoire of specialized RNA-binding protein complexes such as the Piwi proteins and Piwi-interacting RNAs (piRNAs): a germ-cell branch of the RNA interference (RNAi) phenomenon which includes microRNA and endogenous small interfering RNA pathways. Piwi proteins and piRNAs are deeply conserved in animal evolution and play essential roles in fertility and regeneration. Molecular mechanisms for how these ribonucleoproteins act upon the transcriptome and genome are only now coming to light with the application of systems-wide approaches in both invertebrates and vertebrates. Systems biology studies on invertebrates have revealed that transcriptional and heritable silencing is a main mechanism driven by Piwi proteins and piRNA complexes. In vertebrates, Piwi-targeting mechanisms and piRNA biogenesis have progressed, while the discovery that the nuclease activity of Piwi protein is essential for vertebrate germ cell development but not completely required in invertebrates highlights the many complexities of this pathway in different animals. This review recounts how recent systems-wide approaches have rapidly accelerated our appreciation for the broad reach of the Piwi pathway on germline genome regulation and what questions facing the field await to be unraveled.
Collapse
Affiliation(s)
- Josef P. Clark
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| |
Collapse
|
136
|
Abstract
Arginine methylation is an important posttranslational protein modification that modulates protein function for a wide range of biological processes. PIWI proteins, a subclade of the Argonaute family proteins, contain evolutionarily conserved symmetrical dimethylarginines (sDMAs). It has become increasingly apparent that the sDMAs of PIWI proteins serve as binding elements for TUDOR domain-containing proteins and that sDMA-dependent protein interactions play crucial roles in the biogenesis and function of PIWI-interacting RNAs (piRNAs). We describe a method for detecting PIWI sDMAs and purifying PIWI/piRNA complexes using anti-sDMA antibodies.
Collapse
|
137
|
Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev Biol 2013; 386:237-51. [PMID: 24355748 DOI: 10.1016/j.ydbio.2013.12.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 11/24/2022]
Abstract
To preserve genome integrity, an evolutionarily conserved small RNA-based silencing mechanism involving PIWI proteins and PIWI-interacting RNAs (piRNAs) represses potentially deleterious transposons in animals. Although there has been extensive research into PIWI proteins in bilaterians, these proteins remain to be examined in ancient phyla. Here, we investigated the PIWI proteins Hywi and Hyli in the cnidarian Hydra, and found that both PIWI proteins are enriched in multipotent stem cells, germline stem cells, and in the female germline. Hywi and Hyli localize to the nuage, a perinuclear organelle that has been implicated in piRNA-mediated transposon silencing, together with other conserved nuage and piRNA pathway components. Our findings provide the first report of nuage protein localization patterns in a non-bilaterian. Hydra PIWI proteins possess symmetrical dimethylarginines: modified residues that are known to aid in PIWI protein localization to the nuage and proper piRNA loading. piRNA profiling suggests that transposons are the major targets of the piRNA pathway in Hydra. Our data suggest that piRNA biogenesis through the ping-pong amplification cycle occurs in Hydra and that Hywi and Hyli are likely to preferentially bind primary and secondary piRNAs, respectively. Presumptive piRNA clusters are unidirectionally transcribed and primarily give rise to piRNAs that are antisense to transposons. These results indicate that various conserved features of PIWI proteins, the piRNA pathway, and their associations with the nuage were likely established before the evolution of bilaterians.
Collapse
|
138
|
Pek JW, Patil VS, Kai T. piRNA pathway and the potential processing site, the nuage, in the Drosophila germline. Dev Growth Differ 2013; 54:66-77. [PMID: 23741748 DOI: 10.1111/j.1440-169x.2011.01316.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accurate transfer of genetic material in germline cells during the formation of gametes is important for the continuity of the species. However, animal germline cells face challenges from transposons, which seek to spread themselves in the genome. This review focuses on studies in Drosophila melanogaster on how the genome protects itself from such a mutational burden via a class of gonad-specific small interfering RNAs, known as piRNAs (Piwi-interacting RNAs). In addition to silencing transposons, piRNAs also regulate other processes, such as chromosome segregation, mRNA degradation and germline differentiation. Recent studies revealed two modes of piRNA processing – primary processing and secondary processing (also known as ping-pong amplification). The primary processing pathway functions in both germline and somatic cells in the Drosophila ovaries by processing precursor piRNAs into 23–29 nt piRNAs. In contrast, the secondary processing pathway functions only in the germline cells where piRNAs are amplified in a feed-forward loop and require the Piwi-family proteins Aubergine and Argonaute3. Aubergine and Argonaute3 localize to a unique structure found in animal germline cells, the nuage, which has been proposed to function as a compartmentalized site for the ping-pong cycle. The nuage and the localized proteins are well-conserved, implying the importance of the piRNA amplification loop in animal germline cells. Nuage components include various types of proteins that are known to interact both physically and genetically, and therefore appear to be assembled in a sequential order to exert their function, resulting in a macromolecular RNA-protein complex dedicated to the silencing of transposons.
Collapse
Affiliation(s)
- Jun Wei Pek
- Department of Biological Sciences and Temasek Life Sciences Laboratory, 1 Research Link, The National University of Singapore, Singapore 117604, Singapore
| | | | | |
Collapse
|
139
|
Burroughs AM, Ando Y, Aravind L. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:141-81. [PMID: 24311560 DOI: 10.1002/wrna.1210] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/03/2013] [Accepted: 11/01/2013] [Indexed: 12/19/2022]
Abstract
Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs.
Collapse
Affiliation(s)
- Alexander Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | |
Collapse
|
140
|
Dufourt J, Dennis C, Boivin A, Gueguen N, Théron E, Goriaux C, Pouchin P, Ronsseray S, Brasset E, Vaury C. Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis. Nucleic Acids Res 2013; 42:2512-24. [PMID: 24288375 PMCID: PMC3936749 DOI: 10.1093/nar/gkt1184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotransposon in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the 'Piwiless pocket' or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts.
Collapse
Affiliation(s)
- Jérémy Dufourt
- Inserm, UMR1103, F-63001 Clermont-Ferrand, France, CNRS, UMR6293, F-63001 Clermont-Ferrand, France, Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 10448, F-63000 Clermont-Ferrand, France, Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, 9 quai Saint Bernard, 75005 Paris, France and CHU, F-63001 Clermont-Ferrand, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
141
|
Maternal enhancement of cytotype regulation in Drosophila melanogaster by genetic interactions between telomeric P elements and non-telomeric transgenic P elements. Genet Res (Camb) 2013; 94:339-51. [PMID: 23374243 DOI: 10.1017/s0016672312000523] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The X-linked telomeric P elements (TPs) TP5 and TP6 regulate the activity of the entire P element family because they are inserted in a major locus for the production of Piwi-interacting RNAs (piRNAs). The potential for this cytotype regulation is significantly strengthened when either TP5 or TP6 is combined with a non-telomeric X-linked or autosomal transgene that contains a P element. By themselves, none of the transgenic P elements have any regulatory ability. Synergism between the telomeric and transgenic P elements is much greater when the TP is derived from a female. Once an enhanced regulatory state is established in a female, it is transmitted to her offspring independently of either the telomeric or transgenic P elements - that is, it works through a strictly maternal effect. Synergistic regulation collapses when either the telomeric or the transgenic P element is removed from the maternal genotype, and it is significantly impaired when the TPs come from stocks heterozygous for mutations in the genes aubergine, piwi or Su(var)205. The synergism between telomeric and transgenic P elements is consistent with a model in which P piRNAs are amplified by alternating, or ping-pong, targeting of primary piRNAs to sense and antisense P transcripts, with the sense transcripts being derived from the transgenic P element and the antisense transcripts being derived from the TP.
Collapse
|
142
|
Hale BJ, Yang CX, Ross JW. Small RNA regulation of reproductive function. Mol Reprod Dev 2013; 81:148-59. [PMID: 24167089 DOI: 10.1002/mrd.22272] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/20/2013] [Indexed: 12/17/2022]
Abstract
Post-transcriptional gene regulation is one mechanism that occurs "above the genome," allowing the cells of an organism to have dramatically different phenotypes and functions. Non-coding ribonucleic acid (ncRNA) molecules regulate transcript and protein abundance above the level of transcription, and appear to play substantial roles in regulation of reproductive tissues. Three primary classes of small ncRNA are microRNA (miRNA), endogenous small interfering RNA (endo-siRNA), and PIWI-interacting RNA (piRNA). These RNA classes have similarities and clear distinctions between their biogenesis and in the interacting protein machinery that facilitate their effects on cellular phenotype. Characterization of the expression and importance of the critical components for the biogenesis of each class in different tissues is continuously contributing a better understanding of each of these RNA classes in different reproductive cell types. Here, we discuss the expression and potential roles of miRNA, endo-siRNA, and piRNA in reproduction from germ-cell development to pregnancy establishment and placental function. Additionally, the potential contribution of RNA binding proteins, long ncRNAs, and the more recently discovered circular RNAs (circRNAs) in relation to small RNA function is discussed.
Collapse
Affiliation(s)
- Benjamin J Hale
- Department of Animal Science, Iowa State University, Ames, Iowa
| | | | | |
Collapse
|
143
|
YUAN LIQIN, XIAO YUZHONG, ZHOU QIUZHI, YUAN DONGMEI, WU BAIPING, CHEN GANNONG, ZHOU JIANLIN. Proteomic analysis reveals that MAEL, a component of nuage, interacts with stress granule proteins in cancer cells. Oncol Rep 2013; 31:342-50. [DOI: 10.3892/or.2013.2836] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 10/21/2013] [Indexed: 11/06/2022] Open
|
144
|
Ohtani H, Iwasaki YW, Shibuya A, Siomi H, Siomi MC, Saito K. DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary. Genes Dev 2013; 27:1656-61. [PMID: 23913921 DOI: 10.1101/gad.221515.113] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Piwi-piRNA (PIWI-interacting RNA) complex (Piwi-piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. Here, we reveal that DmGTSF1, a Drosophila homolog of gametocyte-specific factor 1 (GTSF1) (which is required for transposon silencing in mouse testes), is necessary for Piwi-piRISC to repress target transposons and neighboring genes. DmGTSF1 depletion affected neither piRNA biogenesis nor nuclear import of Piwi-piRISC. DmGTSF1 mutations caused derepression of transposons and loss of ovary follicle layers, resulting in female infertility. We suggest that DmGTSF1, a nuclear Piwi interactor, is an integral factor in Piwi-piRISC-mediated transcriptional silencing.
Collapse
Affiliation(s)
- Hitoshi Ohtani
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | | | | | | | | | | |
Collapse
|
145
|
Abstract
The past two decades have seen an explosion in research on non-coding RNAs and their physiological and pathological functions. Several classes of small (20-30 nucleotides) and long (>200 nucleotides) non-coding RNAs have been firmly established as key regulators of gene expression in myriad processes ranging from embryonic development to innate immunity. In this review, we focus on our current understanding of the molecular mechanisms underlying the biogenesis and function of small interfering RNAs (siRNAs), microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs). In addition, we briefly review the relevance of small and long non-coding RNAs to human physiology and pathology and their potential to be exploited as therapeutic agents.
Collapse
Affiliation(s)
- Veena S Patil
- Program for RNA Biology, Sanford-Burnham Medical Research Institute , La Jolla, CA , USA
| | | | | |
Collapse
|
146
|
Honda S, Kirino Y, Maragkakis M, Alexiou P, Ohtaki A, Murali R, Mourelatos Z, Kirino Y. Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA (NEW YORK, N.Y.) 2013; 19:1405-18. [PMID: 23970546 PMCID: PMC3854531 DOI: 10.1261/rna.040428.113] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
PIWI proteins and their associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons in animal germlines. The molecular mechanisms and components responsible for piRNA biogenesis remain elusive. PIWI proteins contain conserved symmetrical dimethylarginines (sDMAs) that are specifically targeted by TUDOR domain-containing proteins. Here we report that the sDMAs of PIWI proteins play crucial roles in PIWI localization and piRNA biogenesis in Bombyx mori-derived BmN4 cells, which harbor fully functional piRNA biogenesis machinery. Moreover, RNAi screenings for Bombyx genes encoding TUDOR domain-containing proteins identified BmPAPI, a Bombyx homolog of Drosophila PAPI, as a factor modulating the length of mature piRNAs. BmPAPI specifically recognized sDMAs and interacted with PIWI proteins at the surface of the mitochondrial outer membrane. BmPAPI depletion resulted in 3'-terminal extensions of mature piRNAs without affecting the piRNA quantity. These results reveal the BmPAPI-involved piRNA precursor processing mechanism on mitochondrial outer membrane scaffolds.
Collapse
Affiliation(s)
- Shozo Honda
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Yoriko Kirino
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Akashi Ohtaki
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yohei Kirino
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Corresponding authorE-mail
| |
Collapse
|
147
|
Lim AK, Lorthongpanich C, Chew TG, Tan CWG, Shue YT, Balu S, Gounko N, Kuramochi-Miyagawa S, Matzuk MM, Chuma S, Messerschmidt DM, Solter D, Knowles BB. The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles. Development 2013; 140:3819-25. [PMID: 23924633 DOI: 10.1242/dev.099184] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mobilization of endogenous retrotransposons can destabilize the genome, an imminent danger during epigenetic reprogramming of cells in the germline. The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway is known to silence retrotransposons in the mouse testes. Several piRNA pathway components localize to the unique, germline structure known as the nuage. In this study, we surveyed mouse ovaries and found, for the first time, transient appearance of nuage-like structures in oocytes of primordial follicles. Mouse vasa homolog (MVH), Piwi-like 2 (PIWIL2/MILI) and tudor domain-containing 9 (TDRD9) are present in these structures, whereas aggregates of germ cell protein with ankyrin repeats, sterile alpha motif and leucine zipper (GASZ) localize separately in the cytoplasm. Retrotransposons are silenced in primordial ovarian follicles, and de-repressed upon reduction of piRNA expression in Mvh, Mili or Gasz mutants. However, these null-mutant females, unlike their male counterparts, are fertile, uncoupling retrotransposon activation from sterility.
Collapse
Affiliation(s)
- Ai Khim Lim
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648 Singapore.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
148
|
Vagin VV, Yu Y, Jankowska A, Luo Y, Wasik KA, Malone CD, Harrison E, Rosebrock A, Wakimoto BT, Fagegaltier D, Muerdter F, Hannon GJ. Minotaur is critical for primary piRNA biogenesis. RNA (NEW YORK, N.Y.) 2013; 19:1064-77. [PMID: 23788724 PMCID: PMC3708527 DOI: 10.1261/rna.039669.113] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Piwi proteins and their associated small RNAs are essential for fertility in animals. In part, this is due to their roles in guarding germ cell genomes against the activity of mobile genetic elements. piRNA populations direct Piwi proteins to silence transposon targets and, as such, form a molecular code that discriminates transposons from endogenous genes. Information ultimately carried by piRNAs is encoded within genomic loci, termed piRNA clusters. These give rise to long, single-stranded, primary transcripts that are processed into piRNAs. Despite the biological importance of this pathway, neither the characteristics that define a locus as a source of piRNAs nor the mechanisms that catalyze primary piRNA biogenesis are well understood. We searched an EMS-mutant collection annotated for fertility phenotypes for genes involved in the piRNA pathway. Twenty-seven homozygous sterile strains showed transposon-silencing defects. One of these, which strongly impacted primary piRNA biogenesis, harbored a causal mutation in CG5508, a member of the Drosophila glycerol-3-phosphate O-acetyltransferase (GPAT) family. These enzymes catalyze the first acylation step on the path to the production of phosphatidic acid (PA). Though this pointed strongly to a function for phospholipid signaling in the piRNA pathway, a mutant form of CG5508, which lacks the GPAT active site, still functions in piRNA biogenesis. We have named this new biogenesis factor Minotaur.
Collapse
Affiliation(s)
- Vasily V. Vagin
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yang Yu
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Anna Jankowska
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yicheng Luo
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- College of Pharmaceutical Science, Jilin University, Changchun, Jilin 130021, China P.R
| | - Kaja A. Wasik
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Colin D. Malone
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Emily Harrison
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adam Rosebrock
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Barbara T. Wakimoto
- Department of Biology and Center for Developmental Biology, University of Washington, Seattle, Washington 98195, USA
| | - Delphine Fagegaltier
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Felix Muerdter
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Corresponding authorE-mail
| |
Collapse
|
149
|
Guo M, Wu Y. Fighting an old war with a new weapon-silencing transposons by Piwi-interacting RNA. IUBMB Life 2013; 65:739-47. [DOI: 10.1002/iub.1192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 05/28/2013] [Accepted: 06/01/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Manhong Guo
- Department of Biochemistry; University of Saskatchewan; Saskatoon; Saskatchewan; Canada
| | - Yuliang Wu
- Department of Biochemistry; University of Saskatchewan; Saskatoon; Saskatchewan; Canada
| |
Collapse
|
150
|
Mani SR, Juliano CE. Untangling the web: the diverse functions of the PIWI/piRNA pathway. Mol Reprod Dev 2013; 80:632-64. [PMID: 23712694 DOI: 10.1002/mrd.22195] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/13/2013] [Indexed: 12/26/2022]
Abstract
Small RNAs impact several cellular processes through gene regulation. Argonaute proteins bind small RNAs to form effector complexes that control transcriptional and post-transcriptional gene expression. PIWI proteins belong to the Argonaute protein family, and bind PIWI-interacting RNAs (piRNAs). They are highly abundant in the germline, but are also expressed in some somatic tissues. The PIWI/piRNA pathway has a role in transposon repression in Drosophila, which occurs both by epigenetic regulation and post-transcriptional degradation of transposon mRNAs. These functions are conserved, but clear differences in the extent and mechanism of transposon repression exist between species. Mutations in piwi genes lead to the upregulation of transposon mRNAs. It is hypothesized that this increased transposon mobilization leads to genomic instability and thus sterility, although no causal link has been established between transposon upregulation and genome instability. An alternative scenario could be that piwi mutations directly affect genomic instability, and thus lead to increased transposon expression. We propose that the PIWI/piRNA pathway controls genome stability in several ways: suppression of transposons, direct regulation of chromatin architecture and regulation of genes that control important biological processes related to genome stability. The PIWI/piRNA pathway also regulates at least some, if not many, protein-coding genes, which further lends support to the idea that piwi genes may have broader functions beyond transposon repression. An intriguing possibility is that the PIWI/piRNA pathway is using transposon sequences to coordinate the expression of large groups of genes to regulate cellular function.
Collapse
Affiliation(s)
- Sneha Ramesh Mani
- Yale Stem Cell Center, Yale University, New Haven, Connecticut 06520, USA
| | | |
Collapse
|