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A genetic screen based on in vivo RNA imaging reveals centrosome-independent mechanisms for localizing gurken transcripts in Drosophila. G3-GENES GENOMES GENETICS 2014; 4:749-60. [PMID: 24531791 PMCID: PMC4059244 DOI: 10.1534/g3.114.010462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have screened chromosome arm 3L for ethyl methanesulfonate−induced mutations that disrupt localization of fluorescently labeled gurken (grk) messenger (m)RNA, whose transport along microtubules establishes both major body axes of the developing Drosophila oocyte. Rapid identification of causative mutations by single-nucleotide polymorphism recombinational mapping and whole-genomic sequencing allowed us to define nine complementation groups affecting grk mRNA localization and other aspects of oogenesis, including alleles of elg1, scaf6, quemao, nudE, Tsc2/gigas, rasp, and Chd5/Wrb, and several null alleles of the armitage Piwi-pathway gene. Analysis of a newly induced kinesin light chain allele shows that kinesin motor activity is required for both efficient grk mRNA localization and oocyte centrosome integrity. We also show that initiation of the dorsoanterior localization of grk mRNA precedes centrosome localization, suggesting that microtubule self-organization contributes to breaking axial symmetry to generate a unique dorsoventral axis.
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52
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Fablet M, Akkouche A, Braman V, Vieira C. Variable expression levels detected in the Drosophila effectors of piRNA biogenesis. Gene 2013; 537:149-53. [PMID: 24361206 DOI: 10.1016/j.gene.2013.11.095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 11/30/2013] [Indexed: 11/18/2022]
Abstract
piRNAs (piwi-interacting RNAs) are a class of small interfering RNAs that play a major role in the regulation of transposable elements (TEs) in Drosophila and are considered of fundamental importance in gonadal development. Genes encoding the effectors of the piRNA machinery are thus often thought to be highly constrained. On the contrary, as actors of genetic immunity, these genes have also been shown to evolve rapidly and display a high level of sequence variability. In order to assess the support for these competing models, we analyzed seven genes of the piRNA pathway using a collection of wild-type strains of Drosophila simulans, which are known to display significant variability in their TE content between strains. We showed that these genes exhibited wide variation in transcript levels, and we discuss some evolutionary considerations regarding the observed variability in TE copy numbers.
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Affiliation(s)
- Marie Fablet
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
| | - Abdou Akkouche
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Virginie Braman
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, F-69000 Lyon, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; Institut Universitaire de France.
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53
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Garza-Manero S, Pichardo-Casas I, Arias C, Vaca L, Zepeda A. Selective distribution and dynamic modulation of miRNAs in the synapse and its possible role in Alzheimer's Disease. Brain Res 2013; 1584:80-93. [PMID: 24355599 DOI: 10.1016/j.brainres.2013.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/30/2013] [Accepted: 12/07/2013] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control a wide range of functions in the cell. They act as post-transcriptional gene regulators throughout in development and in adulthood, although recent evidence suggests their potential role in the onset and development of various diseases and neuropathologies. In neurons miRNAs seem to play a key role as regulators of synaptic function. Synapses are vulnerable structures in neurodegenerative diseases. In particular, synaptic loss has been described as an early event in the pathogenesis of Alzheimer's Disease (AD). MicroRNA-mediated gene silencing represents a candidate event for the repression of specific mRNAs and protein synthesis that could account for synaptic dysfunction. In this work, we review the participation of miRNAs in synaptic function and consider their possible role in synaptic alterations in AD. First we review the biogenesis of miRNAs and their role as post-transcriptional regulators. Then we discuss recently published data on the distribution of miRNAs in the brain as well as their role in dynamic regulation at the synapse. In the second part, we briefly introduce the reader to AD, focusing on synaptic alterations in the progression of the pathology. Then we discuss possible implications of miRNAs in the associated synaptic dysfunction.
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Affiliation(s)
- Sylvia Garza-Manero
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México, DF, Mexico.
| | - Israel Pichardo-Casas
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510 México, DF, Mexico.
| | - Clorinda Arias
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México, DF, Mexico.
| | - Luis Vaca
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510 México, DF, Mexico.
| | - Angélica Zepeda
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04510, México, DF, Mexico.
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54
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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.
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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
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55
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Abstract
Ion channels and transporters are expressed in every living cell, where they participate in controlling a plethora of biological processes and physiological functions, such as excitation of cells in response to stimulation, electrical activities of cells, excitation-contraction coupling, cellular osmolarity, and even cell growth and death. Alterations of ion channels/transporters can have profound impacts on the cellular physiology associated with these proteins. Expression of ion channels/transporters is tightly regulated and expression deregulation can trigger abnormal processes, leading to pathogenesis, the channelopathies. While transcription factors play a critical role in controlling the transcriptome of ion channels/transporters at the transcriptional level by acting on the 5'-flanking region of the genes, microribonucleic acids (miRNAs), a newly discovered class of regulators in the gene network, are also crucial for expression regulation at the posttranscriptional level through binding to the 3'untranslated region of the genes. These small noncoding RNAs fine tune expression of genes involved in a wide variety of cellular processes. Recent studies revealed the role of miRNAs in regulating expression of ion channels/transporters and the associated physiological functions. miRNAs can target ion channel genes to alter cardiac excitability (conduction, repolarization, and automaticity) and affect arrhythmogenic potential of heart. They can modulate circadian rhythm, pain threshold, neuroadaptation to alcohol, brain edema, etc., through targeting ion channel genes in the neuronal systems. miRNAs can also control cell growth and tumorigenesis by acting on the relevant ion channel genes. Future studies are expected to rapidly increase to unravel a new repertoire of ion channels/transporters for miRNA regulation.
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Affiliation(s)
- Zhiguo Wang
- Harbin Medical University, Harbin, Heilongjiang, People's Republic of China.
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56
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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.
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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
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57
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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
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58
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Carter JM, Baker SC, Pink R, Carter DRF, Collins A, Tomlin J, Gibbs M, Breuker CJ. Unscrambling butterfly oogenesis. BMC Genomics 2013; 14:283. [PMID: 23622113 PMCID: PMC3654919 DOI: 10.1186/1471-2164-14-283] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/05/2013] [Indexed: 12/16/2022] Open
Abstract
Background Butterflies are popular model organisms to study physiological mechanisms
underlying variability in oogenesis and egg provisioning in response to
environmental conditions. Nothing is known, however, about; the
developmental mechanisms governing butterfly oogenesis, how polarity in the
oocyte is established, or which particular maternal effect genes regulate
early embryogenesis. To gain insights into these developmental mechanisms
and to identify the conserved and divergent aspects of butterfly oogenesis,
we analysed a de novo ovarian transcriptome of the Speckled Wood
butterfly Pararge aegeria (L.), and compared the results with known
model organisms such as Drosophila melanogaster and Bombyx
mori. Results A total of 17306 contigs were annotated, with 30% possibly novel or highly
divergent sequences observed. Pararge aegeria females expressed
74.5% of the genes that are known to be essential for D.
melanogaster oogenesis. We discuss the genes involved in all
aspects of oogenesis, including vitellogenesis and choriogenesis, plus those
implicated in hormonal control of oogenesis and transgenerational hormonal
effects in great detail. Compared to other insects, a number of significant
differences were observed in; the genes involved in stem cell maintenance
and differentiation in the germarium, establishment of oocyte polarity, and
in several aspects of maternal regulation of zygotic development. Conclusions This study provides valuable resources to investigate a number of divergent
aspects of butterfly oogenesis requiring further research. In order to fully
unscramble butterfly oogenesis, we also now also have the resources to
investigate expression patterns of oogenesis genes under a range of
environmental conditions, and to establish their function.
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Affiliation(s)
- Jean-Michel Carter
- Evolutionary Developmental Biology Research Group, Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Headington, Oxford, OX3 0BP, UK
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59
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A mosaic genetic screen for genes involved in the early steps of Drosophila oogenesis. G3-GENES GENOMES GENETICS 2013; 3:409-25. [PMID: 23450845 PMCID: PMC3583450 DOI: 10.1534/g3.112.004747] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
The first hours of Drosophila embryogenesis rely exclusively on maternal information stored within the egg during oogenesis. The formation of the egg chamber is thus a crucial step for the development of the future adult. It has emerged that many key developmental decisions are made during the very first stages of oogenesis. We performed a clonal genetic screen on the left arm of chromosome 2 for mutations affecting early oogenesis. During the first round of screening, we scored for defects in egg chambers morphology as an easy read-out of early abnormalities. In a second round of screening, we analyzed the localization of centrosomes and Orb protein within the oocyte, the position of the oocyte within the egg chamber, and the progression through meiosis. We have generated a collection of 71 EMS-induced mutants that affect oocyte determination, polarization, or localization. We also recovered mutants affecting the number of germline cyst divisions or the differentiation of follicle cells. Here, we describe the analysis of nine complementation groups and eight single alleles. We mapped several mutations and identified alleles of Bicaudal-D, lethal(2) giant larvae, kuzbanian, GDP-mannose 4,6-dehydratase, tho2, and eiF4A. We further report the molecular identification of two alleles of the Drosophila homolog of Che-1/AATF and demonstrate its antiapoptotic activity in vivo. This collection of mutants will be useful to investigate further the early steps of Drosophila oogenesis at a genetic level.
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60
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Lucas K, Raikhel AS. Insect microRNAs: biogenesis, expression profiling and biological functions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:24-38. [PMID: 23165178 PMCID: PMC3534889 DOI: 10.1016/j.ibmb.2012.10.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/24/2012] [Accepted: 10/28/2012] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNA) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that modulate gene expression at the post-transcriptional level via base pairing to target sites within messenger RNAs (mRNA). Typically, the miRNA "seed sequence" (nucleotides 2-8 at the 5' end) binds complementary seed match sites within the 3' untranslated region of mRNAs, resulting in either translational inhibition or mRNA degradation. MicroRNAs were first discovered in Caenorhabditis elegans and were shown to be involved in the timed regulation of developmental events. Since their discovery in the 1990s, thousands of potential miRNAs have since been identified in various organisms through small RNA cloning methods and/or computational prediction, and have been shown to play functionally important roles of gene regulation in invertebrates, vertebrates, plants, fungi and viruses. Numerous functions of miRNAs identified in Drosophila melanogaster have demonstrated a great significance of these regulatory molecules. However, elucidation of miRNA roles in non-drosophilid insects presents a challenging and important task.
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Affiliation(s)
- Keira Lucas
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, CA 92521, U.S.A
| | - Alexander S. Raikhel
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Corresponding author. Department of Entomology, University of California, Riverside, Riverside, CA 92521, U.S.A. Tel. +1 951 827 2129. (Keira Lucas); (Alexander S. Raikhel)
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61
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Zheng YH, Jeang KT, Tokunaga K. Host restriction factors in retroviral infection: promises in virus-host interaction. Retrovirology 2012; 9:112. [PMID: 23254112 PMCID: PMC3549941 DOI: 10.1186/1742-4690-9-112] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 12/09/2012] [Indexed: 01/19/2023] Open
Abstract
Retroviruses have an intricate life cycle. There is much to be learned from studying retrovirus-host interactions. Among retroviruses, the primate lentiviruses have one of the more complex genome structures with three categories of viral genes: structural, regulatory, and accessory genes. Over time, we have gained increasing understanding of the lentivirus life cycle from studying host factors that support virus replication. Similarly, studies on host restriction factors that inhibit viral replication have also made significant contributions to our knowledge. Here, we review recent progress on the rapidly growing field of restriction factors, focusing on the antiretroviral activities of APOBEC3G, TRIM5, tetherin, SAMHD1, MOV10, and cellular microRNAs (miRNAs), and the counter-activities of Vif, Vpu, Vpr, Vpx, and Nef.
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Affiliation(s)
- Yong-Hui Zheng
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
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62
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Abstract
Hybrids of two Drosophila species show transposable element derepression and piRNA pathway malfunction, revealing adaptive evolution of piRNA pathway components. The Piwi-interacting RNA (piRNA) pathway defends the germline of animals from the deleterious activity of selfish transposable elements (TEs) through small-RNA mediated silencing. Adaptation to novel invasive TEs is proposed to occur by incorporating their sequences into the piRNA pool that females produce and deposit into their eggs, which then propagates immunity against specific TEs to future generations. In support of this model, the F1 offspring of crosses between strains of the same Drosophila species sometimes suffer from germline derepression of paternally inherited TE families, caused by a failure of the maternal strain to produce the piRNAs necessary for their regulation. However, many protein components of the Drosophila piRNA pathway exhibit signatures of positive selection, suggesting that they also contribute to the evolution of host genome defense. Here we investigate piRNA pathway function and TE regulation in the F1 hybrids of interspecific crosses between D. melanogaster and D. simulans and compare them with intraspecific control crosses of D. melanogaster. We confirm previous reports showing that intraspecific crosses are characterized by derepression of paternally inherited TE families that are rare or absent from the maternal genome and piRNA pool, consistent with the role of maternally deposited piRNAs in shaping TE silencing. In contrast to the intraspecific cross, we discover that interspecific hybrids are characterized by widespread derepression of both maternally and paternally inherited TE families. Furthermore, the pattern of derepression of TE families in interspecific hybrids cannot be attributed to their paucity or absence from the piRNA pool of the maternal species. Rather, we demonstrate that interspecific hybrids closely resemble piRNA effector-protein mutants in both TE misregulation and aberrant piRNA production. We suggest that TE derepression in interspecific hybrids largely reflects adaptive divergence of piRNA pathway genes rather than species-specific differences in TE-derived piRNAs. Eukaryotic genomes contain large quantities of transposable elements (TEs), short self-replicating DNA sequences that can move within the genome. The selfish replication of TEs has potentially drastic consequences for the host, such as disruption of gene function, induction of sterility, and initiation or exacerbation of some cancers. Like the adaptive immune system that defends our bodies against pathogens, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful effects of TEs. Fundamental to piRNA-mediated defense is the production of small noncoding RNAs that act like antibodies to target replicating TEs for destruction by piRNA-effector proteins. piRNAs are expected to diverge rapidly between species in response to genome infection by increasingly disparate TEs. Here, we tested this hypothesis by examining how differences in piRNAs between two species of fruit fly relate to TE “immunity” in their hybrid offspring. Because piRNAs are maternally deposited, we expected excessive replication of paternal TEs in hybrids. Surprisingly, we observe increased activity of both maternal and paternal TEs, together with defects in piRNA production that are reminiscent of piRNA effector-protein mutants. Our observations reveal that piRNA effector-proteins do not function properly in hybrids, and we propose that adaptive evolution among piRNA effector-proteins contributes to host genome defense and leads to the functional incompatibilities that we observe in hybrids.
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MESH Headings
- Adaptation, Biological
- Animals
- Animals, Genetically Modified/genetics
- Animals, Genetically Modified/metabolism
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Crosses, Genetic
- DNA Transposable Elements
- Drosophila/genetics
- Drosophila/metabolism
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Evolution, Molecular
- Female
- Genetic Complementation Test
- Genome, Insect
- Hybridization, Genetic
- Immunohistochemistry
- Inheritance Patterns
- Male
- Mutation
- Ovary/cytology
- Ovary/metabolism
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Phenotype
- RNA Interference
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Selection, Genetic
- Species Specificity
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Affiliation(s)
- Erin S. Kelleher
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ESK); (DAB)
| | | | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (ESK); (DAB)
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63
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Blockade of pachytene piRNA biogenesis reveals a novel requirement for maintaining post-meiotic germline genome integrity. PLoS Genet 2012; 8:e1003038. [PMID: 23166510 PMCID: PMC3499362 DOI: 10.1371/journal.pgen.1003038] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 09/05/2012] [Indexed: 11/19/2022] Open
Abstract
Piwi-interacting RNAs are a diverse class of small non-coding RNAs implicated in the silencing of transposable elements and the safeguarding of genome integrity. In mammals, male germ cells express two genetically and developmentally distinct populations of piRNAs at the pre-pachytene and pachytene stages of meiosis, respectively. Pre-pachytene piRNAs are mostly derived from retrotransposons and required for their silencing. In contrast, pachytene piRNAs originate from ~3,000 genomic clusters, and their biogenesis and function remain enigmatic. Here, we report that conditional inactivation of the putative RNA helicase MOV10L1 in mouse spermatocytes produces a specific loss of pachytene piRNAs, significant accumulation of pachytene piRNA precursor transcripts, and unusual polar conglomeration of Piwi proteins with mitochondria. Pachytene piRNA-deficient spermatocytes progress through meiosis without derepression of LINE1 retrotransposons, but become arrested at the post-meiotic round spermatid stage with massive DNA damage. Our results demonstrate that MOV10L1 acts upstream of Piwi proteins in the primary processing of pachytene piRNAs and suggest that, distinct from pre-pachytene piRNAs, pachytene piRNAs fulfill a unique function in maintaining post-meiotic genome integrity.
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64
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Gao M, Arkov AL. Next generation organelles: structure and role of germ granules in the germline. Mol Reprod Dev 2012; 80:610-23. [PMID: 23011946 DOI: 10.1002/mrd.22115] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 09/14/2012] [Indexed: 12/20/2022]
Abstract
Germ cells belong to a unique class of stem cells that gives rise to eggs and sperm, and ultimately to an entire organism after gamete fusion. In many organisms, germ cells contain electron-dense structures that are also known as nuage or germ granules. Although germ granules were discovered more than 100 years ago, their composition, structure, assembly, and function are not fully understood. Germ granules contain non-coding RNAs, mRNAs, and proteins required for germline development. Here we review recent studies that highlight the importance of several protein families in germ granule assembly and function, including germ granule inducers, which initiate the granule formation, and downstream components, such as RNA helicases and Tudor domain-Piwi protein-piRNA complexes. Assembly of these components into one granule is likely to result in a highly efficient molecular machine that ensures translational control and protects germline DNA from mutations caused by mobile genetic elements. Furthermore, recent studies have shown that different somatic cells, including stem cells and neurons, produce germ granule components that play a crucial role in stem cell maintenance and memory formation, indicating a much more diverse functional repertoire for these organelles than previously thought.
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Affiliation(s)
- Ming Gao
- Department of Biological Sciences, Murray State University, Murray, Kentucky 42071, USA
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65
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Lasko P. mRNA localization and translational control in Drosophila oogenesis. Cold Spring Harb Perspect Biol 2012; 4:cshperspect.a012294. [PMID: 22865893 DOI: 10.1101/cshperspect.a012294] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Localization of an mRNA species to a particular subcellular region can complement translational control mechanisms to produce a restricted spatial distribution of the protein it encodes. mRNA localization has been studied most in asymmetric cells such as budding yeast, early embryos, and neurons, but the process is likely to be more widespread. This article reviews the current state of knowledge about the mechanisms of mRNA localization and its functions in early embryonic development, focusing on Drosophila where the relevant knowledge is most advanced. Links between mRNA localization and translational control mechanisms also are examined.
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Affiliation(s)
- Paul Lasko
- Department of Biology, Bellini Life Sciences Building, McGill University, Montréal, Québec H3G 0B1, Canada.
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66
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Preall JB, Czech B, Guzzardo PM, Muerdter F, Hannon GJ. shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA (NEW YORK, N.Y.) 2012; 18:1446-57. [PMID: 22753781 PMCID: PMC3404366 DOI: 10.1261/rna.034405.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 05/15/2012] [Indexed: 05/03/2023]
Abstract
In animals, the piRNA pathway preserves the integrity of gametic genomes, guarding them against the activity of mobile genetic elements. This innate immune mechanism relies on distinct genomic loci, termed piRNA clusters, to provide a molecular definition of transposons, enabling their discrimination from genes. piRNA clusters give rise to long, single-stranded precursors, which are processed into primary piRNAs through an unknown mechanism. These can engage in an adaptive amplification loop, the ping-pong cycle, to optimize the content of small RNA populations via the generation of secondary piRNAs. Many proteins have been ascribed functions in either primary biogenesis or the ping-pong cycle, though for the most part the molecular functions of proteins implicated in these pathways remain obscure. Here, we link shutdown (shu), a gene previously shown to be required for fertility in Drosophila, to the piRNA pathway. Analysis of knockdown phenotypes in both the germline and somatic compartments of the ovary demonstrate important roles for shutdown in both primary biogenesis and the ping-pong cycle. shutdown is a member of the FKBP family of immunophilins. Shu contains domains implicated in peptidyl-prolyl cis-trans isomerase activity and in the binding of HSP90-family chaperones, though the relevance of these domains to piRNA biogenesis is unknown.
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Affiliation(s)
- Jonathan B. Preall
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Benjamin Czech
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Paloma M. Guzzardo
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Felix Muerdter
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gregory J. Hannon
- Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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67
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Liu C, Zhang X, Huang F, Yang B, Li J, Liu B, Luo H, Zhang P, Zhang H. APOBEC3G inhibits microRNA-mediated repression of translation by interfering with the interaction between Argonaute-2 and MOV10. J Biol Chem 2012; 287:29373-83. [PMID: 22791714 DOI: 10.1074/jbc.m112.354001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The apolipoprotein-B-mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or A3G) is a potent restrictive factor for human immunodeficiency virus type 1 (HIV-1) and many other retroviruses. It belongs to the cytidine deaminase family. Recent studies have shown that A3G significantly inhibits microRNA (miRNA)-mediated repression of translation. However, the mechanism underlying this action must be clarified. In this report, we have demonstrated that A3G counteracts miRNA-mediated repression of translation by inhibiting the interaction between moloney leukemia virus 10 (MOV10) protein and Argonaute-2 (AGO2), causing either abnormal assembly or abnormal maturation of miRNA-inducing silencing complex (miRISC). Through a series of MOV10 deletions, we found that A3G binds to a domain at the C terminus in MOV10, where it competitively inhibits the binding of AGO2 to that same domain. The interaction between A3G and MOV10 relies on its association with a small RNA named 7SL RNA. The A3G mutant W127L, which is unable to bind to 7SL RNA, shows significantly incapability to counteract the miRNA-mediated repression of translation. Our data demonstrate a novel mechanism involved in the regulation of miRISC activity. Although both A3G and MOV10 belong to the interferon antiviral system and inhibit HIV-1 and other retroviruses, their opposing effects on the cellular miRNA activity suggest that they play much more complicated regulatory roles in various cellular functions.
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Affiliation(s)
- Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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68
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Conservation of the RNA Transport Machineries and Their Coupling to Translation Control across Eukaryotes. Comp Funct Genomics 2012; 2012:287852. [PMID: 22666086 PMCID: PMC3361156 DOI: 10.1155/2012/287852] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 02/09/2012] [Indexed: 01/03/2023] Open
Abstract
Restriction of proteins to discrete subcellular regions is a common mechanism to establish cellular asymmetries and depends on a coordinated program of mRNA localization and translation control. Many processes from the budding of a yeast to the establishment of metazoan embryonic axes and the migration of human neurons, depend on this type of cell polarization. How factors controlling transport and translation assemble to regulate at the same time the movement and translation of transported mRNAs, and whether these mechanisms are conserved across kingdoms is not yet entirely understood. In this review we will focus on some of the best characterized examples of mRNA transport machineries, the "yeast locasome" as an example of RNA transport and translation control in unicellular eukaryotes, and on the Drosophila Bic-D/Egl/Dyn RNA localization machinery as an example of RNA transport in higher eukaryotes. This focus is motivated by the relatively advanced knowledge about the proteins that connect the localizing mRNAs to the transport motors and the many well studied proteins involved in translational control of specific transcripts that are moved by these machineries. We will also discuss whether the core of these RNA transport machineries and factors regulating mRNA localization and translation are conserved across eukaryotes.
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69
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Onal P, Grün D, Adamidi C, Rybak A, Solana J, Mastrobuoni G, Wang Y, Rahn HP, Chen W, Kempa S, Ziebold U, Rajewsky N. Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J 2012; 31:2755-69. [PMID: 22543868 DOI: 10.1038/emboj.2012.110] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/02/2012] [Indexed: 12/13/2022] Open
Abstract
Freshwater planaria possess extreme regeneration capabilities mediated by abundant, pluripotent stem cells (neoblasts) in adult animals. Although planaria emerged as an attractive in vivo model system for stem cell biology, gene expression in neoblasts has not been profiled comprehensively and it is unknown how molecular mechanisms for pluripotency in neoblasts relate to those in mammalian embryonic stem cells (ESCs). We purified neoblasts and quantified mRNA and protein expression by sequencing and shotgun proteomics. We identified ∼4000 genes specifically expressed in neoblasts, including all ∼30 known neoblast markers. Genes important for pluripotency in ESCs, including regulators as well as targets of OCT4, were well conserved and upregulated in neoblasts. We found conserved expression of epigenetic regulators and demonstrated their requirement for planarian regeneration by knockdown experiments. Post-transcriptional regulatory genes characteristic for germ cells were also enriched in neoblasts, suggesting the existence of a common ancestral state of germ cells and ESCs. We conclude that molecular determinants of pluripotency are conserved throughout evolution and that planaria are an informative model system for human stem cell biology.
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Affiliation(s)
- Pinar Onal
- Laboratory of Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
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70
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Wang S, Chen AJ, Shi LJ, Zhao XF, Wang JX. TRBP and eIF6 homologue in Marsupenaeus japonicus play crucial roles in antiviral response. PLoS One 2012; 7:e30057. [PMID: 22279564 PMCID: PMC3261181 DOI: 10.1371/journal.pone.0030057] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022] Open
Abstract
Plants and invertebrates can suppress viral infection through RNA silencing, mediated by RNA-induced silencing complex (RISC). Trans-activation response RNA-binding protein (TRBP), consisting of three double-stranded RNA-binding domains, is a component of the RISC. In our previous paper, a TRBP homologue in Fenneropenaeus chinensis (Fc-TRBP) was reported to directly bind to eukaryotic initiation factor 6 (Fc-eIF6). In this study, we further characterized the function of TRBP and the involvement of TRBP and eIF6 in antiviral RNA interference (RNAi) pathway of shrimp. The double-stranded RNA binding domains (dsRBDs) B and C of the TRBP from Marsupenaeus japonicus (Mj-TRBP) were found to mediate the interaction of TRBP and eIF6. Gel-shift assays revealed that the N-terminal of Mj-TRBP dsRBD strongly binds to double-stranded RNA (dsRNA) and that the homodimer of the TRBP mediated by the C-terminal dsRBD increases the affinity to dsRNA. RNAi against either Mj-TRBP or Mj-eIF6 impairs the dsRNA-induced sequence-specific RNAi pathway and facilitates the proliferation of white spot syndrome virus (WSSV). These results further proved the important roles of TRBP and eIF6 in the antiviral response of shrimp.
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Affiliation(s)
- Shuai Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation of Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, People's Republic of China
- Wuhan Institute of Virology, Chinese Academy of Science, Wuchang, Hubei, People's Republic of China
| | - An-Jing Chen
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation of Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, People's Republic of China
| | - Li-Jie Shi
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation of Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, People's Republic of China
| | - Xiao-Fan Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation of Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, People's Republic of China
| | - Jin-Xing Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation of Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong, People's Republic of China
- * E-mail:
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71
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Abstract
Translational regulation plays an essential role in many phases of the Drosophila life cycle. During embryogenesis, specification of the developing body pattern requires co-ordination of the translation of oskar, gurken and nanos mRNAs with their subcellular localization. In addition, dosage compensation is controlled by Sex-lethal-mediated translational regulation while dFMR1 (the Drosophila homologue of the fragile X mental retardation protein) controls translation of various mRNAs which function in the nervous system. Here we describe some of the mechanisms that are utilized to regulate these various processes. Our review highlights the complexity that can be involved with multiple factors employing different mechanisms to control the translation of a single mRNA.
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Affiliation(s)
- James E Wilhelm
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210, USA
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72
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Muench DG, Zhang C, Dahodwala M. Control of cytoplasmic translation in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:178-94. [DOI: 10.1002/wrna.1104] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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73
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Sato K, Nishida KM, Shibuya A, Siomi MC, Siomi H. Maelstrom coordinates microtubule organization during Drosophila oogenesis through interaction with components of the MTOC. Genes Dev 2011; 25:2361-73. [PMID: 22085963 DOI: 10.1101/gad.174110.111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The establishment of body axes in multicellular organisms requires accurate control of microtubule polarization. Mutations in Drosophila PIWI-interacting RNA (piRNA) pathway genes often disrupt the axes of the oocyte. This results from the activation of the DNA damage checkpoint factor Checkpoint kinase 2 (Chk2) due to transposon derepression. A piRNA pathway gene, maelstrom (mael), is critical for the establishment of oocyte polarity in the developing egg chamber during Drosophila oogenesis. We show that Mael forms complexes with microtubule-organizing center (MTOC) components, including Centrosomin, Mini spindles, and γTubulin. We also show that Mael colocalizes with αTubulin and γTubulin to centrosomes in dividing cyst cells and follicle cells. MTOC components mislocalize in mael mutant germarium and egg chambers, leading to centrosome migration defects. During oogenesis, the loss of mael affects oocyte determination and induces egg chamber fusion. Finally, we show that the axis specification defects in mael mutants are not suppressed by a mutation in mnk, which encodes a Chk2 homolog. These findings suggest a model in which Mael serves as a platform that nucleates other MTOC components to form a functional MTOC in early oocyte development, which is independent of Chk2 activation and DNA damage signaling.
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Affiliation(s)
- Kaoru Sato
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
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74
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The "Special" crystal-Stellate System in Drosophila melanogaster Reveals Mechanisms Underlying piRNA Pathway-Mediated Canalization. GENETICS RESEARCH INTERNATIONAL 2011; 2012:324293. [PMID: 22567384 PMCID: PMC3335654 DOI: 10.1155/2012/324293] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/18/2011] [Accepted: 09/21/2011] [Indexed: 11/18/2022]
Abstract
The Stellate-made crystals formation in spermatocytes is the phenotypic manifestation of a disrupted crystal-Stellate interaction in testes of Drosophila melanogaster. Stellate silencing is achieved by the piRNA pathway, but many features still remain unknown. Here we outline the important role of the crystal-Stellate modifiers. These have shed light on the piRNA pathways that defend genome integrity against transposons and other repetitive elements in the gonads. In particular, we illustrate the finding that HSP90 participates in the molecular pathways of piRNA production. This observation has relevance for the mechanisms underlying the evolutionary canalization process.
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75
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Abstract
Translational control of specific mRNAs is a widespread mechanism of gene regulation, and it is especially important in pattern formation in the oocytes of organisms in which the embryonic axes are established maternally. Drosophila and Xenopus have been especially valuable in elucidating the relevant molecular mechanisms. Here, we comprehensively review what is known about translational control in these two systems, focusing on examples that illustrate key concepts that have emerged. We focus on protein-mediated translational control, rather than regulation mediated by small RNAs, as the former appears to be predominant in controlling these developmental events. Mechanisms that modulate the ability of the specific mRNAs to be recruited to the ribosome, that regulate polyadenylation of specific mRNAs, or that control the association of particular mRNAs into translationally inert ribonucleoprotein complexes will all be discussed.
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Affiliation(s)
- Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01606, USA.
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76
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A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J 2011; 30:3977-93. [PMID: 21863019 DOI: 10.1038/emboj.2011.308] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/03/2011] [Indexed: 11/08/2022] Open
Abstract
PIWI proteins and their bound PIWI-interacting RNAs (piRNAs) form the core of a gonad-specific small RNA silencing pathway that protects the animal genome against the deleterious activity of transposable elements. Recent studies linked the piRNA pathway to TUDOR biology as TUDOR domains of various proteins bind symmetrically methylated Arginine residues in PIWI proteins. We systematically analysed the Drosophila TUDOR protein family and identified four previously not characterized TUDOR domain-containing proteins (CG4771, CG14303, CG11133 and CG31755) as essential piRNA pathway factors. We characterized CG4771 (Vreteno) in detail and demonstrate a critical role for this protein in primary piRNA biogenesis. Vreteno physically and/or genetically interacts with the primary pathway components Piwi, Armitage, Yb and Zucchini. Vreteno also interacts with the Tdrd12 orthologues CG11133 (Brother of Yb) and CG31755 (Sister of Yb), which are essential for the primary piRNA pathway in the germline and probably replace the function of the related but soma-specific factor Yb.
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77
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Zamparini AL, Davis MY, Malone CD, Vieira E, Zavadil J, Sachidanandam R, Hannon GJ, Lehmann R. Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. Development 2011; 138:4039-50. [PMID: 21831924 PMCID: PMC3160098 DOI: 10.1242/dev.069187] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In Drosophila, Piwi proteins associate with Piwi-interacting RNAs (piRNAs) and protect the germline genome by silencing mobile genetic elements. This defense system acts in germline and gonadal somatic tissue to preserve germline development. Genetic control for these silencing pathways varies greatly between tissues of the gonad. Here, we identified Vreteno (Vret), a novel gonad-specific protein essential for germline development. Vret is required for piRNA-based transposon regulation in both germline and somatic gonadal tissues. We show that Vret, which contains Tudor domains, associates physically with Piwi and Aubergine (Aub), stabilizing these proteins via a gonad-specific mechanism that is absent in other fly tissues. In the absence of vret, Piwi-bound piRNAs are lost without changes in piRNA precursor transcript production, supporting a role for Vret in primary piRNA biogenesis. In the germline, piRNAs can engage in an Aub- and Argonaute 3 (AGO3)-dependent amplification in the absence of Vret, suggesting that Vret function can distinguish between primary piRNAs loaded into Piwi-Aub complexes and piRNAs engaged in the amplification cycle. We propose that Vret plays an essential role in transposon regulation at an early stage of primary piRNA processing.
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Affiliation(s)
- Andrea L Zamparini
- HHMI and Kimmel Center for Biology and Medicine at Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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78
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Sokolova OA, Yakushev EY, Stolyarenko AD, Mikhaleva EA, Gvozdev VA, Klenov MS. Interplay of transposon-silencing genes in the germline of Drosophila melanogaster. Mol Biol 2011. [DOI: 10.1134/s0026893311030174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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79
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piR_015520 belongs to Piwi-associated RNAs regulates expression of the human melatonin receptor 1A gene. PLoS One 2011; 6:e22727. [PMID: 21818375 PMCID: PMC3144248 DOI: 10.1371/journal.pone.0022727] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/02/2011] [Indexed: 11/19/2022] Open
Abstract
Piwi-associated RNAs (piRNAs) are a distinct class of 24- to 30-nucleotide-long RNAs produced by a Dicer-independent mechanism, and are associated with Piwi-class Argonaute proteins. In contrast to the several hundred species of microRNAs (miRNAs) identified thus far, piRNAs consist of more than 30,000 different species in humans. Studies in flies, fish and mice implicate these piRNAs in regulating germ line development, the silencing of selfish DNA elements, and maintaining germ line DNA integrity. Most piRNAs map to unique sites in the human genome, including intergenic, intronic, and exonic sequences. However, the role of piRNAs in humans remains to be elucidated. Here, we uncover an unexpected function of the piRNA pathway in humans. We show for the first time, that the piRNA_015520, located in intron 1 of the human Melatonin receptor 1A (MTNR1A) gene, is expressed in adult human tissues (testes and brain) and in the human cell line HEK 293. Although the role of piR_015520 expression in brain tissue remains unknown, the testes-specific expression is consistent with previous findings in several species. Surprisingly, in contrast to the mechanism known for miRNA-mediated modulation of gene expression, piRNA_015520 negatively regulates MTNR1A gene expression by binding to its genomic region. This finding suggests that changes in individual piRNA levels could influence both autoregulatory gene expression and the expression of the gene in which the piRNA is located. These findings offer a new perspective for piRNAs functioning as gene regulators in humans.
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80
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Simonelig M. Developmental functions of piRNAs and transposable elements: a Drosophila point-of-view. RNA Biol 2011; 8:754-9. [PMID: 21712652 DOI: 10.4161/rna.8.5.16042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The primary function of the piRNA pathway is to repress the expression and transposition of transposable elements. However, the piRNA pathway has additional biological and developmental functions. These functions are either a consequence of transposon regulation, or they result from direct roles of transposable elements in chromosome structure and gene regulation through piRNAs. Recent data have extended the functions of transposable elements in gene regulation, revealing a trans-acting role of transposable element piRNAs in the control of gene expression. Over the last few years, extensive studies on the piRNA pathway have rapidly increased our understanding of the relationships between transposable elements and the host genome, and of the essential role of transposable elements in biological and developmental processes.
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Affiliation(s)
- Martine Simonelig
- mRNA Regulation and Development, Institute of Human Genetics, CNRS UPR1142, Montpellier, France.
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81
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Tchurikov NA, Kretova OV. Both piRNA and siRNA pathways are silencing transcripts of the suffix element in the Drosophila melanogaster germline and somatic cells. PLoS One 2011; 6:e21882. [PMID: 21779345 PMCID: PMC3136478 DOI: 10.1371/journal.pone.0021882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/10/2011] [Indexed: 01/22/2023] Open
Abstract
In the Drosophila melanogaster germline, the piRNA pathway silences retrotransposons as well as other transcribed repetitive elements. Suffix is an unusual short retroelement that was identified both as an actively transcribed repetitive element and also as an element at the 3' ends of the Drosophila non-LTR F element. The copies of suffix that are F element-independent are far more actively transcribed than their counterparts on the F element. We studied the patterns of small RNAs targeting both strands of suffix in Drosophila ovaries using an RNase protection assay and the analysis of the corresponding RNA sequences from the libraries of total small RNAs. Our results indicate that suffix sense and antisense transcripts are targeted mainly by 23-29 nucleotides in length piRNAs and also by 21 nucleotides in length siRNAs. Suffix sense transcripts actively form longer RNA species, corresponding either to partial digestion products of the RNAi and Piwi pathways or to another RNA silencing mechanism. Both sense and antisense suffix transcripts accumulated in the ovaries of homozygous spn-E, piwi and aub mutants. These results provide evidence that suffix sense and antisense transcripts in the germ line and soma are targeted by both RNAi and Piwi pathways and that a Dicer-independent pathway of biogenesis of siRNAs could exist in Drosophila cells.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Genome Organization, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Kretova
- Department of Genome Organization, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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82
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DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation. Proc Natl Acad Sci U S A 2011; 108:12007-12. [PMID: 21730191 DOI: 10.1073/pnas.1106245108] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During mitosis, faithful inheritance of genetic material is achieved by chromosome segregation, as mediated by the condensin I and II complexes. Failed chromosome segregation can result in neoplasm formation, infertility, and birth defects. Recently, the germ-line-specific DEAD-box RNA helicase Vasa was demonstrated to promote mitotic chromosome segregation in Drosophila by facilitating robust chromosomal localization of Barren (Barr), a condensin I component. This mitotic function of Vasa is mediated by Aubergine and Spindle-E, which are two germ-line components of the Piwi-interacting RNA pathway. Faithful segregation of chromosomes should be executed both in germ-line and somatic cells. However, whether a similar mechanism also functions in promoting chromosome segregation in somatic cells has not been elucidated. Here, we present evidence that belle (vasa paralog) and the RNA interference pathway regulate chromosome segregation in Drosophila somatic cells. During mitosis, belle promotes robust Barr chromosomal localization and chromosome segregation. Belle's localization to condensing chromosomes depends on dicer-2 and argonaute2. Coimmunoprecipitation experiments indicated that Belle interacts with Barr and Argonaute2 and is enriched at endogenous siRNA (endo-siRNA)-generating loci. Our results suggest that Belle functions in promoting chromosome segregation in Drosophila somatic cells via the endo-siRNA pathway. DDX3 (human homolog of belle) and DICER function in promoting chromosome segregation and hCAP-H (human homolog of Barr) localization in HeLa cells, indicating a conserved function for those proteins in human cells. Our results suggest that the RNA helicase Belle/DDX3 and the RNA interference pathway perform a common role in regulating chromosome segregation in Drosophila and human somatic cells.
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83
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Abstract
Small RNAs with lengths of 20-30 nucleotides, such as microRNAs (miRNAs), play important regulatory roles in various cellular processes. In conventional linear processing pathways, precursors of miRNAs are transported out of the nucleus by the specific nuclear transport receptor, exportin-5. The exported precursors are further processed and eventually incorporated into the RNA-induced silencing complex (RISC), which silences the expression of the target genes by posttranscriptional mechanisms in the cytoplasm. Subsequent identification and characterization of P-element induced wimpy testis (PIWI)-interacting small RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs) revealed that the processing mechanisms of these newly emerging small RNAs differ from those of miRNAs. Moreover, cumulative experimental evidence indicates that the nuclear functions of the small RNAs, such as transcriptional gene silencing, could be widespread in divergent species. These observations appended other interesting features in the biogenesis and nucleocytoplasmic transport mechanisms of these small RNAs. In this review, we discuss the mechanisms and biological significance of the intracellular trafficking of small RNAs in animal cells.
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Affiliation(s)
- Jun Katahira
- Biomolecular Networks Laboratories, Biomolecular Dynamics Laboratory, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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84
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A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods 2011; 8:405-7. [PMID: 21460824 DOI: 10.1038/nmeth.1592] [Citation(s) in RCA: 618] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 03/14/2011] [Indexed: 11/09/2022]
Abstract
Existing transgenic RNAi resources in Drosophila melanogaster based on long double-stranded hairpin RNAs are powerful tools for functional studies, but they are ineffective in gene knockdown during oogenesis, an important model system for the study of many biological questions. We show that shRNAs, modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress toward building a genome-wide shRNA resource.
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85
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Liu L, Qi H, Wang J, Lin H. PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition. Development 2011; 138:1863-73. [PMID: 21447556 DOI: 10.1242/dev.059287] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nuage is a germline-specific perinuclear structure that remains functionally elusive. Recently, the nuage in Drosophila was shown to contain two of the three PIWI proteins - Aubergine and Argonaute 3 (AGO3) - that are essential for germline development. The PIWI proteins bind to PIWI-interacting RNAs (piRNAs) and function in epigenetic regulation and transposon control. Here, we report a novel nuage component, PAPI (Partner of PIWIs), that contains a TUDOR domain and interacts with all three PIWI proteins via symmetrically dimethylated arginine residues in their N-terminal domain. In adult ovaries, PAPI is mainly cytoplasmic and enriched in the nuage, where it partially colocalizes with AGO3. The localization of PAPI to the nuage does not require the arginine methyltransferase dPRMT5 or AGO3. However, AGO3 is largely delocalized from the nuage and becomes destabilized in the absence of PAPI or dPRMT5, indicating that PAPI recruits PIWI proteins to the nuage to assemble piRNA pathway components. As expected, papi deficiency leads to transposon activation, phenocopying piRNA mutants. This further suggests that PAPI is involved in the piRNA pathway for transposon silencing. Moreover, AGO3 and PAPI associate with the P body component TRAL/ME31B complex in the nuage and transposon activation is observed in tral mutant ovaries. This suggests a physical and functional interaction in the nuage between the piRNA pathway components and the mRNA-degrading P-body components in transposon silencing. Overall, our study reveals a function of the nuage in safeguarding the germline genome against deleterious retrotransposition via the piRNA pathway.
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Affiliation(s)
- Li Liu
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06509, USA
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86
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Lasko P. Posttranscriptional regulation in Drosophila oocytes and early embryos. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:408-16. [PMID: 21957026 DOI: 10.1002/wrna.70] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular asymmetries underlying embryonic axis patterning and germ cell specification are established in Drosophila largely by position-dependent translational regulation of maternally expressed messenger RNAs. Here, I review several mechanisms of posttranscriptional regulation in the Drosophila oocyte and syncytial embryo, and how they relate to embryonic patterning, with a strong emphasis on the most recent advances in the area. The review is not exhaustive, but focuses on examples that illustrate the interplay between specific regulatory events and the general metabolic machinery that governs translation and mRNA stability. Biophysical investigations into how the Bicoid gradient is formed are discussed, as are the elaborate mechanisms controlling how the Oskar and Nanos proteins become restricted to the posterior pole of the embryo. Work on Vasa, a translational activator of some germ line mRNAs and on 4EHP, a negative regulator that unproductively binds the 5' cap structure of target mRNAs, is also briefly reviewed. Finally, the emerging understanding of the role of microRNAs in regulating translation of germ line mRNAs is also discussed.
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Affiliation(s)
- Paul Lasko
- Department of Biology, McGill University, Montreal, Quebec, Canada.
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87
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Khurana JS, Theurkauf W. piRNAs, transposon silencing, and Drosophila germline development. ACTA ACUST UNITED AC 2011; 191:905-13. [PMID: 21115802 PMCID: PMC2995163 DOI: 10.1083/jcb.201006034] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transposons are prominent features of most eukaryotic genomes and mobilization of these elements triggers genetic instability. Transposon silencing is particularly critical in the germline, which maintains the heritable genetic complement. Piwi-interacting RNAs (piRNAs) have emerged as central players in transposon silencing and genome maintenance during germline development. In particular, research on Drosophila oogenesis has provided critical insights into piRNA biogenesis and transposon silencing. In this system, the ability to place piRNA mutant phenotypes within a well-defined developmental framework has been instrumental in elucidating the molecular mechanisms underlying the connection between piRNAs and transposon control.
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Affiliation(s)
- Jaspreet S Khurana
- Program in Cell and Developmental Dynamics, and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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88
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Senti KA, Brennecke J. The piRNA pathway: a fly's perspective on the guardian of the genome. Trends Genet 2010; 26:499-509. [PMID: 20934772 DOI: 10.1016/j.tig.2010.08.007] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Revised: 08/27/2010] [Accepted: 08/31/2010] [Indexed: 11/29/2022]
Abstract
Throughout the eukaryotic lineage, small RNA silencing pathways protect the genome against the deleterious influence of selfish genetic elements such as transposons. In animals an elaborate small RNA pathway centered on PIWI proteins and their interacting piRNAs silences transposons within the germline. In contrast to other small RNA silencing pathways, we lack a mechanistic understanding of this genome defense system. However, genetic and molecular studies have uncovered a fascinating conceptual framework for this pathway that is conserved from sponges to mammals. We discuss our current understanding of the piRNA pathway in Drosophila with an emphasis on origin and biogenesis of piRNAs.
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Affiliation(s)
- Kirsten-André Senti
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
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89
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Khurana JS, Xu J, Weng Z, Theurkauf WE. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet 2010; 6:e1001246. [PMID: 21179579 PMCID: PMC3003142 DOI: 10.1371/journal.pgen.1001246] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 11/11/2010] [Indexed: 12/30/2022] Open
Abstract
Transposons and other selfish DNA elements can be found in all phyla, and mobilization of these elements can compromise genome integrity. The piRNA (PIWI-interacting RNA) pathway silences transposons in the germline, but it is unclear if this pathway has additional functions during development. Here we show that mutations in the Drosophila piRNA pathway genes, armi, aub, ago3, and rhi, lead to extensive fragmentation of the zygotic genome during the cleavage stage of embryonic divisions. Additionally, aub and armi show defects in telomere resolution during meiosis and the cleavage divisions; and mutations in lig-IV, which disrupt non-homologous end joining, suppress these fusions. By contrast, lig-IV mutations enhance chromosome fragmentation. Chromatin immunoprecipitation studies show that aub and armi mutations disrupt telomere binding of HOAP, which is a component of the telomere protection complex, and reduce expression of a subpopulation of 19- to 22-nt telomere-specific piRNAs. Mutations in rhi and ago3, by contrast, do not block HOAP binding or production of these piRNAs. These findings uncover genetically separable functions for the Drosophila piRNA pathway. The aub, armi, rhi, and ago3 genes silence transposons and maintain chromosome integrity during cleavage-stage embryonic divisions. However, the aub and armi genes have an additional function in assembly of the telomere protection complex.
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Affiliation(s)
- Jaspreet S. Khurana
- Program in Cell and Developmental Dynamics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jia Xu
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology and Department in Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - William E. Theurkauf
- Program in Cell and Developmental Dynamics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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90
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Nagao A, Mituyama T, Huang H, Chen D, Siomi MC, Siomi H. Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis. RNA (NEW YORK, N.Y.) 2010; 16:2503-15. [PMID: 20980675 PMCID: PMC2995411 DOI: 10.1261/rna.2270710] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/16/2010] [Indexed: 05/25/2023]
Abstract
PIWI-interacting RNAs (piRNAs) silence transposable elements in animal germ cells. In Drosophila ovaries, piRNAs are produced by two distinct pathways: the "ping-pong" amplification cycle that operates in germ cells and a ping-pong-independent pathway termed the primary pathway that mainly operates in somatic cells. AGO3, one of three PIWI proteins in flies, is involved in the ping-pong cycle in ovaries. We characterized AGO3-associated piRNAs in fly testes and found that like in ovaries, AGO3 functions in the ping-pong cycle with Aubergine (Aub) for piRNA production from transposon transcripts. In contrast, most AGO3-associated piRNAs corresponding to Suppressor of Stellate [Su(Ste)] genes are antisense-oriented and bound to Aub. In addition, the vast majority of AGO3-bound piRNAs derived from the AT-chX locus on chromosome X are antisense-oriented and are also found among Aub-associated piRNAs. The presence of very few sense Su(Ste) and AT-chX piRNAs suggests that biogenesis of both Su(Ste) and AT-chX piRNAs by a ping-pong mechanism only is highly unlikely. Nevertheless, the mutual interdependence of AGO3 and Aub for the accumulation of these piRNAs shows that their production relies on both AGO3 and Aub. Analysis of piRNA pathway mutants revealed that although the requirements for piRNA factors for Su(Ste)- and AT-chX-piRNA levels mostly overlap and resemble those for the ping-pong mechanism in the ovaries, Armitage (armi) is not required for the accumulation of AT-chX-1 piRNA. These findings suggest that the impacts of armi mutants on the operation of the piRNA pathway are variable in germ cells of fly testes.
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Affiliation(s)
- Akihiro Nagao
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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91
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Qi H, Watanabe T, Ku HY, Liu N, Zhong M, Lin H. The Yb body, a major site for Piwi-associated RNA biogenesis and a gateway for Piwi expression and transport to the nucleus in somatic cells. J Biol Chem 2010; 286:3789-97. [PMID: 21106531 DOI: 10.1074/jbc.m110.193888] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite exciting progress in understanding the Piwi-interacting RNA (piRNA) pathway in the germ line, less is known about this pathway in somatic cells. We showed previously that Piwi, a key component of the piRNA pathway in Drosophila, is regulated in somatic cells by Yb, a novel protein containing an RNA helicase-like motif and a Tudor-like domain. Yb is specifically expressed in gonadal somatic cells and regulates piwi in somatic niche cells to control germ line and somatic stem cell self-renewal. However, the molecular basis of the regulation remains elusive. Here, we report that Yb recruits Armitage (Armi), a putative RNA helicase involved in the piRNA pathway, to the Yb body, a cytoplasmic sphere to which Yb is exclusively localized. Moreover, co-immunoprecipitation experiments show that Yb forms a complex with Armi. In Yb mutants, Armi is dispersed throughout the cytoplasm, and Piwi fails to enter the nucleus and is rarely detectable in the cytoplasm. Furthermore, somatic piRNAs are drastically diminished, and soma-expressing transposons are desilenced. These observations indicate a crucial role of Yb and the Yb body in piRNA biogenesis, possibly by regulating the activity of Armi that controls the entry of Piwi into the nucleus for its function. Finally, we discovered putative endo-siRNAs in the flamenco locus and the Yb dependence of their expression. These observations further implicate a role for Yb in transposon silencing via both the piRNA and endo-siRNA pathways.
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Affiliation(s)
- Hongying Qi
- Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06511, USA
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92
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Saito K, Ishizu H, Komai M, Kotani H, Kawamura Y, Nishida KM, Siomi H, Siomi MC. Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila. Genes Dev 2010; 24:2493-8. [PMID: 20966047 DOI: 10.1101/gad.1989510] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PIWI-interacting RNAs (piRNAs) protect genome integrity from transposons. In Drosophila ovarian somas, primary piRNAs are produced and loaded onto Piwi. Here, we describe roles for the cytoplasmic Yb body components Armitage and Yb in somatic primary piRNA biogenesis. Armitage binds to Piwi and is required for localizing Piwi into Yb bodies. Without Armitage or Yb, Piwi is freed from the piRNAs and does not enter the nucleus. Thus, piRNA loading is required for Piwi nuclear entry. We propose that a functional Piwi-piRNA complex is formed and inspected in Yb bodies before its nuclear entry to exert transposon silencing.
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93
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Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev 2010; 24:2499-504. [PMID: 20966049 DOI: 10.1101/gad.1968110] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Combining RNAi in cultured cells and analysis of mutant animals, we probed the roles of known Piwi-interacting RNA (piRNA) pathway components in the initiation and effector phases of transposon silencing. Squash associated physically with Piwi, and reductions in its expression led to modest transposon derepression without effects on piRNAs, consistent with an effector role. Alterations in Zucchini or Armitage reduced both Piwi protein and piRNAs, indicating functions in the formation of a stable Piwi RISC (RNA-induced silencing complex). Notably, loss of Zucchini or mutations within its catalytic domain led to accumulation of unprocessed precursor transcripts from flamenco, consistent with a role for this putative nuclease in piRNA biogenesis.
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94
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Becalska AN, Kim YR, Belletier NG, Lerit DA, Sinsimer KS, Gavis ER. Aubergine is a component of a nanos mRNA localization complex. Dev Biol 2010; 349:46-52. [PMID: 20937269 DOI: 10.1016/j.ydbio.2010.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 09/14/2010] [Accepted: 10/01/2010] [Indexed: 01/09/2023]
Abstract
Localization of nanos (nos) mRNA to the posterior pole of the Drosophila oocyte is essential for abdominal segmentation and germline development during embryogenesis. Posterior localization is mediated by a complex cis-acting localization signal in the nos 3' untranslated region that comprises multiple partially redundant elements. Genetic analysis suggests that this signal is recognized by RNA-binding proteins and associated factors that package nos mRNA into a localization competent ribonucleoprotein complex. However, functional redundancy among localization elements has made the identification of individual localization factors difficult. Indeed, only a single direct-acting nos localization factor, Rumpelstiltskin (Rump), has been identified thus far. Through a sensitized genetic screen, we have now identified the Argonaute family member Aubergine (Aub) as a nos localization factor. Aub interacts with nos mRNA in vivo and co-purifies with Rump in an RNA-dependent manner. Our results support a role for Aub, independent of its function in RNA silencing, as a component of a nos mRNA localization complex.
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Affiliation(s)
- Agata N Becalska
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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95
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Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 2010; 467:1128-32. [PMID: 20953170 DOI: 10.1038/nature09465] [Citation(s) in RCA: 328] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 08/27/2010] [Indexed: 12/25/2022]
Abstract
Piwi-associated RNAs (piRNAs), a specific class of 24- to 30-nucleotide-long RNAs produced by the Piwi-type of Argonaute proteins, have a specific germline function in repressing transposable elements. This repression is thought to involve heterochromatin formation and transcriptional and post-transcriptional silencing. The piRNA pathway has other essential functions in germline stem cell maintenance and in maintaining germline DNA integrity. Here we uncover an unexpected function of the piRNA pathway in the decay of maternal messenger RNAs and in translational repression in the early embryo. A subset of maternal mRNAs is degraded in the embryo at the maternal-to-zygotic transition. In Drosophila, maternal mRNA degradation depends on the RNA-binding protein Smaug and the deadenylase CCR4, as well as the zygotic expression of a microRNA cluster. Using mRNA encoding the embryonic posterior morphogen Nanos (Nos) as a paradigm to study maternal mRNA decay, we found that CCR4-mediated deadenylation of nos depends on components of the piRNA pathway including piRNAs complementary to a specific region in the nos 3' untranslated region. Reduced deadenylation when piRNA-induced regulation is impaired correlates with nos mRNA stabilization and translational derepression in the embryo, resulting in head development defects. Aubergine, one of the Argonaute proteins in the piRNA pathway, is present in a complex with Smaug, CCR4, nos mRNA and piRNAs that target the nos 3' untranslated region, in the bulk of the embryo. We propose that piRNAs and their associated proteins act together with Smaug to recruit the CCR4 deadenylation complex to specific mRNAs, thus promoting their decay. Because the piRNAs involved in this regulation are produced from transposable elements, this identifies a direct developmental function for transposable elements in the regulation of gene expression.
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96
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Orsi GA, Joyce EF, Couble P, McKim KS, Loppin B. Drosophila I-R hybrid dysgenesis is associated with catastrophic meiosis and abnormal zygote formation. J Cell Sci 2010; 123:3515-24. [PMID: 20841382 DOI: 10.1242/jcs.073890] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The Drosophila I-R type of hybrid dysgenesis is a sterility syndrome (SF sterility) associated with the mobilization of the I retrotransposon in female germ cells. SF sterility results from a maternal-effect embryonic lethality whose origin has remained unclear since its discovery about 40 years ago. Here, we show that meiotic divisions in SF oocytes are catastrophic and systematically fail to produce a functional female pronucleus at fertilization. As a consequence, most embryos from SF females rapidly arrest their development with aneuploid or damaged nuclei, whereas others develop as non-viable, androgenetic haploid embryos. Finally, we show that, in contrast to mutants affecting the biogenesis of piRNAs, SF egg chambers do not accumulate persistent DNA double-strand breaks, suggesting that I-element activity might perturb the functional organization of meiotic chromosomes without triggering an early DNA damage response.
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Affiliation(s)
- Guillermo A Orsi
- Centre de Génétique Moléculaire et Cellulaire, CNRS UMR5534, University of Lyon, UCBL Lyon1, Villeurbanne, F-69100, France
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97
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van der Heijden GW, Castañeda J, Bortvin A. Bodies of evidence - compartmentalization of the piRNA pathway in mouse fetal prospermatogonia. Curr Opin Cell Biol 2010; 22:752-7. [PMID: 20822889 DOI: 10.1016/j.ceb.2010.08.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 08/10/2010] [Indexed: 10/19/2022]
Abstract
Epigenetic reprogramming of embryonic mouse germ cells involves DNA demethylation of the genome that is accompanied by derepression of transposable elements (TEs). Threatening the genome's integrity, TE activation is efficiently countered by the concerted action of de novo DNA methylation and PIWI-interacting small RNAs (piRNAs). Recent studies have closely examined the subcellular localization of various piRNA pathway proteins in fetal prospermatogonia of wild-type and piRNA pathway mutant mice. Our survey highlights hierarchies and partnerships between the members of this ancient defensive mechanism. Overall, the elaborate cytoplasmic compartmentalization of the piRNA pathway in fetal prospermatogonia provides a highly informative context to aid our understanding of the mouse piRNA pathway.
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98
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Olivieri D, Sykora MM, Sachidanandam R, Mechtler K, Brennecke J. An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J 2010; 29:3301-17. [PMID: 20818334 DOI: 10.1038/emboj.2010.212] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/10/2010] [Indexed: 11/09/2022] Open
Abstract
In Drosophila, PIWI proteins and bound PIWI-interacting RNAs (piRNAs) form the core of a small RNA-mediated defense system against selfish genetic elements. Within germline cells, piRNAs are processed from piRNA clusters and transposons to be loaded into Piwi/Aubergine/AGO3 and a subset of piRNAs undergoes target-dependent amplification. In contrast, gonadal somatic support cells express only Piwi, lack signs of piRNA amplification and exhibit primary piRNA biogenesis from piRNA clusters. Neither piRNA processing/loading nor Piwi-mediated target silencing is understood at the genetic, cellular or molecular level. We developed an in vivo RNAi assay for the somatic piRNA pathway and identified the RNA helicase Armitage, the Tudor domain containing RNA helicase Yb and the putative nuclease Zucchini as essential factors for primary piRNA biogenesis. Lack of any of these proteins leads to transposon de-silencing, to a collapse in piRNA levels and to a failure in Piwi-nuclear accumulation. We show that Armitage and Yb interact physically and co-localize in cytoplasmic Yb bodies, which flank P bodies. Loss of Zucchini leads to an accumulation of Piwi and Armitage in Yb bodies, indicating that Yb bodies are sites of primary piRNA biogenesis.
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Affiliation(s)
- Daniel Olivieri
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
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99
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P body-associated protein Mov10 inhibits HIV-1 replication at multiple stages. J Virol 2010; 84:10241-53. [PMID: 20668078 DOI: 10.1128/jvi.00585-10] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent studies have shown that APOBEC3G (A3G), a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) replication, is localized to cytoplasmic mRNA-processing bodies (P bodies). However, the functional relevance of A3G colocalization with P body marker proteins has not been established. To explore the relationship between HIV-1, A3G, and P bodies, we analyzed the effects of overexpression of P body marker proteins Mov10, DCP1a, and DCP2 on HIV-1 replication. Our results show that overexpression of Mov10, a putative RNA helicase that was previously reported to belong to the DExD superfamily and was recently reported to belong to the Upf1-like group of helicases, but not the decapping enzymes DCP1a and DCP2, leads to potent inhibition of HIV-1 replication at multiple stages. Mov10 overexpression in the virus producer cells resulted in reductions in the steady-state levels of the HIV-1 Gag protein and virus production; Mov10 was efficiently incorporated into virions and reduced virus infectivity, in part by inhibiting reverse transcription. In addition, A3G and Mov10 overexpression reduced proteolytic processing of HIV-1 Gag. The inhibitory effects of A3G and Mov10 were additive, implying a lack of functional interaction between the two inhibitors. Small interfering RNA (siRNA)-mediated knockdown of endogenous Mov10 by 80% resulted in a 2-fold reduction in virus production but no discernible impact on the infectivity of the viruses after normalization for the p24 input, suggesting that endogenous Mov10 was not required for viral infectivity. Overall, these results show that Mov10 can potently inhibit HIV-1 replication at multiple stages.
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100
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Gibbings D, Voinnet O. Control of RNA silencing and localization by endolysosomes. Trends Cell Biol 2010; 20:491-501. [PMID: 20630759 DOI: 10.1016/j.tcb.2010.06.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 05/31/2010] [Accepted: 06/02/2010] [Indexed: 01/24/2023]
Abstract
Recent advances in the cell biology of RNA silencing have unraveled an intriguing association of post-transcriptionally regulated RNA with endolysosomal membranes in several circumstances of mRNA localization, microRNA activity and viral RNA transport and packaging. Endolysosomal membranes are a nexus of communication and transport between cells and their exterior environment for signaling receptors, pathogens and nutrients. Here, we discuss recent data that support a view that endolysosomal positioning of RNA might facilitate intercellular transmission of RNA and host defence against viruses and retrotransposons. Positioning of RNA regulatory mechanisms on endolysosomal membranes might permit rapid and localized control of microRNA (miRNA) gene regulatory programs and mRNA translation in response to environmental signals, such as activated plasma membrane receptors transported on endosomes. Finally, we suggest that the pathology of several conditions, including Huntington's disease, might be a consequence of the disruption of the control of RNA via endolysosomal membranes.
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Affiliation(s)
- Derrick Gibbings
- UPR2357, Centre National de la Recherche Scientifique, Institut de Biologie Moleculaire des Plantes, 12 rue du General Zimmer, 67084 Strasbourg France.
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