scholarly journals piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in the Drosophila germline

2009 ◽  
Vol 186 (3) ◽  
pp. 333-342 ◽  
Author(s):  
Ai Khim Lim ◽  
Liheng Tao ◽  
Toshie Kai
Keyword(s):  
Drosophila Melanogaster ◽  
Messenger Rna ◽  
Mrna Degradation ◽  
Full Length ◽  
Processing Bodies ◽  
Present Evidence ◽  
Maternal Expression ◽  
Germline Cells ◽  
Pirna Pathway

Nuage, a well-conserved perinuclear organelle found in germline cells, is thought to mediate retroelement repression in Drosophila melanogaster by regulating the production of Piwi-interacting RNAs (piRNAs). In this study, we present evidence that the nuage–piRNA pathway components can be found in cytoplasmic foci that also contain retroelement transcripts, antisense piRNAs, and proteins involved in messenger RNA (mRNA) degradation. These mRNA degradation proteins, decapping protein 1/2 (DCP1/2), Me31B (maternal expression at 31B), and pacman (PCM), are normally thought of as components of processing bodies. In spindle-E (spn-E) and aubergine (aub) mutants that lack piRNA production, piRNA pathway proteins no longer overlap the mRNA degradation proteins. Concomitantly, spn-E and aub mutant ovaries show an accumulation of full-length retroelement transcripts and prolonged stabilization of HeT-A mRNA, supporting the role of piRNAs in mediating posttranscriptional retroelement silencing. HeT-A mRNA is derepressed in mRNA degradation mutants twin, dcp1, and ski3, indicating that these enzymes also aid in removing full-length transcripts and/or decay intermediates.

scholarly journals The RNA-binding protein Y14 inhibits mRNA decapping and modulates processing body formation

2013 ◽  
Vol 24 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Tzu-Wei Chuang ◽  
Wei-Lun Chang ◽  
Kuo-Ming Lee ◽  
Woan-Yuh Tarn
Keyword(s):  
Rna Binding ◽  
Mrna Degradation ◽  
Exon Junction Complex ◽  
Processing Bodies ◽  
Body Formation ◽  
Mrna Decapping ◽  
Mrna Metabolism ◽  
Processing Body

The exon-junction complex (EJC) deposited on a newly spliced mRNA plays an important role in subsequent mRNA metabolic events. Here we show that an EJC core heterodimer, Y14/Magoh, specifically associates with mRNA-degradation factors, including the mRNA-decapping complex and exoribonucleases, whereas another core factor, eIF4AIII/MLN51, does not. We also demonstrate that Y14 interacts directly with the decapping factor Dcp2 and the 5′ cap structure of mRNAs via different but overlapping domains and that Y14 inhibits the mRNA-decapping activity of Dcp2 in vitro. Accordingly, overexpression of Y14 prolongs the half-life of a reporter mRNA. Therefore Y14 may function independently of the EJC in preventing mRNA decapping and decay. Furthermore, we observe that depletion of Y14 disrupts the formation of processing bodies, whereas overexpression of a phosphomimetic Y14 considerably increases the number of processing bodies, perhaps by sequestering the mRNA-degradation factors. In conclusion, this report provides unprecedented evidence for a role of Y14 in regulating mRNA degradation and processing body formation and reinforces the influence of phosphorylation of Y14 on its activity in postsplicing mRNA metabolism.

scholarly journals Germline silencing of UASt depends on the piRNA pathway

2018 ◽  
Author(s):  
Yi-Chun Huang ◽  
Henry Moreno ◽  
Sarayu Row ◽  
Dongyu Jia ◽  
Wu-Min Deng
Keyword(s):  
Binary System ◽  
Small Rnas ◽  
Transgene Expression ◽  
Rna Seq ◽  
Somatic Tissues ◽  
Germline Expression ◽  
Germline Cells ◽  
Pirna Pathway ◽  
Nonsense Mediated Rna Decay

AbstractOne of the most extensively used techniques in Drosophila is the Gal4/UAS binary system, which allows tissue-specific misexpression or knockdown of specific genes of interest. The original UAS vector, UASt, can only be activated for transgene expression in somatic tissues and not in the germline cells. Rørth (1998) generated UASp, a modified UAS vector that is responsive to Gal4 in both somatic and germline tissues, by replacing both the hsp70 promoter and the SV40 3’UTR with the P transposase promoter and the K10 3’UTR respectively. At present, the mechanisms by which UASt is silenced in germline cells are not fully understood. Here, we report that the piRNA pathway is involved in suppressing UASt expression in ovarian germline cells. Individually knocking down or mutating components of the piRNA biogenesis pathway (e.g., Piwi, AGO3, Aub, Spn-E, and Vasa) resulted in the expression of the UASt-reporter (GFP or RFP) in the germline. An RNA-seq analysis of small RNAs revealed that the hsp70 promoter of UASt is targeted by piRNAs, and in the aub mutant ovary, the amount of piRNAs targeting the hsp70 promoter is reduced by around 40 folds. In contrast, the SV40 3’UTR of the UASt, which happens to be targeted by the Nonsense-mediated RNA decay (NMD) pathway, is not responsible for germline UASt suppression, as UASt-reporters with NMD-insensitive 3’UTRs fail to show germline expression. Taken together, our studies reveal a crucial role of the piRNA pathway, potentially via the suppression of the hsp70 promoter, in germline UASt silencing in Drosophila ovaries.

scholarly journals The “Special” crystal-Stellate System in Drosophila melanogaster Reveals Mechanisms Underlying piRNA Pathway-Mediated Canalization

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Maria Pia Bozzetti ◽  
Laura Fanti ◽  
Silvia Di Tommaso ◽  
Lucia Piacentini ◽  
Maria Berloco ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Repetitive Elements ◽  
Genome Integrity ◽  
Molecular Pathways ◽  
Phenotypic Manifestation ◽  
Pirna Pathway ◽  
Shed Light

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.

scholarly journals AGO3 Slicer activity regulates mitochondria–nuage localization of Armitage and piRNA amplification

2014 ◽  
Vol 206 (2) ◽  
pp. 217-230 ◽  
Author(s):  
Haidong Huang ◽  
Yujing Li ◽  
Keith E. Szulwach ◽  
Guoqiang Zhang ◽  
Peng Jin ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Subcellular Localization ◽  
Mitochondrial Fraction ◽  
Rna Cleavage ◽  
Independent Manner ◽  
Ping Pong ◽  
Pirna Pathway

In Drosophila melanogaster the reciprocal “Ping-Pong” cycle of PIWI-interacting RNA (piRNA)–directed RNA cleavage catalyzed by the endonuclease (or “Slicer”) activities of the PIWI proteins Aubergine (Aub) and Argonaute3 (AGO3) has been proposed to expand the secondary piRNA population. However, the role of AGO3/Aub Slicer activity in piRNA amplification remains to be explored. We show that AGO3 Slicer activity is essential for piRNA amplification and that AGO3 inhibits the homotypic Aub:Aub Ping-Pong process in a Slicer-independent manner. We also find that expression of an AGO3 Slicer mutant causes ectopic accumulation of Armitage, a key component in the primary piRNA pathway, in the Drosophila melanogaster germline granules known as nuage. AGO3 also coexists and interacts with Armitage in the mitochondrial fraction. Furthermore, AGO3 acts in conjunction with the mitochondria-associated protein Zucchini to control the dynamic subcellular localization of Armitage between mitochondria and nuage in a Slicer-dependent fashion. Collectively, our findings uncover a new mechanism that couples mitochondria with nuage to regulate secondary piRNA amplification.

scholarly journals A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

2021 ◽  
Author(s):  
Julius Brennecke ◽  
Mostafa F ElMaghraby ◽  
Tirian Laszlo ◽  
Kirsten A Senti ◽  
Katharina Meixner
Keyword(s):  
Drosophila Melanogaster ◽  
Cyst Formation ◽  
Resource Center ◽  
Experimental Systems ◽  
Transposon Silencing ◽  
Rna Export ◽  
Nuclear Rna Export ◽  
Pirna Pathway ◽  
Genetic Toolkit

Argonaute proteins of the PIWI class complexed with PIWI-interacting RNAs (piRNAs) protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only after germ cell cyst formation. Stage-specific RNAi allows us to investigate the role of genes essential for germline cell survival, for example nuclear RNA export or the SUMOylation pathway, in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit provided by the Vienna Drosophila Resource Center.

scholarly journals A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

Genetics ◽  
2021 ◽  
Author(s):  
Mostafa F ElMaghraby ◽  
Laszlo Tirian ◽  
Kirsten-André Senti ◽  
Katharina Meixner ◽  
Julius Brennecke
Keyword(s):  
Drosophila Melanogaster ◽  
Cyst Formation ◽  
Resource Center ◽  
Experimental Systems ◽  
Transposon Silencing ◽  
Rna Export ◽  
Nuclear Rna Export ◽  
Pirna Pathway ◽  
Genetic Toolkit

Abstract Argonaute proteins of the PIWI clade complexed with PIWI-interacting RNAs (piRNAs) protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that combines germline transgenic RNAi, GFP marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only after germ cell cyst formation. Stage-specific RNAi allows us to investigate the role of genes essential for germline cell survival, for example nuclear RNA export or the SUMOylation pathway, in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit provided by the Vienna Drosophila Resource Center.

Improving the questions we ask, with Psychology and Cognitive Conflict.

2018 ◽  
Author(s):  
Brett Buttliere
Keyword(s):  
Problem Solving ◽  
Scientific Method ◽  
Meaning Making ◽  
Cognitive Conflict ◽  
Empirical Literature ◽  
Present Evidence ◽  
Scientific Papers ◽  
Science In Society

Over the last decade, there have been many suggestions to improve how scientists answer their questions, but far fewer attempt to improve the questions scientists are asking in the first place. The goal of the paper is then to examine and summarize synthesize the evidence on how to ask the best questions possible. First is a brief review of the philosophical and empirical literature on how the best science is done, which implicitly but not explicitly mentions the role of psychology and especially cognitive conflict. Then we more closely focus on the psychology of the scientist, finding that they are humans, engaged in a meaning making process, and that cognitive conflict is a necessary input for any learning or change in the system. The scientific method is, of course, a specialized meaning making process. We present evidence for this central role of cognitive conflict in science by examining the most discussed scientific papers between 2013 and 2017, which are, in general, controversial and about big problems (e.g., whether vaccines cause autism, how often doctors kill us with their mistakes). Toward the end we discuss the role of science in society, suggesting science itself is an uncertainty reducing and problem solving enterprise. From this basis we encourage scientists to take riskier stances on bigger topics, for the good of themselves and society generally.

scholarly journals Structure of the full-length human Pannexin1 channel and insights into its role in pyroptosis

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Sensen Zhang ◽  
Baolei Yuan ◽  
Jordy Homing Lam ◽  
Jun Zhou ◽  
Xuan Zhou ◽  
...  
Keyword(s):  
Md Simulation ◽  
Potential Role ◽  
Md Simulations ◽  
Full Length ◽  
Inflammasome Activation ◽  
Simulation Studies ◽  
Cryo Electron Microscopy ◽  
Gating Mechanism ◽  
Atp Efflux

AbstractPannexin1 (PANX1) is a large-pore ATP efflux channel with a broad distribution, which allows the exchange of molecules and ions smaller than 1 kDa between the cytoplasm and extracellular space. In this study, we show that in human macrophages PANX1 expression is upregulated by diverse stimuli that promote pyroptosis, which is reminiscent of the previously reported lipopolysaccharide-induced upregulation of PANX1 during inflammasome activation. To further elucidate the function of PANX1, we propose the full-length human Pannexin1 (hPANX1) model through cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulation studies, establishing hPANX1 as a homo-heptamer and revealing that both the N-termini and C-termini protrude deeply into the channel pore funnel. MD simulations also elucidate key energetic features governing the channel that lay a foundation to understand the channel gating mechanism. Structural analyses, functional characterizations, and computational studies support the current hPANX1-MD model, suggesting the potential role of hPANX1 in pyroptosis during immune responses.

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