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https://www.readbyqxmd.com/read/28094937/click-qms-identifies-piwil3-as-a-mechanistic-target-of-rna-interference-activator-enoxacin-in-cancer-cells
#1
Nathan Abell, Marvin Mercado, Tatiana Cañeque, Raphaël Rodriguez, Blerta Xhemalce
Enoxacin is a small molecule that stimulates RNA interference (RNAi) and acts as a growth inhibitor selectively in cancer but not in untransformed cells. Here, we used alkenox, a clickable enoxacin surrogate, coupled with quantitative Mass Spectrometry, to identify PIWIL3 as a mechanistic target of enoxacin. PIWIL3 is an Argonaut protein of the PIWI subfamily that is mainly expressed in the germline and that mediates RNAi through piRNAs. Our results suggest that cancer cells re-express PIWIL3 to repress RNAi through miRNAs and thus open a new opportunity for cancer specific targeting...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28091568/identification-of-misexpressed-genetic-elements-in-hybrids-between-drosophila-related-species
#2
Hélène Lopez-Maestre, Elias A G Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron, Claudia M A Carareto, Cristina Vieira
Crosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, we performed reciprocal crosses between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. We performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28087276/drosophila-argonaute2-turnover-is-regulated-by-the-ubiquitin-proteasome-pathway
#3
Madoka Chinen, Elissa P Lei
Argonaute (AGO) proteins play a central role in the RNA interference (RNAi) pathway, which is a cytoplasmic mechanism important for post-transcriptional regulation of gene expression. In Drosophila, AGO2 also functions in the nucleus to regulate chromatin insulator activity and transcription. Although there are a number of studies focused on AGO2 function, the regulation of AGO2 turnover is not well understood. We found that mutation of T1149 or R1158 in the conserved PIWI domain causes AGO2 protein instability, but only T1149 affects RNAi activity...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28072387/embryonic-origin-of-adult-stem-cells-required-for-tissue-homeostasis-and-regeneration
#4
Erin L Davies, Kai Lei, Christopher W Seidel, Amanda E Kroesen, Sean A McKinney, Longhua Guo, Sofia Mc Robb, Eric J Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Planarian neoblasts are pluripotent, adult somatic stem cells and lineage-primed progenitors required for production and maintenance of all differentiated cell types, including the germline. Neoblasts, originally defined as undifferentiated cells residing in the adult parenchyma, are frequently compared to embryonic stem cells yet their developmental origin remains obscure. We investigated the provenance of neoblasts during S. mediterranea embryogenesis, and report that neoblasts arise from an anarchic, cycling piwi-1+ population wholly responsible for production of all temporary and definitive organs during embryogenesis...
January 10, 2017: ELife
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#5
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28060823/the-antiviral-rnai-response-in-vector-and-non-vector-cells-against-orthobunyaviruses
#6
Isabelle Dietrich, Xiaohong Shi, Melanie McFarlane, Mick Watson, Anne-Lie Blomström, Jessica K Skelton, Alain Kohl, Richard M Elliott, Esther Schnettler
BACKGROUND: Vector arthropods control arbovirus replication and spread through antiviral innate immune responses including RNA interference (RNAi) pathways. Arbovirus infections have been shown to induce the exogenous small interfering RNA (siRNA) and Piwi-interacting RNA (piRNA) pathways, but direct antiviral activity by these host responses in mosquito cells has only been demonstrated against a limited number of positive-strand RNA arboviruses. For bunyaviruses in general, the relative contribution of small RNA pathways in antiviral defences is unknown...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28057684/ismart-a-toolkit-for-a-comprehensive-analysis-of-small-rna-seq-data
#7
Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato
: The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT (integrative Small RNA Tool-kit), an automated pipeline to analyze smallRNA-Seq data...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28053272/trans-generational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-non-coding-rna-loci
#8
Brian M Farley, Kathleen Collins
Trans-generational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of trans-generational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of trans-generational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated trans-generational regulation to include unique non-coding RNA loci. Ciliates such as Tetrahymena have a phenotypically silent germline micronucleus and an expressed somatic macronucleus, which is differentiated anew from a germline genome copy in sexual reproduction...
January 4, 2017: RNA
https://www.readbyqxmd.com/read/28052756/small-rna-sequencing-of-cryopreserved-semen-from-single-bull-revealed-altered-mirnas-and-pirnas-expression-between-high-and-low-motile-sperm-populations
#9
E Capra, F Turri, B Lazzari, P Cremonesi, T M Gliozzi, I Fojadelli, A Stella, F Pizzi
BACKGROUND: Small RNAs present in bovine ejaculate can be linked to sperm abnormalities and fertility disorders. At present, quality parameters routinely used in semen evaluation are not fully reliable to predict bull fertility. In order to provide additional quality measurements for cryopreserved semen used for breeding, a method based on deep sequencing of sperm microRNA (miRNA) and Piwi-interacting RNA (piRNA) from individual bulls was developed. To validate our method, two populations of spermatozoa isolated from high and low motile fractions separated by Percoll were sequenced, and their small RNAs content characterized...
January 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28039207/nup358-binds-to-ago-proteins-through-its-sumo-interacting-motifs-and-promotes-the-association-of-target-mrna-with-mirisc
#10
Manas Ranjan Sahoo, Swati Gaikwad, Deepak Khuperkar, Maitreyi Ashok, Mary Helen, Santosh Kumar Yadav, Aditi Singh, Indrasen Magre, Prachi Deshmukh, Supriya Dhanvijay, Pabitra Kumar Sahoo, Yogendra Ramtirtha, Mallur Srivatsan Madhusudhan, Pananghat Gayathri, Vasudevan Seshadri, Jomon Joseph
MicroRNA (miRNA)-guided mRNA repression, mediated by the miRNA-induced silencing complex (miRISC), is an important component of post-transcriptional gene silencing. However, how miRISC identifies the target mRNA in vivo is not well understood. Here, we show that the nucleoporin Nup358 plays an important role in this process. Nup358 localizes to the nuclear pore complex and to the cytoplasmic annulate lamellae (AL), and these structures dynamically associate with two mRNP granules: processing bodies (P bodies) and stress granules (SGs)...
December 30, 2016: EMBO Reports
https://www.readbyqxmd.com/read/28033427/piwis-go-viral-arbovirus-derived-pirnas-in-vector-mosquitoes
#11
REVIEW
Pascal Miesen, Joep Joosten, Ronald P van Rij
Vector mosquitoes are responsible for transmission of the majority of arthropod-borne (arbo-) viruses. Virus replication in these vectors needs to be sufficiently high to permit efficient virus transfer to vertebrate hosts. The mosquito immune response therefore is a key determinant for arbovirus transmission. Mosquito antiviral immunity is primarily mediated by the small interfering RNA pathway. Besides this well-established antiviral machinery, the PIWI-interacting RNA (piRNA) pathway processes viral RNA into piRNAs...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/28031481/xenopus-piwi-proteins-interact-with-a-broad-proportion-of-the-oocyte-transcriptome
#12
James A Toombs, Yuliya A Sytnikova, Gung-Wei Chirn, Ignatius Ang, Nelson C Lau, Michael D Blower
Piwi proteins utilize small RNAs (piRNAs) to recognize and repress target transcripts such as transposable elements (TE). However, the extensive diversity in piRNA sequences also suggests that Piwi/piRNA complexes interact with many transcripts beyond TEs. To examine the extent of Piwi interaction with target RNAs, we used Ribonucleoprotein-Immunoprecipitation (RIP) and Cross-linking and Immunoprecipitation (CLIP) to identify thousands of transcripts that associate with the Piwi proteins XIWI and XILI (Piwi-protein-Associated Transcripts, PATs) from early stage oocytes of X...
December 28, 2016: RNA
https://www.readbyqxmd.com/read/28025795/possible-role-of-hiwi2-in-modulating-tight-junction-proteins-in-retinal-pigment-epithelial-cells-through-akt-signaling-pathway
#13
Suganya Sivagurunathan, Karthikka Palanisamy, Jayamuruga Pandian Arunachalam, Subbulakshmi Chidambaram
PIWI subfamily of proteins is shown to be primarily expressed in germline cells. They maintain the genomic integrity by silencing the transposable elements. Although the role of PIWI proteins in germ cells has been documented, their presence and function in somatic cells remains unclear. Intriguingly, we detected all four members of PIWI-like proteins in human ocular tissues and somatic cell lines. When HIWI2 was knocked down in retinal pigment epithelial cells, the typical honeycomb morphology was affected...
December 26, 2016: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28018141/what-drives-positive-selection-in-the-drosophila-pirna-machinery-the-genomic-autoimmunity-hypothesis
#14
REVIEW
Justin P Blumenstiel, Alexandra A Erwin, Lucas W Hemmer
In animals, PIWI-interacting RNAs (piRNAs) play a crucial role in genome defense. Moreover, because piRNAs can be maternally transmitted, they contribute to the epigenetic profile of inheritance. Multiple studies, especially in Drosophila, have demonstrated that the machinery of piRNA biogenesis is often the target of positive selection. Because transposable elements (TEs) are a form of genetic parasite, positive selection in the piRNA machinery is often explained by analogy to the signatures of positive selection commonly observed in genes that play a role in host-parasite dynamics...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28005467/defining-the-purity-of-exosomes-required-for-diagnostic-profiling-of-small-rna-suitable-for-biomarker-discovery
#15
Camelia Quek, Shayne A Bellingham, Chol-Hee Jung, Benjamin J Scicluna, Mitch C Shambrook, Robyn A Sharples, Lesley Cheng, Andrew F Hill
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated...
December 22, 2016: RNA Biology
https://www.readbyqxmd.com/read/28003471/pirna-associated-proteins-and-retrotransposons-are-differentially-expressed-in-murine-testis-and-ovary-of-aryl-hydrocarbon-receptor-deficient-mice
#16
Eva M Rico-Leo, Nuria Moreno-Marín, Francisco J González-Rico, Eva Barrasa, Cristina Ortega-Ferrusola, Patricia Martín-Muñoz, Luis O Sánchez-Guardado, Elena Llano, Alberto Alvarez-Barrientos, Ascensión Infante-Campos, Inmaculada Catalina-Fernández, Matías Hidalgo-Sánchez, Dirk G de Rooij, Alberto M Pendás, Fernando J Peña, Jaime M Merino, Pedro M Fernández-Salguero
Previous studies suggested that the aryl hydrocarbon receptor (AhR) contributes to mice reproduction and fertility. However, the mechanisms involved remain mostly unknown. Retrotransposon silencing by Piwi-interacting RNAs (piRNAs) is essential for germ cell maturation and, remarkably, AhR has been identified as a regulator of murine B1-SINE retrotransposons. Here, using littermate AhR(+/+) and AhR(-/-) mice, we report that AhR regulates the general course of spermatogenesis and oogenesis by a mechanism likely to be associated with piRNA-associated proteins, piRNAs and retrotransposons...
December 2016: Open Biology
https://www.readbyqxmd.com/read/28000665/a-somatic-pirna-pathway-in-the-drosophila-fat-body-ensures-metabolic-homeostasis-and-normal-lifespan
#17
Brian C Jones, Jason G Wood, Chengyi Chang, Austin D Tam, Michael J Franklin, Emily R Siegel, Stephen L Helfand
In gonadal tissues, the Piwi-interacting (piRNA) pathway preserves genomic integrity by employing 23-29 nucleotide (nt) small RNAs complexed with argonaute proteins to suppress parasitic mobile sequences of DNA called transposable elements (TEs). Although recent evidence suggests that the piRNA pathway may be present in select somatic cells outside the gonads, the role of a non-gonadal somatic piRNA pathway is not well characterized. Here we report a functional somatic piRNA pathway in the adult Drosophila fat body including the presence of the piRNA effector protein Piwi and canonical 23-29 nt long TE-mapping piRNAs...
December 21, 2016: Nature Communications
https://www.readbyqxmd.com/read/27966078/analysis-of-pirna-like-small-non-coding-rnas-present-in-axons-of-adult-sensory-neurons
#18
Monichan Phay, Hak Hee Kim, Soonmoon Yoo
Small non-coding RNAs (sncRNAs) have been shown to play pivotal roles in spatiotemporal-specific gene regulation that is linked to many different biological functions. PIWI-interacting RNAs (piRNAs), typically 25-34-nucleotide long, are originally identified and thought to be restricted in germline cells. However, recent studies suggest that piRNAs associate with neuronal PIWI proteins, contributing to neuronal development and function. Here, we identify a cohort of piRNA-like sncRNAs (piLRNAs) in rat sciatic nerve axoplasm and directly contrast temporal changes of piLRNA levels in the nerve following injury, as compared with those in an uninjured nerve using deep sequencing...
December 13, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27965401/bovine-pirna-like-rnas-are-associated-with-both-mobile-elements-and-mrnas
#19
Stewart J Russell, Mehool Patel, Graham Gilchrist, Leanne Stalker, Daniel Gillis, David Rosenkranz, Jonathan LaMarre
PIWI proteins and their associated piRNAs have been the focus of intensive research for the past decade, and their participation in the maintenance of genomic integrity during spermatogenesis has been well established. Recent studies have suggested important roles for the PIWI/piRNA system outside of gametogenesis, based on the presence of piRNAs and PIWI proteins in several somatic tissues, cancers, and the early embryo. Here we investigated the small-RNA complement present in bovine gonads, gametes, and embryos through next generation sequencing...
December 13, 2016: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/27951720/-involvement-of-piwi-interacting-rnas-in-cancerogenesis-via-the-regulation-of-gene-expression
#20
S Rybecká, K Štítkovcová, P Vychytilová-Faltejsková, O Slabý
BACKGROUND: In the past few years, a number of studies have suggested that small non-coding RNAs could be promising diagnostic, prognostic and predictive biomarkers in oncology. Recently, small RNAs interacting with PIWI proteins (piRNAs) have been described. These small RNAs regulate gene expression at transcriptional and post-transcriptional levels; however, they appear to be specifically involved in silencing the transposable elements LINE and SINE and are thus considered to contribute to genomic stability...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
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