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https://www.readbyqxmd.com/read/28103247/bombyx-mori-p-element-somatic-inhibitor-bmpsi-is-a-key-auxiliary-factor-for-silkworm-male-sex-determination
#1
Jun Xu, Shuqing Chen, Baosheng Zeng, Anthony A James, Anjiang Tan, Yongping Huang
Manipulation of sex determination pathways in insects provides the basis for a wide spectrum of strategies to benefit agriculture and public health. Furthermore, insects display a remarkable diversity in the genetic pathways that lead to sex differentiation. The silkworm, Bombyx mori, has been cultivated by humans as a beneficial insect for over two millennia, and more recently as a model system for studying lepidopteran genetics and development. Previous studies have identified the B. mori Fem piRNA as the primary female determining factor and BmMasc as its downstream target, while the genetic scenario for male sex determination was still unclear...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28094937/click-qms-identifies-piwil3-as-a-mechanistic-target-of-rna-interference-activator-enoxacin-in-cancer-cells
#2
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
#3
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/28063496/measuring-phospholipase-d-enzymatic-activity-through-biochemical-and-imaging-methods
#4
F Philip, E E Ha, M A Seeliger, M A Frohman
The phospholipase D (PLD) enzymatic superfamily regulates a wide range of cell biological and physiological pathways, including platelet activation, immune responses, cancer, and spermatogenesis. The three main enzymatic actions of the superfamily entail (i) hydrolyzing membrane phospholipids (phosphatidylcholine (PC) and cardiolipin) to generate choline and the second messenger signaling lipid phosphatidic acid (PA), (ii) using ethanol to transphosphatidylate PC to generate the long-lived metabolite phosphatidylethanol, and (iii) hydrolyzing RNA transcripts to generate piRNAs, the third form of endogenous RNAi...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28060823/the-antiviral-rnai-response-in-vector-and-non-vector-cells-against-orthobunyaviruses
#5
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/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#6
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
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/28053118/a-meiosis-specific-spt5-homolog-involved-in-non-coding-transcription
#8
Julita Gruchota, Cyril Denby Wilkes, Olivier Arnaiz, Linda Sperling, Jacek K Nowak
Spt5 is a conserved and essential transcriptional regulator that binds directly to RNA polymerase and is involved in transcription elongation, polymerase pausing and various co-transcriptional processes. To investigate the role of Spt5 in non-coding transcription, we used the unicellular model Paramecium tetraurelia In this ciliate, development is controlled by epigenetic mechanisms that use different classes of non-coding RNAs to target DNA elimination. We identified two SPT5 genes. One (STP5v) is involved in vegetative growth, while the other (SPT5m) is essential for sexual reproduction...
January 3, 2017: Nucleic Acids Research
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/28033427/piwis-go-viral-arbovirus-derived-pirnas-in-vector-mosquitoes
#10
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
#11
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/28018141/what-drives-positive-selection-in-the-drosophila-pirna-machinery-the-genomic-autoimmunity-hypothesis
#12
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/28003516/linking-maternal-and-somatic-5s-rrna-types-with-different-sequence-specific-non-ltr-retrotransposons
#13
Mauro D Locati, Johanna F B Pagano, Wim A Ensink, Marina van Olst, Selina van Leeuwen, Ulrike Nehrdich, Kongju Zhu, Herman P Spaink, Geneviève Girard, Han Rauwerda, Martijs J Jonker, Rob J Dekker, Timo M Breit
5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo and adult tissue, identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions...
December 21, 2016: RNA
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
#14
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
#15
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
#16
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
#17
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
#18
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
https://www.readbyqxmd.com/read/27940613/evaluation-of-possible-proximate-mechanisms-underlying-the-kinship-theory-of-intragenomic-conflict-in-social-insects
#19
David A Galbraith, Soojin V Yi, Christina M Grozinger
Kinship theory provides a universal framework in which to understand the evolution of altruism, but there are many molecular and genetic mechanisms that can generate altruistic behaviors. Interestingly, kinship theory specifically predicts intragenomic conflict between maternally-derived alleles (matrigenes) and paternally-derived alleles (patrigenes) over the generation of altruistic behavior in cases where the interests of the matrigenes and patrigenes are not aligned. Under these conditions, individual differences in selfish versus altruistic behavior are predicted to arise from differential expression of the matrigenes and patrigenes (parent-specific gene expression or PSGE) that regulate selfish versus altruistic behaviors...
December 2016: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/27939293/telomeric-retrotransposon-het-a-contains-a-bidirectional-promoter-that-initiates-divergent-transcription-of-pirna-precursors-in-drosophila-germline
#20
Elizaveta Radion, Sergei Ryazansky, Natalia Akulenko, Yakov Rozovsky, Dmitry Kwon, Valeriya Morgunova, Ivan Olovnikov, Alla Kalmykova
PIWI-interacting RNAs (piRNAs) provide the silencing of transposable elements in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. Here, we performed a deletion analysis of the HeT-A promoter and show that common regulatory elements are shared by sense and antisense promoters of HeT-A...
December 7, 2016: Journal of Molecular Biology
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