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https://www.readbyqxmd.com/read/28204592/tetools-facilitates-big-data-expression-analysis-of-transposable-elements-and-reveals-an-antagonism-between-their-activity-and-that-of-pirna-genes
#1
Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira
No abstract text is available yet for this article.
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#2
Joseph A Karam, Rasesh Y Parikh, Dhananjaya Nayak, David Rosenkranz, Vamsi K Gangaraju
piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90 Organizing Protein Homolog (Hop), a co-chaperone, interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28178889/v-elmpirnapred-identification-of-human-pirnas-by-the-voting-based-extreme-learning-machine-v-elm-with-a-new-hybrid-feature
#3
Cong Pian, Yuan-Yuan Chen, Jin Zhang, Zhi Chen, Guang-Le Zhang, Qiang Li, Tao Yang, Liang-Yun Zhang
Piwi-interacting RNAs (piRNAs) were recently discovered as endogenous small noncoding RNAs. Some recent research suggests that piRNAs may play an important role in cancer. So the precise identification of human piRNAs is a significant work. In this paper, we introduce a series of new features with 80 dimension called short sequence motifs (SSM). A hybrid feature vector with 1444 dimension can be formed by combining 1364 features of [Formula: see text]-mer strings and 80 features of SSM features. We optimize the 1444 dimension features using the feature score criterion (FSC) and list them in descending order according to the scores...
January 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28131900/non-coding-rnas-and-neuroprotection-after-acute-cns-injuries
#4
Raghavendar Chandran, Suresh L Mehta, Raghu Vemuganti
Accumulating evidence indicates that various classes of non-coding RNAs (ncRNAs) including microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and long non-coding RNAs (lncRNAs) play important roles in normal state as well as the diseases of the CNS. Interestingly, ncRNAs have been shown to interact with messenger RNA, DNA and proteins, and these interactions could induce epigenetic modifications and control transcription and translation, thereby adding a new layer of genomic regulation. The ncRNA expression profiles are known to be altered after acute CNS injuries including stroke, traumatic brain injury and spinal cord injury that are major contributors of morbidity and mortality worldwide...
January 26, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/28127595/small-rna-sequencing-revealed-dysregulated-pirnas-in-alzheimer-s-disease-and-their-probable-role-in-pathogenesis
#5
Jyoti Roy, Arijita Sarkar, Sibun Parida, Zhumur Ghosh, Bibekanand Mallick
PIWI-interacting RNAs (piRNAs), ∼23-36 nucleotide-long small non-coding RNAs, earlier believed to be germline-specific, have now been identified in somatic cells including neural cells. However, piRNAs have not yet been studied in the human brain (HB) and Alzheimer's disease (AD)-affected brain. In this study, by next-generation small RNA sequencing, 564 and 451 piRNAs were identified in the HB and AD-affected brain respectively. The majority of the neuronal piRNAs have intronic origin wherein primary piRNAs are mostly from the negative strand...
January 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28115634/roles-of-miwi-mili-and-pld6-in-small-rna-regulation-in-mouse-growing-oocytes
#6
Yuka Kabayama, Hidehiro Toh, Ami Katanaya, Takayuki Sakurai, Shinichiro Chuma, Satomi Kuramochi-Miyagawa, Yumiko Saga, Toru Nakano, Hiroyuki Sasaki
The mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26-30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood. In the present study, we investigated the consequences of loss of piRNA-pathway components in growing oocytes. When MILI (or PIWIL2), a PIWI family member, was depleted by gene knockout, almost all piRNAs disappeared. This severe loss of piRNA was accompanied by an increase in transcripts derived from specific retrotransposons, especially IAPs...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28115625/histone-derived-pirna-biogenesis-depends-on-the-ping-pong-partners-piwi5-and-ago3-in-aedes-aegypti
#7
Erika Girardi, Pascal Miesen, Bas Pennings, Lionel Frangeul, Maria-Carla Saleh, Ronald P van Rij
The piRNA pathway is of key importance in controlling transposable elements in most animal species. In the vector mosquito Aedes aegypti, the presence of eight PIWI proteins and the accumulation of viral piRNAs upon arbovirus infection suggest additional functions of the piRNA pathway beyond genome defense. To better understand the regulatory potential of this pathway, we analyzed in detail host-derived piRNAs in A. aegypti Aag2 cells. We show that a large repertoire of protein-coding genes and non-retroviral integrated RNA virus elements are processed into genic piRNAs by different combinations of PIWI proteins...
January 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28109471/smoking-status-regulates-a-novel-panel-of-piwi-interacting-rnas-in-head-and-neck-squamous-cell-carcinoma
#8
Aswini R Krishnan, Avinaash Korrapati, Angela E Zou, Yuanhao Qu, Xiao Qi Wang, Joseph A Califano, Jessica Wang-Rodriguez, Scott M Lippman, Melbourne F Hovell, Weg M Ongkeko
OBJECTIVE: Smoking remains a primary etiological factor in head and neck squamous cell carcinoma (HNSCC). Given that non-coding RNAs (ncRNAs), including PIWI-interacting RNAs (piRNAs), have emerged as mediators of initiation and progression in head and neck malignancies, we undertook a global study of piRNA expression patterns in smoking-associated HNSCC. MATERIALS AND METHODS: Using RNA-sequencing data from 256 current smoker and lifelong nonsmoker samples in The Cancer Genome Atlas (TCGA), we analyzed the differential expression patterns of 27,127 piRNAs across patient cohorts stratified by tobacco use, with HPV16 status and tumor status taken into account...
February 2017: Oral Oncology
https://www.readbyqxmd.com/read/28103247/bombyx-mori-p-element-somatic-inhibitor-bmpsi-is-a-key-auxiliary-factor-for-silkworm-male-sex-determination
#9
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 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28094937/click-quantitative-mass-spectrometry-identifies-piwil3-as-a-mechanistic-target-of-rna-interference-activator-enoxacin-in-cancer-cells
#10
Nathan S 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 Argonaute 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...
February 1, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28091568/identification-of-misexpressed-genetic-elements-in-hybrids-between-drosophila-related-species
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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