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https://www.readbyqxmd.com/read/28292424/btbd18-regulates-a-subset-of-pirna-generating-loci-through-transcription-elongation-in-mice
#1
Liquan Zhou, Bertram Canagarajah, Yangu Zhao, Boris Baibakov, Keizo Tokuhiro, Dragan Maric, Jurrien Dean
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development. Despite intense investigation of post-transcriptional processing, chromatin regulators for piRNA biogenesis in mammals remain largely unexplored. Here we document that BTBD18 is a pachytene nuclear protein in mouse testes that occupies a subset of pachytene piRNA-producing loci. Ablation of Btbd18 in mice disrupts piRNA biogenesis, prevents spermiogenesis, and results in male sterility. Transcriptome profiling, chromatin accessibility, and RNA polymerase II occupancy demonstrate that BTBD18 facilitates expression of pachytene piRNA precursors by promoting transcription elongation...
March 13, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28289238/stroke-and-circulating-extracellular-rnas
#2
Eric Mick, Ravi Shah, Kahraman Tanriverdi, Venkatesh Murthy, Mark Gerstein, Joel Rozowsky, Robert Kitchen, Martin G Larson, Daniel Levy, Jane E Freedman
BACKGROUND AND PURPOSE: There is increasing interest in extracellular RNAs (ex-RNAs), with numerous reports of associations between selected microRNAs (miRNAs) and a variety of cardiovascular disease phenotypes. Previous studies of ex-RNAs in relation to risk for cardiovascular disease have investigated small numbers of patients and assayed only candidate miRNAs. No human studies have investigated links between novel ex-RNAs and stroke. METHODS: We conducted unbiased next-generation sequencing using plasma from 40 participants of the FHS (Framingham Heart Study; Offspring Cohort Exam 8) followed by high-throughput polymerase chain reaction of 471 ex-RNAs...
March 13, 2017: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/28283070/circular-concatemers-of-ultra-short-dna-segments-produce-regulatory-rnas
#3
Sarah E Allen, Iris Hug, Sylwia Pabian, Iwona Rzeszutek, Cristina Hoehener, Mariusz Nowacki
In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28254886/tex19-paralogs-are-new-members-of-the-pirna-pathway-controlling-retrotransposon-suppression
#4
Yara Tarabay, Mayada Achour, Marius Teletin, Tao Ye, Aurélie Teissandier, Manuel Mark, Déborah Bourc'his, Stéphane Viville
Tex19 genes are mammalian specific and duplicated in Tex19.1 and Tex19.2 in some species, such as the mouse and rat. It has been demonstrated that mutant Tex19.1 males display a variable degree of infertility whereas they all upregulate MMERVK10C transposons in their germ line. In order to study the function of both paralogs in the mouse, we generated and studied double knockout (Tex19DKO) mutant mice. Adult Tex19DKO males exhibited a fully penetrant phenotype, similar to the most severe phenotype observed in single Tex19...
March 2, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#5
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/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#6
REVIEW
Eugene V Koonin
Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes...
February 10, 2017: Biology Direct
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
#7
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...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28131900/non-coding-rnas-and-neuroprotection-after-acute-cns-injuries
#8
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
#9
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
#10
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
#11
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
#12
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/28094937/click-quantitative-mass-spectrometry-identifies-piwil3-as-a-mechanistic-target-of-rna-interference-activator-enoxacin-in-cancer-cells
#13
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
#14
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
#15
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...
February 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28072387/embryonic-origin-of-adult-stem-cells-required-for-tissue-homeostasis-and-regeneration
#16
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 that are required for the 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 Schmidtea 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
#17
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
#18
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
#19
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. AVAILABILITY AND IMPLEMENTATION: iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI)...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28053272/transgenerational-function-of-tetrahymena-piwi-protein-twi8p-at-distinctive-noncoding-rna-loci
#20
Brian M Farley, Kathleen Collins
Transgenerational transmission of genome-regulatory epigenetic information can determine phenotypes in the progeny of sexual reproduction. Sequence specificity of transgenerational regulation derives from small RNAs assembled into Piwi-protein complexes. Known targets of transgenerational regulation are primarily transposons and transposon-derived sequences. Here, we extend the scope of Piwi-mediated transgenerational regulation to include unique noncoding 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...
April 2017: RNA
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