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https://www.readbyqxmd.com/read/28540181/dynamic-regulation-of-small-rnaome-during-the-early-stage-of-cardiac-differentiation-from-pluripotent-embryonic-stem-cells
#1
Yue Li, An Zeng, Ge Li, Ya-Na Guan, Huang-Tian Yang, Bairong Shen, Qing Jing
Embryonic stem cells (mESCs), having potential to differentiate into three germ-layer cells including cardiomyocytes, shall be a perfect model to help understanding heart development. Here, using small RNA deep sequencing, we studied the small RNAome in the early stage of mouse cardiac differentiation. We found that the expression pattern of most microRNA (miRNA) were highly enriched at the beginning and declined thereafter, some were still insufficiently expressed on day 6, and most miRNAs recovered in the following days...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28539933/mal-de-r%C3%A3-o-cuarto-virus-infection-triggers-the-production-of-distinctive-viral-derived-sirna-profiles-in-wheat-and-its-planthopper-vector
#2
Luis A de Haro, Analía D Dumón, María F Mattio, Evangelina Beatriz Argüello Caro, Gabriela Llauger, Diego Zavallo, Hervé Blanc, Vanesa C Mongelli, Graciela Truol, María-Carla Saleh, Sebastián Asurmendi, Mariana Del Vas
Plant reoviruses are able to multiply in gramineae plants and delphacid vectors encountering different defense strategies with unique features. This study aims to comparatively assess alterations of small RNA (sRNA) populations in both hosts upon virus infection. For this purpose, we characterized the sRNA profiles of wheat and planthopper vectors infected by Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) and quantified virus genome segments by quantitative reverse transcription PCR We provide evidence that plant and insect silencing machineries differentially recognize the viral genome, thus giving rise to distinct profiles of virus-derived small interfering RNAs (vsiRNAs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28539440/uncovering-the-repertoire-of-endogenous-flaviviral-elements-in-aedes-mosquito-genomes
#3
Yasutsugu Suzuki, Lionel Frangeul, Laura B Dickson, Hervé Blanc, Yann Verdier, Joelle Vinh, Louis Lambrechts, Maria-Carla Saleh
Endogenous viral elements derived from non-retroviral RNA viruses were described in various animal genomes. Whether they have a biological function such as host immune protection against related viruses is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Ae. albopictus and one from Ae. aegypti cell lines. However, in-depth characterization of EFVEs in wild-type mosquito populations and individuals in vivo has not been performed...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28538188/identification-and-characterization-of-a-class-of-malat1-like-genomic-loci
#4
Bin Zhang, Yuntao S Mao, Sarah D Diermeier, Irina V Novikova, Eric P Nawrocki, Tom A Jones, Zsolt Lazar, Chang-Shung Tung, Weijun Luo, Sean R Eddy, Karissa Y Sanbonmatsu, David L Spector
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a noncoding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using an RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3' end triple-helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a co-occurrence of components of the 3' end module...
May 23, 2017: Cell Reports
https://www.readbyqxmd.com/read/28536021/effect-of-dietary-astragalus-polysaccharide-supplements-on-testicular-pirna-expression-profiles-of-breeding-cocks
#5
Shengru Wu, Yulong Li, Si Chen, Saisai Liang, Xiaochun Ren, Wei Guo, Qingzhu Sun, Xiaojun Yang
Astragalus polysaccharide (APS), as the main active ingredient of Astragalus membranaceus, has extensive biological activities related to immune, metabolic, and anti-oxidative regulatory processes. Previous studies have proven that piRNAs could play important roles in genital gland. This study aimed to identify the differentially expressed piRNAs in chicken testes in response to dietary APS supplements and further evaluate the roles of these piRNAs related to the effect of dietary APS supplements on testicular changes...
May 20, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28530707/a-mili-independent-pirna-biogenesis-pathway-empowers-partial-germline-reprogramming
#6
Lina Vasiliauskaitė, Dimitrios Vitsios, Rebecca V Berrens, Claudia Carrieri, Wolf Reik, Anton J Enright, Dónal O'Carroll
In mice, the pathway involving PIWI and PIWI-interacting RNA (PIWI-piRNA) is essential to re-establish transposon silencing during male-germline reprogramming. The cytoplasmic PIWI protein MILI mediates piRNA-guided transposon RNA cleavage as well as piRNA amplification. MIWI2's binding to piRNA and its nuclear localization are proposed to be dependent upon MILI function. Here, we demonstrate the existence of a piRNA biogenesis pathway that sustains partial MIWI2 function and reprogramming activity in the absence of MILI...
May 22, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28529570/the-meaning-of-piwi-proteins-in-cancer-development
#7
Monika Litwin, Anna Szczepańska-Buda, Aleksandra Piotrowska, Piotr Dzięgiel, Wojciech Witkiewicz
Cancer is a histologically and genetically heterogeneous population of tumor cells that exhibits distinct molecular profiles determined by epigenetic alterations. P-element-induced wimpy testis (PIWI) proteins in complex with PIWI-interacting RNA (piRNA) have been previously demonstrated to be involved in epigenetic regulation in germline cells. Recently, reactivation of PIWI expression, primarily PIWI-like protein 1 and 2, through aberrant DNA methylation resulting in genomic silencing has been identified in various types of tumors...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28509881/dfmr1-plays-roles-in-small-rna-pathways-of-drosophila-melanogaster
#8
REVIEW
Valeria Specchia, Simona D'Attis, Antonietta Puricella, Maria Pia Bozzetti
Fragile-X syndrome is the most common form of inherited mental retardation accompanied by other phenotypes, including macroorchidism. The disorder originates with mutations in the Fmr1 gene coding for the FMRP protein, which, with its paralogs FXR1 and FXR2, constitute a well-conserved family of RNA-binding proteins. Drosophila melanogaster is a good model for the syndrome because it has a unique fragile X-related gene: dFmr1. Recently, in addition to its confirmed role in the miRNA pathway, a function for dFmr1 in the piRNA pathway, operating in Drosophila gonads, has been established...
May 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28505386/c-d-box-snornas-form-methylating-and-non-methylating-ribonucleoprotein-complexes-old-dogs-show-new-tricks
#9
REVIEW
Marina Falaleeva, Justin R Welden, Marilyn J Duncan, Stefan Stamm
C/D box snoRNAs (SNORDs) are an abundantly expressed class of short, non-coding RNAs that have been long known to perform 2'-O-methylation of rRNAs. However, approximately half of human SNORDs have no predictable rRNA targets, and numerous SNORDs have been associated with diseases that show no defects in rRNAs, among them Prader-Willi syndrome, Duplication 15q syndrome and cancer. This apparent discrepancy has been addressed by recent studies showing that SNORDs can act to regulate pre-mRNA alternative splicing, mRNA abundance, activate enzymes, and be processed into shorter ncRNAs resembling miRNAs and piRNAs...
June 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28497119/aedes-aegypti-piwi4-is-a-noncanonical-piwi-protein-involved-in-antiviral-responses
#10
Margus Varjak, Kevin Maringer, Mick Watson, Vattipally B Sreenu, Anthony C Fredericks, Emilie Pondeville, Claire L Donald, Jelle Sterk, Joy Kean, Marie Vazeille, Anna-Bella Failloux, Alain Kohl, Esther Schnettler
The small interfering RNA (siRNA) pathway is a major antiviral response in mosquitoes; however, another RNA interference pathway, the PIWI-interacting RNA (piRNA) pathway, has been suggested to be antiviral in mosquitoes. Piwi4 has been reported to be a key mediator of this response in mosquitoes, but it is not involved in the production of virus-specific piRNAs. Here, we show that Piwi4 associates with members of the antiviral exogenous siRNA pathway (Ago2 and Dcr2), as well as with proteins of the piRNA pathway (Ago3, Piwi5, and Piwi6) in an Aedes aegypti-derived cell line, Aag2...
May 2017: MSphere
https://www.readbyqxmd.com/read/28497117/rna-interference-restricts-rift-valley-fever-virus-in-multiple-insect-systems
#11
Isabelle Dietrich, Stephanie Jansen, Gamou Fall, Stephan Lorenzen, Martin Rudolf, Katrin Huber, Anna Heitmann, Sabine Schicht, El Hadji Ndiaye, Mick Watson, Ilaria Castelli, Benjamin Brennan, Richard M Elliott, Mawlouth Diallo, Amadou A Sall, Anna-Bella Failloux, Esther Schnettler, Alain Kohl, Stefanie C Becker
The emerging bunyavirus Rift Valley fever virus (RVFV) is transmitted to humans and livestock by a large number of mosquito species. RNA interference (RNAi) has been characterized as an important innate immune defense mechanism used by mosquitoes to limit replication of positive-sense RNA flaviviruses and togaviruses; however, little is known about its role against negative-strand RNA viruses such as RVFV. We show that virus-specific small RNAs are produced in infected mosquito cells, in Drosophila melanogaster cells, and, most importantly, also in RVFV vector mosquitoes...
May 2017: MSphere
https://www.readbyqxmd.com/read/28486636/natural-variation-in-the-distribution-and-abundance-of-transposable-elements-across-the-caenorhabditis-elegans-species
#12
K M Laricchia, S Zdraljevic, D E Cook, E C Andersen
Transposons are mobile DNA elements that generate both adaptive and deleterious phenotypic variation thereby driving genome evolution. For these reasons, genomes have mechanisms to regulate transposable element (TE) activity. Approximately 12-16% of the Caenorhabditis elegans genome is composed of TEs, of which the majority are likely inactive. However, most studies of TE activity have been conducted in the laboratory strain N2, which limits our knowledge of the effects of these mobile elements across natural populations...
May 9, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28472469/piwi-interacts-with-chromatin-at-nuclear-pores-and-promiscuously-binds-nuclear-transcripts-in-drosophila-ovarian-somatic-cells
#13
Artem A Ilyin, Sergei S Ryazansky, Semen A Doronin, Oxana M Olenkina, Elena A Mikhaleva, Evgeny Y Yakushev, Yuri A Abramov, Stepan N Belyakin, Anton V Ivankin, Alexey V Pindyurin, Vladimir A Gvozdev, Mikhail S Klenov, Yuri Y Shevelyov
Piwi in a complex with Piwi-interacting RNAs (piRNAs) triggers transcriptional silencing of transposable elements (TEs) in Drosophila ovaries, thus ensuring genome stability. To do this, Piwi must scan the nascent transcripts of genes and TEs for complementarity to piRNAs. The mechanism of this scanning is currently unknown. Here we report the DamID-seq mapping of multiple Piwi-interacting chromosomal domains in somatic cells of Drosophila ovaries. These domains significantly overlap with genomic regions tethered to Nuclear Pore Complexes (NPCs)...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472327/contrasting-sex-and-caste-dependent-pirna-profiles-in-the-transposon-depleted-haplodiploid-honeybee-apis-mellifera
#14
Wei-Wen Wang, Regan Ashby, Hua Ying, Ryszard Maleszka, Sylvain Forêt
Protecting genome integrity against transposable elements is achieved by intricate molecular mechanisms involving PIWI proteins, their associated small RNAs (piRNAs), and epigenetic modifiers such as DNA methylation. Eusocial bees, in particular the Western honeybee, Apis mellifera, have one of the lowest contents of transposable elements in the animal kingdom, and, unlike other animals with a functional DNA methylation system, do not methylate their transposons. This raises the question of whether the PIWI machinery has been retained in this species...
May 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28461596/a-transit-amplifying-population-underpins-the-efficient-regenerative-capacity-of-the-testis
#15
Claudia Carrieri, Stefano Comazzetto, Amit Grover, Marcos Morgan, Andreas Buness, Claus Nerlov, Dónal O'Carroll
The spermatogonial stem cell (SSC) that supports spermatogenesis throughout adult life resides within the GFRα1-expressing A type undifferentiated spermatogonia. The decision to commit to spermatogenic differentiation coincides with the loss of GFRα1 and reciprocal gain of Ngn3 (Neurog3) expression. Through the analysis of the piRNA factor Miwi2 (Piwil4), we identify a novel population of Ngn3-expressing spermatogonia that are essential for efficient testicular regeneration after injury. Depletion of Miwi2-expressing cells results in a transient impact on testicular homeostasis, with this population behaving strictly as transit amplifying cells under homeostatic conditions...
May 1, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28460486/small-rna-sequencing-reveals-metastasis-related-micrornas-in-lung-adenocarcinoma
#16
Iben Daugaard, Morten T Venø, Yan Yan, Tina E Kjeldsen, Philippe Lamy, Henrik Hager, Jørgen Kjems, Lise Lotte Hansen
The majority of lung cancer deaths are caused by metastatic disease. MicroRNAs (miRNAs) are posttranscriptional regulators of gene expression and miRNA dysregulation can contribute to metastatic progression. Here, small RNA sequencing was used to profile the miRNA and piwi-interacting RNA (piRNA) transcriptomes in relation to lung cancer metastasis. RNA-seq was performed using RNA extracted from formalin-fixed paraffin embedded (FFPE) lung adenocarcinomas (LAC) and brain metastases from 8 patients, and LACs from 8 patients without detectable metastatic disease...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28459978/short-and-long-term-evolutionary-dynamics-of-subtelomeric-pirna-clusters-in-drosophila
#17
Amna Asif-Laidin, Valérie Delmarre, Jeanne Laurentie, Wolfgang J Miller, Stéphane Ronsseray, Laure Teysset
Two Telomeric Associated Sequences, TAS-R and TAS-L, form the principal subtelomeric repeat families identified in Drosophila melanogaster. They are PIWI-interacting RNA (piRNA) clusters involved in repression of Transposable Elements. In this study, we revisited TAS structural and functional dynamics in D. melanogaster and in related species. In silico analysis revealed that TAS-R family members are composed of previously uncharacterized domains. This analysis also showed that TAS-L repeats are composed of arrays of a region we have named "TAS-L like" (TLL) identified specifically in one TAS-R family member, X-TAS...
April 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28457744/piwi-is-required-during-drosophila-embryogenesis-to-license-dual-strand-pirna-clusters-for-transposon-repression-in-adult-ovaries
#18
Abdou Akkouche, Bruno Mugat, Bridlin Barckmann, Carolina Varela-Chavez, Blaise Li, Raoul Raffel, Alain Pélisson, Séverine Chambeyron
Most piRNAs in the Drosophila female germline are transcribed from heterochromatic regions called dual-strand piRNA clusters. Histone 3 lysine 9 trimethylation (H3K9me3) is required for licensing piRNA production by these clusters. However, it is unclear when and how they acquire this permissive heterochromatic state. Here, we show that transient Piwi depletion in Drosophila embryos results in H3K9me3 decrease at piRNA clusters in ovaries. This is accompanied by impaired biogenesis of ovarian piRNAs, accumulation of transposable element transcripts, and female sterility...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28449079/small-non-coding-rna-and-cancer
#19
Giulia Romano, Dario Veneziano, Mario Acunzo, Carlo M Croce
The ENCODE project has reported that at least 80% of the human genome is biologically active, yet only a small part of human DNA encodes for protein. The massive amount of RNA transcribed but not translated into protein can be classified as housekeeping RNA (such as rRNA, tRNA) and regulatory RNA (such as miRNA, piRNA, lncRNA). Small non-coding RNAs, in particular, have been the focus of many studies in the last 20 years and their fundamental role in many human diseases is currently well established. Inter alia, their role in cancer development and progression, as well as in drug resistance, is being increasingly investigated...
May 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28448516/natural-variation-of-pirna-expression-affects-immunity-to-transposable-elements
#20
Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, Maria Y Kordyukova, Ivan Olovnikov, Alla Kalmykova
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements...
April 2017: PLoS Genetics
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