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https://www.readbyqxmd.com/read/28633017/distinct-roles-of-rna-helicases-mvh-and-tdrd9-in-piwi-slicing-triggered-mammalian-pirna-biogenesis-and-function
#1
Joanna M Wenda, David Homolka, Zhaolin Yang, Pietro Spinelli, Ravi Sachidanandam, Radha Raman Pandey, Ramesh S Pillai
Small RNAs called PIWI-interacting RNAs (piRNAs) act as an immune system to suppress transposable elements in the animal gonads. A poorly understood adaptive pathway links cytoplasmic slicing of target RNA by the PIWI protein MILI to loading of target-derived piRNAs into nuclear MIWI2. Here we demonstrate that MILI slicing generates a 16-nt by-product that is discarded and a pre-piRNA intermediate that is used for phased piRNA production. The ATPase activity of Mouse Vasa Homolog (MVH) is essential for processing the intermediate into piRNAs, ensuring transposon silencing and male fertility...
June 19, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28633014/a-krabsody-for-embryo-placental-development
#2
Didier Trono
Many of the hundreds of KRAB zinc finger proteins encoded by human and mouse are involved in taming the transcriptional regulatory potential of transposable elements. Reporting recently in Science, Yang et al. (2017) reveal that one murine family member, ZFP568, controls Igf2 expression for proper embryonic and placental development.
June 19, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28618303/transcriptomic-response-of-the-insect-vector-peregrinus-maidis-to-maize-mosaic-rhabdovirus-and-identification-of-conserved-responses-to-propagative-viruses-in-hopper-vectors
#3
Kathleen M Martin, Karen Barandoc-Alviar, Derek J Schneweis, Catherine L Stewart, Dorith Rotenberg, Anna E Whitfield
Maize mosaic virus (MMV) is a plant-pathogenic rhabdovirus that is transmitted by the corn planthopper, Peregrinus maidis, in a propagative manner. P. maidis supports long-term MMV infections with no negative effects on insect performance. To elucidate whole-body transcriptome responses to virus infection, RNA-Seq was used to examine differential gene expression of virus-infected adult insects, and libraries were prepared from replicated groups of virus-exposed insects and non-exposed insects. From the 68,003 de novo-assembled transcripts, 144 were differentially-expressed (DE) during viral infection with comparable numbers up- and down-regulated...
June 12, 2017: Virology
https://www.readbyqxmd.com/read/28611826/the-evolution-of-bacterial-genome-architecture
#4
REVIEW
Louis-Marie Bobay, Howard Ochman
The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28611742/analysis-of-the-genome-and-mobilome-of-a-dissimilatory-arsenate-reducing-aeromonas-sp-o23a-reveals-multiple-mechanisms-for-heavy-metal-resistance-and-metabolism
#5
Witold Uhrynowski, Przemyslaw Decewicz, Lukasz Dziewit, Monika Radlinska, Pawel S Krawczyk, Leszek Lipinski, Dorota Adamska, Lukasz Drewniak
Aeromonas spp. are among the most ubiquitous microorganisms, as they have been isolated from different environmental niches including waters, soil, as well as wounds and digestive tracts of poikilothermic animals and humans. Although much attention has been paid to the pathogenicity of Aeromonads, the role of these bacteria in environmentally important processes, such as transformation of heavy metals, remains to be discovered. Therefore, the aim of this study was a detailed genomic characterization of Aeromonas sp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28606835/identification-and-characterization-of-mobile-genetic-elements-lines-from-brassica-genome
#6
Faisal Nouroz, Shumaila Noreen, Muhammad Fiaz Khan, Shehzad Ahmed, J S Pat Heslop-Harrison
Among transposable elements (TEs), the LTR retrotransposons are abundant followed by non-LTR retrotransposons in plant genomes, the lateral being represented by LINEs and SINEs. Computational and molecular approaches were used for the characterization of Brassica LINEs, their diversity and phylogenetic relationships. Four autonomous and four non-autonomous LINE families were identified and characterized from Brassica. Most of the autonomous LINEs displayed two open reading frames, ORF1 and ORF2, where ORF1 is a gag protein domain, while ORF2 encodes endonuclease (EN) and a reverse transcriptase (RT)...
June 9, 2017: Gene
https://www.readbyqxmd.com/read/28605751/improved-maize-reference-genome-with-single-molecule-technologies
#7
Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Liang, Michelle C Stitzer, Bo Wang, Michael S Campbell, Joshua C Stein, Xuehong Wei, Chen-Shan Chin, Katherine Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L Schneider, Thomas K Wolfgruber, Michael R May, Nathan M Springer, Eric Antoniou, W Richard McCombie, Gernot G Presting, Michael McMullen, Jeffrey Ross-Ibarra, R Kelly Dawe, Alex Hastie, David R Rank, Doreen Ware
Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping...
June 12, 2017: Nature
https://www.readbyqxmd.com/read/28605523/retrotransposons-are-specified-as-dna-replication-origins-in-the-gene-poor-regions-of-arabidopsis-heterochromatin
#8
Zaida Vergara, Joana Sequeira-Mendes, Jordi Morata, Ramón Peiró, Elizabeth Hénaff, Celina Costas, Josep M Casacuberta, Crisanto Gutierrez
Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family...
June 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28602845/silencing-of-transposable-elements-by-pirnas-in-drosophila-an-evolutionary-perspective
#9
REVIEW
Shiqi Luo, Jian Lu
Transposable elements (TEs) are DNA sequences that can move within the genome. TEs have greatly shaped the genomes, transcriptomes, and proteomes of the host organisms through a variety of mechanisms. However, TEs generally disrupt genes and destabilize the host genomes, which substantially reduce fitness of the host organisms. Understanding the genomic distribution and evolutionary dynamics of TEs will greatly deepen our understanding of the TE-mediated biological processes. Most TE insertions are highly polymorphic in Drosophila melanogaster, providing us a good system to investigate the evolution of TEs at the population level...
June 8, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28602519/diversity-of-plasmids-harboring-blacmy-2-in-multidrug-resistant-escherichia-coli-isolated-from-poultry-in-brazil
#10
Joseane Cristina Ferreira, Rafael Antonio Casarin Penha Filho, Leonardo Neves Andrade, Angelo Berchieri Junior, Ana Lúcia Costa Darini
Multidrug-resistance (MDR) has been increasingly reported in Gram-negative bacteria from the intestinal microbiota, environment and food-producing animals. Resistance plasmids able to harbor different transposable elements are capable to mobilize antimicrobial resistance genes and transfer to other bacterial hosts. Plasmids carrying blaCMY are frequently associated with MDR. The present study assessed the presence of plasmid-encoded ampC genes (blacmy, blamox, blafox, blalat, blaact, blamir, bladha, blamor) in commensal E...
May 3, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28601066/induction-of-transposon-silencing-in-the-drosophila-germline
#11
REVIEW
S S Ryazansky, A D Stolyarenko, M S Klenov, V A Gvozdev
In this review we consider the role of the piRNA system in transposable element silencing in the Drosophila melanogaster germline. We focus on new data that demonstrate the mechanisms of initiation of piRNA biogenesis in ovarian germinal cells and the role of Piwi protein in this process, including our own results.
May 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28597534/whole-genome-patterns-of-linkage-disequilibrium-across-flycatcher-populations-clarify-the-causes-and-consequences-of-fine-scale-recombination-rate-variation-in-birds
#12
Takeshi Kawakami, Carina F Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds, Hans Ellegren
Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years)...
June 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28594822/hybridization-and-polyploidy-enable-genomic-plasticity-without-sex-in-the-most-devastating-plant-parasitic-nematodes
#13
Romain Blanc-Mathieu, Laetitia Perfus-Barbeoch, Jean-Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martin-Jimenez, Marc Bailly-Bechet, Philippe Castagnone-Sereno, Jean-François Flot, Djampa K Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yu-Jin Kim-Jo, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G J Danchin
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28591649/activation-of-lineage-regulators-and-transposable-elements-across-a%C3%A2-pluripotent-spectrum
#14
Jamie A Hackett, Toshihiro Kobayashi, Sabine Dietmann, M Azim Surani
Embryonic stem cells (ESCs) are characterized by the pluripotent capacity to generate all embryonic lineages. Here, we show that ESCs can occupy a spectrum of distinct transcriptional and epigenetic states in response to varied extrinsic conditions. This spectrum broadly corresponds to a developmental continuum of pluripotency and is coupled with a gradient of increasing global DNA methylation. Each pluripotent state is linked with activation of distinct classes of transposable elements (TEs), which in turn influence ESCs through generating chimeric transcripts...
June 6, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28591571/global-hypertranscription-in-the-mouse-embryonic-germline
#15
Michelle Percharde, Priscilla Wong, Miguel Ramalho-Santos
Primordial germ cells (PGCs) are vital for inheritance and evolution. Their transcriptional program has been extensively studied and is assumed to be well known. We report here a remarkable global upregulation of the transcriptome of mouse PGCs compared to somatic cells. Using cell-number-normalized genome-wide analyses, we uncover significant transcriptional amplification in PGCs, including mRNAs, rRNA, and transposable elements. Hypertranscription preserves tissue-specific gene expression patterns, correlates with cell size, and can still be detected in E15...
June 6, 2017: Cell Reports
https://www.readbyqxmd.com/read/28586403/evolution-of-class-1-integrons-mobilization-and-dispersal-via-food-borne-bacteria
#16
Timothy M Ghaly, Louise Chow, Amy J Asher, Liette S Waldron, Michael R Gillings
Class 1 integrons have played a major role in the global dissemination of antibiotic resistance. Reconstructing the history of class 1 integrons might help us control further spread of antibiotic resistance by understanding how human activities influence microbial evolution. Here we describe a class 1 integron that represents an intermediate stage in the evolutionary history of clinical integrons. It was embedded in a series of nested transposons, carried on an IncP plasmid resident in Enterobacter, isolated from the surface of baby spinach leaves...
2017: PloS One
https://www.readbyqxmd.com/read/28581499/high-quality-de-novo-assembly-of-the-apple-genome-and-methylome-dynamics-of-early-fruit-development
#17
Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jérôme Gouzy, D Jasper G Rees, Philippe Guérif, Hélène Muranty, Charles-Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg, Hadi Quesneville, Detlef Weigel, Eric van de Weg, Michela Troggio, Etienne Bucher
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28580197/transposable-elements-in-drosophila
#18
REVIEW
Tabitha J McCullers, Mindy Steiniger
Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28580196/somatizing-the-transposons-action
#19
REVIEW
Elgion L S Loreto, Camila Moura Pereira
The somatic mobilization of transposable elements is more common than previously thought. In this review we discuss how the intensity and the biologic consequences of somatic mobilization are dependent on the transposable elements landscapes of each genome, and on the "momentum" of each particular TE with respect to the mechanisms that control its transposition and the possibility to escape this control. Additionally, the biologic consequences of somatic mobilization vary among organisms that show an early separation between the germline and somatic cells and those organisms that do not exhibit this separation or that reproduce asexually...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28580133/the-elephant-shark-methylome-reveals-conservation-of-epigenetic-regulation-across-jawed-vertebrates
#20
Julian R Peat, Oscar Ortega-Recalde, Olga Kardailsky, Timothy A Hore
BACKGROUND: Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates...
2017: F1000Research
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