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https://www.readbyqxmd.com/read/29236253/iclip-of-the-piwi-protein-aubergine-in-drosophila-embryos
#1
Bridlin Barckmann, Jérémy Dufourt, Martine Simonelig
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs bound to specific Argonaute proteins, the PIWI proteins. piRNAs target mRNAs by complementarity to silence them; they play an important role in the repression of transposable elements in the germ line of many species. piRNAs and PIWI proteins are also involved in diverse biological processes through their role in the regulation of cellular mRNAs. In the Drosophila embryo, they contribute to the maternal mRNA decay occurring during the maternal-to-zygotic transition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29228286/cut-and-paste-transposons-in-fungi-with-diverse-lifestyles
#2
Anna Muszewska, Kamil Steczkiewicz, Marta Stepniewska-Dziubinska, Krzysztof Ginalski
Transposons (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighbourhoods and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut and paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29228262/ltr-retrotransposons-show-low-levels-of-unequal-recombination-and-high-rates-of-intraelement-gene-conversion-in-large-plant-genomes
#3
Rosa Maria Cossu, Claudio Casola, Stefania Giacomello, Amaryllis Vidalis, Douglas G Scofield, Andrea Zuccolo
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, Long Terminal Repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited...
December 8, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29225705/using-bioinformatic-and-phylogenetic-approaches-to-classify-transposable-elements-and-understand-their-complex-evolutionary-histories
#4
REVIEW
Irina R Arkhipova
In recent years, much attention has been paid to comparative genomic studies of transposable elements (TEs) and the ensuing problems of their identification, classification, and annotation. Different approaches and diverse automated pipelines are being used to catalogue and categorize mobile genetic elements in the ever-increasing number of prokaryotic and eukaryotic genomes, with little or no connectivity between different domains of life. Here, an overview of the current picture of TE classification and evolutionary relationships is presented, updating the diversity of TE types uncovered in sequenced genomes...
2017: Mobile DNA
https://www.readbyqxmd.com/read/29224155/targeted-bisulfite-sequencing-using-the-seqcap-epi-enrichment-system
#5
Jennifer Wendt, Heidi Rosenbaum, Todd A Richmond, Jeffrey A Jeddeloh, Daniel L Burgess
Cytosine methylation has been shown to have a role in a host of biological processes. In mammalian biology these include stem cell differentiation, embryonic development, genomic imprinting, inflammation, and silencing of transposable elements. Given the central importance of these processes, it is not surprising to find aberrant cytosine methylation patterns associated with many disorders in humans, including cancer, cardiovascular disease, and neurological disease. While whole genome shotgun bisulfite sequencing (WGBS) has recently become feasible, generating high sequence coverage data for the entire genome is expensive, both in terms of money and analysis time, when generally only a small subset of the genome is of interest to most researchers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29219079/computational-identification-of-harmful-mutation-regions-to-the-activity-of-transposable-elements
#6
Lingling Jin, Ian McQuillan, Longhai Li
BACKGROUND: Transposable elements (TEs) are interspersed DNA sequences that can move or copy to new positions within a genome. TEs are believed to promote speciation and their activities play a significant role in human disease. In the human genome, the 22 AluY and 6 AluS TE subfamilies have been the most recently active, and their transposition has been implicated in many inherited human diseases and in various forms of cancer. Therefore, understanding their transposition activity is very important and identifying the factors that affect their transpositional activity is of great interest...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29218879/an-ultra-fast-and-scalable-quantification-pipeline-for-transposable-elements-from-next-generation-sequencing-data
#7
Hyun-Hwan Jeong, Hari Krishna Yalamanchili, Caiwei Guo, Joshua M Shulman, Zhandong Liu
Transposable elements (TEs) are DNA sequences which are capable of moving from one location to another and represent a large proportion (45%) of the human genome. TEs have functional roles in a variety of biological phenomena such as cancer, neurodegenerative disease, and aging. Rapid development in RNA-sequencing technology has enabled us, for the first time, to study the activity of TE at the systems level.However, efficient TE analysis tools are not yet developed. In this work, we developed SalmonTE, a fast and reliable pipeline for the quantification of TEs from RNA-seq data...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29217755/pollen-differentiation-as-well-as-pollen-tube-guidance-and-discharge-are-independent-of-the-presence-of-gametes
#8
Barbara Glöckle, Wojciech J Urban, Shiori Nagahara, Ellen D Andersen, Tetsuya Higashiyama, Paul E Grini, Arp Schnittger
After meiosis, an unequal cell division generates the male gamete lineage in flowering plants. The generative cell will undergo a second division, giving rise to the two gametes, i.e. the sperm cells. The other cell will develop into the vegetative cell that plays a crucial role in pollen tube formation and sperm delivery. Recently, the vegetative cell has been implicated to be important for programming of the chromatin state in sperm cells and/or the resulting fertilization products. Blocking the initial unequal division genetically, we first highlight that the default differentiation state after male meiosis is a vegetative fate consistent with earlier work...
December 7, 2017: Development
https://www.readbyqxmd.com/read/29211860/changes-in-the-epigenome-and-transcriptome-of-the-poplar-shoot-apical-meristem-in-response-to-water-availability-affect-preferentially-hormone-pathways
#9
Clément Lafon-Placette, Anne-Laure Le Gac, Didier Chauveau, Vincent Segura, Alain Delaunay, Marie-Claude Lesage-Descauses, Irène Hummel, David Cohen, Béline Jesson, Didier Le Thiec, Marie-Béatrice Bogeat-Triboulot, Franck Brignolas, Stéphane Maury
The adaptive capacity of long-lived organisms such as trees to the predicted climate changes, including severe and successive drought episodes, will depend on the presence of genetic diversity and phenotypic plasticity. Here, the involvement of epigenetic mechanisms in phenotypic plasticity toward soil water availability was examined in Populus×euramericana. This work aimed at characterizing (i) the transcriptome plasticity, (ii) the genome-wide plasticity of DNA methylation, and (iii) the function of genes affected by a drought-rewatering cycle in the shoot apical meristem...
December 2, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29211718/pirna-mediated-regulation-of-transposon-alternative-splicing-in-the-soma-and-germ-line
#10
Felipe Karam Teixeira, Martyna Okuniewska, Colin D Malone, Rémi-Xavier Coux, Donald C Rio, Ruth Lehmann
Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The Piwi-interacting small RNA (piRNA) pathway is vital for the regulation of transposable elements, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. Here we show that piRNAs and piRNA biogenesis components regulate precursor mRNA splicing of P-transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in Drosophila germ cells...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29211708/selective-silencing-of-euchromatic-l1s-revealed-by-genome-wide-screens-for-l1-regulators
#11
Nian Liu, Cameron H Lee, Tomek Swigut, Edward Grow, Bo Gu, Michael Bassik, Joanna Wysocka
Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in genome evolution and regulation1-6. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease1-7. Nonetheless, how L1 activity is controlled and what function L1s play in host gene regulation remain incompletely understood...
December 6, 2017: Nature
https://www.readbyqxmd.com/read/29206283/transposable-element-mediated-innovation-in-gene-regulatory-landscapes-of-cells-re-visiting-the-gene-battery-model
#12
REVIEW
Vasavi Sundaram, Ting Wang
Transposable elements (TEs) are no longer considered to be "junk" DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic...
December 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29206242/corrigendum-the-diversity-of-sequence-and-chromosomal-distribution-of-new-transposable-element-related-segments-in-the-rye-genome-revealed-by-fish-and-lineage-annotation
#13
Yingxin Zhang, Chengming Fan, Shuangshuang Li, Yuhong Chen, Richard R-C Wang, Xiangqi Zhang, Fangpu Han, Zanmin Hu
[This corrects the article on p. 1706 in vol. 8, PMID: 29046683.].
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29203920/pan-arthropod-analysis-reveals-somatic-pirnas-as-an-ancestral-defence-against-transposable-elements
#14
Samuel H Lewis, Kaycee A Quarles, Yujing Yang, Melanie Tanguy, Lise Frézal, Stephen A Smith, Prashant P Sharma, Richard Cordaux, Clément Gilbert, Isabelle Giraud, David H Collins, Phillip D Zamore, Eric A Miska, Peter Sarkies, Francis M Jiggins
In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods...
December 4, 2017: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29201017/characterization-of-metagenomes-in-urban-aquatic-compartments-reveals-high-prevalence-of-clinically-relevant-antibiotic-resistance-genes-in-wastewaters
#15
Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H Koh, Timothy M S Barkham, Karina Y-H Gin
The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29199607/transposable-elements-human-endogenous-retroviruses-in-cancer
#16
Muhammad Imran Qadir, Muhammad Usman, Muhammad Sajid Hamid Akash
Transposable elements (TEs) have shown a great significance in regulatory elements research, being responsible for different types of cancers. They are divided into three classes on the basis of their mode of transposition, structural properties, and their homology with DNA sequence. In evaluating their role in cancers and other pathologies, researchers have found extensive evidence of their involvement. TEs can also be used as genetic markers for cancers and help in identifying potential therapeutic targets...
2017: Critical Reviews in Eukaryotic Gene Expression
https://www.readbyqxmd.com/read/29194997/piecing-together-cis-regulatory-networks-insights-from-epigenomics-studies-in-plants
#17
REVIEW
Shao-Shan Huang, Joseph Ecker
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell...
November 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29194487/comparative-genomics-of-an-unusual-biogeographic-disjunction-in-the-cotton-tribe-gossypieae-yields-insights-into-genome-downsizing
#18
Corrinne E Grover, Mark A Arick, Justin L Conover, Adam Thrash, Guanjing Hu, William S Sanders, Hsu Chuan-Yu, Rubab Zahra Naqvi, Muhammad Farooq, Xiaochong Li, Lei Gong, Joann Mudge, Thiru Ramaraj, Joshua A Udall, Daniel G Peterson, Jonathan F Wendel
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple trans-oceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium...
November 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29187220/genomic-copy-number-variation-analysis-in-multiple-system-atrophy
#19
Yuka Hama, Masataka Katsu, Ichigaku Takigawa, Ichiro Yabe, Masaaki Matsushima, Ikuko Takahashi, Takayuki Katayama, Jun Utsumi, Hidenao Sasaki
Genomic variation includes single-nucleotide variants, small insertions or deletions (indels), and copy number variants (CNVs). CNVs affect gene expression by altering the genome structure and transposable elements within a region. CNVs are greater than 1 kb in size; hence, CNVs can produce more variation than can individual single-nucleotide variations that are detected by next-generation sequencing. Multiple system atrophy (MSA) is an α-synucleinopathy adult-onset disorder. Pathologically, it is characterized by insoluble aggregation of filamentous α-synuclein in brain oligodendrocytes...
November 29, 2017: Molecular Brain
https://www.readbyqxmd.com/read/29186298/simulate-simulating-complex-landscapes-of-transposable-elements-of-populations
#20
Robert Kofler
Motivation: Estimating the abundance of transposable elements (TEs) in populations (or tissues) promises to answer many open research questions. However, progress is hampered by the lack of concordance between different approaches for TE identification and thus potentially unreliable results. Results: To address this problem, we developed SimulaTE a tool that generates TE landscapes for populations using a newly developed domain specific language (DSL). The simple syntax of our DSL allows for easily building even complex TE landscapes that have, for example, nested, truncated and highly diverged TE insertions...
November 27, 2017: Bioinformatics
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