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Retrotransposon

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https://www.readbyqxmd.com/read/29777105/phenotypic-diversification-by-enhanced-genome-restructuring-after-induction-of-multiple-dna-double-strand-breaks
#1
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa, Kunihiro Ohta
DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29774526/retrotransposable-genetic-elements-causing-neutrophil-defects
#2
REVIEW
Dirk Roos, Martin de Boer
Retrotransposable elements are stretches of DNA that encode proteins with the inherent ability to insert their own RNA or another RNA by reverse transcriptase as DNA into a new genomic location. In humans, the only autonomous retrotransposable elements are members of the Long INterspersed Element-1 (LINE-1) family. LINE-1s may cause gene inactivation and human disease. We present a brief summary of the published knowledge about LINE-1s in humans and the RNAs that these elements can transpose, and we focus on the effect of LINE-1-mediated retrotransposition on human neutrophil function...
May 17, 2018: European Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29774045/transposon-derived-non-coding-rnas-and-their-function-in-plants
#3
REVIEW
Jungnam Cho
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans -acting regulatory roles of TE-derived RNAs have been rarely studied...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29762876/constant-conflict-between-gypsy-ltr-retrotransposons-and-chh-methylation-within-a-stress-adapted-mangrove-genome
#4
Yushuai Wang, Weiqi Liang, Tian Tang
The evolutionary dynamics of the conflict between transposable elements (TEs) and their host genome remain elusive. This conflict will be intense in stress-adapted plants as stress can often reactivate TEs. Mangroves reduce TE load convergently in their adaptation to intertidal environments and thus provide a unique opportunity to address the host-TE conflict and its interaction with stress adaptation. Using the mangrove Rhizophora apiculata as a model, we investigated methylation and short interfering RNA (siRNA) targeting patterns in relation to the abundance and age of long terminal repeat (LTR) retrotransposons...
May 15, 2018: New Phytologist
https://www.readbyqxmd.com/read/29761210/biochemical-properties-of-bacterial-reverse-transcriptase-related-rvt-gene-products-multimerization-protein-priming-and-nucleotide-preference
#5
Irina A Yushenova, Irina R Arkhipova
Cellular reverse transcriptase-related (rvt) genes represent a novel class of reverse transcriptases (RTs), which are only distantly related to RTs of retrotransposons and retroviruses, but, similarly to telomerase RTs, are immobilized in the genome as single-copy genes. They have been preserved by natural selection throughout the evolutionary history of large taxonomic groups, including most fungi, a few plants and invertebrates, and even certain bacteria, being the only RTs present across different domains of life...
May 14, 2018: Current Genetics
https://www.readbyqxmd.com/read/29757394/a-barley-powdery-mildew-fungus-non-autonomous-retrotransposon-encodes-a-peptide-that-supports-penetration-success-on-barley
#6
Mathias Nottensteiner, Bernd Zechmann, Christopher McCollum, Ralph Hückelhoven
Pathogens overcome plant immunity by the means of secreted effectors. Host effector targets often act in pathogen defense but might also support fungal accommodation or nutrition. The barley ROP GTPase HvRACB is involved in accommodation of fungal haustoria of the powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh) in barley epidermal cells. We found that HvRACB interacts with the ROP-interactive peptide 1 (ROPIP1) that is encoded on the active non-long terminal repeat retroelement Eg-R1 of Bgh. Over-expression of ROPIP1 in barley epidermal cells and host-induced post-transcriptional gene silencing (HIGS) of ROPIP1 suggested that ROPIP1 is involved in virulence of Bgh...
May 11, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29753892/next-generation-sequencing-reveals-packaging-of-host-rnas-by-brome-mosaic-virus
#7
N Shrestha, P H Weber, S V Burke, W Wysocki, M R Duvall, J J Bujarski
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol...
May 10, 2018: Virus Research
https://www.readbyqxmd.com/read/29739818/spermiogenesis-and-male-fertility-require-the-function-of-suppressor-of-hairy-wing-in-somatic-cyst-cells-of-drosophila
#8
Tingting Duan, Pamela K Geyer
Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is an example of a multivalent transcription factor. Although best known for its role in establishing the chromatin insulator of the gypsy retrotransposon, Su(Hw) functions as an activator and repressor at non- gypsy genomic sites. It remains unclear how the different regulatory activities of Su(Hw) are utilized during development. Motivated from observations of spatially restricted expression of Su(Hw) in the testis, we investigated the role of Su(Hw) in spermatogenesis to advance an understanding of its developmental contributions as an insulator, repressor and activator protein...
May 8, 2018: Genetics
https://www.readbyqxmd.com/read/29739320/mobilization-of-retrotransposons-as-a-cause-of-chromosomal-diversification-and-rapid-speciation-the-case-for-the-antarctic-teleost-genus-trematomus
#9
J Auvinet, P Graça, L Belkadi, L Petit, E Bonnivard, A Dettaï, W H Detrich, C Ozouf-Costaz, D Higuet
BACKGROUND: The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29728366/the-hush-complex-cooperates-with-trim28-to-repress-young-retrotransposons-and-new-genes
#10
Luisa Robbez-Masson, Christopher H C Tie, Lucia Conde, Hale Tunbak, Connor Husovsky, Iva A Tchasovnikarova, Richard T Timms, Javier Herrero, Paul J Lehner, Helen M Rowe
Retrotransposons encompass half of the human genome and contribute to the formation of heterochromatin, which provides nuclear structure and regulates gene expression. Here, we asked if the human silencing hub (HUSH) complex is necessary to silence retrotransposons and whether it collaborates with TRIM28 and the chromatin remodeler ATRX at specific genomic loci. We show that the HUSH complex contributes to de novo repression and DNA methylation of a SVA retrotransposon reporter. By using naïve vs. primed mouse pluripotent stem cells, we reveal a critical role for the HUSH complex in naïve cells, implicating it in programming epigenetic marks in development...
May 4, 2018: Genome Research
https://www.readbyqxmd.com/read/29724131/cycling-to-maintain-and-improve-fitness-line-1-modes-of-nuclear-entrance-and-retrotransposition
#11
Paolo Mita, Jef D Boeke
The LINE-1/L1 retrotransposon is a transposable element still active in the human genome. Most retrotransposons in the genome are inactive or repressed by several host mechanisms. In specific contexts, active L1 retrotransposons may evade repression and copy themselves into new genomic loci. Despite a general knowledge of the L1 life cycle, little was known about the dynamics of L1 proteins and function during the different stages of the host cell cycle. Our work highlighted a well-orchestrated localization of L1 proteins and mRNA that take advantage of mitotic nuclear membrane breakdown...
April 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29717194/author-correction-recurrent-acquisition-of-cytosine-methyltransferases-into-eukaryotic-retrotransposons
#12
Alex de Mendoza, Amandine Bonnet, Dulce B Vargas-Landin, Nanjing Ji, Hongfei Li, Feng Yang, Ling Li, Koichi Hori, Jahnvi Pflueger, Sam Buckberry, Hiroyuki Ohta, Nedeljka Rosic, Pascale Lesage, Senjie Lin, Ryan Lister
The original version of this Article contained an error in the spelling of the author Hongfei Li, which was incorrectly given as Fei Hong. This has now been corrected in both the PDF and HTML versions of the Article.
May 1, 2018: Nature Communications
https://www.readbyqxmd.com/read/29713390/retrotransposon-targeting-to-rna-polymerase-iii-transcribed-genes
#13
REVIEW
Stephanie Cheung, Savrina Manhas, Vivien Measday
Retrotransposons are genetic elements that are similar in structure and life cycle to retroviruses by replicating via an RNA intermediate and inserting into a host genome. The Saccharomyces cerevisiae ( S. cerevisiae ) Ty1-5 elements are long terminal repeat (LTR) retrotransposons that are members of the Ty1- copia ( Pseudoviridae ) or Ty3- gypsy ( Metaviridae ) families. Four of the five S. cerevisiae Ty elements are inserted into the genome upstream of RNA Polymerase (Pol) III-transcribed genes such as transfer RNA (tRNA) genes...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29709066/heritable-l1-retrotransposition-events-during-development-understanding-their-origins-examination-of-heritable-endogenous-l1-retrotransposition-in-mice-opens-up-exciting-new-questions-and-research-directions
#14
REVIEW
Sandra R Richardson, Geoffrey J Faulkner
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, "Heritable L1 retrotransposition in the mouse primordial germline and early embryo," we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes...
April 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29705598/the-retrotransposon-storm-and-the-dangers-of-a-collyer-s-genome
#15
REVIEW
Josh Dubnau
Like the famous Collyer's mansion in NY, our genomes have accumulated vast quantities of sequences that have been referred to as 'junk DNA,' much of which consists of retrotransposons (RTEs). A recent literature establishes the phenomenology that many RTEs become expressed at progressively higher levels during the course of normal aging. This seems to reflect gradual loss of heterochromatin in old age. In addition, RTEs appear to be precociously expressed in brains of younger animals that are experiencing neurodegenerative decline...
April 26, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29699487/the-parthenocarpic-gene-pat-k-is-generated-by-a-natural-mutation-of-slagl6-affecting-fruit-development-in-tomato-solanum-lycopersicum-l
#16
Rihito Takisawa, Tetsuya Nakazaki, Tsukasa Nunome, Hiroyuki Fukuoka, Keiko Kataoka, Hiroki Saito, Tsuyoshi Habu, Akira Kitajima
BACKGROUND: Parthenocarpy is a desired trait in tomato because it can overcome problems with fruit setting under unfavorable environmental conditions. A parthenocarpic tomato cultivar, 'MPK-1', with a parthenocarpic gene, Pat-k, exhibits stable parthenocarpy that produces few seeds. Because 'MPK-1' produces few seeds, seedlings are propagated inefficiently via cuttings. It was reported that Pat-k is located on chromosome 1. However, the gene had not been isolated and the relationship between the parthenocarpy and low seed set in 'MPK-1' remained unclear...
April 27, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29697392/line-1-methylation-in-blood-and-tissues-of-patients-with-breast-cancer
#17
K Kankava, E Kvaratskhelia, G Burkadze, I Kokhreidze, N Gogokhia, E Abzianidze
Methylation is an epigenetic alteration proved to be involved in many disease processes including cancer. This change affects mainly gene promoters and repetitive sequences in genome. Long Interspersed Nuclear Element-1 (LINE-1) is a family of retrotransposons - repetitive elements that modify gene activity and can themselves be targeted by epigenetic mechanisms. LINE-1 methylation level is a surrogate marker for global methylation. In many conditions this parameter is found to be altered not only in affected cell groups, but also throughout other tissues...
March 2018: Georgian Medical News
https://www.readbyqxmd.com/read/29696298/mechanisms-origin-and-heredity-of-glu-1ay-silencing-in-wheat-evolution-and-domestication
#18
Guangbin Luo, Shuyi Song, Liru Zhao, Lisha Shen, Yanhong Song, Xin Wang, Kang Yu, Zhiyong Liu, Yiwen Li, Wenlong Yang, Xin Li, Kehui Zhan, Aimin Zhang, Dongcheng Liu
Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41...
April 25, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29694349/control-of-yeast-retrotransposons-mediated-through-nucleoporin-evolution
#19
Paul A Rowley, Kurt Patterson, Suzanne B Sandmeyer, Sara L Sawyer
Yeasts serve as hosts to several types of genetic parasites. Few studies have addressed the evolutionary trajectory of yeast genes that control the stable co-existence of these parasites with their host cell. In Saccharomyces yeasts, the retrovirus-like Ty retrotransposons must access the nucleus. We show that several genes encoding components of the yeast nuclear pore complex have experienced natural selection for substitutions that change the encoded protein sequence. By replacing these S. cerevisiae genes with orthologs from other Saccharomyces species, we discovered that natural sequence changes have affected the mobility of Ty retrotransposons...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29688421/differential-effect-of-selection-against-line-retrotransposons-among-vertebrates-inferred-from-whole-genome-data-and-demographic-modeling
#20
Alexander T Xue, Robert P Ruggiero, Michael J Hickerson, Stéphane Boissinot
Variation in LINE composition is one of the major determinants for the substantial size and structural differences among vertebrate genomes. In particular, the larger genomes of mammals are characterized by hundreds of thousands of copies from a single LINE clade, L1, whereas non-mammalian vertebrates possess a much greater diversity of LINEs, yet with orders of magnitude less in copy number. It has been proposed that such variation in copy number among vertebrates is due to differential effect of LINE insertions on host fitness...
April 23, 2018: Genome Biology and Evolution
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