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https://www.readbyqxmd.com/read/28551392/transposable-phages-dna-reorganization-and-transfer
#1
REVIEW
Ariane Toussaint, Phoebe A Rice
Transposable bacteriophages have long been known to necessarily and randomly integrate their DNA in their host genome, where they amplify by successive rounds of replicative transposition, profoundly reorganizing that genome. As a result of such transposition, a conjugative element (plasmid or genomic island), can either become integrated in the chromosome or receive chromosome segments, which can then be transferred to new hosts by conjugation. In recent years, more and more transposable phages have been isolated or detected by sequence similarity searches in a wide range of bacteria, supporting the idea that this mode of HGT may be pervasive in natural bacterial populations...
May 25, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28549443/quantitative-analysis-of-cryptic-splicing-associated-with-tdp-43-depletion
#2
Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M Isaacs, Vincent Plagnol
BACKGROUND: Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown...
May 26, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28546999/a-birth-of-bipartite-exon-by-intragenic-deletion
#3
Kandai Nozu, Kazumoto Iijima, Toru Igarashi, Shiro Yamada, Jana Kralovicova, Yoshimi Nozu, Tomohiko Yamamura, Shogo Minamikawa, Ichiro Morioka, Takeshi Ninchoji, Hiroshi Kaito, Koichi Nakanishi, Igor Vorechovsky
BACKGROUND: Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS: We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS: The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28544196/analysis-of-transcriptional-and-epigenetic-changes-in-hybrid-vigor-of-allopolyploid-brassica-napus-uncovers-key-roles-for-small-rnas
#4
Yifei Shen, Shuo Sun, Shuijin Hua, Enhui Shen, Chu-Yu Ye, Daguang Cai, Michael P Timko, Qian-Hao Zhu, Longjiang Fan
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared to its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study, we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines...
May 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28541415/transcriptome-wide-identification-and-expression-analysis-of-divaricata-and-radialis-like-genes-of-the-mediterranean-orchid-orchis-italica
#5
Maria Carmen Valoroso, Sofia De Paolo, Giovanni Iazzetti, Serena Aceto
Bilateral symmetry of flowers is a relevant novelty that has occurred many times throughout the evolution of flowering plants. In Antirrhinum majus, establishment of flower dorso-ventral asymmetry is mainly due to interaction of TCP (CYC and DICH) and MYB (DIV, RAD and DRIF) transcription factors. In the present study, we characterized 8 DIV-, 4 RAD- and 2 DRIF-like genes from the transcriptome of Orchis italica, an orchid species with bilaterally symmetric and resupinate flowers. We found a similar number of DIV- and RAD-like genes within the genomes of Phalaenopsis equestris and Dendrobium catenatum orchids...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28537264/draft-genome-of-spinach-and-transcriptome-diversity-of-120-spinacia-accessions
#6
Chenxi Xu, Chen Jiao, Honghe Sun, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Yi Zheng, Wenli Liu, Xuepeng Sun, Yimin Xu, Jie Deng, Zhonghua Zhang, Sanwen Huang, Shaojun Dai, Beiquan Mou, Quanxi Wang, Zhangjun Fei, Quanhua Wang
Spinach is an important leafy vegetable enriched with multiple necessary nutrients. Here we report the draft genome sequence of spinach (Spinacia oleracea, 2n=12), which contains 25,495 protein-coding genes. The spinach genome is highly repetitive with 74.4% of its content in the form of transposable elements. No recent whole genome duplication events are observed in spinach. Genome syntenic analysis between spinach and sugar beet suggests substantial inter- and intra-chromosome rearrangements during the Caryophyllales genome evolution...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28536590/miniature-inverted-repeat-transposable-element-insertions-provide-a-source-of-intron-length-polymorphism-markers-in-the-carrot-daucus-carota-l
#7
Katarzyna Stelmach, Alicja Macko-Podgórni, Gabriela Machaj, Dariusz Grzebelus
The prevalence of non-autonomous class II transposable elements (TEs) in plant genomes may serve as a tool for relatively rapid and low-cost development of gene-associated molecular markers. Miniature inverted-repeat transposable element (MITE) copies inserted within introns can be exploited as potential intron length polymorphism (ILP) markers. ILPs can be detected by PCR with primers anchored in exon sequences flanking the target introns. Here, we designed primers for 209 DcSto (Daucus carota Stowaway-like) MITE insertion sites within introns along the carrot genome and validated them as candidate ILP markers in order to develop a set of markers for genotyping the carrot...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28536194/wild-tobacco-genomes-reveal-the-evolution-of-nicotine-biosynthesis
#8
Shuqing Xu, Thomas Brockmöller, Aura Navarro-Quezada, Heiner Kuhl, Klaus Gase, Zhihao Ling, Wenwu Zhou, Christoph Kreitzer, Mario Stanke, Haibao Tang, Eric Lyons, Priyanka Pandey, Shree P Pandey, Bernd Timmermann, Emmanuel Gaquerel, Ian T Baldwin
Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis...
May 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28528908/the-new-red-algal-subphylum-proteorhodophytina-comprises-the-largest-and-most-divergent-plastid-genomes-known
#9
Sergio A Muñoz-Gómez, Fabián G Mejía-Franco, Keira Durnin, Morgan Colp, Cameron J Grisdale, John M Archibald, Claudio H Slamovits
Red algal plastid genomes are often considered ancestral and evolutionarily stable, and thus more closely resembling the last common ancestral plastid genome of all photosynthetic eukaryotes [1, 2]. However, sampling of red algal diversity is still quite limited (e.g., [2-5]). We aimed to remedy this problem. To this end, we sequenced six new plastid genomes from four undersampled and phylogenetically disparate red algal classes (Porphyridiophyceae, Stylonematophyceae, Compsopogonophyceae, and Rhodellophyceae) and discovered an unprecedented degree of genomic diversity among them...
May 17, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28527116/genome-editing-in-drosophila-melanogaster-from-basic-genome-engineering-to-the-multipurpose-crispr-cas9-system
#10
REVIEW
Xingjie Ren, Kristof Holsteens, Haiyi Li, Jin Sun, Yifan Zhang, Lu-Ping Liu, Qingfei Liu, Jian-Quan Ni
Nowadays, genome editing tools are indispensable for studying gene function in order to increase our knowledge of biochemical processes and disease mechanisms. The extensive availability of mutagenesis and transgenesis tools make Drosophila melanogaster an excellent model organism for geneticists. Early mutagenesis tools relied on chemical or physical methods, ethyl methane sulfonate (EMS) and X-rays respectively, to randomly alter DNA at a nucleotide or chromosomal level. Since the discovery of transposable elements and the availability of the complete fly genome, specific genome editing tools, such as P-elements, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have undergone rapid development...
May 1, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28524723/l1-retrotransposition-is-activated-by-ten-eleven-translocation-protein-1-and-repressed-by-methyl-cpg-binding-proteins
#11
Peng Zhang, Anne K Ludwig, Florian D Hastert, Cathia Rausch, Anne Lehmkuhl, Ines Hellmann, Martha Smets, Heinrich Leonhardt, M Cristina Cardoso
One of the major functions of DNA methylation is the repression of transposable elements, such as the long-interspersed nuclear element 1 (L1). The underlying mechanism(s), however, are unclear. Here, we addressed how retrotransposon activation and mobilization are regulated by methyl-cytosine modifying ten-eleven-translocation (Tet) proteins and how this is modulated by methyl-CpG binding domain (MBD) proteins. We show that Tet1 activates both, endogenous and engineered L1 retrotransposons. Furthermore, we found that Mecp2 and Mbd2 repress Tet1-mediated activation of L1 by preventing 5hmC formation at the L1 promoter...
May 19, 2017: Nucleus
https://www.readbyqxmd.com/read/28517033/high-throughput-sequencing-of-transposable-element-insertions-suggests-adaptive-evolution-of-the-invasive-asian-tiger-mosquito-towards-temperate-environments
#12
Clément Goubert, Hélène Henri, Guillaume Minard, Claire Valiente Moro, Patrick Mavingui, Cristina Vieira, Matthieu Boulesteix
Invasive species represent unique opportunities to evaluate the role of local adaptation during colonization of new environments. Among these species, the Asian tiger mosquito, Aedes albopictus, is a threatening vector of several human viral diseases, including dengue and chikungunya, and raises concerns about the Zika fever. Its broad presence in both temperate and tropical environments has been considered the reflection of great "ecological plasticity". However, no study has been conducted to assess the role of adaptive evolution in the ecological success of Ae...
May 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28507606/transcription-and-chromatin-determinants-of-de-novo-dna-methylation-timing-in-oocytes
#13
Lenka Gahurova, Shin-Ichi Tomizawa, Sébastien A Smallwood, Kathleen R Stewart-Morgan, Heba Saadeh, Jeesun Kim, Simon R Andrews, Taiping Chen, Gavin Kelsey
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28505370/the-complete-nucleotide-sequence-of-an-incp-2-megaplasmid-unveils-a-mosaic-architecture-comprising-a-putative-novel-blavim-2-harbouring-transposon-in-pseudomonas-aeruginosa
#14
João Botelho, Filipa Grosso, Sandra Quinteira, Aymen Mabrouk, Luísa Peixe
Objectives: In Pseudomonas aeruginosa , bla VIM-2 has been mostly associated with a chromosomal location and rarely with a plasmid backbone. Until now, only three complete bla VIM-2 -carrying plasmid sequences have been described in this species. Here we explore the modular structure of pJB37, the first bla VIM-2 -carrying megaplasmid described in P. aeruginosa . Methods: The complete nucleotide sequence of plasmid pJB37 was determined with an Illumina HiSeq, with de novo assembly by SPAdes, annotation by RAST and searching for antimicrobial resistance genes and virulence factors...
May 12, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28504702/pgbd5-promotes-site-specific-oncogenic-mutations-in-human-tumors
#15
Anton G Henssen, Richard Koche, Jiali Zhuang, Eileen Jiang, Casie Reed, Amy Eisenberg, Eric Still, Ian C MacArthur, Elias Rodríguez-Fos, Santiago Gonzalez, Montserrat Puiggròs, Andrew N Blackford, Christopher E Mason, Elisa de Stanchina, Mithat Gönen, Anne-Katrin Emde, Minita Shah, Kanika Arora, Catherine Reeves, Nicholas D Socci, Elizabeth Perlman, Cristina R Antonescu, Charles W M Roberts, Hanno Steen, Elizabeth Mullen, Stephen P Jackson, David Torrents, Zhiping Weng, Scott A Armstrong, Alex Kentsis
Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase expressed in the majority of childhood solid tumors, including lethal rhabdoid tumors. Using assembly-based whole-genome DNA sequencing, we found previously undefined genomic rearrangements in human rhabdoid tumors. These rearrangements involved PGBD5-specific signal (PSS) sequences at their breakpoints and recurrently inactivated tumor-suppressor genes...
May 15, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28499400/epiteome-simultaneous-detection-of-transposable-element-insertion-sites-and-their-dna-methylation-levels
#16
Josquin Daron, R Keith Slotkin
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads...
May 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28498935/the-association-of-changes-in-dna-methylation-with-temperature-dependent-sex-determination-in-cucumber
#17
Yun-Song Lai, Xiaohui Zhang, Wei Zhang, Di Shen, Haiping Wang, Yudong Xia, Yang Qiu, Jiangping Song, Chenchen Wang, Xixiang Li
Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation...
May 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28494505/genome-wide-analysis-of-somatic-copy-number-alterations-and-chromosomal-breakages-in-osteosarcoma
#18
Jan Smida, Hongen Xu, Yanping Zhang, Daniel Baumhoer, Sebastian Ribi, Michal Kovac, Irene von Luettichau, Stefan Bielack, Valerie B O'Leary, Christine Leib-Mösch, Dmitrij Frishman, Michaela Nathrath
Osteosarcoma (OS) is the most common primary malignant bone tumor in children and adolescents. It is characterized by highly complex karyotypes with structural and numerical chromosomal alterations. The observed OS-specific characteristics in localization and frequencies of chromosomal breakages strongly implicate a specific set of responsible driver genes or a specific mechanism of fragility induction. In this study, a comprehensive assessment of somatic copy number alterations (SCNAs) was performed in 160 OS samples using whole-genome CytoScan High Density arrays (Affymetrix, Santa Clara, CA)...
May 11, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28493303/comprehensive-profiling-of-rhizome-associated-alternative-splicing-and-alternative-polyadenylation-in-moso-bamboo-phyllostachys-edulis
#19
Taotao Wang, Huiyuan Wang, Dawei Cai, Yubang Gao, Hangxiao Zhang, Yongsheng Wang, Chentao Lin, Liuyin Ma, Lianfeng Gu
Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system...
May 10, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#20
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
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