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transposable elements

Christian Parisod
Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences...
2017: Methods in Molecular Biology
Jingzhong Xie, Naxin Huo, Shenghui Zhou, Yi Wang, Guanghao Guo, Karin R Deal, Shuhong Ouyang, Yong Liang, Zhenzhong Wang, Lichan Xiao, Tingting Zhu, Tiezhu Hu, Vijay Tiwari, Jianwei Zhang, Hongxia Li, Zhongfu Ni, Yingyin Yao, Huiru Peng, Shengli Zhang, Olin D Anderson, Patrick E McGuire, Jan Dvorak, Ming-Cheng Luo, Zhiyong Liu, Yong Q Gu, Qixin Sun
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4...
October 5, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
Adam M Session, Yoshinobu Uno, Taejoon Kwon, Jarrod A Chapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui, Akira Hikosaka, Atsushi Suzuki, Mariko Kondo, Simon J van Heeringen, Ian Quigley, Sven Heinz, Hajime Ogino, Haruki Ochi, Uffe Hellsten, Jessica B Lyons, Oleg Simakov, Nicholas Putnam, Jonathan Stites, Yoko Kuroki, Toshiaki Tanaka, Tatsuo Michiue, Minoru Watanabe, Ozren Bogdanovic, Ryan Lister, Georgios Georgiou, Sarita S Paranjpe, Ila van Kruijsbergen, Shengquiang Shu, Joseph Carlson, Tsutomu Kinoshita, Yuko Ohta, Shuuji Mawaribuchi, Jerry Jenkins, Jane Grimwood, Jeremy Schmutz, Therese Mitros, Sahar V Mozaffari, Yutaka Suzuki, Yoshikazu Haramoto, Takamasa S Yamamoto, Chiyo Takagi, Rebecca Heald, Kelly Miller, Christian Haudenschild, Jacob Kitzman, Takuya Nakayama, Yumi Izutsu, Jacques Robert, Joshua Fortriede, Kevin Burns, Vaneet Lotay, Kamran Karimi, Yuuri Yasuoka, Darwin S Dichmann, Martin F Flajnik, Douglas W Houston, Jay Shendure, Louis DuPasquier, Peter D Vize, Aaron M Zorn, Michihiko Ito, Edward M Marcotte, John B Wallingford, Yuzuru Ito, Makoto Asashima, Naoto Ueno, Yoichi Matsuda, Gert Jan C Veenstra, Asao Fujiyama, Richard M Harland, Masanori Taira, Daniel S Rokhsar
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma...
October 19, 2016: Nature
Maelin da Silva, Patricia Barbosa, Roberto F Artoni, Eliana Feldberg
Gymnotidae is a family of electric fish endemic to the Neotropics consisting of 2 genera: Electrophorus and Gymnotus. The genus Gymnotus is widely distributed and is found in all of the major Brazilian river systems. Physical and molecular mapping data for the ribosomal DNA (rDNA) in this genus are still scarce, with its chromosomal location known in only 11 species. As other species of Gymnotus with 2n = 54 chromosomes from the Paraná-Paraguay basin, G. mamiraua was found to have a large number of 5S rDNA sites...
October 18, 2016: Cytogenetic and Genome Research
M J Madison-Villar, Cheng Sun, Nelson C Lau, Matthew L Settles, Rachel Lockridge Mueller
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules...
October 14, 2016: Journal of Molecular Evolution
Hidenori Nishihara, Naoki Kobayashi, Chiharu Kimura-Yoshida, Kuo Yan, Olga Bormuth, Qiong Ding, Akiko Nakanishi, Takeshi Sasaki, Mika Hirakawa, Kenta Sumiyama, Yasuhide Furuta, Victor Tarabykin, Isao Matsuo, Norihiro Okada
Acquisition of cis-regulatory elements is a major driving force of evolution, and there are several examples of developmental enhancers derived from transposable elements (TEs). However, it remains unclear whether one enhancer element could have been produced via cooperation among multiple, yet distinct, TEs during evolution. Here we show that an evolutionarily conserved genomic region named AS3_9 comprises three TEs (AmnSINE1, X6b_DNA and MER117), inserted side-by-side, and functions as a distal enhancer for wnt5a expression during morphogenesis of the mammalian secondary palate...
October 2016: PLoS Genetics
Teresa Graziano, Angela Amoruso, Stefania Nicola, Francesca Deidda, Serena Allesina, Marco Pane, Pietro Piffanelli, Francesco Strozzi, Luca Mogna, Mario Del Piano
GOALS: The aim of the study was to unequivocally demonstrate the nontransmissibility of the genes mediating the resistance of the strain Bifidobacterium longum W11 (LMG P-21586) to rifaximin. BACKGROUND: Most antibiotic treatments can induce unfavorable side effects such as antibiotic-associated diarrhea, which is largely attributable to the disruption of the intestinal microbiota. The parallel intake of probiotic bacteria might reduce these events, even if with generally very poor results...
November 2016: Journal of Clinical Gastroenterology
Nathalie Feiner
Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes...
October 12, 2016: Proceedings. Biological Sciences
Leandro Quadrana, Vincent Colot
Transgenerational epigenetics is defined in opposition to developmental epigenetics and implies an absence of resetting of epigenetic states between generations. Unlike mammals, plants appear to be particularly prone to this type of inheritance. In this review, we summarize our knowledge about transgenerational epigenetics in plants, which entails heritable changes in DNA methylation. We emphasize the role of transposable elements and other repeat sequences in the creation of epimutable alleles. We also argue that because reprogramming of DNA methylation across generations seems limited in plants, the inheritance of DNA methylation defects results from the failure to reinforce rather than reset this modification during sexual reproduction...
October 6, 2016: Annual Review of Genetics
Songmi Kim, Chun-Sung Cho, Kyudong Han, Jungnam Lee
Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery...
September 2016: Genomics & Informatics
Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher, Ales Pecinka
BACKGROUND: The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. RESULTS: We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A...
October 11, 2016: Genome Biology
Ferdinand von Meyenn, Rebecca V Berrens, Simon Andrews, Fátima Santos, Amanda J Collier, Felix Krueger, Rodrigo Osorno, Wendy Dean, Peter J Rugg-Gunn, Wolf Reik
Primordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells. Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation-resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster...
October 10, 2016: Developmental Cell
Antoine Porquier, Guillaume Morgant, Javier Moraga, Bérengère Dalmais, Isabelle Luyten, Adeline Simon, Jean-Marc Pradier, Joëlle Amselem, Isidro González Collado, Muriel Viaud
Botrydial (BOT) is a non-host specific phytotoxin produced by the polyphagous phytopathogenic fungus Botrytis cinerea. The genomic region of the BOT biosynthetic gene cluster was investigated and revealed two additional genes named Bcbot6 and Bcbot7. Analysis revealed that the G+C/A+T-equilibrated regions that contain the Bcbot genes alternate with A+T-rich regions made of relics of transposable elements that have undergone repeat-induced point mutations (RIP). Furthermore, BcBot6, a Zn(II)2Cys6 putative transcription factor was identified as a nuclear protein and the major positive regulator of BOT biosynthesis...
October 6, 2016: Fungal Genetics and Biology: FG & B
Xianzong Wang, Xiaolin Liu
BACKGROUND: Horizontal transfer (HT) of genetic materials is increasingly being found in both animals and plants and mainly concerns transposable elements (TEs). Many crustaceans have big genome sizes and are thus likely to harbor high TE contents. Their habitat might offer them ample opportunities to exchange genetic materials with organisms that are ecologically close but taxonomically distant to them. RESULTS: In this study, we analyzed the transcriptome of Pacific white shrimp (Litopenaeus vannamei), an important economic crustacean, to explore traces of HT events...
October 7, 2016: BMC Evolutionary Biology
Petr Ráb, Cassia F Yano, Sébastien Lavoué, Oladele I Jegede, Luiz A C Bertollo, Tariq Ezaz, Zuzana Majtánová, Ezequiel A de Oliveira, Marcelo B Cioffi
The monophyletic order Osteoglossiformes represents one of the most ancestral groups of teleosts and has at least 1 representative in all continents of the southern hemisphere, with the exception of Antarctica. However, despite its phylogenetic and biogeographical importance, cytogenetic data in Osteoglossiformes are scarce. Here, karyotype and chromosomal characteristics of the lower Niger River population of the African butterfly fish Pantodon buchholzi, the sole species of the family Pantodontidae (Osteoglossiformes), were examined using conventional and molecular cytogenetic approaches...
October 7, 2016: Cytogenetic and Genome Research
R C R Noronha, L M R Barros, R E F Araújo, D F Marques, C Y Nagamachi, C Martins, J C Pieczarka
BACKGROUND: Cytogenetic studies were conducted in the Brazilian Amazon turtles, Podocnemis expansa Schweigger, 1912 (PEX) and Podocnemis unifilis Troschel, 1848 (PUN) to understand their karyoevolution. Their chromosomal complements were compared using banding techniques (C, G-, Ag-NOR and Chromomycin A3) and fluorescence in situ hybridization (FISH), and efforts were made to establish evolutionary chromosomal relationships within the Podocnemidae family. RESULTS: Our results revealed that both species have a chromosome complement of 2n = 28...
2016: Molecular Cytogenetics
Kiyomi Abe, Hiroaki Ichikawa
Identification and elucidation of functions of plant genes is valuable for both basic and applied research. In addition to natural variation in model plants, numerous loss-of-function resources have been produced by mutagenesis with chemicals, irradiation, or insertions of transposable elements or T-DNA. However, we may be unable to observe loss-of-function phenotypes for genes with functionally redundant homologs and for those essential for growth and development. To offset such disadvantages, gain-of-function transgenic resources have been exploited...
2016: Frontiers in Plant Science
Wei Yin, Zong-Ji Wang, Qi-Ye Li, Jin-Ming Lian, Yang Zhou, Bing-Zheng Lu, Li-Jun Jin, Peng-Xin Qiu, Pei Zhang, Wen-Bo Zhu, Bo Wen, Yi-Jun Huang, Zhi-Long Lin, Bi-Tao Qiu, Xing-Wen Su, Huan-Ming Yang, Guo-Jie Zhang, Guang-Mei Yan, Qi Zhou
Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes...
October 6, 2016: Nature Communications
Jürgen Schmitz, Angela Noll, Carsten A Raabe, Gennady Churakov, Reinhard Voss, Martin Kiefmann, Timofey Rozhdestvensky, Jürgen Brosius, Robert Baertsch, Hiram Clawson, Christian Roos, Aleksey Zimin, Patrick Minx, Michael J Montague, Richard K Wilson, Wesley C Warren
Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syrichta), and provide extended analyses of the genome and detailed history of transposable element insertion events...
October 6, 2016: Nature Communications
S B Im, S-J Kwon, J Ryu, S W Jeong, J B Kim, J-W Ahn, S H Kim, Y D Jo, H-I Choi, S-Y Kang
Under certain circumstances, transposable elements (TE) can create or reverse mutations and alter the genome size of a cell. Sorghum (Sorghum bicolor L.) is promising for plant transposon tagging due to its small genome size and its low content of repetitive DNA. We developed a marker system based on targeted region amplification polymorphisms (TE-TRAP) that uses the terminal inverted repeats (TIRs) of transposons. A total of 3816 class 2 transposons belonging to the PIF/Harbinger family were identified from the whole sorghum genome that produced five primers, including eight types of TIRs...
September 16, 2016: Genetics and Molecular Research: GMR
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