Genomes and Genes
dna transposable elements
Summary: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Publications217 found, 100 shown here
- Genome sequence of Aedes aegypti, a major arbovirus vectorVishvanath Nene
Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 316:1718-23. 2007..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
- Initial sequencing and analysis of the human genomeE S Lander
Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
Nature 409:860-921. 2001..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
- Discrete small RNA-generating loci as master regulators of transposon activity in DrosophilaJulius Brennecke
Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
Cell 128:1089-103. 2007..Thus, sense piRNAs, formed following cleavage of transposon mRNAs may enhance production of antisense piRNAs, complementary to active elements, by directing cleavage of transcripts from master control loci...
- The TIGR Rice Genome Annotation Resource: improvements and new featuresShu Ouyang
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
Nucleic Acids Res 35:D883-7. 2007..Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads...
- The B73 maize genome: complexity, diversity, and dynamicsPatrick S Schnable
Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA
Science 326:1112-5. 2009..These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize...
- Repbase Update, a database of eukaryotic repetitive elementsJ Jurka
Genetic Information Research Institute, Mountain View, CA 94043, USA
Cytogenet Genome Res 110:462-7. 2005..Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst.org/Repbase_Update.html...
- Transposable elements and the epigenetic regulation of the genomeR Keith Slotkin
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
Nat Rev Genet 8:272-85. 2007..In addition, new insights have been gained into how this silencing has been co-opted to serve essential functions in 'host' cells, highlighting the importance of TEs in the epigenetic regulation of the genome...
- Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and CensorOleksiy Kohany
Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA
BMC Bioinformatics 7:474. 2006..Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases...
- A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in miceAlexei A Aravin
Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Mol Cell 31:785-99. 2008..This implicates piRNAs as specificity determinants of DNA methylation in germ cells...
- ISfinder: the reference centre for bacterial insertion sequencesP Siguier
, C.N.R.S. 118, route de Narbonne, F-31062 Toulouse Cedex, France
Nucleic Acids Res 34:D32-6. 2006..Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication...
- Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cellsMegha Ghildiyal
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
Science 320:1077-81. 2008..We propose that endo-siRNAs generated by the fly RNAi pathway silence selfish genetic elements in the soma, much as Piwi-interacting RNAs do in the germ line...
- Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposonKosuke Yusa
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Methods 6:363-9. 2009..iPSCs fulfilled all criteria of pluripotency, such as pluripotency gene expression, teratoma formation and contribution to chimeras. piggyBac transposon-based reprogramming may be used to generate therapeutically applicable iPSCs...
- An epigenetic role for maternally inherited piRNAs in transposon silencingJulius Brennecke
Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory CSHL, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Science 322:1387-92. 2008..This indicates that maternally deposited piRNAs are important for mounting an effective silencing response and that a lack of maternal piRNA inheritance underlies hybrid dysgenesis...
- Simultaneous assay of every Salmonella Typhi gene using one million transposon mutantsGemma C Langridge
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
Genome Res 19:2308-16. 2009..Typhi in the gall bladder. This screen validated our hypothesis that we can simultaneously assay every gene in the genome to identify niche-specific essential genes...
- The complete genome sequence of Escherichia coli K-12F R Blattner
Laboratory of Genetics, University of Wisconsin Madison, 445 Henry Mall, Madison, WI 53706, USA
Science 277:1453-62. 1997..The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer...
- A modular master on the move: the Tn916 family of mobile genetic elementsAdam P Roberts
Division of Microbial Diseases, UCL Eastman Dental Institute, 256 Gray s Inn Road, London, WC1X 8LD, UK
Trends Microbiol 17:251-8. 2009..Therefore, the study of this family of mobile genetic elements is essential for a better understanding and control of the current rise of antibiotic resistance among pathogenic bacteria...
- DNA transposons and the evolution of eukaryotic genomesCEDRIC FESCHOTTE
Department of Biology, University of Texas, Arlington, TX 76019, USA
Annu Rev Genet 41:331-68. 2007..Finally, we highlight how the distinctive biological features of DNA transposons have contributed to shape genome architecture and led to the emergence of genetic innovations in different eukaryotic lineages...
- A unified classification system for eukaryotic transposable elementsThomas Wicker
Institute of Plant Biology, University Zurich, Zollikerstrasse 107, Ch 8008 Zurich, Switzerland
Nat Rev Genet 8:973-82. 2007..The system and nomenclature is kept up to date at the WikiPoson web site...
- Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebratesLajos Mátés
Max Delbruck Center for Molecular Medicine, Berlin, Germany
Nat Genet 41:753-61. 2009....
- The genome of the Western clawed frog Xenopus tropicalisUffe Hellsten
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 328:633-6. 2010..The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage...
- The carnegie protein trap library: a versatile tool for Drosophila developmental studiesMichael Buszczak
Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21218, USA
Genetics 175:1505-31. 2007....
- A transposon-based genetic screen in mice identifies genes altered in colorectal cancerTimothy K Starr
Department of Genetics, Cell Biology and Development, Center for Genome Engineering, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
Science 323:1747-50. 2009..These genes include APC, PTEN, and SMAD4. The screen also identified 17 candidate genes that had not previously been implicated in CRC, including POLI, PTPRK, and RSPO2...
- Epigenetic reprogramming and small RNA silencing of transposable elements in pollenR Keith Slotkin
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Cell 136:461-72. 2009..We propose a conserved role for reprogramming in germline companion cells, such as nurse cells in insects and vegetative nuclei in plants, to reveal intact TEs in the genome and regulate their activity in gametes...
- Mobile elements create structural variation: analysis of a complete human genomeJinchuan Xing
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84109, USA
Genome Res 19:1516-26. 2009....
- Chromosomal transposition of PiggyBac in mouse embryonic stem cellsWei Wang
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
Proc Natl Acad Sci U S A 105:9290-5. 2008..The comprehensive information from this study should facilitate further exploration of the potential of PB and SB DNA transposons in mammalian genetics...
- Insertion sequences in prokaryotic genomesPatricia Siguier
, route de Narbonne, F-31062 Toulouse Cedex, France
Curr Opin Microbiol 9:526-31. 2006..In addition, defective (non- autonomous) elements, which can be complemented by related active elements in the same cell, are often overlooked in genome annotations but also contribute to the evolution of genome organisation...
- Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence setsNicolas Buisine
Unite de Recherche en Genomique Vegetale, INRA UMR1165 CNRS UMR8114 Université d Evry Val d Essonne, 2 rue Gaston Cremieux, 91057 Evry, France
Genomics 91:467-75. 2008..Significantly, we find that TE detection could be readily optimized using only two reference sets, one containing true consensus sequences and the other mosaic sequences that capture the structural diversity of TE copies within a family...
- Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture...
- Extensive demethylation of repetitive elements during seed development underlies gene imprintingMary Gehring
Howard Hughes Medical Institute HHMI, Fred Hutchinson Cancer Research Center FHCRC, 1100 Fairview Avenue North, Seattle, WA 98109, USA
Science 324:1447-51. 2009..These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous...
- Transposition of cloned P elements into Drosophila germ line chromosomesA C Spradling
Science 218:341-7. 1982..Thus P elements can efficiently and selectively transpose from extrachromosomal DNA to the DNA of germ line chromosomes in Drosophila embryos. These observations provide the basis for efficient DNA-mediated gene transfer in Drosophila...
- Transposable elements and the evolution of regulatory networksCEDRIC FESCHOTTE
Department of Biology, Life Science Building, Box 19498, University of Texas, Arlington, Texas 76019, USA
Nat Rev Genet 9:397-405. 2008..Here I revisit and expand earlier models and propose that genomic repeats, and in particular transposable elements, have been a rich source of material for the assembly and tinkering of eukaryotic gene regulatory systems...
- ISCR elements: novel gene-capturing systems of the 21st century?Mark A Toleman
Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
Microbiol Mol Biol Rev 70:296-316. 2006..It appears that ISCR elements have now firmly established themselves within that regimen...
- The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrataSteven Lockton
Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
BMC Evol Biol 10:10. 2010..We analyzed seven TE families in four natural populations of each species to tease apart the effects of mating system, demography, transposition, and selection in determining patterns of TE diversity...
- Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?N Zamudio
Inserm U934 UMR3215, Institut Curie, Paris, France
Heredity (Edinb) 105:92-104. 2010..An organized cross-talk between PIWI-interacting small RNAs (piRNAs) and various nuclear and cytoplasmic accessories provides this potent and multi-layered response to retrotransposon unleashing in early germ cells...
- Conserved themes in small-RNA-mediated transposon controlAngelique Girard
Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Trends Cell Biol 18:136-48. 2008....
- SOS response promotes horizontal dissemination of antibiotic resistance genesJohn W Beaber
Department of Microbiology, Tufts University School of Medicine and Howard Hughes Medical Institute, 136 Harrison Avenue, Boston, Massachusetts 02111, USA
Nature 427:72-4. 2004..Thus, we present a mechanism by which therapeutic agents can promote the spread of antibiotic resistance genes...
- Critical roles for Dicer in the female germlineElizabeth P Murchison
Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA
Genes Dev 21:682-93. 2007..Our studies identify Dicer as central to a regulatory network that controls oocyte gene expression programs and that promotes genomic integrity in a cell type notoriously susceptible to aneuploidy...
- Genome-wide demethylation of Arabidopsis endospermTzung Fu Hsieh
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
Science 324:1451-4. 2009..Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo...
- Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spacesFrédéric Choulet
Institut National de la Recherche Agronomique, Universite Blaise Pascal, Unité Mixte de Recherche 1095 Genetics Diversity and Ecophysiology of Cereals, F 63100 Clermont Ferrand, France
Plant Cell 22:1686-701. 2010....
- Jumping genes and epigenetics: Towards new speciesRita Rebollo
CNRS, UMR558, Laboratoire de Biometrie et Biologie Evolutive, Universite Lyon 1, Villeurbanne, France
Gene 454:1-7. 2010..We propose to focus on recent data that demonstrate the correlation between changes in the epigenetic control of TEs in species/populations and genome evolution...
- Functions required for extracellular quinolone signaling by Pseudomonas aeruginosaLarry A Gallagher
Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
J Bacteriol 184:6472-80. 2002..Others of the pleiotropic phenazine-minus mutations appear to inactivate novel components of the quorum-sensing regulatory network, including one regulator (np20) previously shown to be required for virulence in neutropenic mice...
- Genes required for mycobacterial growth defined by high density mutagenesisChristopher M Sassetti
Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard Medical School, Boston, MA 02115, USA
Mol Microbiol 48:77-84. 2003....
- Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH)Roy R Chaudhuri
Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
BMC Genomics 10:291. 2009..An important starting point for the development of new antimicrobial drugs is the identification of "essential" genes that are important for bacterial survival and growth...
- P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogasterKoen J T Venken
Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
Science 314:1747-51. 2006..This transgenesis platform should greatly facilitate structure/function analyses of most Drosophila genes...
- The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plantsY Notsu
Department of Genetic Diversity, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
Mol Genet Genomics 268:434-45. 2002....
- Sequence and comparative analysis of the maize NB mitochondrial genomeSandra W Clifton
Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
Plant Physiol 136:3486-503. 2004..After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function...
- Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programsE Lerat
Universite de Lyon, F 6900 Lyon
Heredity (Edinb) 104:520-33. 2010..However, this makes it essential to verify the results provided by each program independently. The ideal solution would be to test all programs against the same data set to obtain a true comparison of their actual performance...
- Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expressionJesse D Hollister
Department of Ecology and Evolutionary Biology, University of Californina, Irvine, Irvine, California 92697 2525, USA
Genome Res 19:1419-28. 2009..This mechanism implies an evolutionary tradeoff in which the benefit of TE silencing imposes a fitness cost via deleterious effects on the expression of nearby genes...
- MUST: a system for identification of miniature inverted-repeat transposable elements and applications to Anabaena variabilis and Haloquadratum walsbyiYong Chen
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, 120 Green Street Athens, GA 30602, USA
Gene 436:1-7. 2009..bmb.uga.edu/ffzhou/MUST/ (the standalone version is available upon request). Supplementary data associated with this article are available in the online version or at: http://csbl1.bmb.uga.edu/ffzhou/MUST/supp/...
- A Tn7-based broad-range bacterial cloning and expression systemKyoung-Hee Choi
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
Nat Methods 2:443-8. 2005..pestis. This system will thus have widespread biomedical and environmental applications, especially in environments where plasmids and antibiotic selection are not feasible, namely in plant and animal models or biofilms...
- Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in DrosophilaJian Lu
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
Genome Res 20:212-27. 2010....
- Conjugative transposons: the tip of the icebergVincent Burrus
, UMR INRA-UHP 1128, IFR110, , , BP239, , France
Mol Microbiol 46:601-10. 2002..These elements evolve by acquisition or exchanges of modules with various transferable elements including at least ICEs and plasmids. The ICEs are probably widespread among the bacteria...
- Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locusJoshua M Schmidt
Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
PLoS Genet 6:e1000998. 2010..Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession...
- Transposable elements in reptilian and avian (sauropsida) genomesD Kordis
Department of Molecular and Biomedical Sciences, J Stefan Institute, Ljubljana, Slovenia
Cytogenet Genome Res 127:94-111. 2009..The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context...
- Genome-wide patterns of adaptation to temperate environments associated with transposable elements in DrosophilaJosefa González
Department of Biology, Stanford University, Stanford, California, United States of America
PLoS Genet 6:e1000905. 2010..We argue that reverse population genomic analyses, as the one described in this work, are necessary to arrive at a comprehensive picture of adaptation...
- Repeated horizontal transfer of a DNA transposon in mammals and other tetrapodsJohn K Pace
Department of Biology, University of Texas at Arlington, P O Box 19498, Arlington, TX 76019, USA
Proc Natl Acad Sci U S A 105:17023-8. 2008..In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species...
- The evolution of RNAi as a defence against viruses and transposable elementsDarren J Obbard
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King s Buildings, Edinburgh EH9 3JT, UK
Philos Trans R Soc Lond B Biol Sci 364:99-115. 2009..Over longer time scales, key RNAi genes are repeatedly duplicated or lost across the metazoan phylogeny, with important implications for RNAi as an immune defence...
- Molecular domestication of transposable elements: from detrimental parasites to useful host genesL Sinzelle
Max Delbruck Center for Molecular Medicine, Berlin, Germany
Cell Mol Life Sci 66:1073-93. 2009..Our knowledge on the structure, distribution, evolution and mechanism of transposons will continue to provide important contributions to our understanding of host genome functions...
- Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81Nicholas J Croucher
Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, United Kingdom
J Bacteriol 191:1480-9. 2009..However, further sequencing of other pandemic clones will be required to establish whether there are any general attributes shared by these strains that are responsible for their international success...
- Bursts of retrotransposition reproduced in ArabidopsisSayuri Tsukahara
Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411 8540, Japan
Nature 461:423-6. 2009....
- A triptych of the evolution of plant transposable elementsMaud I Tenaillon
CNRS, UMR 0320 UMR8120 Génétique Végétale, F 91190 Gif sur Yvette, France
Trends Plant Sci 15:471-8. 2010..Finally, we focus on the often-ignored third panel of our triptych - the population processes that determine the ultimate evolutionary fate of TE insertions...
- Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lungJeffrey D Gawronski
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, 55 Lake Avenue North, S6 242, Worcester, MA 01655, USA
Proc Natl Acad Sci U S A 106:16422-7. 2009....
- A modified sleeping beauty transposon system that can be used to model a wide variety of human cancers in miceAdam J Dupuy
Department of Anatomy and Cell Biology, Center for Bioinformatics, Computational Biology and Biomedical Engineering, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
Cancer Res 69:8150-6. 2009..These novel alleles provide additional tools for the SB system and provide some insight into how this mutagenesis system can be manipulated to model cancer in mice...
- The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clustersCarla Klattenhoff
University of Massachusetts Medical School, Worcester, MA 01605, USA
Cell 138:1137-49. 2009..Rhino thus appears to promote transcription of dual-strand clusters, leading to production of piRNAs that drive the ping-pong amplification cycle...
- Complete genome sequence of a virulent isolate of Streptococcus pneumoniaeH Tettelin
The Institute for Genomic Research (TIGR, 9712 Medical Center Drive, Rockville, MD 20850, USA
Science 293:498-506. 2001..Comparative genome hybridization with DNA arrays revealed strain differences in S. pneumoniae that could contribute to differences in virulence and antigenicity...
- The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolutionKeisuke Nakayama
Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki, Japan
DNA Res 15:185-99. 2008..tsutsugamushi and the pathogenesis of 'Tsutsugamushi' disease...
- Horizontal gene transfer in eukaryotic evolutionPatrick J Keeling
Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z, Canada
Nat Rev Genet 9:605-18. 2008..Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages...
- Changes in Hox genes' structure and function during the evolution of the squamate body planNicolas Di-Poï
National Research Center Frontiers in Genetics, Department of Zoology and Animal Biology, University of Geneva, Sciences III, 1211 Geneva 4, Switzerland
Nature 464:99-103. 2010....
- High rate of recent transposable element-induced adaptation in Drosophila melanogasterJosefa González
Department of Biology, Stanford University, Stanford, California, United States of America
PLoS Biol 6:e251. 2008..Such a high rate of TE-induced adaptation is inconsistent with the number of fixed TEs in the D. melanogaster genome, and we discuss possible explanations for this discrepancy...
- CRISPR-based adaptive and heritable immunity in prokaryotesJohn van der Oost
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
Trends Biochem Sci 34:401-7. 2009..Recent analyses of key Cas proteins indicate that, despite some functional analogies, this fascinating prokaryotic system shares no phylogenetic relation with the eukaryotic RNA interference system...
- A role for host-parasite interactions in the horizontal transfer of transposons across phylaClément Gilbert
Department of Biology, University of Texas, Arlington, Texas 76019, USA
Nature 464:1347-50. 2010..Furthermore, the large amount of DNA generated by the amplification of the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution...
- Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogenDragana Ajdic
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
Proc Natl Acad Sci U S A 99:14434-9. 2002....
- Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomesO Raskina
Institute of Evolution, University of Haifa, Israel
Cytogenet Genome Res 120:351-7. 2008....
- An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutantsNicole T Liberati
Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
Proc Natl Acad Sci U S A 103:2833-8. 2006..Comparison of the genes disrupted in the PA14 transposon insertion library with an independently constructed insertion library in P. aeruginosa strain PAO1 provides an estimate of the number of P. aeruginosa essential genes...
- Repeats in genomic DNA: mining and meaningJ Jurka
Genetic Information Research Institute, Sunnyvale, CA 94089, USA
Curr Opin Struct Biol 8:333-7. 1998..Analysis of these sequences, combined with experimental research, reveals a history of complex 'intracellular ecosystems' of transposable elements that are inseparably associated with genomic evolution...
- Pig transgenesis by Sleeping Beauty DNA transpositionJannik E Jakobsen
Department of Human Genetics, University of Aarhus, Wilh Meyers Allé 1240, 8000, Aarhus C, Denmark
Transgenic Res 20:533-45. 2011....
- Transposed genes in Arabidopsis are often associated with flanking repeatsMargaret R Woodhouse
Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
PLoS Genet 6:e1000949. 2010..We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition...
- A c-Myc regulatory subnetwork from human transposable element sequencesJianrong Wang
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
Mol Biosyst 5:1831-9. 2009..These data point to a substantial contribution of TEs to the regulation of human genes by c-Myc. Genes that are regulated by TE-derived c-Myc binding sites appear to form a distinct c-Myc regulatory subnetwork...
- Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profileMichael Reuter
European Molecular Biology Laboratory, Grenoble Outstation, France
Nat Struct Mol Biol 16:639-46. 2009..Our data suggest that Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool...
- Stable integration and conditional expression of electroporated transgenes in chicken embryosYuki Sato
Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916 5, Takayama, Ikoma, Nara, 630 0192, Japan
Dev Biol 305:616-24. 2007..Thus, the techniques proposed in this study provide a novel approach to study the mechanisms of late organogenesis, for which chickens are most suitable model animals...
- sigmaB regulates IS256-mediated Staphylococcus aureus biofilm phenotypic variationJaione Valle
Instituto de Agrobiotecnologia, Universidad Publica de Navarra, Pamplona 31006, Spain
J Bacteriol 189:2886-96. 2007..Overall, our results identify a new role for sigma(B) as a negative regulator of insertion sequence transposition and support the idea that deregulation of IS256 activity abrogates biofilm formation capacity in S. aureus...
- Dynamic landscapes of four histone modifications during deetiolation in ArabidopsisJean Benoit F Charron
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520, USA
Plant Cell 21:3732-48. 2009....
- High-throughput identification of protein localization dependency networksBeat Christen
Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 107:4681-6. 2010....
- Post-integration stability of piggyBac in Aedes aegyptiNagaraja Sethuraman
Center for Biosystems Research, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
Insect Biochem Mol Biol 37:941-51. 2007..The post-integration mobility properties of piggyBac in Ae. aegypti enhance the utility of this gene vector for certain applications, particularly those where any level of vector remobilization is unacceptable...
- Detailed analysis of a contiguous 22-Mb region of the maize genomeFusheng Wei
Arizona Genomics Institute, School of Plant Sciences and Department of Ecology, BIO5 Institute for Collaborative Research, University of Arizona, Tucson, Arizona, United States of America
PLoS Genet 5:e1000728. 2009..Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses...
- Comparative analysis of transposable element vector systems in human cellsIvana Grabundzija
Max Delbruck Center for Molecular Medicine, Berlin, Germany
Mol Ther 18:1200-9. 2010..SB, Tol2, and PB constitute complementary research tools for gene transfer in mammalian cells with important implications for fundamental and translational research...
- Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomesJon Reinders
Department of Plant Biology, University of Geneva, Sciences III, Geneva, Switzerland
Genes Dev 23:939-50. 2009..Such persistently "unstable" epigenetic states complicate linkage-based epigenomic mapping. Thus, future epigenomic analyses should consider possible genetic instabilities and alternative mapping strategies...
- Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomesTomas Cermak
Laboratory of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, CZ 61265, Brno, Czech Republic
Chromosome Res 16:961-76. 2008..The unique pattern of repeat distribution is found on the Y chromosome, where some elements are accumulated while other elements are conspicuously absent, which probably reflects different forces shaping the Y chromosome...
- Control of female gamete formation by a small RNA pathway in ArabidopsisVianey Olmedo-Monfil
Grupo de Desarrollo Reproductivo y Apomixis, Laboratorio Nacional de Genómica para la Biodiversidad y Departamento de Ingeniería Genética de Plantas, Cinvestav Irapuato CP36500 Guanajuato, Mexico
Nature 464:628-32. 2010..Our results show that AGO9-dependent sRNA silencing is crucial to specify cell fate in the Arabidopsis ovule, and that epigenetic reprogramming in companion cells is necessary for sRNA-dependent silencing in plant gametes...
- In vivo random mutagenesis of Bacillus subtilis by use of TnYLB-1, a mariner-based transposonYoann Le Breton
Department of Microbiology and Immunology, MSC 7758, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229 3900, USA
Appl Environ Microbiol 72:327-33. 2006..Two auxotrophic mutants were identified among the 200 transposants, one with an insertion in lysA and another in a gene (yjzB) whose function is unknown...
- The AmpC phenotype in Norwegian clinical isolates of Escherichia coli is associated with an acquired ISEcp1-like ampC element or hyperproduction of the endogenous AmpCBjørg Haldorsen
Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
J Antimicrob Chemother 62:694-702. 2008..The aim of the study was to examine resistance mechanisms associated with an AmpC phenotype in Norwegian clinical isolates of Escherichia coli...
- Isolation of predation-deficient mutants of Bdellovibrio bacteriovorus by using transposon mutagenesisJohn J Tudor
Department of Biology, Saint Joseph s University, 5600 City Avenue, Philadelphia, PA 19131, USA
Appl Environ Microbiol 74:5436-43. 2008....
- Systematic insertional mutagenesis of a streptomycete genome: a link between osmoadaptation and antibiotic productionAmy Bishop
School of Biological Sciences, University of Wales Swansea, Singleton Park, Swansea SA2 8PP, UK
Genome Res 14:893-900. 2004....
- Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo redZhaohui Xiong
State Key Laboratory for Molecular Virology and Genetic Engineering, Beijing 100052, China
Sci China C Life Sci 49:141-8. 2006..Whether these genes determine the Crb function requires continued investigation...
- Xenorhabdus nematophila lrhA is necessary for motility, lipase activity, toxin expression, and virulence in Manduca sexta insectsGregory R Richards
Department of Bacteriology, University of Wisconsin Madison, Madison, Wisconsin, USA
J Bacteriol 190:4870-9. 2008..nematophila pathogenesis and expression of surface-localized and secreted factors. Future research is aimed at identifying and characterizing virulence factors within the LrhA regulon...
- Tol2 transposon-mediated transgenesis in Xenopus tropicalisMichelle R Johnson Hamlet
Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
Genesis 44:438-45. 2006..Here, we show that the Medaka fish transposon, Tol2, is able to stably integrate into the X. tropicalis genome and will serve as a powerful tool for insertional mutagenesis strategies in the frog...
- Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factorR Horak
Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, EE2400 Tartu, Estonia
J Bacteriol 180:2822-9. 1998..Also, an in vitro binding assay demonstrated that both ends of Tn4652 bind IHF from a cell lysate of E. coli...
- Sub-terminal sequences modulating IS30 transposition in vivo and in vitroMonika Szabo
Agricultural Biotechnology Center, 4 Szent Györgyi Albert Str, H 2100, Godollo, Hungary
J Mol Biol 375:337-52. 2008..In vitro kinetic experiments suggest that the sub-terminal enhancers may, at least partly, be transposase-dependent. Such enhancers may reflect a subtle regulatory mechanism for IS30 transposition...
- Comparison of virulence plasmids among Clostridium perfringens type E isolatesJihong Li
Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
Infect Immun 75:1811-9. 2007..Further iap/ibp plasmid diversity occurred when either the iap/ibp genes later remobilized and inserted onto other conjugative plasmids or some iap/ibp plasmids acquired additional DNA sequences...
- Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic organization of IncP-7 TOL plasmid pWW53 and related mobile genetic elementsHirokazu Yano
Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980 8577, Japan
J Mol Biol 369:11-26. 2007....
- Putative surface proteins encoded within a novel transferable locus confer a high-biofilm phenotype to Enterococcus faecalisPreeti M Tendolkar
Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, P.O. Box 26901, Oklahoma City, OK 73190, USA
J Bacteriol 188:2063-72. 2006..faecalis strains. This represents the first instance of the identification of a mobile genetic element conferring biofilm-forming property in E. faecalis...
Research Grants143 found, 100 shown here
- Transposon Mediated Insertional Mutagenesis in MiceDAVID LARGAESPADA; Fiscal Year: 2003..element called Sleeping Beauty (SB), which is a reconstructed member of the Tcl/mariner family of DNA transposable elements. We have demonstrated that efficient mobilization of SB transposons can be made to occur in the germline ..
- RNAi, Histone Modification and the DDB1/CPSF-like Complex Rik1Robert A Martienssen; Fiscal Year: 2010..Transposable elements and other repeats are common to all of these genomes, and may hold the key to epigenetic mechanisms of gene regulation and chromosome function. ..
- RNAi, Histone Modification and the DDB1/CPSF-like Complex Rik1Robert Martienssen; Fiscal Year: 2007..Transposable elements and other repeats are common to all of these genomes, and may hold the key to epigenetic mechanisms of gene regulation and chromosome function. ..
- Selenium, Aminothiols, and RadiationAlan Diamond; Fiscal Year: 2004..Collectively, these studies will provide new insight on how selenium protects cells from radiation-induced mutagenesis and may lead to novel approaches to increase the beneficial properties of this nutrient. ..
- Human DNA transposons: evolutionary history and genomic impactCEDRIC FESCHOTTE; Fiscal Year: 2010..We will combine comparative and evolutionary sequence analyses to in vitro and in vivo assays to test whether these proteins (or other candidate identified in the course of this research) have retained their catalytic activities. ..
- Human DNA transposons: evolutionary history and genomic impactCEDRIC FESCHOTTE; Fiscal Year: 2007..We will combine comparative and evolutionary sequence analyses to in vitro and in vivo assays to test whether these proteins (or other candidate identified in the course of this research) have retained their catalytic activities. ..
- REGULATION OF AMPICILLIN RESISTANCE IN E FACEIUMLouis Rice; Fiscal Year: 2004..They will also yield important new information on mechanisms of cell wall synthesis in E. faecium and other Gram-positive bacteria as well as on the mechanisms by which ampicillin resistance in E. faecium is regulated. ..
- Ampicillin resistance mechanisms in E. faeciumLouis Rice; Fiscal Year: 2007..abstract_text> ..
- Cell wall synthesis enzymes and beta-lactam resistance in Enterococcus faeciumLouis B Rice; Fiscal Year: 2010..This project aims to identify and characterize the complex and redundant mechanisms of ?-lactam resistance in an effort to better understand enterococcal physiology and promote identification of novel therapeutic targets. ..
- Genetic methods using the Tol2 transposable elementKoichi Kawakami; Fiscal Year: 2006..abstract_text> ..
- HOBO-LIKE ELEMENTS IN INSECTSDAVID O BROCHTA; Fiscal Year: 2004..5) develop a functional anopheline hAT element-based gene vector system. These aims will be accomplished using genetic and molecular genetic methods. ..
- HOBO-LIKE ELEMENTS IN INSECTSDAVID O BROCHTA; Fiscal Year: 2007..gambiae populations, 3) develop Herves into a mosquito gene vector. These aims will be accomplished by performing a combination of laboratory and field-based studies using molecular and population genetics tools. ..
- Genetic Manipulation of InsectsDAVID O BROCHTA; Fiscal Year: 2004..The meeting is an uncommon opportunity for graduate students and postdoctoral fellows to obtain a high level synopsis of the field of insect molecular genetics and to make important career-advancing interactions. ..
- Tn5 as an insect genomics toolDAVID O BROCHTA; Fiscal Year: 2002..gambiae make this is a high risk project but one whose impact on the field of medical entomology and efforts to control the transmission of malaria will be enormous if it is successful. ..
- Gene drive potential of transposable elements in Anopheles gambiae.DAVID O BROCHTA; Fiscal Year: 2009..gambiae will be known. This project involves the use of Animals but does not involve Human Subjects. ..
- HOBO-LIKE TRANSPOSABLE ELEMENTS IN INSECTSDAVID O BROCHTA; Fiscal Year: 1993....
- HOBO-LIKE TRANSPOSABLE ELEMENTS IN INSECTSDAVID O BROCHTA; Fiscal Year: 1999....
- Gene drive potential of transposable elements in Anopheles gambiae.DAVID A O apos BROCHTA; Fiscal Year: 2010..gambiae will be known. This project involves the use of Animals but does not involve Human Subjects. ..
- Identification of Tetrahymena DNA Rearrangement GenesDOUGLAS LEE CHALKER; Fiscal Year: 2010..abstract_text> ..
- MECHANISMS OF MYCOPLASMA-INDUCED ARTHRITISKevin Dybvig; Fiscal Year: 2002..arthritidis by affecting interactions with host factors such as B and T cells and complement. Thus, the process of dissecting the function of MAV1 in virulence will be begun. ..
- Molecular Epidemiology of Community-Associated MRSASANJAY SHUKLA; Fiscal Year: 2007..We will determine the presence or absences of 40 different virulence factor genes in all 320 isolates listed in aim 2 and determine evolution of virulence factor genes in contemporary CA-MRSA. ..
- GENETIC RECOMBINATION IN MYCOPLASMASKevin Dybvig; Fiscal Year: 2004..In aim 2, mutants with defects in putative DNA recombinases and V-I protein production will be examined to study the mechanisms of gene rearrangements and phenotypic switching. ..
- Tandemly Repetitive Proteins in MycoplasmasKevin Dybvig; Fiscal Year: 2007..By understanding the role of repetitive proteins in the disease process, it is anticipated that improved measures to control the infections of these significant human pathogens will be developed. ..
- ANTIGENIC VARIATION IN MYCOPLASMASKevin Dybvig; Fiscal Year: 2004....
- ROLE OF RHOMBOID HOMOLOGUES IN MYCOBACTERIA SIGNALINGMoses Joloba; Fiscal Year: 2006..This will expand our understanding of mycobacterial biology and may provide novel candidate vaccines and drug targets. ..
- RHEUMATOLOGY RESEARCH TRAINING PROGRAMMARY CROW; Fiscal Year: 2007..Support is requested for 3 MD, MD-PhD, or PhD trainees who will gain the skills required to make important advances in the health of patients with rheumatic disease. ..
- RNA Polymerase III transcription in Leishmania majorSANTIAGO MARTINEZ CALVILLO; Fiscal Year: 2007..The tandem affinity purification (TAP-tag) method will be used to purify Pol III transcriptional complexes. The protein components in these complexes will be identified by mass-spectrometry analysis. ..
- Improved Brucella Vaccine StrainsThomas Ficht; Fiscal Year: 2009..abstract_text> ..
- Interferon in Systemic Lupus ErythematosusMARY CROW; Fiscal Year: 2009..Elucidation of this important pathway should lead to more targeted modulation of disease mediators in systemic autoimmune diseases. ..
- CELL TO CELL SIGNALING IN MYCOBACTERIAMOSES LUTAAKOME JOLOBA; Fiscal Year: 2010..This will enrich our knowledge on mycobacterial biology and may reveal novel drug and vaccine targets. ..
- REQUIREMENTS FOR BACTERIAL COLONIZATION OF ANIMAL TISSUEKaren L Visick; Fiscal Year: 2010....
- REQUIREMENTS FOR BACTERIAL COLONIZATION OF ANIMAL TISSUEKAREN VISICK; Fiscal Year: 2007..parahaemolyticus and V. vulnificus. Studying this model may also lead to approaches that prevent, reduce or treat such infections. ..
- Interferon in Systemic Lupus ErythematosusMary K Crow; Fiscal Year: 2010..Elucidation of this important pathway should lead to more targeted modulation of disease mediators in systemic autoimmune diseases. ..
- CELL TO CELL SIGNALING IN MYCOBACTERIAMoses Joloba; Fiscal Year: 2007..This will enrich our knowledge on mycobacterial biology and may reveal novel drug and vaccine targets. ..
- RNA Polymerase III transcription in Leishmania majorSANTIAGO MARTINEZ CALVILLO; Fiscal Year: 2009..The tandem affinity purification (TAP-tag) method will be used to purify Pol III transcriptional complexes. The protein components in these complexes will be identified by mass-spectrometry analysis. ..
- Identification of Rheumatic Disease GenesMARY CROW; Fiscal Year: 2004..abstract_text> ..