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.
Publications252 found, 100 shown here
- 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...
- 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...
- 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....
- 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...
- 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...
- 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...
- 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...
- 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...
- Repetitive elements may comprise over two-thirds of the human genomeA P Jason De Koning
Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
PLoS Genet 7:e1002384. 2011..These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed...
- 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...
- 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...
- 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...
- 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...
- Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammalsVincent J Lynch
Department of Ecology and Evolutionary Biology and Yale Systems Biology Institute, Yale University, New Haven, Connecticut, USA
Nat Genet 43:1154-9. 2011....
- Transposable elements have rewired the core regulatory network of human embryonic stem cellsGalih Kunarso
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
Nat Genet 42:631-4. 2010..These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells...
- 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...
- Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestansBrian J Haas
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
Nature 461:393-8. 2009..infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential...
- 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...
- 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...
- 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...
- ISfinder: the reference centre for bacterial insertion sequencesP Siguier
Laboratoire de Microbiologie et Genetique Moleculaires, 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...
- 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...
- 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...
- Efficient transposition of the piggyBac (PB) transposon in mammalian cells and miceSheng Ding
Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
Cell 122:473-83. 2005..These data provide a first and critical step toward a highly efficient transposon system for a variety of genetic manipulations including transgenesis and insertional mutagenesis in mice and other vertebrates...
- An active DNA transposon family in riceNing Jiang
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
Nature 421:163-7. 2003..Since the domestication of rice mPing MITEs have been amplified preferentially in cultivars adapted to environmental extremes-a situation that is reminiscent of the genomic shock theory for transposon activation...
- Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolutionSarah Schaack
Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
Trends Ecol Evol 25:537-46. 2010..We argue that the introduction of transposable elements by horizontal transfer in eukaryotic genomes has been a major force propelling genomic variation and biological innovation...
- 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...
- Origin of primate orphan genes: a comparative genomics approachMacarena Toll-Riera
Evolutionary Genomics Group, Biomedical Informatics Research Programme, Fundació Institut Municipal d Investigació Mèdica, Barcelona, Spain
Mol Biol Evol 26:603-12. 2009..This indicates frequent recruitment of TEs as part of novel genes. Finally, we also obtain evidence that a small fraction of primate orphan genes, around 5.5%, might have originated de novo from mammalian noncoding genomic regions...
- 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....
- 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...
- Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotesJean Nicolas Volff
Biofuture Research Group, Physiologische Chemie I, Biozentrum, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
Bioessays 28:913-22. 2006..Many new candidates for domesticated sequences have been revealed by sequencing projects. Their functional analysis will uncover new aspects of evolutionary alchemy, the turning of junk into gold within genomes...
- The struggle for life of the genome's selfish architectsAurelie Hua-Van
Laboratoire Evolution, Génomes, Spéciation, CNRS UPR9034 Université Paris Sud, Gif sur Yvette, France
Biol Direct 6:19. 2011..We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution...
- 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...
- 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...
- 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...
- piggyBac transposition reprograms fibroblasts to induced pluripotent stem cellsKnut Woltjen
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
Nature 458:766-70. 2009..We anticipate that the unique properties of this virus-independent simplification of iPS cell production will accelerate this field further towards full exploration of the reprogramming process and future cell-based therapies...
- 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...
- Epigenetic regulation of transposable elements in plantsDamon Lisch
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Annu Rev Plant Biol 60:43-66. 2009..Together, these observations suggest that naturally occurring changes in transposon activity may have had an important impact on the causes and consequences of epigenetic silencing in plants...
- Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrataJesse D Hollister
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
Proc Natl Acad Sci U S A 108:2322-7. 2011..Our results suggest that the efficacy of RNA-directed DNA methylation silencing is lower in A. lyrata, a finding that may shed light on the causes of differential TE proliferation among species...
- 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...
- Dual coding of siRNAs and miRNAs by plant transposable elementsJittima Piriyapongsa
School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 0230, USA
RNA 14:814-21. 2008..The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression...
- Unexpected consequences of a sudden and massive transposon amplification on rice gene expressionKen Naito
Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
Nature 461:1130-4. 2009..As such, this study provides evidence for models first proposed previously for the involvement of transposable elements and other repetitive sequences in genome restructuring and gene regulation...
- Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteriaM Herrero
GBF National Research Centre for Biotechnology, Braunschweig, Federal Republic of Germany
J Bacteriol 172:6557-67. 1990..g., in open systems and natural environments), and that do not carry antibiotic resistance markers characteristic of most available cloning vectors (as is currently required of live bacterial vaccines)...
- Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cellsZ Ivics
Department of Genetics and Cell Biology, University of Minnesota, St Paul 55108 1095, USA
Cell 91:501-10. 1997..Sleeping Beauty is an active DNA-transposon system from vertebrates for genetic transformation and insertional mutagenesis...
- DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivoSunil Gangadharan
Department of Molecular Biology and Genetics, Division of Biostatistics and Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Proc Natl Acad Sci U S A 107:21966-72. 2010..We have also discovered a long-range sequence motif that defines S. cerevisiae nucleosome-free regions...
- Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutationsThierry Rouxel
INRA Bioger, UR1290, Avenue Lucien Brétignières, BP 01, Thiverval Grignon F 78850, France
Nat Commun 2:202. 2011..This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints...
- The essential genome of a bacteriumBeat Christen
Department of Developmental Biology, Stanford University, Stanford, CA, USA
Mol Syst Biol 7:528. 2011..The high-resolution strategy used here is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments in a broad class of bacterial species...
- 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....
- Mobile elements: drivers of genome evolutionHaig H Kazazian
Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Science 303:1626-32. 2004..Although the host can often control their numbers, massive expansions of retrotransposons have been tolerated during evolution. Now mobile elements are becoming useful tools for learning more about genome evolution and gene function...
- Transposable elements: powerful facilitators of evolutionKeith R Oliver
School of Biological Sciences and Biotechnology, Faculty of Sustainability, Environmental and Life Sciences, Murdoch University, Perth, Australia
Bioessays 31:703-14. 2009..We propose a general and holistic synthesis on how the presence of TEs within genomes makes them flexible and dynamic, so that genomes themselves are powerful facilitators of their own evolution...
- 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...
- The catalytic domain of all eukaryotic cut-and-paste transposase superfamiliesYao Wu Yuan
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
Proc Natl Acad Sci U S A 108:7884-9. 2011Cut-and-paste DNA transposable elements are major components of eukaryotic genomes and are grouped into superfamilies (e.g., hAT, P) based on sequence similarity of the element-encoded transposase...
- Massive horizontal gene transfer in bdelloid rotifersEugene A Gladyshev
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Science 320:1210-3. 2008..One such gene, apparently of bacterial origin, was overexpressed in Escherichia coli and yielded an active enzyme. The capture and functional assimilation of exogenous genes may represent an important force in bdelloid evolution...
- 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...
- 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....
- 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...
- Insertion sequences in prokaryotic genomesPatricia Siguier
Laboratoire de Microbiologie et Génétique Moléculaires UMR5100 CNRS Campus Université Paul Sabatier 118, 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...
- 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...
- 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...
- 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....
- Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITEGuojun Yang
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
Science 325:1391-4. 2009..The MITE contains internal sequences that enhance transposition. These findings suggest that MITEs achieve high transposition activity by scavenging transposases encoded by distantly related and self-restrained autonomous elements...
- 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....
- Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytesOliver H Tam
Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
Nature 453:534-8. 2008..Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals...
- Small RNA-mediated quiescence of transposable elements in animalsKuniaki Saito
Department of Molecular Biology, Keio University School of Medicine, Tokyo 160 8582, Japan
Dev Cell 19:687-97. 2010....
- Selfish genetic elements, genetic conflict, and evolutionary innovationJohn H Werren
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Proc Natl Acad Sci U S A 108:10863-70. 2011..The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs...
- Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEsHanhui Kuang
Plant Gene Expression Center, Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
Genome Res 19:42-56. 2009..We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae...
- 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...
- Revisiting horizontal transfer of transposable elements in DrosophilaE L S Loreto
UFSM Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
Heredity (Edinb) 100:545-54. 2008..We discuss the methods used to infer HT, their limits and the putative vectors of transposable elements. We outline all the alternative hypotheses and ask how we can be almost certain that phylogenetic inconsistencies are due to HT...
- 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...
- A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogateLarry A Gallagher
Department of Genome Sciences, University of Washington, Campus Box 355065, 1705 NE Pacific Street, Seattle, WA 98195, USA
Proc Natl Acad Sci U S A 104:1009-14. 2007..The library provides a resource for virtually complete identification of genes involved in virulence and other nonessential processes...
- Isolation of human iPS cells using EOS lentiviral vectors to select for pluripotencyAkitsu Hotta
Developmental and Stem Cell Biology Program, Toronto, Ontario, Canada
Nat Methods 6:370-6. 2009..Finally, we used EOS selection to establish Rett syndrome-specific mouse and human iPS cell lines with known mutations in MECP2...
- 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...
- 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...
- Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatinNicole C Riddle
Department of Biology, Washington University St Louis, Missouri 63130, USA
Genome Res 21:147-63. 2011..This comprehensive analysis provides a foundation for future studies of gene activity and chromosomal functions that are influenced by or dependent upon heterochromatin...
- Gene transfer efficiency and genome-wide integration profiling of Sleeping Beauty, Tol2, and piggyBac transposons in human primary T cellsXin Huang
Division of Pediatric Blood and Marrow Transplantation, University of Minnesota Medical School, Minneapolis, Minnesota, USA
Mol Ther 18:1803-13. 2010....
- PiggyBac transposon mutagenesis: a tool for cancer gene discovery in miceRoland Rad
Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridge CB10 1SA, UK
Science 330:1104-7. 2010..Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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....
- 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...
- 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....
- 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...
- 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....
- 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/...
- 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...
- 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...
- 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...
- 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...
- 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....
- 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...
- Conjugative transposons: the tip of the icebergVincent Burrus
Laboratoire de Génétique et Microbiologie, UMR INRA UHP 1128, IFR110, Faculte des Sciences et Techniques, Universite Henri Poincare Nancy 1, BP239, 54506 Vandoeuvre les Nancy, 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...
- 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...
- 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...
- 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...
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 ..
- 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. ..
- 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. ..
- 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> ..