Genomic Impact of Eukaryotic Transposable Elements
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Insertion Site Preference of Mu, Tn5, and Tn7 Transposons. Brian Green, Christiane Bouchier, Cécile Fairhead, Nancy Craig, Brendan Cormack
Insertion site preference of Mu, Tn5, and Tn7 transposons. Brian Green, Christiane Bouchier, Cécile Fairhead, Nancy Craig, Brendan Cormack To cite this version: Brian Green, Christiane Bouchier, Cécile Fairhead, Nancy Craig, Brendan Cormack. Insertion site preference of Mu, Tn5, and Tn7 transposons.. Mobile DNA, BioMed Central, 2012, 3 (1), pp.3. 10.1186/1759-8753-3-3. pasteur-00675691 HAL Id: pasteur-00675691 https://hal-pasteur.archives-ouvertes.fr/pasteur-00675691 Submitted on 1 Mar 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Green et al. Mobile DNA 2012, 3:3 http://www.mobilednajournal.com/content/3/1/3 SHORTREPORT Open Access Insertion site preference of Mu, Tn5, and Tn7 transposons Brian Green1, Christiane Bouchier2, Cécile Fairhead3, Nancy L Craig4 and Brendan P Cormack1* Abstract Background: Transposons, segments of DNA that can mobilize to other locations in a genome, are often used for insertion mutagenesis or to generate priming sites for sequencing of large DNA molecules. For both of these uses, a transposon with minimal insertion bias is desired to allow complete coverage with minimal oversampling. Findings: Three transposons, Mu, Tn5, and Tn7, were used to generate insertions in the same set of fosmids containing Candida glabrata genomic DNA. -
Epigenetic Regulation of the Human Genome by Transposable Elements
EPIGENETIC REGULATION OF THE HUMAN GENOME BY TRANSPOSABLE ELEMENTS A Dissertation Presented to The Academic Faculty By Ahsan Huda In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy in Bioinformatics in the School of Biology Georgia Institute of Technology August 2010 EPIGENETIC REGULATION OF THE HUMAN GENOME BY TRANSPOSABLE ELEMENTS Approved by: Dr. I. King Jordan, Advisor Dr. John F. McDonald School of Biology School of Biology Georgia Institute of Technology Georgia Institute of Technology Dr. Leonardo Mariño-Ramírez Dr. Jung Choi NCBI/NLM/NIH School of Biology Georgia Institute of Technology Dr. Soojin Yi, School of Biology Georgia Institute of Technology Date Approved: June 25, 2010 To my mother, your life is my inspiration... ACKNOWLEDGEMENTS I am evermore thankful to my advisor Dr. I. King Jordan for his guidance, support and encouragement throughout my years as a PhD student. I am very fortunate to have him as my mentor as he is instrumental in shaping my personal and professional development. His contributions will continue to impact my life and career and for that I am forever grateful. I am also thankful to my committee members, John McDonald, Leonardo Mariño- Ramírez, Soojin Yi and Jung Choi for their continued support during my PhD career. Through my meetings and discussions with them, I have developed an appreciation for the scientific method and a thorough understanding of my field of study. I am especially grateful to my friends and colleagues, Lee Katz and Jittima Piriyapongsa for their support and presence, which brightened the atmosphere in the lab in the months and years past. -
Small Genomes
81h INTERNATIONAL CONFERENCE ON Small Genomes 1J.00.""", 1. " 400.000 Rsr II 900.000 September 24 -28, 2000 UCLA CONFERENCE CENTER LAKE ARROWHEAD CALIFORNIA . SCIENTIFIC PROGRAM ORGANIZERS Dr. Jeffrey H. Miller, Chair University of California, Los Angeles Dr. George Weinstock University of Texas-Houston Health Sciences Center Dr. Jizhong Zhou Oak Ridge National Laboratory Dr. Monica Riley Woods Hole Dr. Elisabeth Raleigh New England Biolabs Dr. Theresa (Terry) Gaasterland Rockefeller University ACKNOWLEDGEMENTS The Organizers of the conference gratefully acknowledge the contributions of the following for their support: Amgen Oak Ridge National Laboratory Diversa Corp. National Science Foundation DNASTAR Inc. Department of Energy Dupont De Nemours National Institute of Allergy and Infectious Diseases, National Institutes of Genencor Health Integrated Genomics, Inc. Merck New England Biolabs Pharmacia & Upjohn Co. Proctor & Gamble SmithKline Beecham CONTACT NUMBER The Arrowhead Conference Center Phone number is: (909) 337-2478 SCIENTIFIC PROGRAM SUNDAY, SEPTEMBER 24 4:00-6:00 pm Arrival and Check-in at Lake Arrowhead Conference Center 6:15-7:45 pm Dinner (Dining Room) Opening of Meeting (Pineview Room) 7:45-8:10 pm Jeffrey H. Miller University of California, Los Angeles Welcome 8:10-9:00 pm Keynote Address Julian Davies TerraGen Discovery, Inc. "Evolution of Microbial Resistance to Antibiotics" 9:00 pm Reception (Iris Room) MONDAY, SEPTEMBER 25 7:45-8:30 am Breakfast (Dining Room) Session I Genomes of Pathogens (Pineview Room) 8:45-9:00 -
UNIVERSITY of CALIFORNIA RIVERSIDE Dissecting the Hermes
UNIVERSITY OF CALIFORNIA RIVERSIDE Dissecting the Hermes Transposase: Residues Important for Target DNA Binding and Phosphorylation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Biochemistry and Molecular Biology by Joshua Allen Knapp December 2011 Dissertation Committee: Dr. Peter W. Atkinson, Chairperson Dr. Julia Bailey-Serres Dr. Howard Judelson Copyright by Joshua Allen Knapp 2011 The Dissertation of Joshua Allen Knapp is approved: ________________________________________________________________________ ________________________________________________________________________ _______________________________________________________________________ Chairperson University of California, Riverside ACKNOWLEDGEMENTS Firstly, I would like to thank my advisor Dr. Peter Atkinson. He has been an outstanding mentor over these years and has helped me grow as a scientist and provided me with amazing research opportunities. I would like to thank my committee members Dr. Howard Judelson and Dr. Julia Bailey-Serres for all of their guidance and valuable input that has enhanced the quality of my dissertation research. I would also like to thank my undergraduate advisor Dr. Martin Case who taught me how to write scientifically. Members of the Atkinson lab have become a family for me – one of them literally. I met my wife and the love of my life, Jennifer Wright, in the Atkinson lab. She has been a rock for me, providing me with love and support in so many ways. I feel blessed to have her my life. I would not be the scientist that I am with out Rob Hice. He has taught me more about science than anyone else in my academic career and I am thankful to have him in my life as both a teacher and a friend. -
JOURNAL of BACTERIOLOGY VOLUME 169 DECEMBER 1987 NUMBER 12 Samuel Kaplan, Editor in Chief (1992) Kenneth N
JOURNAL OF BACTERIOLOGY VOLUME 169 DECEMBER 1987 NUMBER 12 Samuel Kaplan, Editor in Chief (1992) Kenneth N. Timmis, Editor (1992) University of Illinois, Urbana Richard M. Losick, Editor (1988) Centre Medical Universitaire, James D. Friesen, Editor (1992) Harvard University, Cambridge, Mass. Geneva, Switzerland University of Toronto, L. Nicholas Ornston, Editor (1992) Graham C. Walker, Editor (1990) Toronto, Canada Yale University, New Haven, Conn. Massachusetts Institute of Stanley C. Holt, Editor (1987) Robert H. Rownd, Editor (1990) Technology, Cambridge, Mass. The University of Texas Health Northwestern Medical School, Robert A. Weisberg, Editor (1990) Science Center, San Antonio Chicago, Ill. National Institute of Child June J. Lascelles, Editor (1989) Health and Human University of California, Los Angeles Development, Bethesda, Md. EDITORIAL BOARD David Apirion (1988) James G. Ferry (1989) Eva R. Kashket (1987) Palmer Rogers (1987) Stuart J. Austin (1987) David Figurski (1987) David E. Kennell (1988) Barry P. Rosen (1989) Frederick M. Ausubel (1989) Timothy J. Foster (1989) Wil N. Konings (1987) Lucia B. Rothman-Denes (1989) Barbara Bachmann (1987) Robert T. Fraley (1988) Jordan Konisky (1987) Rudiger Schmitt (1989) Manfred E. Bayer (1988) David I. Friedman (1989) Dennis J. Kopecko (1987) June R. Scott (1987) Margret H. Bayer (1989) Masamitsu Futai (1988) Viji Krishnapillai (1988) Jane K. Setlow (1987) Claire M. Berg (1989) Robert Gennis (1988) Terry Krulwich (1987) Peter Setlow (1987) Helmut Bertrand (1988) Jane Gibson (1988) Lasse Lindahl (1987) James A. Shapiro (1988) Terry J. Beveridge (1988) Robert D. Goldman (1988) Jack London (1987) Louis A. Sherman (1988) Donald A. Bryant (1988) Susan Gottesman (1989) Sharon Long (1989) Howard A. -
The Struggle for Life of the Genomels Selfish Architects
Hua-Van et al. Biology Direct 2011, 6:19 http://www.biology-direct.com/content/6/1/19 REVIEW Open Access The struggle for life of the genome’s selfish architects Aurélie Hua-Van*, Arnaud Le Rouzic, Thibaud S Boutin, Jonathan Filée and Pierre Capy Abstract Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin’s theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome) evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution. Reviewers: This article was reviewed by Jerzy Jurka, Jürgen Brosius and I. King Jordan. For complete reports, see the Reviewers’ reports section. Background 1930s and 1940s by Fisher, Wright, Haldane, Dobz- For a century and half, from the publication of “On the hansky, Mayr, and Simpson among others), and finally Origin of Species by Means of Natural Selection, or the molecular dimension (Kimura’s neutral evolution the Preservation of Favoured Races in the Struggle for theory, Pauling and Zuckerkandl’s molecular clock con- Life“ by Darwin [1] to the present day, thinking about cept). -
DNA Damage and Tn7 Target Activation Page 1 1 2 DNA Damage
Genetics: Published Articles Ahead of Print, published on June 18, 2008 as 10.1534/genetics.108.088161 DNA damage and Tn7 target activation 1 2 3 DNA damage differentially activates regional chromosomal loci for Tn7 4 transposition in E. coli 5 6 7 Qiaojuan Shi, Adam R. Parks, Benjamin D. Potter, Ilan J. Safir, Yun Luo, Brian 8 M. Forster, Joseph E. Peters* 9 10 Department of Microbiology, Cornell University, Ithaca NY USA 11 12 13 14 15 16 17 18 19 20 21 22 23 *To whom correspondences should be addressed Page 1 DNA damage and Tn7 target activation 1 2 3 Running title: DNA damage and Tn7 target activation 4 5 Key Words: replication restart, target site selection, DNA double strand break 6 repair, chromosome structure 7 8 Corresponding authors contact information 9 175A Wing Hall 10 Ithaca, NY 14853 11 Ph.607-255-2271 12 FAX.607-255-3904 13 [email protected] 14 15 16 Page 2 DNA damage and Tn7 target activation 1 ABSTRACT 2 The bacterial transposon Tn7 recognizes replicating DNA as a target with 3 a preference for the region where DNA replication terminates in the Escherichia 4 coli chromosome. It was previously shown that DNA double strand breaks in the 5 chromosome stimulate Tn7 transposition where transposition events occur 6 broadly around the point of the DNA break. We show that individual DNA breaks 7 actually activate a series of small regional hotspots in the chromosome for Tn7 8 insertion. These hotspots are fixed and only become active when a DNA break 9 occurs in the same region of the chromosome. -
Profile of Nancy L. Craig
PROFILE Profile of Nancy L. Craig ancy Craig studies how DNA again. This triggers the transformation moves from place to place: from a quiet hitchhiker in the bacterial Na deceptively simple quest that genome to an active virus bent on repli- has revealed how transposons, cating itself and destroying the bacterial or so-called “DNA cut-and-paste ele- cell (1). ments,” snip themselves from one loca- tion on the chromosome and resettle in From Virus to Transposon another. Craig, a professor of molecular Craig’s love of cutting and pasting led her biology and genetics at Johns Hopkins to the National Institutes of Health University School of Medicine (Baltimore, (NIH) for a postdoctoral position in the MD), an investigator with the Howard laboratory of Howard Nash, inventor of Hughes Medical Institute, and a recently the first in vitro system for studying site- elected member of the National Academy specific recombination, such as the in- of Sciences, has helped uncover how tegration and excision cycle of phage transposable elements jump from one po- lambda. Under his guidance, Craig hoped sition to another to cause disease and to determine molecules necessary to re- sculpt the seemingly infinite variety of locate the virus within the genome. genomes on Earth. While she was at the NIH, a 1982 Even before scientists revealed in 2001 Nature article (2) piqued her interest. that half of the human genome was packed “It was about the seventh transposable with transposable elements, it was clear element described so far, aptly named from Barbara McClintock’s classic studies Tn7, that inserted into a single specific in the 1940s that these so-called “jumping site. -
Chromatic Bacteria – a Broad Host-Range Plasmid and Chromosomal Insertion Toolbox for Fluorescent Protein Expression in Bacteria
bioRxiv preprint doi: https://doi.org/10.1101/402172; this version posted September 7, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Chromatic bacteria – A broad host-range plasmid and chromosomal insertion toolbox for fluorescent protein expression in bacteria Rudolf O. Schlechter1,2, Hyunwoo Jun1#, Michał Bernach1,2#, Simisola Oso1, Erica Boyd1, Dian A. Muñoz-Lintz1, Renwick C. J. Dobson1,2,3, Daniela M. Remus1,2,4, and Mitja N. P. Remus-Emsermann1,2* 1School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. 2Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand. 3Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia. 4Protein Science & Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand. # Both authors contributed equally to this work * Correspondence: Mitja N. P. Remus-Emsermann [email protected] Keywords: fluorophore, fluorescent labelling, tagging, Tn5, Tn7, transposon bioRxiv preprint doi: https://doi.org/10.1101/402172; this version posted September 7, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Differential fluorescent labelling of bacteria has become instrumental for many aspects of microbiological research, such as the study of biofilm formation, bacterial individuality, evolution, and bacterial behaviour in complex environments. -
Structural Basis for DNA Targeting by the Tn7 Transposon
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.24.445525; this version posted May 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Structural basis for DNA targeting by the Tn7 transposon Yao Shen1,2, Josue Gomez-Blanco1,2, Michael T. Petassi3, Joseph E. Peters3, Joaquin Ortega2,4, Alba Guarné1,2,5,* 1Department of Biochemistry, McGill University, Montreal (QC), Canada. 2Centre de Recherche and Biologie Structurale, McGill University, Montreal (QC), Canada. 3Department of Microbiology, Cornell University, Ithaca (NY), USA. 4Department of Anatomy and Cell Biology, McGill University Montreal (QC), Canada. 5Lead Contact *Correspondence: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.05.24.445525; this version posted May 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Tn7 transposable elements are unique for their highly specific, and sometimes programmable, target-site selection mechanisms and precise insertions. All the elements in the Tn7-family utilize a AAA+ adaptor (TnsC) to coordinates target-site selection with transposase activation and prevent insertions at sites already containing a Tn7 element. Due to its multiple functions, TnsC is considered the linchpin in the Tn7 element. Here we present the high-resolution cryo- EM structure of TnsC bound to DNA using a gain-of-function variant of the protein and a DNA substrate that together recapitulate the recruitment to a specific DNA target site. -
Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution
Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution by Tyler Adam Elliott A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Doctor of Philosophy in Integrative Biology Guelph, Ontario, Canada © Tyler Adam Elliott, December, 2016 ABSTRACT Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution Tyler Adam Elliott Advisor: University of Guelph, 2016 Professor T.R. Gregory Transposable elements (TEs), mobile pieces of self-replicating DNA, are one of the driving forces behind genomic evolution in eukaryotic organisms. Their contribution to genome size variation and as mutagens has led researchers to pursue their study in the hope of better understanding the evolution of genomic properties and organismal phenotypes But TEs can also be thought of in a multi-level evolutionary context, with TEs best understood as evolving populations residing within (and interacting with) the host genome. I argue, with empirical evidence from the literature, that the multi-level approach advocated by the classic ―selfish DNA‖ papers of 1980 has become less commonly invoked over the past 35 years, in a favour of a strictly organism-centric view. I also make the case that an exploration of evolution at the level of TEs within genomes is required, one which articulates the similarities and differences between a TE population and a traditional population of organisms. A comprehensive analysis of sequenced eukaryote genomes outlines the landscape of how TE superfamilies are distributed, but also reveals that how TEs are reported needs to be addressed. A proper exploration of evolution at the TE level will require a dramatic change to how TE information is annotated, curated, and stored, and I make several specific recommendations in this regard. -
![Jump Around: Transposons in and out of the Laboratory[Version 1; Peer Review: 2 Approved]](https://docslib.b-cdn.net/cover/5835/jump-around-transposons-in-and-out-of-the-laboratory-version-1-peer-review-2-approved-3745835.webp)
Jump Around: Transposons in and out of the Laboratory[Version 1; Peer Review: 2 Approved]
F1000Research 2020, 9(F1000 Faculty Rev):135 Last updated: 11 MAR 2020 REVIEW Jump around: transposons in and out of the laboratory [version 1; peer review: 2 approved] Anuj Kumar 1,2 1Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA 2Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA First published: 24 Feb 2020, 9(F1000 Faculty Rev):135 ( Open Peer Review v1 https://doi.org/10.12688/f1000research.21018.1) Latest published: 24 Feb 2020, 9(F1000 Faculty Rev):135 ( https://doi.org/10.12688/f1000research.21018.1) Reviewer Status Abstract Invited Reviewers Since Barbara McClintock’s groundbreaking discovery of mobile DNA 1 2 sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, version 1 genome evolution, and human health. Transposable elements are a major 24 Feb 2020 constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is F1000 Faculty Reviews are written by members of profound, as over 100 human heritable diseases have been attributed to the prestigious F1000 Faculty. They are transposon insertions. Transposition can be highly mutagenic, perturbing commissioned and are peer reviewed before genome integrity and gene expression in a wide range of organisms. This publication to ensure that the final, published version mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the is comprehensive and accessible.