“What You Need, Baby, I Got It”: Transposable Elements As Suppliers of Cis-Operating Sequences in Drosophila
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Copy Number of P Elements, KP/Full-Sized P Element Ratio and Their Relationships with Environmental Factors in Brazilian Drosophila Melanogaster Populations
Heredity (2003) 91, 570–576 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Copy number of P elements, KP/full-sized P element ratio and their relationships with environmental factors in Brazilian Drosophila melanogaster populations MT Ruiz and CMA Carareto Departamento de Biologia, IBILCE, Universidade Estadual Paulista, Rua Cristo´va˜o Colombo, 2265, Jardim Nazare´,Sa˜o Jose´ do Rio Preto 15054-000, SP, Brazil The P transposable element copy numbers and the KP/full- and the strains from less extreme latitudes had many sized P element ratios were determined in eight Brazilian more full-sized P than KP elements. However, no clinal strains of Drosophila melanogaster. Strains from tropical variation was observed. Strains from different localities, regions showed lower overall P element copy numbers previously classified as having P cytotype, displayed a higher than did strains from temperate regions. Variable numbers of or a lower proportion of KP elements than of full-sized full-sized and defective elements were detected, but the P elements, as well as an equal number of the two element full-sized P and KP elements were the predominant classes types, showing that the same phenotype may be produced of elements in all strains. The full-sized P and KP element by different underlying genomic components of the P–M ratios were calculated and compared with latitude. The system. northernmost and southernmost Brazilian strains showed Heredity (2003) 91, 570–576, advance online publication, fewer full-sized elements than KP elements per genome, 17 September 2003; doi:10.1038/sj.hdy.6800360 Keywords: P transposable elements; KP elements; KP/full-sized P elements; P–M systems; Drosophila melanogaster Introduction elements, allows P element transposition (Engels, 1983). -
Interspecific DNA Transformation in Drosophila (Drosophila Melanogaster/Drosophila Simulans/Rosy Gene/P Element/Transposable Element) NANCY J
Proc. Nati. Acad. Sci. USA Vol. 81, pp. 7515-7519, December 1984 Genetics Interspecific DNA transformation in Drosophila (Drosophila melanogaster/Drosophila simulans/rosy gene/P element/transposable element) NANCY J. SCAVARDA AND DANIEL L. HARTL Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110 Communicated by Peter H. Raven, August 7, 1984 ABSTRACT A DNA fragment that includes the wild-type (4). Use of an average rate of synonymous substitutions in rosy (ry+) gene of Drosophila melanogaster has been intro- coding regions of 5.1 + 0.3 x 10-9 per nucleotide site per yr duced by microinjection into the germ line of the reproductive- (9, 10) results in an estimated time since separation of 4.1 + ly isolated species Drosophila simulans and incorporated into 0.2 million yr, but analogous estimates based on rates of nu- the D. simulans genome. Transformation was mediated by the cleotide substitution in intervening sequences range from 3.8 transposable element P, which occurs in the genome of most to 6.8 million yr. These estimates are uncertain because av- natural populations ofD. melanogaster but not in D. simulans. erage rates of substitution in other organisms may have little Rubin and Spradling [Rubin, G. M. & Spradling, A. C. relevance to insects, and because evolutionary change in the (1982) Science 218, 348-353] have previously shown that the gene coding for alcohol dehydrogenase may be atypical. ry' DNA fragment, which is flanked by recognition sequences Although D. melanogaster and D. simulans are reproduc- of P element, can transform the germ line ofD. -
Evolution of Pogo, a Separate Superfamily of IS630-Tc1-Mariner
Gao et al. Mobile DNA (2020) 11:25 https://doi.org/10.1186/s13100-020-00220-0 RESEARCH Open Access Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates Bo Gao, Yali Wang, Mohamed Diaby, Wencheng Zong, Dan Shen, Saisai Wang, Cai Chen, Xiaoyan Wang and Chengyi Song* Abstracts Background: Tc1/mariner and Zator, as two superfamilies of IS630-Tc1-mariner (ITm) group, have been well-defined. However, the molecular evolution and domestication of pogo transposons, once designated as an important family of the Tc1/mariner superfamily, are still poorly understood. Results: Here, phylogenetic analysis show that pogo transposases, together with Tc1/mariner,DD34E/Gambol,and Zator transposases form four distinct monophyletic clades with high bootstrap supports (> = 74%), suggesting that they are separate superfamilies of ITm group. The pogo superfamily represents high diversity with six distinct families (Passer, Tigger, pogoR, Lemi, Mover,andFot/Fot-like) and wide distribution with an expansion spanning across all the kingdoms of eukaryotes. It shows widespread occurrences in animals and fungi, but restricted taxonomic distribution in land plants. It has invaded almost all lineages of animals—even mammals—and has been domesticated repeatedly in vertebrates, with 12 genes, including centromere-associated protein B (CENPB), CENPB DNA-binding domain containing 1 (CENPBD1), Jrk helix–turn–helix protein (JRK), JRK like (JRKL), pogo transposable element derived with KRAB domain (POGK), and with ZNF domain (POGZ), and Tigger transposable element-derived 2 to 7 (TIGD2–7), deduced as originating from this superfamily. Two of them (JRKL and TIGD2) seem to have been co-domesticated, and the others represent independent domestication events. -
Genome of Drosophila Guanche WOLFGANG J
Proc. Nati. Acad. Sci. USA Vol. 89, pp. 4018-4022, May 1992 Genetics P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche WOLFGANG J. MILLER*, SYLVIA HAGEMANNt, ELEONORE REITERt, AND WILHELM PINSKERtt *Institut fur Botanik, Abteilung Cytologie und Genetik, Rennweg 14, A-1030 Vienna, Austria; and tInstitut fur Allgemeine Biologie, Abteilung Genetik, Wahringerstrasse 17, A-1090 Vienna, Austria Communicated by Bruce Wallace, December 23, 1991 ABSTRACT In Drosophila guanche, P-homologous se- In germ-line cells, the copy number of P elements is quences were found to be located in a tandem repetitive array genetically regulated by a complex mixture of chromosomal (copy number: 20-50) at a single genomic site. The cytological and cytoplasmic factors (11). At least two mechanisms can be position on the polytene chromosomes was determined by in situ distinguished: the maternally transmitted cytotype (12) and a hybridization (chromosome 0: 85C). Sequencing of one com- chromosomally inherited control system (13). In the P cyto- plete repeat unit (3.25 kilobases) revealed high sequence simi- type, the cytoplasmic state of P-strain individuals, transpo- larity between the central coding region comprising exons 0 to sition is repressed in somatic cells and in the germ line. In 2 and the corresponding section of the Drosophila melanogaster general the P cytotype develops gradually as a result of the P element. The rest of the sequence has diverged considerably. increasing number of P-element copies. M-strains, on the Exon 3 has no coding function and the inverted repeats have other hand, have genomes devoid of P elements. -
History to the Rescue Pseudogenes Get Some Respect Flyin' Pain Free
RESEARCH NOTES Pseudogenes get some respect adenoviral entry is mediated by interaction between RGD motifs and integrins, they went on to engineer a virus with an RGD peptide. This Pseudogenes are the non-functional remnants of genes that have version of the modified virus specifically infected tumor cells and repli- been thought to do nothing more than take up space. A new cated more effectively than Delta-24. When injected directly into report by Shinji Hirotsune and colleagues provides evidence that human gliomas xenografted into mice, Delta-24-RGD allowed signifi- at least one such pseudogene has an essential role as a regulator of cantly longer survival than did Delta-24 or an inactivated virus control. gene expression (Nature 423, 91–96; 2003). A fortuitous insertion More impressively, 60% of mice treated with Delta-24-RGD were long- of a transgene into the Makorin1-p1 locus generated a mouse term survivors (compared with 15% of those treated with Delta-24 with a bone deformity and polycystic kidneys. Makorin1-p1 is a characterized by complete tumor regression). MH pseudogene that is normally transcribed, although no functional protein product can be produced. Strikingly, the transgene insertion reduced not only the transcription of Makorin1-p1, but RNAi on or off target? that of its functional homolog, Makorin1, as well. In vitro Two new reports examine the specificity of RNA interference (RNAi) in experiments show that an intact Makorin1-p1 locus stabilizes the human cells using genome-wide expression profiling. Targeting exoge- Makorin1 mRNA, and a rescue of the original transgenic mouse nous GFP in human embryonic kidney cells, Jen-Tsan Chi and col- with Makorin1-p1 proves that the pseudogene is required for leagues report efficient and specific knockdown using two different normal expression of Makorin1. -
Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using White Co-Conversion
G3: Genes|Genomes|Genetics Early Online, published on August 26, 2016 as doi:10.1534/g3.116.032557 Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Co-Conversion Daniel Tianfang Ge*,†,1, Cindy Tipping*,‡,1, Michael H. Brodsky§, Phillip D. Zamore*,‡,**,2 *RNA Therapeutics Institute, †Interdisciplinary Graduate Program, ‡Howard Hughes Medical Institute, §Department of Molecular, Cell and Cancer Biology, **Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA 1These authors contributed equally to this work. 2To whom correspondence should be addressed. 1 © The Author(s) 2013. Published by the Genetics Society of America. Running title: Rapid Screening for CRISPR Editing Keywords: Cas9; Co-Conversion; Genetic Screen; Microhomology-Mediated End Joining; Homologous Recombination Corresponding author: Phillip D. Zamore Address: 368 Plantation Street, AS4-2053, Worcester, MA 01605 Tel.: 508-856-2191 E-mail: [email protected] 2 1 ABSTRACT 2 Adoption of a streamlined version of the bacterial CRISPR/Cas9 defense system has 3 accelerated targeted genome engineering. The Streptococcus pyogenes Cas9 protein, 4 directed by a simplified, CRISPR-like single guide RNA, catalyzes a double-stranded 5 DNA break at a specific genomic site; subsequent repair by end joining can introduce 6 mutagenic insertions or deletions, while repair by homologous recombination using an 7 exogenous DNA template can incorporate new sequence at the target locus. However, 8 the efficiency of Cas9-directed mutagenesis is low in Drosophila melanogaster. Here, we 9 describe a strategy that reduces the time and effort required to identify flies with 10 targeted genomic changes. -
Evaluating the Probability of CRISPR-Based Gene Drive Contaminating Another Species
bioRxiv preprint doi: https://doi.org/10.1101/776609; this version posted September 19, 2019. 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 4.0 International license. Evaluating the Probability of CRISPR-based Gene Drive Contaminating Another Species 1 2 3 4 Virginie Courtier-Orgogozo , Antoine Danchin , Pierre-Henri Gouyon and Christophe Boëte 1 I nstitut Jacques Monod, CNRS, UMR 7592, Université de Paris, Paris, France 2 I nstitut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris Descartes, Paris, France 3 I nstitut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France 4 I SEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France Abstract The probability D that a given CRISPR-based gene drive element contaminates another, non-target species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = (hyb+transf).express.cut.flank.immune.nonextinct with hyb = probability of hybridization between the target species and a non-target species transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a non-target species (with no hybridization) express = probability that the Cas9 and guide RNA genes are expressed cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host flank = probability that the gene drive cassette inserts at the cut site immune = probability that the immune system does not reject Cas9-expressing cells nonextinct = probability of invasion of the drive within the population We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. -
The Evolutionary Life History of P Transposons: from Horizontal Invaders to Domesticated Neogenes
Chromosoma (2001) 110:148–158 DOI 10.1007/s004120100144 CHROMOSOMA FOCUS Wilhelm Pinsker · Elisabeth Haring Sylvia Hagemann · Wolfgang J. Miller The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes Received: 5 February 2001 / In revised form: 15 March 2001 / Accepted: 15 March 2001 / Published online: 3 May 2001 © Springer-Verlag 2001 Abstract P elements, a family of DNA transposons, are uct of their self-propagating lifestyle. One of the most known as aggressive intruders into the hitherto uninfected intensively studied examples is the P element of Dro- gene pool of Drosophila melanogaster. Invading through sophila, a family of DNA transposons that has proved horizontal transmission from an external source they useful not only as a genetic tool (e.g., transposon tag- managed to spread rapidly through natural populations ging, germline transformation vector), but also as a model within a few decades. Owing to their propensity for rapid system for investigating general features of the evolu- propagation within genomes as well as within popula- tionary behavior of mobile DNA (Kidwell 1994). P ele- tions, they are considered as the classic example of self- ments were first discovered as the causative agent of hy- ish DNA, causing havoc in a genomic environment per- brid dysgenesis in Drosophila melanogaster (Kidwell et missive for transpositional activity. Tracing the fate of P al. 1977) and were later characterized as a family of transposons on an evolutionary scale we describe differ- DNA transposons -
Helitronscanner Uncovers a Large Overlooked Cache of Helitron Transposons in Many Plant Genomes
HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes Wenwei Xionga, Limei Heb, Jinsheng Laic, Hugo K. Doonerb,d,1, and Chunguang Dua,1 aDepartment of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043; bWaksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854; cNational Maize Improvement Center, China Agricultural University, Beijing 100083, China; and dDepartment of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08801 Contributed by Hugo K. Dooner, June 6, 2014 (sent for review January 28, 2014) Transposons make up the bulk of eukaryotic genomes, but are content of maize (14). This tool was based on conserved sequences difficult to annotate because they evolve rapidly. Most of the at the termini of most Helitrons (5′-TC and CTAG-3′)andacon- unannotated portion of sequenced genomes is probably made up served 16- to 20-bp palindromic structure located 10–15 bp up- of various divergent transposons that have yet to be categorized. stream of the 3′ terminus. Using HelitronFinder, we identified Helitrons are unusual rolling circle eukaryotic transposons that almost 3,000 new Helitrons intheB73maizegenome(12). often capture gene sequences, making them of considerable evo- HelSearch (15), another computational tool, is very similar lutionary importance. Unlike other DNA transposons, Helitrons do to HelitronFinder in terms of identifying the 3′ end of Helitrons. not end in inverted repeats or create target site duplications, so Both programs look for the hairpin structure and the CTRR 3′ they are particularly challenging to identify. Here we present terminus. The difference is that users of HelSearch have to ′ HelitronScanner, a two-layered local combinational variable (LCV) manually search for the 5 end of Helitrons, whereas HelitronFinder ′ tool for generalized Helitron identification that represents a major can identify the 5 end automatically. -
Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum Violaceum
Copyright © 2005 by the Genetics Society of America DOI: 10.1534/genetics.105.042564 Repeat-Induced Point Mutation and the Population Structure of Transposable Elements in Microbotryum violaceum Michael E. Hood,*,1 Melanie Katawczik† and Tatiana Giraud‡ *Department of Biology, University of Virginia, Charlottesville, Virginia 22903, †Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695 and ‡Ecologie, Syste´matique et Evolution, Universite´ Paris-Sud, F-91405 Orsay Cedex, France Manuscript received February 25, 2005 Accepted for publication April 12, 2005 ABSTRACT Repeat-induced point mutation (RIP) is a genome defense in fungi that hypermutates repetitive DNA and is suggested to limit the accumulation of transposable elements. The genome of Microbotryum violaceum has a high density of transposable elements compared to other fungi, but there is also evidence of RIP activity. This is the first report of RIP in a basidiomycete and was obtained by sequencing multiple copies of the integrase gene of a copia-type transposable element and the helicase gene of a Helitron-type element. In M. violaceum, the targets for RIP mutations are the cytosine residues of TCG trinucleotide combinations. Although RIP is a linkage-dependent process that tends to increase the variation among repetitive se- quences, a chromosome-specific substructuring was observed in the transposable element population. The observed chromosome-specific patterns are not consistent with RIP, but rather suggest an effect of gene conversion, which is also a linkage-dependent process but results in a homogenization of repeated se- quences. Particular sequences were found more widely distributed within the genome than expected by chance and may reflect the recently active variants. -
The Future of Transposable Element Annotation and Their Classification in the Light of Functional Genomics
The future of transposable element annotation and their classification in the light of functional genomics -what we can learn from the fables of Jean de la Fontaine? Peter Arensburger, Benoit Piegu, Yves Bigot To cite this version: Peter Arensburger, Benoit Piegu, Yves Bigot. The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from thefables of Jean de la Fontaine?. Mobile Genetic Elements, Taylor & Francis, 2016, 6 (6), pp.e1256852. 10.1080/2159256X.2016.1256852. hal-02385838 HAL Id: hal-02385838 https://hal.archives-ouvertes.fr/hal-02385838 Submitted on 27 May 2020 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. Copyright The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine? Peter Arensburger1, Benoît Piégu2, and Yves Bigot2 1 Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768 - United States of America. 2 Physiologie de la reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly – France Corresponding author address: Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768 - United States of America. -
Repeated Horizontal Transfers of Four DNA Transposons in Invertebrates and Bats Zhou Tang1†, Hua-Hao Zhang2†, Ke Huang3, Xiao-Gu Zhang2, Min-Jin Han1 and Ze Zhang1*
Tang et al. Mobile DNA (2015) 6:3 DOI 10.1186/s13100-014-0033-1 RESEARCH Open Access Repeated horizontal transfers of four DNA transposons in invertebrates and bats Zhou Tang1†, Hua-Hao Zhang2†, Ke Huang3, Xiao-Gu Zhang2, Min-Jin Han1 and Ze Zhang1* Abstract Background: Horizontal transfer (HT) of transposable elements (TEs) into a new genome is considered as an important force to drive genome variation and biological innovation. However, most of the HT of DNA transposons previously described occurred between closely related species or insects. Results: In this study, we carried out a detailed analysis of four DNA transposons, which were found in the first sequenced twisted-wing parasite, Mengenilla moldrzyki. Through the homology-based strategy, these transposons were also identified in other insects, freshwater planarian, hydrozoans, and bats. The phylogenetic distribution of these transposons was discontinuous, and they showed extremely high sequence identities (>87%) over their entire length in spite of their hosts diverging more than 300 million years ago (Mya). Additionally, phylogenies and comparisons of transposons versus orthologous gene identities demonstrated that these transposons have transferred into their hosts by independent HTs. Conclusions: Here, we provided the first documented example of HT of CACTA transposons, which have been so far extensively studied in plants. Our results demonstrated that bats had continuously acquired new DNA elements via HT. This implies that predation on a large quantity of insects might increase bat exposure to HT. In addition, parasite-host interaction might facilitate exchanging of their genetic materials. Keywords: Horizontal transfer, CACTA transposons, Mammals, Recent activity Background or isolated species.