DOCSLIB.ORG

The Saccharomyces Ty5 Retrotransposon Family Is Associated with Origins of DNA Replication at the Telomeres and the Silent Mating Locus HMR SIGE Zou, DAVID A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Saccharomyces Ty5 Retrotransposon Family Is Associated with Origins of DNA Replication at the Telomeres and the Silent Mating Locus HMR SIGE Zou, DAVID A Proc. Natl. Acad. Sci. USA Vol. 92, pp. 920-924, January 1995 Genetics The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR SIGE Zou, DAVID A. WRIGHT, AND DANIEL F. VOYTAS* Department of Zoology and Genetics, Iowa State University, Ames, IA 50011 Communicated by Mary Lou Pardue, Massachusetts Institute of Technology, Cambridge, MA, October 3, 1994 ABSTRACT We have characterized the genomic organi- with tRNA genes has been well documented, and most Ty3 zation of the TyS retrotransposons among diverse strains of insertions are located within a few bases of the transcription Saccharomyces cerevisiae and the related species Saccharomyces start site of genes transcribed by RNA polymerase III (pol III) paradoxus. The S. cerevisiae strain S288C (or its derivatives) (4). The fourth retrotransposon family, Ty4, is represented by carries eight Ty5 insertions. Six of these are located near the a single insertion on chr III. This element is within 300 bp of telomeres, and five are found within 500 bp of autonomously a tRNA gene, and tRNA genes are associated with 10 of 12 Ty4 replicating sequences present in the type X subtelomeric insertions currently in the sequence data base (GenBank, repeat. The remaining two S. cerevisiae elements are adjacent release 83.0). Thus, a target bias, and in particular a preference to the silent mating locus HMR and are located within 500 bp for tRNA genes, is readily apparent from the genomic orga- of the origin of replication present in the transcriptional nization of endogenous Tyl-4 elements. silencer HMR-E. Although the S. cerevisiae TyS elements no Transposition assays have made it possible to monitor the longer appear capable of transposition, some strains of S. target choice of de novo Tyl or Ty3 transposition events. For paradoxus have numerous Ty5 insertions, suggesting that example, Tyl target preference was analyzed by determining transposition is occurring in this species. Most of these integration sites for 32 independent transposition events onto elements are adjacent to type X telomeric repeats, and regions chr III (3). Over half (57%) were within 400 bp upstream of flanking four of five characterized S. paradoxus insertions tRNA genes. Similarly, Ty3 integrates within 1-4 nt of the carry autonomously replicating sequences. The genomic or- transcription start site of genes transcribed by pol III (5-7). ganization of the Ty5 elements is in marked contrast to the Target specificity for Ty3 requires the assembly of the pol III other S. cerevisiae retrotransposon families (Tyl-4), which are transcription complex, and the transcription factor TFIIIB has typically located within 500 bp of tRNA genes. For Ty3, this been directly implicated in directing Ty3 integration (6, 7). The association reflects an interaction between Ty3 and the RNA target bias observed from the genomic organization ofTyl and polymerase III transcription complex, which appears to direct Ty3 insertions, therefore, apparently reflects a mechanism that integration [Chalker, D. L. & Sandmeyer, S. B. (1992) Genes directs these elements to particular sites in the genome and, at Dev. 6, 117-128]. By analogy to Ty3, we predict that Ty5 target least for Ty3, to the pol III transcription complex. choice is specified by interactions with factors present at both An additional S. cerevisiae retrotransposon family, desig- the telomeres and HMR that are involved in DNA replication, nated TyS, was discovered upon examination of the DNA transcriptional silencing, or the maintenance of the unique sequence of chr III (8). In contrast to the other Ty element chromatin structure at these sites. families, none of the three TyS insertions on chr III resides near tRNA genes (3). We have analyzed additional Ty5 target sites Retrotransposons are mobile genetic elements that replicate among S. cerevisiae strains and species closely related to S. by reverse transcription of an RNA intermediate. The final cerevisiae to determine whether the Ty5 family has a target site step in the retrotransposon life cycle is the integration of an bias and to characterize the nature of such sites.t element into a new site in the host genome. Integration may be deleterious to the host cell because it can cause mutations or MATERIALS AND METHODS lead to chromosome rearrangements. Mechanisms that mini- mize this damage preserve the host's genetic integrity and also Strains. Table 1 lists yeast strains used in this study, with the allow retrotransposons to replicate and maintain viable pop- exception of YH51 (MATa, his4-539, lys2-801, spt3-202, ura3- ulations. In the yeast, Saccharomyces cerevisiae mechanisms 52) (gift of J. Boeke, Johns Hopkins School of Medicine, have evolved that limit the negative consequences of integra- Baltimore), which was used to assay replication activity. tion by directing transposition to specific sites in the genome. DNA Manipulations. Southern hybridization filters contain- Target preference of the S. cerevisiae retrotransposons has ing yeast genomic DNA or yeast chromosomes that had been been made strikingly evident by the recent genome sequencing separated on pulsed-field gels were prepared as described (9). efforts. Insertions of the four best-characterized retrotrans- Filters were hybridized as in ref. 10 with DNA fragments that poson families (Tyl-4) are found within the nucleotide se- had been radiolabeled by random priming (Promega). Hybrid- quences of chromosomes III and XI (chr III and chr XI, ization probes included either restriction fragments of the respectively) (1, 2). Of the 28 insertions representing the TyS-1 element (see Fig. 1A) or long terminal repeat (LTR) closely related Tyl and Ty2 retrotransposons, 27 are found and type X repeat probes generated by PCR amplification (9). within 500 bp of tRNA genes (or 500 bp from a Ty element in The LTR probes were generated from the TyS-1 element of S. cases of multiple insertions at a single tRNA gene) (3). For the cerevisiae (DVO115 = AGTAATGCTTTAGTATTG; Ty3 element family, a single insertion is found on chr XI within the promoter region of a tRNA gene. The association of Ty3 Abbreviations: chr, chromosome; pol III, RNA polymerase III; LTR, long terminal repeat; ARS, autonomously replicating sequence; ACS, autonomously replicating consensus sequence. The publication costs of this article were defrayed in part by page charge *To whom reprint requests should be addressed. payment. This article must therefore be hereby marked "advertisement" in tThe sequences reported in this paper have been deposited in the accordance with 18 U.S.C. §1734 solely to indicate this fact. GenBank data base (accession nos. U19263 and U19264). 920 Downloaded by guest on September 28, 2021 Genetics: Zou et al. Proc. Natl. Acad. Sci. USA 92 (1995) 921 DVO116 = TAGTAAGTTTATTGGACC) or the Ty5-5 el- Table 1. Yeast strains used in this study ement from Saccharomyces paradoxus (DVO182 = GGGTA- Strain Ty5 copy ATGTTTCAGT; DVO116). The X probe was amplified with designation no.* Sourcet primers whose sequences were derived from the X repeat at Species the left telomere of chr III (DVO196 = TGCTCGAGTATAT- Saccharomyces cerevisiae Y-12632 0 NRRL ACCATCTCAAA; DVO197 = AGGTCGACTCATATCAT- S. cerevisiae A364a 2 J. Boeke GCTATTGG). Filters of overlapping phage A clones of S. S. cerevisiae S288C 1 J. Boeke cerevisiae strain AB972 were obtained from the American S. cerevisiae SKi 1 J. Boeke Type Culture Collection. An S. paradoxus minilibrary was Saccharomyces chevalierit Y-12633 0 NRRL constructed in pBluescript (Stratagene) with size-selected Saccharomyces italicust Y-12649 2 NRRL DNA from strain NRRL Y-17217. Ligation products were Saccharomyces norbensist Y-12656 2 NRRL introduced into Escherichia coli by electroporation, and de- Saccharomyces oleaceust Y-12657 1 NRRL sired recombinants were identified by colony hybridization Saccharomyces diastaticust Y-2416 2 NRRL using the internal probe from Ty5-1 (see Fig. 1A) (9). DNA Saccharomyces hienipiensist Y-6677 2 NRRL sequences were determined with the fmol DNA sequencing kit Saccharomyces oleaginosust Y-6679 2 NRRL (Promega), or by the Nucleic Acid Facility of Iowa State Saccharomyces heterogenicus Y-1354 0 NRRL University. Sequence analysis was performed by using Genet- Saccharomyces bayanus Y-12624 0 NRRL ics Computer Group computer programs (11). Saccharomyces kluyveri Y-12651 0 NRRL Test for DNA Replication Activity. Several TyS elements and Saccharomyces dairensis Y-12639 0 NRRL their flanking sequences were tested for the ability to sustain Saccharomyces exiguus Y-12640 0 NRRL plasmid replication in S. cerevisiae. For Ty5-S, the 3' flanking Saccharomyces unisporus Y-1556 0 NRRL region was subcloned into the URA3-derived integration plas- Saccharomyces servazzii Y-12661 0 NRRL mid pRS406 (12) to create the test plasmid pSZ107. Plasmids Saccharomyces castellii Y-12630 0 NRRL identified from the minilibrary that carried the Ty5-6, Ty5-12, Saccharomyces paradoxus Y-17217 5-8 NRRL and Ty5-14 elements were directly modified by the addition of S. paradoxus Y-17218 1 NRRL the URA3 gene, resulting in test plasmids pSZ120, pSZ119, and S. paradoxus 2980 0 CBS pSZ121, respectively. Test plasmids were introduced into the S. paradoxus 7400 0 CBS ura3 S. cerevisiae strain YH51 by electroporation (9). Yeast S. paradoxus 6303 0 DBVPG cells were plated on synthetic medium without uracil, and S. paradoxus 6304 0 DBVPG Ural colonies were counted after 48 hr at 30°C. S. paradoxus 6489 3 DBVPG S. paradoxus 6490 3 DBVPG S. paradoxus 6492 3 DBVPG RESULTS Candida albicans YDV84 0 F. Spencer Distribution of the TyS Elements in S. cerevisiae. Eleven S. Candida utilis F608 0 J. Boeke cerevisiae strains were analyzed by Southern hybridization to Kluyveromyces lactis F645 0 J. Boeke determine TyS copy number. Although many of these strains Pichia rhodanensis F612 0 J. Boeke are designated as separate species, recent assessments of DNA Saccharomycopsis lipolytica F613 0 J. Boeke divergence indicate that all are likely to be isolates of S.
Load more

Recommended publications
  • "Evolutionary Emergence of Genes Through Retrotransposition"
    Evolutionary Emergence of Advanced article Genes Through Article Contents . Introduction Retrotransposition . Gene Alteration Following Retrotransposon Insertion . Retrotransposon Recruitment by Host Genome . Retrotransposon-mediated Gene Duplication Richard Cordaux, University of Poitiers, Poitiers, France . Conclusion Mark A Batzer, Department of Biological Sciences, Louisiana State University, Baton Rouge, doi: 10.1002/9780470015902.a0020783 Louisiana, USA Variation in the number of genes among species indicates that new genes are continuously generated over evolutionary times. Evidence is accumulating that transposable elements, including retrotransposons (which account for about 90% of all transposable elements inserted in primate genomes), are potent mediators of new gene origination. Retrotransposons have fostered genetic innovation during human and primate evolution through: (i) alteration of structure and/or expression of pre-existing genes following their insertion, (ii) recruitment (or domestication) of their coding sequence by the host genome and (iii) their ability to mediate gene duplication via ectopic recombination, sequence transduction and gene retrotransposition. Introduction genes, respectively, and de novo origination from previ- ously noncoding genomic sequence. Genome sequencing Variation in the number of genes among species indicates projects have also highlighted that new gene structures can that new genes are continuously generated over evolution- arise as a result of the activity of transposable elements ary times. Although the emergence of new genes and (TEs), which are mobile genetic units or ‘jumping genes’ functions is of central importance to the evolution of that have been bombarding the genomes of most species species, studies on the formation of genetic innovations during evolution. For example, there are over three million have only recently become possible.
    [Show full text]
  • B2 and ALU Retrotransposons Are Self-Cleaving Ribozymes Whose Activity Is Enhanced by EZH2
    B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2 Alfredo J. Hernandeza,1, Athanasios Zovoilisb,c,1,2, Catherine Cifuentes-Rojasb,c,1,3, Lu Hanb,c, Bojan Bujisicb,c, and Jeannie T. Leeb,c,4 aDepartment of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; bDepartment of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; and cDepartment of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA 02114 Contributed by Jeannie T. Lee, November 18, 2019 (sent for review October 9, 2019; reviewed by Vivian G. Cheung and Karissa Y. Sanbonmatsu) Transposable elements make up half of the mammalian genome. B2s are present in ∼350,000 copies in the mouse genome (10) One of the most abundant is the short interspersed nuclear and give rise to 180- to 200-nucleotide (nt) polymerase III complex element (SINE). Among their million copies, B2 accounts for (POL-III) transcripts. B2 SINEs are transcriptionally active, with ∼350,000 in the mouse genome and has garnered special interest expression being highest in germ cells and in early development, because of emerging roles in epigenetic regulation. Our recent work after which they become epigenetically silenced. However, one of demonstrated that B2 RNA binds stress genes to retard transcription the most intriguing aspects of SINE biology is that these elements elongation. Although epigenetically silenced, B2s become massively become highly up-regulated when somatic cells are acutely stressed up-regulated during thermal and other types of stress. Specifically, (11–13), including during viral infection (8, 11), autoimmune pro- an interaction between B2 RNA and the Polycomb protein, EZH2, cesses such as macular degeneration (14, 15), and progression to results in cleavage of B2 RNA, release of B2 RNA from chromatin, cancer (16, 17).
    [Show full text]
  • Stable Integration of Transgenes Delivered by a Retrotransposon–Adenovirus Hybrid Vector
    HUMAN GENE THERAPY 12:1417–1428 (July 20, 2001) Mary Ann Liebert, Inc. Stable Integration of Transgenes Delivered by a Retrotransposon–Adenovirus Hybrid Vector HARRIS SOIFER, 1,2 COLLIN HIGO, 1,2 HAIG H. KAZAZIAN, JR., 3 JOHN V. MORAN, 4 KOHNOSUKE MITANI, 5 and NORIYUKI KASAHARA 1,2,6 ABSTRACT Helper-dependent adenoviruses show great promise as gene delivery vectors. However, because they do not integrate into the host chromosome, transgene expression cannot be maintained indefinitely. To overcome these limitations, we have inserted an L1 retrotransposon/transgene element into a helper-dependent adeno- virus to create a novel chimeric gene delivery vector. Efficient adenovirus-mediated delivery of the L1 ele- ment into cultured human cells results in subsequent retrotransposition and stable integration of the trans- gene. L1 retrotransposition frequency was found to correlate with increasing multiplicity of infection by the chimeric vector, and further retrotransposition from newly integrated elements was not observed on pro- longed culture. Therefore, this vector, which utilizes components of low immunogenic potential, represents a novel two-stage gene delivery system capable of achieving high titers via the initial helper-dependent adeno- virus stage and permanent transgene integration via the retrotransposition stage. OVERVIEW SUMMARY ing to achieve efficient gene transfer, a variety of viruses have been adapted for use as gene delivery vectors, including retro- A retrotransposition-competent LINE-1 element (RC-L1) virus, adenovirus, and adeno-associated virus. Of these, ade- was inserted into a helper-dependent adenovirus (HDAd) to noviral vectors are capable of achieving high titers and have generate a hybrid adenovirus–retrotransposon vector.
    [Show full text]
  • The Enigma of Y Chromosome Degeneration: T', a Novel Retrotransposon Is Preferentially Located on the Neey Chromosome of Drosophila Miranda
    Copyright 0 1997 by the Genetics Society of America The Enigma of Y Chromosome Degeneration: T', a Novel Retrotransposon is Preferentially Located on the NeeY Chromosome of Drosophila miranda Manfred Steinemann and Sigrid Steinemann Institut fur Genetik, Heinrich-Heine-Universitat Dusseldorf; 0-40225 Dusseldorf, Germany Manuscript received July 16, 1996 Accepted for publication October 17, 1996 ABSTRACT We have cloned a novel transposable element from the nepY chromosome of Drosophila miranda. The size of the element, designated asTRAM, is 3.452 bp, including on both sides long terminal direct repeats (LTRs)of 372 bp, respectively. The element is flanked by a 5-bp target site duplication, ATATG. The putative primer binding site (PBS) for minus-strand priming is complementary to 18 nucleotides of the 3"end of tRNATv. Data base screens for DNA sequence identities were negative, apart from the sequence motif of the PBS. The deduced amino acid sequence from the large ORF does not' reveal identities described for other transposons. In situ hybridizations with TRAM subclones show a biased distribution in the genome, with a massive accumulation of TRAM in the neo-Y chromosome, while the former homologue, the XZchromosomeis devoid of TRAMsites. The enriched occurrence of the TRAM element at the evolving neo-Y chromosome of D.miranda adds compelling evidencein favor of the view that Y chromosome degeneration is driven by the accumulation of transposable elements. CHROMOSOME degeneration (MULLER1918, polytene chromosome squashes, the male X chromo- Y 1932) is a process that involves structural changes some in Drosophila can be distinguished by the pres- in chromosome architecture and expansionof genetic ence of an isoform of histone H4 acetylated at lysine 16, inertness along theY chromosome (6CHARLESWORTH H4.Ac16.
    [Show full text]
  • Like Retrotransposon (Transposable Dement/Interspedflc Hybridization/Zea/Tnpsacum/Waxy Alde) MICHAEL D
    Proc. Nati. Acad. Sci. USA Vol. 91, pp. 11674-11678, November 1994 Evolution Molecular evolution of magellan, a maize Ty3/gypsy- like retrotransposon (transposable dement/interspedflc hybridization/Zea/Tnpsacum/waxy alde) MICHAEL D. PURUGGANAN*t AND SUSAN R. WESSLER*t§ Departments of *Botany and *Genetics, University of Georgia, Athens, GA 30602 Communicated by Wyatt W. Anderson, July 28, 1994 ABSTRACT The magelan transposable element is respon- Understanding the evolutionary biology of retrotrans- sible for a spontaneous 5.7-kb insertion in the maize wx-M posons requires data on the extent and patterns of molecular allele. This element has the sequence and structural charac- variation within element families. In this report, we describe teristics of a Ty3/gypsy-like retrotransposon. The maeln a low-copy-number retrotransposon whose presence within element is present in all Zea species and Tripsacum andersonu; the phylogenetically well-defined genus Zea makes it an It is absent, however, in the genomes of all other Tripsacum excellent subject for the study of retrotransposon evolution. species analyzed. The genetic distances between magellan ele- This Ty3/gypsy-like retrotransposon, which we have named ments suggest that this retrotransposon is evolving faster than magellan, is responsible for a 5.7-kb insertion in a sponta- other Zea nuclear loci. The phylogeny of magelan within Zea neous mutant allele of the maize waxy (wx) locus. The and T. andersonf also reveals a pattern of interspecies trans- magellan element is also found in Tripsacum andersonii but fers, resulting in the movement of mageflan subfmles be- is absent in all other Tripsacum species tested.
    [Show full text]
  • Downloads/Repeatmaskedgenomes
    Kojima Mobile DNA (2018) 9:2 DOI 10.1186/s13100-017-0107-y REVIEW Open Access Human transposable elements in Repbase: genomic footprints from fish to humans Kenji K. Kojima1,2 Abstract Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades (L1, CR1, L2, Crack, RTE, RTEX, R4, Vingi, Tx1 and Penelope) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (SINE1/7SL, SINE2/tRNA, and SINE3/5S) of short interspersed elements (SINEs), 1 composite retrotransposon (SVA) family, 5 classes (ERV1, ERV2, ERV3, Gypsy and DIRS) of LTR retrotransposons, and 12 superfamilies (Crypton, Ginger1, Harbinger, hAT, Helitron, Kolobok, Mariner, Merlin, MuDR, P, piggyBac and Transib) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome. Keywords: Human repeat, Transposable elements, Repbase, Non-LTR retrotransposons, LTR retrotransposons, DNA transposons, SINE, Crypton, MER, UCON Background contrast, MER4 was revealed to be comprised of LTRs of Repbase and conserved noncoding elements endogenous retroviruses (ERVs) [1]. Right now, Repbase Repbase is now one of the most comprehensive data- keeps MER1 to MER136, some of which are further bases of eukaryotic transposable elements and repeats divided into several subfamilies.
    [Show full text]
  • Developmental Retrotransposon Activation Primes Host Immunity for Future Viral- Clearance
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263293; this version posted August 24, 2020. 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. Developmental retrotransposon activation primes host immunity for future viral- clearance Lu Wang1, Lauren Tracy1, ZZ Zhao Zhang1,2,* 1Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, USA. 2Regeneration Next, Duke University School of Medicine, Durham, USA. *Corresponding author: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263293; this version posted August 24, 2020. 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 Transposons are thought to be largely suppressed under physiological conditions, ensuring that their mobilization is a rare event. By tracking mobilization, we show that during metamorphosis at the Drosophila pupal stage, the Gypsy retrotransposon selectively mobilizes in regenerating tissues. In the newly formed tissues, this wave of Gypsy activation primes the host’s innate immune system by inducing the production of antimicrobial peptides (AMPs). Moreover, early immune-priming functions of Gypsy are essential for combating viral invasion in adult flies: flies with Gypsy being silenced at the pupal stage are unable to clear viruses and succumb to viral infection. Our data reveal that regulated activation of transposons during animal developmental endows a long-term benefit in pathogen warfare. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.263293; this version posted August 24, 2020.
    [Show full text]
  • Arabidopsis Retrotransposon Virus-Like Particles and Their Regulation by Epigenetically Activated Small RNA
    Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA Seung Cho Lee,1,3 Evan Ernst,1,3 Benjamin Berube,2 Filipe Borges,1 Jean-Sebastien Parent,1 Paul Ledon,2 Andrea Schorn,2 and Robert A. Martienssen1,2 1Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 2Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA In Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated siRNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR retrotransposons without the need for mapping transpo- sition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nu- clear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon “suicide” by auto-integration within the VLP. easiRNA targeted EVADE geno- mic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethy- lation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels.
    [Show full text]
  • The Mechanism of Integration Preference to Heterochromatin of Yeast Retrotransposon Ty5 Weiwu Xie Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2003 The mechanism of integration preference to heterochromatin of yeast retrotransposon Ty5 Weiwu Xie Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Genetics Commons, and the Molecular Biology Commons Recommended Citation Xie, Weiwu, "The mechanism of integration preference to heterochromatin of yeast retrotransposon Ty5 " (2003). Retrospective Theses and Dissertations. 1475. https://lib.dr.iastate.edu/rtd/1475 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. The mechanism of integration preference to heterochromatin of yeast retrotransposon Ty5 by Weiwu Xie A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Genetics (Computational Molecular Biology) Program of Study Committee: Daniel F. Voytas, Major Professor John May field Alan Myers David Oliver Jo Anne Powell-Coffman Iowa State University Ames, Iowa 2003 UMI Number: 3105118 UMI UMI Microform 3105118 Copyright 2003 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 ii Graduate College Iowa State University This is to certify that the doctoral dissertation of Weiwu Xie Has met the dissertation requirements of Iowa State University Signature was redacted for privacy.
    [Show full text]
  • Genome-Wide Analysis of Long Terminal Repeat Retrotransposons
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452536; this version posted July 15, 2021. 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. Research Report Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon Nusrat Sultanaa,b*, Gerhard Menzelb, Kathrin M. Seibtb, Sònia Garciac, Beatrice Weberb, Sedat Serçed, and Tony Heitkamb* aDepartment of Botany, Faculty of Life and Earth Sciences, Jagannath University, Dhaka 1100, Bangladesh bInstitute of Botany, Technische Universität Dresden, D-01062 Dresden, Germany (present address) cInstitut Bota`nic de Barcelona (IBB-CSIC), 08038 Barcelona, Catalonia, Spain dDepartment of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240, Niğde, Turkey Running title: Retrotransposons in cranberry Words: 7057 (main text) + 2650 (references) + 555 (figure legends) *Corresponding authors: [email protected], [email protected] Page 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.15.452536; this version posted July 15, 2021. 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. 1 ABSTRACT 2 BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant 3 genomes and play a large role in the generation of genomic variation.
    [Show full text]
  • HDV Family of Self-Cleaving Ribozymes
    Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use. This chapter was originally published in the book Progress in Molecular Biology and Translational Science, Vol. 120, published by Elsevier, and the attached copy is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who know you, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier's permissions site at: http://www.elsevier.com/locate/permissionusematerial From: Nathan Riccitelli, Andrej Lupták, HDV Family of Self-Cleaving Ribozymes. In Garrett A. Soukup, editor: Progress in Molecular Biology and Translational Science, Vol. 120, Burlington: Academic Press, 2013, pp. 123-171. ISBN: 978-0-12-381286-5 © Copyright 2013 Elsevier Inc. Academic Press Author's personal copy CHAPTER FOUR HDV Family of Self-Cleaving Ribozymes Nathan Riccitelli*, Andrej Lupták*,†,{ *Department of Chemistry, University of California, Irvine, California, USA †Department of Pharmaceutical Sciences, University of California, Irvine, California, USA { Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA Contents 1. Introduction 124 2. Hepatitis Delta Virus 124 3. HDV Ribozymes 127 3.1 Ribozyme structure 127 3.2 Ribozyme folding 129 4.
    [Show full text]
  • Retrotransposons That Maintain Chromosome Ends
    SACKLER SPECIAL FEATURE: PERSPECTIVE Retrotransposons that maintain chromosome ends Mary-Lou Pardue1 and P. G. DeBaryshe Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Joan Curcio, Wadsworth Center, New York State Department of Health, Albany, NY, and accepted by the Editorial Board June 28, 2011 (received for review January 30, 2011) Reverse transcriptases have shaped genomes in many ways. A remarkable example of this shaping is found on telomeres of the genus Drosophila, where retrotransposons have a vital role in chromosome structure. Drosophila lacks telomerase; instead, three telomere- specific retrotransposons maintain chromosome ends. Repeated transpositions to chromosome ends produce long head to tail arrays of these elements. In both form and function, these arrays are analogous to the arrays of repeats added by telomerase to chromosomes in other organisms. Distantly related Drosophila exhibit this variant mechanism of telomere maintenance, which was established before the separation of extant Drosophila species. Nevertheless, the telomere-specific elements still have the hallmarks that characterize non-long terminal repeat (non-LTR) retrotransposons; they have also acquired characteristics associated with their roles at telomeres. These telomeric retrotransposons have shaped the Drosophila genome, but they have also been shaped by the genome. Here, we discuss ways in which these three telomere-specific retrotransposons have been modified for their roles in Drosophila chromosomes. centromeres | chromosome evolution | heterochromatin | euchromatin | Y chromosome ells invest an unexpected amount HeT-A, TART, and TAHRE: A Ménage cessive transpositions produce long arrays of their resources in what might à Trois? of these elements, all oriented with their Cseem to be relatively insignificant Like other complex repeat sequences, 5′ ends toward the end of the chromo- parts of the chromosome, their telomere database entries are prone to some, and many showing some truncation telomeres.
    [Show full text]