DOCSLIB.ORG

The Enigma of Y Chromosome Degeneration: T', a Novel Retrotransposon Is Preferentially Located on the Neey Chromosome of Drosophila Miranda

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read 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. Staining D. miranda with H4.Ac16 antibodies 1978,1991,1996; LUCCHESI1978,1994; CHARLESWORTH showed that dosage compensation extends across part and CHARLESWORTH1979; BULL1983; RICE 1987,1994; of the X2 (STEINEMANNet al. 1996). The X2 shows a STEINEMANNand STEINEMANN1992). It is generally as- muchbrighter staining over -90% chromosome sumed that the heteromorphic sex chromosome pair length, reflecting thepredominant association of has developed from a pairof homologues. Causes of the H4.Ac16. A terminal region constituting -10% of the evolution of the structurally and functionally different X X2 chromosome is not labeled. This finding fits nicely and Y chromosomes have been the object of specula- with quantitative autoradiographic studies,showing tion sincethe discovery of sex chromosomes.To analyze that RNA synthesis in this region is not upregulated themolecular basis of this evolutionary process we (STROBELet al. 1978). chose a model system, Drosophila miranda. D. miranda Here we describe a novel LTR-retrotransposon cloned belongs to theAmerican representatives of the obscura fromthe neo-Y-chromosomal Lcpl-4 locus. While the group. The separationof D. mirandu from its next rela- neo-Y shows an enrichment of TRAM sites (-50-60), tives D. pseudoobscura and D. persimilis occurred relatively we find the former homologue, the X2 chromosome, recently, about 2 mya ago according to mtDNA restric- to be devoid of sites. Together with the distribution of tion analysis (BARRIOet al. 1992). Due to the fusion of the non-LTR TRIM retrotransposon (STEINEMANNand one of the autosomes to the Y chromosome, a neo-Y STEINEMANN1991) and the ISY3 insertionelements chromosome and a neo-X chromosome, designated as (STEINEMANNand STEINEMANN 1992, 1993),we present X2, were formed (DOBZHANSKY1935; MACKNIGHT 1939; compelling evidence that the first step in Y chromo- STEINEMANN1982). Thusformerly autosomal genes are some degeneration is driven by the accumulation of transmitted in association with the sex chromosomes. transposable elements, especially retrotransposons. We have cloned the larval cuticle protein (Lcp) genes from the X2 and neo-Y chromosome (STEINEMANNand MATERIALS AND METHODS STEINEMANN1990). Analyzing the DNA sequences from Cloning of the TRAM element from theneo-Y chromosome the X2and neo-Y region, we observed amassive accumu- and the homologous region on the X2 chromosome: High lation of DNA insertions on the neo-Y chromosome. In molecularweight DNA from D. miranda was isolatedac- cording to STEINEMANN1982. GenomicEMBL4 lambda librar- Corresponding author; Manfred Steinemann, Institutfur Genetik, ies from partial Sau3A (Boehringer Mannheim) digests were Heinrich HeineUnivenitat Dusseldorf, Univeniatsstr. 1, D40225 described in STEINEMANNand STEINEMANN(1990). Using a Dtisseldorf, FR Germany. polymorphic restriction site, overlapping clones with X2 or E-mail: [email protected] neo-Y chromosomal origin were isolated, covering -30 kb Genetics 145 261-266 (February, 1997) 262 Steinemann and Steinemann T terminalrepeat (LTR)-type (XIONGand EICKBUSH TRAM 1990). The 5'- and 3'-LTRs are 372 bp in size (Figure RA P 3). They show identical sequences except forone point H A PXhRX xcx cxh H mutation, an exchange of a C base us. T at position 17. I I I II Ill Ill I I1 I 4 " The internal central region of the TRAM element is + 4"- t- e bordered by sequences that are conserved in retrovi- 4 f" . - - 6 ruses. At the 5' end,a stretch of DNA shows sequence b"----) - - identity to the primer bindingsite (PBS), which is com- FIGURE1.-Restriction map of the TRAM element and se- plementary to 18 nucleotidesof the 3' end of the trypto- quencing strategy. Fragments were subcloned in Ml3mpl8/ 19 and sequenced on both strands. Arrows below the map phan tRNA (tRNA"rP). Indata base screens, we ob- indicate the sequencing strategy.H, HindIII; A, AccI; P, PstI; taineda 100% identity for this TRAM DNA region Xh, XhoI; R, EcoRI; X, XbaI; C, ClaI. (377-399, 23 bp) with Myeloblastosis-associated virus type 2 (accession number L10924), Rous sarcoma virus (RSV, from both locations, respectively (STEINEMANNand STEINE- 378-399, 22 bp; accession number U41731), chicken MANN 1990). For detailed restriction mapping, the regions c-erbB oncogene (378-399, 22 bp; accession number containing the Lcp genes on the X2 and neo-Y chromosome M10066, M13881) and chicken endogenous rav-RAV-0 were subcloned into pUCl8. The DNA was sequenced on both strands from M13mp18/19 subclones by the dideoxy chain avian virus (378-399,22 bp; accession numberJ02015). termination method accordingto the protocol suppliedwith The RTV PBS sequence is complementary to the ac- Sequenase (United States Biochemical). Forthe Xba-Xba frag- ceptorstem of the tRNA"'P (SCHWARTZet al. 1983). ments, we proved the correctorientation by sequencing from Thus, we conclude that TRAM could potentially use flanking sequences over the Xba sites (Figure 1). Standard tRNATrpto prime the replication of its minus strand. DNA techniques were carried out according to SAMBROOK, The 3' end of theinternal domain shows a short FRITSCHand MANIATIS (1989). Computer analysis: The DNA data base screening with polypurine tract (PPT), a characteristic domain in re- BLASTN (ALTSCHUL et ul. 1990) and the Genetics Computer troviruses, which is believed to serve as a primer for the Group SequenceAnalysis Package (DEVEREUXet al. 1984) was replication of the plus DNA strand (VARMUS1983). done using the updated (May 1996) EMBL and GenBank Integration site and codingcapacity of the TRAM nucleotide Sequence Data Library (EMBL, Heidelberg; Gen- Bank, NCBI, Washington). SwissProt data librarywas used for element: The TRAM element has integrated between the screening of the deduced amino acid sequence of the the Lcp3 and Lcp4 locus, 433 bp upstream of the tran- large TRAM ORF. The TRAM sequence is deposited in the scription start of the neo-Y chromosomal Lcp4 (Figure EMBL gene bank, accession number Y08905. 2). The elementhas induced a 5-bp target site duplica- Chromosome in situ hybridizationand D. miranda tion, ATATG (Figure 4). The site of integration of strains: D.miranda flies were cultured on standard Drosoph- ila food at 18". The 111/30 strain is an isoline from single TRAM lies within a sequence showing a palindrome females collected in the wild. D. miranda MPI is a strain of structure. Of interestis the notion that the neighboring unknown origin fromour laboratory. Fragmentsof the TRAM TRIM retrotransposon has integrated in a similar se- element were subcloned into pUCl8. The cloneswere labeled quence structure (STEINEMANNand STEINEMANN 1991). withBiotin-16-dUTP (Boehringer, Mannheim) by the nick In the latter case, the integration was accompanied by translation reaction and hybridized at 58" overnight to alkali an 11-bp deletion, while the integration oc- denatured chromosome squashes (STEINEMANNand STEINE- TRAM MANN 1991). The slides were washed three times in 2X SSC curred without one. In addition to the induced target at 53". Signal detection followed the protocol for immunoper- site duplication, we found two base substitutions at the oxidasestaining supplied with the DETEK I-hrp kit used right hand side of the integration site (Figure 4). (Enzo Diagnostics, New York). The intensity and contrast of The deduced aminoacid sequence of the TRAM ele- the diaminobenzidine (DAB) precipitate were enhanced us- ment reveals one large open reading frame of ing a silver DAB enhancement kit (Amersham). Photomicro- (OW) graphs of the chromosome squasheswere made with an Agfa- 2013 bp (positions 1092-3104) with the first methio- pan 25 film. nine at position 1158. The ORF terminates within the 3'-LTR. Data base screening with the
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]
  • 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.
    [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]
  • 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]