Strategies for Re-Targeting the Non-LTR Retrotransposon Alu

Total Page:16

File Type:pdf, Size:1020Kb

Strategies for Re-Targeting the Non-LTR Retrotransposon Alu Strategies for re-targeting the non-LTR retrotransposon Alu AN ABSTRACT SUBMITTED ON THE FIFTH DAY OF SEPTEMBER OF 2017 TO THE DEPARTMENT OF CELL AND MOLECULAR BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS OF THE TULANE UNIVERSITY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY BY Catherine M. Ade APPROVED: AstridJ. Engel, David A. Mullin, Ph.D William C. Wimley, Ph.D. ABSTRACT Genetic engineering of biological molecules has provided the ability to create improved tools that have been applied in numerous fields including re- search, agriculture, industrial biotechnology, and medicine. Mobile elements are the perfect platform for developing gene targeting systems in humans, as they are endogenous and capable of mobilizing genetic material. Here, I present data demonstrating the first successful genetic engineering of a human non-LTR ele- ment protein to promote site-specific insertions. I tested two distinct strategies to target Alu insertions to specific sites in the human genome. The first strategy consisted of fusing a site-specific DNA binding domain (DBD) to the L1 ORF2 protein to favor Alu insertions to the target site. Five distinct DNA binding do- mains targeting specific sequences were tested: the Adeno associated virus (AAV) REP proteins, a TAL effector, the Cre recombinase, several zinc fingers, and the catalytically inactive dCas9. The second strategy utilized the CRISPR system, fusing a catalytically active Cas9 protein to an endonuclease deficient L1 ORF2 protein, the targeting abilities provided by a gRNA. I was successful at en- riching insertions of Alu insertions within in 1.2 kb window around the target se- quence by 47 fold by fusing a six-finger zinc finger, ZF4, to the N-terminus of the ORF2 protein. Recovered insertions showed a distinct bias, inserting upstream of the ZF4 target sequence when compared to recovered Alu insertions driven by unfused L1 ORF2. Other DBDs were unable to alter targeting preference of the ORF2 protein. However, the data provided valuable information on the require- ments for designing successful genetic engineering approaches. My findings demonstrate that multiple factors including target site abundance, linker selec- tion, terminus for fusion, size of DNA binding domain, and overall complexity of the system play an important role in designing fusion proteins with targeting ca- pabilities. The data demonstrate that it is possible to redirect insertion prefer- ence of human non-LTR-retroelements. Strategies for re-targeting the non-LTR retrotransposon Alu A DISSERTATION SUBMITTED ON THE FIFTH DAY OF SEPTEMBER OF 2017 TO THE DEPARTMENT OF CELL AND MOLECULAR BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS OF THE TULANE UNIVERSITY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY BY rll Catherine M. Ade APPROVED: gel^Ph.D h.D. William C. Wimley, Ph.D. © Copyright by Catherine M. Ade, 2017 All Rights Reserved ACKNOWLEDGEMENTS . I need to first express my gratitude to Astrid Engel, for taking a chance on an awkward CMB student. You have been a great mentor in and outside the lab, giving me countless opportunities to grow and succeed. Without your guidance, wisdom, kindness, and patience, I would not be the person I am today. To the former members of the lab, Dr. Brad Wagstaff and Rebecca Derbes: thank you for training and helping me get through the first few years of graduate school. Without your advice, experience, and humor, this experience would have been quite different. To the members of COMET, especially Dr. Maria Morales in the Deininger lab: thank you for reigning in, dealing with, and sometimes partici- pating in the crazy. All y’all made it an easy decision to join Astrid’s lab. To everyone I consider family- biological relatives, Virginia band geeks, Ohio nerds, and New Orleans comrades- thank you. Thank you for all of your unwa- vering support, lending me your ears and minds. Without you all, this process would not have been as rewarding or entertaining. Finally, extra scritches and cuddles to my fur babies Tazo, Vinnie, Violet, Blue, Frisco, and Boudreaux. You always know how to make me smile. TABLE OF CONTENTS LIST OF TABLES………………………………………………………………………vi LIST OF FIGURES…………………………………………………………………….viii CHAPTER 1. INTRODUCTION……………………………………………………….1 1.1 Mobile elements in the human genome 1.2 LINE-1 1.2.1 LINE-1 Structure 1.2.2 LINE-1 transcription, translation, and expression 1.2.3 LINE-1 replication cycle 1.2.4 Non-Autonomous elements mobilized by LINE-1 1.3 Alu elements 1.3.1 Origin of Alu elements 1.3.2 Alu Mobilization 1.4 Retrotransposons contribute to human diseases 1.4.1 Insertional mutagenesis 1.4.2 Non-allelic Homologous recombination (NAHR) events 1.4.3 Adverse effects from L1 protein expression 1.5 Retroelement activity and expression in cancer 1.6 Environmental influences on mobile element activity 1.7 Host suppression mechanisms i 1.8 Assays to detect retrotransposition events 1.8.1 Alu and L1 retrotransposition assay 1.8.2 Alu and L1 rescue assay 1.8.3 Next-generation sequencing assays to detect new insertions 1.9 Naturally occurring elements exhibit site-specific insertions 1.10 DNA binding domains with targeting capabilities 1.10.1 Adeno-associated viral proteins (AAV) 1.10.2 Cre recombinase 1.10.3 TALENS 1.10.4 Zinc fingers 1.10.5 The CRISPR/Cas9 targeting system 1.11 Engineering mobile elements to promote site-specific insertions CHAPTER 2. MATERIALS & METHODS……………………………59 2.1 Constructs 2.1.A Alu Constructs 2.1.B Creating the fusion proteins: LZ-ORF2 and TZ-ORF2 and Cre- ORF2 (Chapter 3) 2.1.C Creation of the fusion proteins: TAL-ORF2 (Chapter 4) 2.1.D Creation of the fusion proteins: ZF2.17-ORF2,ZF2.18-ORF2, and ZF2.1817-ORF2 (Chapter 5) 2.1.E Creation of the fusion proteins: N-ZF4-ORF2, N-ZF2-ORF2, C-ZF4- ORF2, and C-ZF2-ORF2 with GHL, FL4, and HL4 linkers (Chapters 6) ii 2.1.F Creation of the CRISPR/Cas9 fusion proteins and gRNAs (Chapter 7) 2.2. Retrotransposition, Alu Rescue assay and insert analysis 2.3. Creation of a HeLa-LoxP cell line and HeLa-EGFP cell line. 2.4 Western Blot Analysis CHAPTER 3. The effect of the multimeric DNA binding proteins, TZ and LZ and Cre on redirecting ORF2p targeting capabilities…………………………….84 3.1. Introduction 3.2. Results 3.2.1 Evaluation of the retrotransposition capability of the ORF2-fusion pro- teins. 3.2.2 Expression of the ORF2 fusion proteins 3.2.3 Evaluation of the capability of the ORF2 -fusion proteins to redirect in- sertion preference of the Alu. 3.3. Discussion CHAPTER 4. The Transcription Activator-like Effector: The effect of mono- meric DNA binding domains with a few genomic target sequences on tar- geting capabilities……………………………………………………….………….102 4.1. Introduction 4.2. Results 4.2.1 Evaluation of the retrotransposition capability of the ORF2-fusion pro- teins. 4.2.2 Expression of the TAL-ORF2 fusion protein iii 4.2.3 Evaluation of the capability of the TAL-ORF2 -fusion proteins to redirect insertion preference of the Alu. 4.3 Discussion CHAPTER 5. Zinc finger proteins: The effect of monomeric DNA binding domains with a few genomic target sequences on targeting capabili- ties……………………………………………………………………………..………111 5.1 Introduction 5.2 Results 5.2.1 Evaluation of the retrotransposition capability of the ORF2-fusion pro- teins. 5.2.2 Evaluation of the capability of the ORF2-fusion proteins to redirect inser- tion preference of the Alu. 5.3 Discussion CHAPTER 6. Six-fingered zinc fingers that target multiple sites in the ge- nome enrich for Alu insertions when fused to ORF2.................................117 6.1. Introduction 6.2. Results 6.2.1 Evaluation of the retrotransposition capability of the ORF2-fusion pro- teins. 6.2.2 Expression of the ORF2 fusion proteins 6.2.3 Evaluation of the capability of the ORF2 -fusion proteins to redirect in- sertion preference of the Alu. 6.2.4 Insertion bias observed due to availability of endo site 6.3. Discussion iv CHAPTER 7. Adapting the CRISPR system to the ORF2 protein in order to target Alu insertions………………………………………………………………..142 7.1 Introduction 7.2 Results 7.2.1 Evaluation of the Cas9 targeting capability of the Cas9-ORF2-fusion proteins. 7.2.2 Evaluation of the retrotransposition capability of the functional Cas9- endonuclease defective ORF2-fusion proteins. 7.2.3 Evaluation of the capability of the functional Cas9-endonuclease defec- tive ORF2-fusion proteins to redirect insertion preference of Alu. 7.2.4 Evaluation of the capability of the dCas9-ORF2 (defective Cas9- functional ORF2)-fusion proteins to redirect insertion preferences of Alu. 7.2.5 Using an MS2-ORF2 fusion protein to increase the interaction a MS2- gRNA-Cas9 complex to increase efficiency of targeting Alu insertions 7.2.6 Re-designing the A-tail of the Alu Rescue Cassette to promote se- quence homology between a specific genomic target and Alu insert. 7.3: Discussion CHAPTER 8. CONCLUSIONS……………………………………………...……..168 BIBLIOGRAPHY……………………………………………………………………..174 APPENDIX……………………………………………………………………………203 BIOGRAPHY…………………………………………………………………………264 v LIST OF TABLES Table 1. Relative retrotransposition rates of Alu when driven by ORF2 or by the indicated fusion protein………………………………………………………………..93 Table 2. Relative retrotransposition rates of Alu when driven by ORF2 or by N- terminally fused TAL effector………………………………………………………. 106 Table 3. Two potential Alu targeting events when Alu is driven by TAL- ORF2…………………………………………………………………………………..108 Table 4. Relative retrotransposition rates of Alu when driven by ORF2 or by N- terminally fused EGFP targeting zinc fingers…………………………………… 114 Table 5. Relative retrotransposition rates of Alu when driven by ORF2 or by the N-ZF4-ORF2 fusion protein…………………………………………………………119 Table 6. Recovered Alu Retrotransposition events driven by the ORF2 and the N-ZF4-ORF2 fusion construct………………………………………………………122 Table 7.
Recommended publications
  • Interfering with Retrotransposition by Two Types of CRISPR Effectors
    Zhang et al. Cell Discovery (2020) 6:30 Cell Discovery https://doi.org/10.1038/s41421-020-0164-0 www.nature.com/celldisc ARTICLE Open Access Interfering with retrotransposition by two types of CRISPR effectors: Cas12a and Cas13a Niubing Zhang1,2, Xinyun Jing1, Yuanhua Liu3, Minjie Chen1,2, Xianfeng Zhu2, Jing Jiang2, Hongbing Wang4, Xuan Li1 and Pei Hao3 Abstract CRISPRs are a promising tool being explored in combating exogenous retroviral pathogens and in disabling endogenous retroviruses for organ transplantation. The Cas12a and Cas13a systems offer novel mechanisms of CRISPR actions that have not been evaluated for retrovirus interference. Particularly, a latest study revealed that the activated Cas13a provided bacterial hosts with a “passive protection” mechanism to defend against DNA phage infection by inducing cell growth arrest in infected cells, which is especially significant as it endows Cas13a, a RNA-targeting CRISPR effector, with mount defense against both RNA and DNA invaders. Here, by refitting long terminal repeat retrotransposon Tf1 as a model system, which shares common features with retrovirus regarding their replication mechanism and life cycle, we repurposed CRISPR-Cas12a and -Cas13a to interfere with Tf1 retrotransposition, and evaluated their different mechanisms of action. Cas12a exhibited strong inhibition on retrotransposition, allowing marginal Tf1 transposition that was likely the result of a lasting pool of Tf1 RNA/cDNA intermediates protected within virus-like particles. The residual activities, however, were completely eliminated with new constructs for persistent crRNA targeting. On the other hand, targeting Cas13a to Tf1 RNA intermediates significantly inhibited Tf1 retrotransposition. However, unlike in bacterial hosts, the sustained activation of Cas13a by Tf1 transcripts did not cause cell growth arrest in S.
    [Show full text]
  • A Species-Specific Retrotransposon Drives a Conserved Cdk2ap1 Isoform Essential for Preimplantation Development
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.24.436683; this version posted March 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. Title: A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development Authors: Andrew Modzelewski1†, Wanqing Shao2†, Jingqi Chen1, Angus Lee1, Xin Qi1, Mackenzie Noon1, Kristy Tjokro1, Gabriele Sales3, Anne Biton4, Terence Speed5, Zhenyu Xuan6, Ting Wang2#, Davide Risso3# and Lin He1# Affiliations: 1 Division of Cellular and Developmental Biology, MCB department, University of California at Berkeley, Berkeley, CA, USA. 2 Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA 3 Department of Statistical Sciences, University of Padova, Italy. 4 Division of Biostatistics, University of California at Berkeley, Berkeley, CA 94720, USA. 5 Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia. 6 Department of Biological Sciences, The University of Texas at Dallas, Richardson Texas, USA # Correspondence to: [email protected], [email protected] and [email protected] †These authors contributed equally. Abstract: Retrotransposons mediate gene regulation in multiple developmental and pathological processes. Here, we characterized the transient retrotransposon induction in preimplantation development of eight mammalian species. While species-specific in sequences, induced retrotransposons exhibit a similar preimplantation profile, conferring gene regulatory activities particularly through LTR retrotransposon promoters. We investigated a mouse-specific MT2B2 retrotransposon promoter, which generates an N-terminally truncated, preimplantation-specific Cdk2ap1ΔN isoform to promote cell proliferation. Cdk2ap1ΔN functionally contrasts to the canonical Cdk2ap1, which represses cell proliferation and peaks in mid-gestation stage.
    [Show full text]
  • LINE1 Inhibition (With Nucleoside Reverse Transcriptase Inhibitors)
    Cognitive Vitality Reports® are reports written by neuroscientists at the Alzheimer’s Drug Discovery Foundation (ADDF). These scientific reports include analysis of drugs, drugs-in- development, drug targets, supplements, nutraceuticals, food/drink, non-pharmacologic interventions, and risk factors. Neuroscientists evaluate the potential benefit (or harm) for brain health, as well as for age-related health concerns that can affect brain health (e.g., cardiovascular diseases, cancers, diabetes/metabolic syndrome). In addition, these reports include evaluation of safety data, from clinical trials if available, and from preclinical models. LINE1 inhibition (with nucleoside reverse transcriptase inhibitors) Evidence Summary L1 activation may be associated with age-related diseases, and nucleoside reverse transcriptase inhibitors (NRTIs) suppress L1 activation and may be beneficial in age-related diseases. Neuroprotective Benefit: Increased retrotransposition of transposable elements is implicated in neurodegenerative diseases, so NRTIs could theoretically reverse these actions, but only preclinical evidence exists to date. Aging and related health concerns: Preclinical studies suggest that NRTIs may be an effective anti-aging therapy, and clinical studies suggest they may be effective for cancer. Safety: NRTIs are associated with some mild side effects and rare severe, possibly life- threatening, side effects. 1 Availability: Available with Dose: Depends on the Molecular Formula: N/A prescription (as generics) NRTI Molecular weight: N/A Half-life: Depends on the BBB: Possibly penetrant NRTI in animal models Clinical trials: Many for HIV, Observational studies: one for ALS Many What is it? Retrotransposons are stretches of DNA that can replicate and reinsert into other parts of the genome. Their presence in the DNA comes from retroviral infection of germline cells throughout evolutionary history.
    [Show full text]
  • Multiple Non-LTR Retrotransposons in the Genome of Arabidqpsis Thulium
    Copyright 0 1996 by the Genetics Society of America Multiple Non-LTR Retrotransposons in the Genome of ArabidqPsis thulium David A. Wright,* Ning Ke," Jan Smalle,t" Brian M. Hauge,t'2Howard M. Goodmant and Daniel F. Voytas* *Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011 and tDepartment of Genetics, Haward Medical School and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 021 14 Manuscript received June 13, 1995 Accepted for publication October 14, 1995 ABSTRACT DNA sequence analysis near the Arabidopsis thaliana AB13 gene revealed the presence of a non-LTR retrotransposon insertion thatwe have designated Tal 1-1.This insertion is 6.2 kb in length and encodes two overlapping reading frames with similarity to non-LTR retrotransposon proteins, including reverse transcriptase. A polymerase chain reaction assaywas developed based on conserved amino acid sequences shared between the Tall-1 reverse transcriptase and those of non-LTR retrotransposons from other species. Seventeen additionalA. thaliana reverse transcriptases were identified that range in nucleotide similarity from 4848% (Ta12-Ta28). Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over mostof their evolutionary history. One sequence, Ta17,is located in the mitochondrial genome. The remaining are nuclear andof low copy number among 17 diverse A. thaliana ecotypes tested, suggesting that they are not highly active in transposition. The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families.
    [Show full text]
  • Sap1 Dependent Replication Fork Barriers Guide Integration of Ltr Retrotransposons in S
    SAP1 DEPENDENT REPLICATION FORK BARRIERS GUIDE INTEGRATION OF LTR RETROTRANSPOSONS IN S. POMBE By! JAKE ZACHARY JACOBS A Dissertation submitted to the! Graduate School-New Brunswick! Rutgers, The State University of New Jersey !In partial fulfillment of the requirements! For the degree of !Doctor of Philosophy !Graduate Program in Biochemistry !Written under the direction of Dr. Mikel Zaratiegui, Ph.D.! And approved by _____________________________________________________ _____________________________________________________ _____________________________________________________ _____________________________________________________! New Brunswick, New Jersey! October 2016 ABSTRACT OF THE DISSERTATION SAP1 DEPENDENT REPLICATION FORK BARRIERS GUIDE INTEGRATION OF LTR RETROTRANSPOSONS IN S. POMBE By! JAKE ZACHARY JACOBS Dissertation Director: Dr. Mikel Zaratiegui Long Terminal Repeat retrotransposable elements (LTR-TEs) are a large group of eukaryotic Transposable Elements characterized by flanking repeats in tandem orientation—the LTRs. The LTRs of these elements contain sequences that recruit proteins involved in their expression, replication, silencing, organization, and stability. A successful transposable element must maximize its reproductive amplification without jeopardizing its host, and several characterized LTR-TEs appear to accomplish this through the selection of integration sites away from protein coding sequences. However, despite their high relatedness, a universal mechanism that explains how these parasitic elements avoid
    [Show full text]
  • Genome-Wide Mapping and Characterization of Microsatellites In
    www.nature.com/scientificreports OPEN Genome-wide mapping and characterization of microsatellites in the swamp eel genome Received: 14 February 2017 Zhigang Li, Feng Chen, Chunhua Huang, Weixin Zheng, Chunlai Yu, Hanhua Cheng & Accepted: 26 April 2017 Rongjia Zhou Published: xx xx xxxx We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics. Swamp eel (Monopterus albus) taxonomically belongs to teleosts, the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, and Vertebrata).
    [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]
  • Drosophila: Retrotransposons Making up Telomeres
    Review Drosophila: Retrotransposons Making up Telomeres Elena Casacuberta Institute of Evolutionary Biology, IBE, CSIC—Pompeu Fabra University, Barcelona Spain, Passeig de la Barceloneta 37‐49, 08003 Barcelona, Spain; [email protected]‐csic.es; Tel.: +34‐932309637; Fax: +34‐932309555 Guest Editors: Paul M. Liebermann and Benedikt B. Kaufer Received: 9 June 2017; Accepted: 17 July 2017; Published: 19 July 2017 Abstract: Drosophila and extant species are the best‐studied telomerase exception. In this organism, telomere elongation is coupled with targeted retrotransposition of Healing Transposon (HeT‐A) and Telomere Associated Retrotransposon (TART) with sporadic additions of Telomere Associated and HeT‐A Related (TAHRE), all three specialized non‐Long Terminal Repeat (non‐LTR) retrotransposons. These three very special retroelements transpose in head to tail arrays, always in the same orientation at the end of the chromosomes but never in interior locations. Apparently, retrotransposon and telomerase telomeres might seem very different, but a detailed view of their mechanisms reveals similarities explaining how the loss of telomerase in a Drosophila ancestor could successfully have been replaced by the telomere retrotransposons. In this review, we will discover that although HeT‐A, TART, and TAHRE are still the only examples to date where their targeted transposition is perfectly tamed into the telomere biology of Drosophila, there are other examples of retrotransposons that manage to successfully integrate inside and at the end of telomeres. Because the aim of this special issue is viral integration at telomeres, understanding the base of the telomerase exceptions will help to obtain clues on similar strategies that mobile elements and viruses could have acquired in order to ensure their survival in the host genome.
    [Show full text]
  • Pericentromeric Regions of Soybean (Glycine Max L. Merr
    Copyright © 2005 by the Genetics Society of America DOI: 10.1534/genetics.105.041616 Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile Jer-Young Lin,* Barbara Hass Jacobus,* Phillip SanMiguel,† Jason G. Walling,* Yinan Yuan,* Randy C. Shoemaker,‡ Nevin D. Young§ and Scott A. Jackson*,1 *Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, †Purdue University Genomics Core, Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, ‡USDA-ARS-CICGR and Department of Agronomy, Iowa State University, Ames, Iowa 50011 and §Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108 Manuscript received February 3, 2005 Accepted for publication April 1, 2005 ABSTRACT Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102- bp repeat (STR120). Fragments-120ف bp tandem repeat with sequence identity to a previously characterized of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G.
    [Show full text]
  • Tandem Repeats Derived from Centromeric Retrotransposons Anupma Sharma, Thomas K Wolfgruber and Gernot G Presting*
    Sharma et al. BMC Genomics 2013, 14:142 http://www.biomedcentral.com/1471-2164/14/142 RESEARCH ARTICLE Open Access Tandem repeats derived from centromeric retrotransposons Anupma Sharma, Thomas K Wolfgruber and Gernot G Presting* Abstract Background: Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotransposons, are enriched at centromeres. Some satellite repeats have homology to retrotransposons and several mechanisms have been proposed to explain the expansion, contraction as well as homogenization of tandem repeats. However, the origin and evolution of tandem repeat loci remain largely unknown. Results: CRM1TR and CRM4TR are novel tandem repeats that we show to be entirely derived from CR elements belonging to two different subfamilies, CRM1 and CRM4. Although these tandem repeats clearly originated in at least two separate events, they are derived from similar regions of their respective parent element, namely the long terminal repeat (LTR) and untranslated region (UTR). The 5’ ends of the monomer repeat units of CRM1TR and CRM4TR map to different locations within their respective LTRs, while their 3’ ends map to the same relative position within a conserved region of their UTRs. Based on the insertion times of heterologous retrotransposons that have inserted into these tandem repeats, amplification of the repeats is estimated to have begun at least ~4 (CRM1TR) and ~1 (CRM4TR) million years ago. Distinct CRM1TR sequence variants occupy the two CRM1TR loci, indicating that there is little or no movement of repeats between loci, even though they are separated by only ~1.4 Mb.
    [Show full text]
  • Transposable Elements and Stress in Vertebrates: an Overview
    International Journal of Molecular Sciences Review Transposable Elements and Stress in Vertebrates: An Overview Anna Maria Pappalardo 1,*,†, Venera Ferrito 1,†, Maria Assunta Biscotti 2 , Adriana Canapa 2 and Teresa Capriglione 3 1 Department of Biological, Geological and Environmental Sciences—Section of Animal Biology “M. La Greca”, University of Catania, Via Androne 81, 95124 Catania, Italy; [email protected] 2 Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy; [email protected] (M.A.B.); [email protected] (A.C.) 3 Department of Biology, University of Naples “Federico II”, Via Cinthia 21—Ed7, 80126 Naples, Italy; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Abstract: Since their identification as genomic regulatory elements, Transposable Elements (TEs) were considered, at first, molecular parasites and later as an important source of genetic diversity and regulatory innovations. In vertebrates in particular, TEs have been recognized as playing an important role in major evolutionary transitions and biodiversity. Moreover, in the last decade, a significant number of papers has been published highlighting a correlation between TE activity and exposition to environmental stresses and dietary factors. In this review we present an overview of the impact of TEs in vertebrate genomes, report the silencing mechanisms adopted by host genomes to regulate TE activity, and finally we explore the effects of environmental and dietary factor exposures on TE activity in mammals, which is the most studied group among vertebrates. The studies here reported evidence that several factors can induce changes in the epigenetic status of TEs and silencing mechanisms leading to their activation with consequent effects on the host genome.
    [Show full text]
  • Activation of a LTR-Retrotransposon by Telomere Erosion
    Activation of a LTR-retrotransposon by telomere erosion Derek T. Scholes, Alison E. Kenny, Eric R. Gamache*, Zhongming Mou, and M. Joan Curcio† Laboratory of Developmental Genetics, Wadsworth Center, and Department of Biomedical Sciences, University at Albany School of Public Health, P. O. Box 22002, Albany, NY 12201-2002 Communicated by Marlene Belfort, New York State Department of Health, Albany, NY, October 13, 2003 (received for review August 18, 2003) Retrotransposons can facilitate repair of broken chromosomes, and as sensors is not required for the telomere checkpoint. Interest- therefore an important question is whether the host can activate ingly, DNA-damage transducer proteins Rad9 and Rad53 are retrotransposons in response to chromosomal lesions. Here we also dispensable for the telomere checkpoint; however, they are show that Ty1 elements, which are LTR-retrotransposons in Sac- activated in response to telomere erosion and required for charomyces cerevisiae, are mobilized when DNA lesions are cre- induction of a DNA damage-response gene (15, 16). ated by the loss of telomere function. Inactivation of telomerase in A common feature of transposons is their responsiveness to yeast results in progressive shortening of telomeric DNA, eventu- genetic and environmental stresses (21), yet little is known about ally triggering a DNA-damage checkpoint that arrests cells in G2͞M. the signals that activate transposition or the pathways through A fraction of cells, termed survivors, recover from arrest by forming which they are transduced. Although it has been suggested that alternative telomere structures. When telomerase is inactivated, DNA lesions can trigger the activation of transposition, the idea Ty1 retrotransposition increases substantially in parallel with telo- has not been addressed directly by analyzing the effects of mere erosion and then partially declines when survivors emerge.
    [Show full text]