Somatic and Germinal Recombination of a Direct Repeat in Arabidopsis
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Yeast Telomeres Exert a Position Effect on Recombination Between Internal Tracts of Yeast Telomeric DNA
Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Yeast telomeres exert a position effect on recombination between internal tracts of yeast telomeric DNA Jeffrey B. Stavenhagen1,2 and Virginia A. Zakian Princeton University, Department of Molecular Biology, Princeton, New Jersey 08544-1014 USA; 1Biology Department, University of Dayton, Dayton, Ohio 45469-2320 USA. In Saccharomyces cerevisiae, proximity to a telomere affects both transcription and replication of adjacent DNA. In this study, we show that telomeres also impose a position effect on mitotic recombination. The rate of recombination between directly repeated tracts of telomeric C1–3A/TG1–3 DNA was reduced severely by proximity to a telomere. In contrast, recombination of two control substrates was not affected by telomere proximity. Thus, unlike position effects on transcription or replication, inhibition of recombination was sequence specific. Moreover, the repression of recombination was not under the same control as transcriptional repression (telomere position effect; TPE), as mutations in genes essential for TPE did not alleviate telomeric repression of recombination. The reduction in recombination between C1–3A/TG1–3 tracts near the telomere was caused by an absence of Rad52p-dependent events as well as a reduction in Rad1p-dependent events. The sequence-specific repression of recombination near the telomere was eliminated in cells that overexpressed the telomere-binding protein Rap1p, a condition that also increased recombination between C1–3A/TG1–3 tracts at internal positions on the chromosome. We propose that the specific inhibition between C1–3A/TG1–3 tracts near the telomere occurs through the action of a telomere-specific end-binding protein that binds to the single-strand TG1–3 tail generated during the processing of recombination intermediates. -
Genetic Effects on Microsatellite Diversity in Wild Emmer Wheat (Triticum Dicoccoides) at the Yehudiyya Microsite, Israel
Heredity (2003) 90, 150–156 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Genetic effects on microsatellite diversity in wild emmer wheat (Triticum dicoccoides) at the Yehudiyya microsite, Israel Y-C Li1,3, T Fahima1,MSRo¨der2, VM Kirzhner1, A Beiles1, AB Korol1 and E Nevo1 1Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel; 2Institute for Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466 Gatersleben, Germany This study investigated allele size constraints and clustering, diversity. Genome B appeared to have a larger average and genetic effects on microsatellite (simple sequence repeat number (ARN), but lower variance in repeat number 2 repeat, SSR) diversity at 28 loci comprising seven types of (sARN), and smaller number of alleles per locus than genome tandem repeated dinucleotide motifs in a natural population A. SSRs with compound motifs showed larger ARN than of wild emmer wheat, Triticum dicoccoides, from a shade vs those with perfect motifs. The effects of replication slippage sun microsite in Yehudiyya, northeast of the Sea of Galilee, and recombinational effects (eg, unequal crossing over) on Israel. It was found that allele distribution at SSR loci is SSR diversity varied with SSR motifs. Ecological stresses clustered and constrained with lower or higher boundary. (sun vs shade) may affect mutational mechanisms, influen- This may imply that SSR have functional significance and cing the level of SSR diversity by both processes. natural constraints. -
Capture of a Recombination Activating Sequence from Mammalian Cells
Gene Therapy (1999) 6, 1819–1825 1999 Stockton Press All rights reserved 0969-7128/99 $15.00 http://www.stockton-press.co.uk/gt Capture of a recombination activating sequence from mammalian cells P Olson and R Dornburg The Dorrance H Hamilton Laboratories, Center for Human Virology, Division of Infectious Diseases, Jefferson Medical College, Thomas Jefferson University, Jefferson Alumni Hall, 1020 Locust Street, Rm 329, Philadelphia, PA 19107, USA We have developed a genetic trap for identifying revealed a putative recombination signal (CCCACCC). sequences that promote homologous DNA recombination. When this heptamer or an abbreviated form (CCCACC) The trap employs a retroviral vector that normally disables were reinserted into the vector, they stimulated vector itself after one round of replication. Insertion of defined repair and other DNA rearrangements. Mutant forms of DNA sequences into the vector induced the repair of a 300 these oligomers (eg CCCAACC or CCWACWS) did not. base pair deletion, which restored its ability to replicate. Our data suggest that the recombination events occurred Tests of random sequence libraries made in the vector within 48 h after transfection. Keywords: recombination; retroviral vector; vector stability; gene conversion; gene therapy Introduction scripts are still made from the intact left LTR, but reverse transcription copies the deletion to both LTRs, disabling Recognition of cis-acting DNA signals occupies a central the daughter provirus.15–17 We found that the SIN vectors role in both site-specific and general recombination path- that could escape this programmed disablement did so 1–6 ways. Signals in site-specific pathways define the by recombinationally repairing the U3-deleted LTR. -
Conversion Between 100-Million-Year-Old Duplicated Genes Contributes to Rice Subspecies Divergence
Wei et al. BMC Genomics (2021) 22:460 https://doi.org/10.1186/s12864-021-07776-y RESEARCH Open Access Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence Chendan Wei1†, Zhenyi Wang1†, Jianyu Wang1†, Jia Teng1, Shaoqi Shen1, Qimeng Xiao1, Shoutong Bao1, Yishan Feng1, Yan Zhang1, Yuxian Li1, Sangrong Sun1, Yuanshuai Yue1, Chunyang Wu1, Yanli Wang1, Tianning Zhou1, Wenbo Xu1, Jigao Yu2,3, Li Wang1* and Jinpeng Wang1,2,3* Abstract Background: Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution. Results: Using comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19–5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at ~ 0.4 mya, with more (7.77–9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. -
A Long Polymorphic GT Microsatellite Within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a Cpg Island in a Goldfish Inter-Strain Hybrid
International Journal of Molecular Sciences Article A Long Polymorphic GT Microsatellite within a Gene Promoter Mediates Non-Imprinted Allele-Specific DNA Methylation of a CpG Island in a Goldfish Inter-Strain Hybrid 1,2, , 2, 2 Jianbo Zheng * y , Haomang Xu y and Huiwen Cao 1 Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China 2 College of Life Sciences, Zhejiang University, Hangzhou 310058, China * Correspondence: [email protected]; Tel.: +86-572-204-5681 These authors equally contributed to this work. y Received: 26 June 2019; Accepted: 6 August 2019; Published: 12 August 2019 Abstract: It is now widely accepted that allele-specific DNA methylation (ASM) commonly occurs at non-imprinted loci. Most of the non-imprinted ASM regions observed both within and outside of the CpG island show a strong correlation with DNA polymorphisms. However, what polymorphic cis-acting elements mediate non-imprinted ASM of the CpG island remains unclear. In this study, we investigated the impact of polymorphic GT microsatellites within the gene promoter on non-imprinted ASM of the local CpG island in goldfish. We generated various goldfish heterozygotes, in which the length of GT microsatellites or some non-repetitive sequences in the promoter of no tail alleles was different. By examining the methylation status of the downstream CpG island in these heterozygotes, we found that polymorphisms of a long GT microsatellite can lead to the ASM of the downstream CpG island during oogenesis and embryogenesis, polymorphisms of short GT microsatellites and non-repetitive sequences in the promoter exhibited no significant effect on the methylation of the CpG island. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
High-Frequency Germ Line Gene Conversion in Transgenic Mice J
MOLECULAR AND CELLULAR BIOLOGY, June 1992, p. 2545-2552 Vol. 12, No. 6 0270-7306/92/062545-08$02.00/0 Copyright ©) 1992, American Society for Microbiology High-Frequency Germ Line Gene Conversion in Transgenic Mice J. RAMANA MURTI, MICHAEL BUMBULIS, AND JOHN C. SCHIMENTI* Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 45106 Received 8 November 1991/Accepted 28 February 1992 Gene conversion is the nonreciprocal transfer of genetic information between two related genes or DNA sequences. It can influence the evolution of gene families, having the capacity to generate both diversity and homogeneity. The potential evolutionary significance of this process is directly related to its frequency in the germ line. While measurement of meiotic inter- and intrachromosomal gene conversion frequency is routine in fungal systems, it has hitherto been impractical in mammals. We have designed a system for identifying and quantitating germ line gene conversion in mice by analyzing transgenic male gametes for a contrived recombination event. Spermatids which undergo the designed intrachromosomal gene conversion produce functional 13-galactosidase (encoded by the lacZ gene), which is visualized by histochemical staining. We observed a high incidence of lacZ-positive spermatids (-2%), which were produced by a combination of meiotic and mitotic conversion events. These results demonstrate that gene conversion in mice is an active recombinational process leading to nonparental gametic haplotypes. This high frequency of intrachromosomal gene conversion seems incompatible with the evolutionary divergence of newly duplicated genes. Hence, a process may exist to uncouple gene pairs from frequent conversion-mediated homogenization. Gene (or DNA) duplication is a major molecular mecha- aptation. -
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http://www.diva-portal.org This is the published version of a paper published in Genome Biology and Evolution. Citation for the original published paper (version of record): Cossu, R M., Casola, C., Giacomello, S., Vidalis, A., Scofield, D G. et al. (2017) LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes Genome Biology and Evolution, 9(12): 3449-3462 https://doi.org/10.1093/gbe/evx260 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-144974 GBE LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes Rosa Maria Cossu1,2,†, Claudio Casola3,†, Stefania Giacomello4,5, Amaryllis Vidalis6,7, Douglas G. Scofield6,8,9,*, and Andrea Zuccolo1,10,* 1Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy 2Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy 3Department of Ecosystem Science and Management, Texas A&M University 4Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden 5Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden 6Department of Ecology and Environmental Science, Umea˚ University, Sweden 7Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universitat€ Mu¨ nchen, Freising, Germany 8Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden 9Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden 10Istituto di Genomica Applicata, Udine, Italy †These authors contributed equally to this work. -
Transposable Elements in Sexual and Asexual Animals
Transposable elements in sexual and asexual animals Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades „Doctor rerum naturalium“ der Georg-August-Universität Göttingen im Promotionsprogramm Biologie der Georg-August University School of Science (GAUSS) vorgelegt von Diplom-Biologe J e n s B a s t aus Bad Bergzabern Göttingen, 2014 Betreuungsausschuss Prof. Dr. Stefan Scheu, Tierökologie, J.F. Blumenbach Institut PD Dr. Mark Maraun, Tierökologie, J.F. Blumenbach Institut Dr. Marina Schäfer, Tierökologie, J.F. Blumenbach Institut Mitglieder der Prüfungskommision Referent: Prof. Dr. Stefan Scheu, Tierökologie, J.F. Blumenbach Institut Korreferent: PD Dr. Mark Maraun, Tierökologie, J.F. Blumenbach Institut Weitere Mitglieder der Prüfungskommision: Prof. Dr. Elvira Hörandl, Systematische Botanik, Albrecht von Haller Institut Prof. Dr. Ernst Wimmer, Entwicklungsbiologie, J.F. Blumenbach Institut Prof. Dr. Ulrich Brose, Systemische Naturschutzbiologie, J.F. Blumenbach Institut PD Dr. Marko Rohlfs, Tierökologie, J.F. Blumenbach Institut Tag der mündlichen Prüfung: 30.01.2015 2 Wahrlich es ist nicht das Wissen, sondern das Lernen, nicht das Besitzen, sondern das Erwerben, nicht das Da-Seyn, sondern das Hinkommen, was den grössten Genuss gewährt. – Schreiben Gauss an Wolfgang Bolyai, 1808 3 Curriculum Vitae PERSONAL DETAILS NAME Jens Bast BIRTH January, 31 1983 in Bad Bergzabern NATIONALITY German EDUCATION 2011-2015 PhD thesis (biology) Georg-August University Goettingen Title: 'Transposable elements in sexual and -
Characterisation of Repeat and Palindrome Elements in Patients
1of4 ONLINE MUTATION REPORT J Med Genet: first published as 10.1136/jmg.40.7.e86 on 1 July 2003. Downloaded from Characterisation of repeat and palindrome elements in patients harbouring single deletions of mitochondrial DNA A Solano, J Gámez, F J Carod, M Pineda, A Playán, E López-Gallardo, A L Andreu, J Montoya ............................................................................................................................. J Med Genet 2003;40:e86(http://www.jmedgenet.com/cgi/content/full/40/7/e86) ingle deletions of mitochondrial DNA (mtDNA) were the Key points first pathogenic mutations to be identified in human mtDNA. In a seminal paper, Holt et al1 reported the pres- S • We report the molecular findings in a series of 18 ence of single deletions of the mitochondrial genome in patients in whom we have identified single deletions of patients presenting with mitochondrial myopathies, and since their mitochondrial DNA (mtDNA). then, the field has experienced enormous progress. To date, 97 different deletions have been reported in MITOMAP,the main • From a clinical point of view, patients fall into two cat- international database for mtDNA related disorders (www- egories: chronic progressive external ophthalmoplegia .mitomap.org), and most of these deletions are associated (CPEO) and Kearns-Sayre syndrome (KSS). with two clinical presentations: chronic progressive external • After mapping the deletion breakpoints, we report nine ophthalmoplegia (CPEO) and Kearns-Sayre syndrome (KSS). novel deletions varying in size and heteroplasmy levels, Here, we report the molecular characterisation of a series of 18 in which direct tandem repeat elements are involved. patients in whom we have identified single deletions of Also, several palindrome sequences within or near the mtDNA. -
A Highly Accurate and Sensitive Program for Identification of LTR
bioRxiv preprint doi: https://doi.org/10.1101/137141; this version posted May 12, 2017. 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. LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons Shujun Ou and Ning Jiang* Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA ORCID IDs: 0000-0001-5938-7180 (S.O.); 0000-0002-2776-6669 (N.J.) * To whom correspondence should be addressed. Tel: +1 (517) 353-0381; Fax: +1 (517) 353-0890; Email: [email protected] ABSTRACT Long terminal repeat retrotransposons (LTR-RTs) are prevalent in most plant genomes. Identification of LTR-RTs is critical for achieving high-quality gene annotation. The sequences of LTR-RTs are diverse among species, yet the structure of the element is well conserved. Based on the conserved structure, multiple programs were developed for de novo identification of LTR-RTs. Most of these programs are associated with low specificity, and excessive curation is required since false positives are very detrimental for downstream analyses. Here we report LTR_retriever, a multithreading empowered Perl program that identifies LTR retrotransposons and generates high- quality LTR libraries from genomes with various assembly qualities. LTR_retriever demonstrated significant improvements by achieving high levels of sensitivity, specificity, accuracy, and precision, which are 91.7%, 96.9%, 95.7%, and 90.0%, respectively, in rice (Oryza sativa). Besides LTR-RTs with canonical ends (TG..CA), LTR_retriever also identifies non-canonical LTRs accurately. -
The Role of Gene Conversion Between Transposable Elements in Rewiring Regulatory Networks
GBE The Role of Gene Conversion between Transposable Elements in Rewiring Regulatory Networks Jeffrey A. Fawcett1,* and Hideki Innan2,* 1RIKEN iTHEMS, Wako, Saitama, Japan 2SOKENDAI, Hayama, Kanagawa, Japan *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: June 11, 2019 Abstract Nature has found many ways to utilize transposable elements (TEs) throughout evolution. Many molecular and cellular processes depend on DNA-binding proteins recognizing hundreds or thousands of similar DNA motifs dispersed throughout the genome that are often provided by TEs. It has been suggested that TEs play an important role in the evolution of such systems, in particular, the rewiring of gene regulatory networks. One mechanism that can further enhance the rewiring of regulatory networks is nonallelic gene conversion between copies of TEs. Here, we will first review evidence for nonallelic gene conversion in TEs. Then, we will illustrate the benefits nonallelic gene conversion provides in rewiring regulatory networks. For instance, nonallelic gene conversion between TE copies offers an alternative mechanism to spread beneficial mutations that improve the network, it allows multiple mutations to be combined and transferred together, and it allows natural selection to work efficiently in spreading beneficial mutations and removing disadvantageous mutations. Future studies examining the role of nonallelic gene conversion in the evolution of TEs should help us to better understand how TEs have contributed to evolution. Key words: transposable elements, rewiring regulatory network, gene conversion. Evolution of Regulatory Networks species. Many sets of motifs appear to be subject to a high Eukaryotic genomes contain many DNA-binding proteins birth-and-death rate, providing ample opportunities for new which bind to thousands of sites in the genome sharing a genes to be wired in to the network (fig.