Bursts of retrotransposition reproduced in Arabidopsis
Retrotransposons, which proliferate by reverse transcription of RNA intermediates, comprise a major portion of plant genomes. Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon s...
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| Veröffentlicht in: | Nature (London) 2009-09, Vol.461 (7262), p.423-426 |
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| creator | Tsukahara, Sayuri Kobayashi, Akie Kawabe, Akira Mathieu, Olivier Miura, Asuka Kakutani, Tetsuji |
| description | Retrotransposons, which proliferate by reverse transcription of RNA intermediates, comprise a major portion of plant genomes. Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon sequences throughout the Arabidopsis thaliana genome and the trans-acting mutations affecting epigenetic states make it an ideal model organism with which to study transposon dynamics. Here we report the mobilization of various families of endogenous A. thaliana LTR retrotransposons identified through genetic and genomic approaches with high-resolution genomic tiling arrays and mutants in the chromatin-remodelling gene DDM1 (DECREASE IN DNA METHYLATION 1). Using multiple lines of self-pollinated ddm1 mutant, we detected an increase in copy number, and verified this for various retrotransposons in a gypsy family (ATGP3) and copia families (ATCOPIA13, ATCOPIA21, ATCOPIA93), and also for a DNA transposon of a Mutator family, VANDAL21. A burst of retrotransposition occurred stochastically and independently for each element, suggesting an additional autocatalytic process. Furthermore, comparison of the identified LTR retrotransposons in related Arabidopsis species revealed that a lineage-specific burst of retrotransposition of these elements did indeed occur in natural Arabidopsis populations. The recent burst of retrotransposition in natural population is targeted to centromeric repeats, which is presumably less harmful than insertion into genes. The ddm1-induced retrotransposon proliferations and genome rearrangements mimic the transposon-mediated genome dynamics during evolution and provide experimental systems with which to investigate the controlling molecular factors directly. |
| doi_str_mv | 10.1038/nature08351 |
| format | Article |
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Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon sequences throughout the Arabidopsis thaliana genome and the trans-acting mutations affecting epigenetic states make it an ideal model organism with which to study transposon dynamics. Here we report the mobilization of various families of endogenous A. thaliana LTR retrotransposons identified through genetic and genomic approaches with high-resolution genomic tiling arrays and mutants in the chromatin-remodelling gene DDM1 (DECREASE IN DNA METHYLATION 1). Using multiple lines of self-pollinated ddm1 mutant, we detected an increase in copy number, and verified this for various retrotransposons in a gypsy family (ATGP3) and copia families (ATCOPIA13, ATCOPIA21, ATCOPIA93), and also for a DNA transposon of a Mutator family, VANDAL21. A burst of retrotransposition occurred stochastically and independently for each element, suggesting an additional autocatalytic process. Furthermore, comparison of the identified LTR retrotransposons in related Arabidopsis species revealed that a lineage-specific burst of retrotransposition of these elements did indeed occur in natural Arabidopsis populations. The recent burst of retrotransposition in natural population is targeted to centromeric repeats, which is presumably less harmful than insertion into genes. The ddm1-induced retrotransposon proliferations and genome rearrangements mimic the transposon-mediated genome dynamics during evolution and provide experimental systems with which to investigate the controlling molecular factors directly.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/nature08351</identifier><identifier>PMID: 19734880</identifier><identifier>CODEN: NATUAS</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>Agronomy. Soil science and plant productions ; Arabidopsis - classification ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis thaliana ; Biological and medical sciences ; Centromere - genetics ; centromeres ; Deoxyribonucleic acid ; DNA ; DNA Methylation ; DNA Transposable Elements - genetics ; DNA, Satellite - genetics ; DNA-Binding Proteins - genetics ; Epigenesis, Genetic ; Evolution, Molecular ; Fundamental and applied biological sciences. Psychology ; Gene Dosage - genetics ; Genetic aspects ; Genetics and breeding of economic plants ; Genome, Plant - genetics ; Genomic Instability ; Genomics ; Humanities and Social Sciences ; letter ; Life Sciences ; multidisciplinary ; Mutagenesis, Insertional - genetics ; Phenotype ; Phylogeny ; Plant genetics ; Properties ; Recombination, Genetic - genetics ; repetitive sequences ; Retroelements - genetics ; retrotransposition ; Retrotransposons ; Reverse transcriptase ; Ribonucleic acid ; RNA ; Science ; Science (multidisciplinary) ; Stochastic Processes ; terminal repeat sequences ; Transcription Factors - genetics ; transposition (genetics)</subject><ispartof>Nature (London), 2009-09, Vol.461 (7262), p.423-426</ispartof><rights>Macmillan Publishers Limited. All rights reserved 2009</rights><rights>2015 INIST-CNRS</rights><rights>COPYRIGHT 2009 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Sep 17, 2009</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c807t-42826d72fa9e2ccd9a129ac9c1a7156d17cde99b083a48c8bd7fea09244779c33</citedby><cites>FETCH-LOGICAL-c807t-42826d72fa9e2ccd9a129ac9c1a7156d17cde99b083a48c8bd7fea09244779c33</cites><orcidid>0000-0001-5302-1102</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nature08351$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature08351$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21901351$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19734880$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://uca.hal.science/hal-01917186$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Tsukahara, Sayuri</creatorcontrib><creatorcontrib>Kobayashi, Akie</creatorcontrib><creatorcontrib>Kawabe, Akira</creatorcontrib><creatorcontrib>Mathieu, Olivier</creatorcontrib><creatorcontrib>Miura, Asuka</creatorcontrib><creatorcontrib>Kakutani, Tetsuji</creatorcontrib><title>Bursts of retrotransposition reproduced in Arabidopsis</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>Retrotransposons, which proliferate by reverse transcription of RNA intermediates, comprise a major portion of plant genomes. Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon sequences throughout the Arabidopsis thaliana genome and the trans-acting mutations affecting epigenetic states make it an ideal model organism with which to study transposon dynamics. Here we report the mobilization of various families of endogenous A. thaliana LTR retrotransposons identified through genetic and genomic approaches with high-resolution genomic tiling arrays and mutants in the chromatin-remodelling gene DDM1 (DECREASE IN DNA METHYLATION 1). Using multiple lines of self-pollinated ddm1 mutant, we detected an increase in copy number, and verified this for various retrotransposons in a gypsy family (ATGP3) and copia families (ATCOPIA13, ATCOPIA21, ATCOPIA93), and also for a DNA transposon of a Mutator family, VANDAL21. 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Soil science and plant productions</subject><subject>Arabidopsis - classification</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis thaliana</subject><subject>Biological and medical sciences</subject><subject>Centromere - genetics</subject><subject>centromeres</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA Transposable Elements - genetics</subject><subject>DNA, Satellite - genetics</subject><subject>DNA-Binding Proteins - genetics</subject><subject>Epigenesis, Genetic</subject><subject>Evolution, Molecular</subject><subject>Fundamental and applied biological sciences. 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Plants often change the genome size and organization during evolution by rapid proliferation and deletion of long terminal repeat (LTR) retrotransposons. Precise transposon sequences throughout the Arabidopsis thaliana genome and the trans-acting mutations affecting epigenetic states make it an ideal model organism with which to study transposon dynamics. Here we report the mobilization of various families of endogenous A. thaliana LTR retrotransposons identified through genetic and genomic approaches with high-resolution genomic tiling arrays and mutants in the chromatin-remodelling gene DDM1 (DECREASE IN DNA METHYLATION 1). Using multiple lines of self-pollinated ddm1 mutant, we detected an increase in copy number, and verified this for various retrotransposons in a gypsy family (ATGP3) and copia families (ATCOPIA13, ATCOPIA21, ATCOPIA93), and also for a DNA transposon of a Mutator family, VANDAL21. A burst of retrotransposition occurred stochastically and independently for each element, suggesting an additional autocatalytic process. Furthermore, comparison of the identified LTR retrotransposons in related Arabidopsis species revealed that a lineage-specific burst of retrotransposition of these elements did indeed occur in natural Arabidopsis populations. The recent burst of retrotransposition in natural population is targeted to centromeric repeats, which is presumably less harmful than insertion into genes. The ddm1-induced retrotransposon proliferations and genome rearrangements mimic the transposon-mediated genome dynamics during evolution and provide experimental systems with which to investigate the controlling molecular factors directly.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>19734880</pmid><doi>10.1038/nature08351</doi><tpages>4</tpages><orcidid>https://orcid.org/0000-0001-5302-1102</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0028-0836 |
| ispartof | Nature (London), 2009-09, Vol.461 (7262), p.423-426 |
| issn | 0028-0836 1476-4687 |
| language | eng |
| recordid | cdi_hal_primary_oai_HAL_hal_01917186v1 |
| source | MEDLINE; Springer Nature - Complete Springer Journals; Nature Journals Online |
| subjects | Agronomy. Soil science and plant productions Arabidopsis - classification Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis thaliana Biological and medical sciences Centromere - genetics centromeres Deoxyribonucleic acid DNA DNA Methylation DNA Transposable Elements - genetics DNA, Satellite - genetics DNA-Binding Proteins - genetics Epigenesis, Genetic Evolution, Molecular Fundamental and applied biological sciences. Psychology Gene Dosage - genetics Genetic aspects Genetics and breeding of economic plants Genome, Plant - genetics Genomic Instability Genomics Humanities and Social Sciences letter Life Sciences multidisciplinary Mutagenesis, Insertional - genetics Phenotype Phylogeny Plant genetics Properties Recombination, Genetic - genetics repetitive sequences Retroelements - genetics retrotransposition Retrotransposons Reverse transcriptase Ribonucleic acid RNA Science Science (multidisciplinary) Stochastic Processes terminal repeat sequences Transcription Factors - genetics transposition (genetics) |
| title | Bursts of retrotransposition reproduced in Arabidopsis |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-30T22%3A04%3A34IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_hal_p&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Bursts%20of%20retrotransposition%20reproduced%20in%20Arabidopsis&rft.jtitle=Nature%20(London)&rft.au=Tsukahara,%20Sayuri&rft.date=2009-09-17&rft.volume=461&rft.issue=7262&rft.spage=423&rft.epage=426&rft.pages=423-426&rft.issn=0028-0836&rft.eissn=1476-4687&rft.coden=NATUAS&rft_id=info:doi/10.1038/nature08351&rft_dat=%3Cgale_hal_p%3EA208694911%3C/gale_hal_p%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=204549365&rft_id=info:pmid/19734880&rft_galeid=A208694911&rfr_iscdi=true |