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Different mutational function of low‐ and high‐linear energy transfer heavy‐ion irradiation demonstrated by whole‐genome resequencing of Arabidopsis mutants
Summary Heavy‐ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double‐stranded break induction along the particle path...
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| Published in: | The Plant journal : for cell and molecular biology 2017-12, Vol.92 (6), p.1020-1030 |
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| container_end_page | 1030 |
| container_issue | 6 |
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| container_title | The Plant journal : for cell and molecular biology |
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| creator | Kazama, Yusuke Ishii, Kotaro Hirano, Tomonari Wakana, Taeko Yamada, Mieko Ohbu, Sumie Abe, Tomoko |
| description | Summary
Heavy‐ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double‐stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm−1) and C ions (LET: 30.0 keV μm−1), by whole‐genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Conversely, C ions induced more single‐base substitutions and small indels ( |
| doi_str_mv | 10.1111/tpj.13738 |
| format | article |
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Heavy‐ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double‐stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm−1) and C ions (LET: 30.0 keV μm−1), by whole‐genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Conversely, C ions induced more single‐base substitutions and small indels (<100 bp) than Ar ions, with 28.1 and 56.9 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Moreover, the rearrangements induced by Ar‐ion irradiation were more complex than those induced by C‐ion irradiation, and tended to accompany single base substitutions or small indels located close by. In conjunction with the detection of causative genes through high‐throughput sequencing, selective irradiation by beams with different effects will be a powerful tool for forward genetics as well as studies on chromosomal rearrangements.
Significance Statement
In the heavy‐ion irradiation, the value of linear energy transfer (LET) can be manipulated by the selection of ion species and particle velocity. Here, we show that the type of induced mutations is affected by the value of LET. Our findings will allow researchers to select the mutation spectrum depending on the purpose of their research.</description><identifier>ISSN: 0960-7412</identifier><identifier>EISSN: 1365-313X</identifier><identifier>DOI: 10.1111/tpj.13738</identifier><identifier>PMID: 29024116</identifier><language>eng</language><publisher>England: Blackwell Publishing Ltd</publisher><subject>Arabidopsis ; Arabidopsis - genetics ; Arabidopsis - physiology ; Arabidopsis - radiation effects ; Arabidopsis thaliana ; Beams (radiation) ; chromosomal rearrangement ; Chromosome Aberrations - radiation effects ; Chromosome rearrangements ; Deoxyribonucleic acid ; DNA ; Energy transfer ; Gene Rearrangement ; Gene sequencing ; Genetics ; Genomes ; Heavy Ions ; heavy‐ion beam ; High-Throughput Nucleotide Sequencing ; Ion irradiation ; Ions ; Irradiation ; linear energy transfer ; Linear energy transfer (LET) ; Linear Energy Transfer - radiation effects ; Mutagenesis ; Mutants ; Mutation ; mutation spectrum ; Next-generation sequencing ; Radiation, Ionizing ; Sequence Analysis, DNA ; Sequence Deletion - radiation effects</subject><ispartof>The Plant journal : for cell and molecular biology, 2017-12, Vol.92 (6), p.1020-1030</ispartof><rights>2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd</rights><rights>2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.</rights><rights>Copyright © 2017 John Wiley & Sons Ltd and the Society for Experimental Biology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4548-304aa57a77befff7db5378cf7ba21980394746ebc1d105a96ffe02fa8fff3fc83</citedby><cites>FETCH-LOGICAL-c4548-304aa57a77befff7db5378cf7ba21980394746ebc1d105a96ffe02fa8fff3fc83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29024116$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kazama, Yusuke</creatorcontrib><creatorcontrib>Ishii, Kotaro</creatorcontrib><creatorcontrib>Hirano, Tomonari</creatorcontrib><creatorcontrib>Wakana, Taeko</creatorcontrib><creatorcontrib>Yamada, Mieko</creatorcontrib><creatorcontrib>Ohbu, Sumie</creatorcontrib><creatorcontrib>Abe, Tomoko</creatorcontrib><title>Different mutational function of low‐ and high‐linear energy transfer heavy‐ion irradiation demonstrated by whole‐genome resequencing of Arabidopsis mutants</title><title>The Plant journal : for cell and molecular biology</title><addtitle>Plant J</addtitle><description>Summary
Heavy‐ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double‐stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm−1) and C ions (LET: 30.0 keV μm−1), by whole‐genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Conversely, C ions induced more single‐base substitutions and small indels (<100 bp) than Ar ions, with 28.1 and 56.9 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Moreover, the rearrangements induced by Ar‐ion irradiation were more complex than those induced by C‐ion irradiation, and tended to accompany single base substitutions or small indels located close by. In conjunction with the detection of causative genes through high‐throughput sequencing, selective irradiation by beams with different effects will be a powerful tool for forward genetics as well as studies on chromosomal rearrangements.
Significance Statement
In the heavy‐ion irradiation, the value of linear energy transfer (LET) can be manipulated by the selection of ion species and particle velocity. Here, we show that the type of induced mutations is affected by the value of LET. Our findings will allow researchers to select the mutation spectrum depending on the purpose of their research.</description><subject>Arabidopsis</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis - physiology</subject><subject>Arabidopsis - radiation effects</subject><subject>Arabidopsis thaliana</subject><subject>Beams (radiation)</subject><subject>chromosomal rearrangement</subject><subject>Chromosome Aberrations - radiation effects</subject><subject>Chromosome rearrangements</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Energy transfer</subject><subject>Gene Rearrangement</subject><subject>Gene sequencing</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Heavy Ions</subject><subject>heavy‐ion beam</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Ion irradiation</subject><subject>Ions</subject><subject>Irradiation</subject><subject>linear energy transfer</subject><subject>Linear energy transfer (LET)</subject><subject>Linear Energy Transfer - radiation effects</subject><subject>Mutagenesis</subject><subject>Mutants</subject><subject>Mutation</subject><subject>mutation spectrum</subject><subject>Next-generation sequencing</subject><subject>Radiation, Ionizing</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Deletion - radiation effects</subject><issn>0960-7412</issn><issn>1365-313X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNp1kc9O3DAQhy0EKlvaAy-ALHFpDwE7duLkiOg_EFJ7oFJv0SQZ73qV2IuddJVbH6EP0Sfrk9TZBQ5I9cUj-fM3Y_8IOeXsgsd1OWzWF1woURyQBRd5lggufhySBStzlijJ02PyOoQ1Y1yJXL4ix2nJUsl5viB_Phit0aMdaD8OMBhnoaN6tM1cUqdp57Z_f_2mYFu6MstVrDtjETxFi3450cGDDVFBVwg_p3g83zPeQ2t2Otpi72yI2IAtrSe6XbkOI7dE63qkHgM-jGgbY5dzvysPtWndJpiwG8kO4Q050tAFfPu4n5Dvnz7eX39J7r5-vrm-uksamckiEUwCZAqUqlFrrdo6E6potKoh5WXBRCmVzLFueMtZBmUeX85SDUWEhW4KcULe7b0b7-JIYah6ExrsOrDoxlDxMpMsF7xMI3r-Al270ce_mymVFirLVRap93uq8S4Ej7raeNODnyrOqjm6KkZX7aKL7Nmjcax7bJ_Jp6wicLkHtqbD6f-m6v7b7V75D4R6q6o</recordid><startdate>201712</startdate><enddate>201712</enddate><creator>Kazama, Yusuke</creator><creator>Ishii, Kotaro</creator><creator>Hirano, Tomonari</creator><creator>Wakana, Taeko</creator><creator>Yamada, Mieko</creator><creator>Ohbu, Sumie</creator><creator>Abe, Tomoko</creator><general>Blackwell Publishing Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201712</creationdate><title>Different mutational function of low‐ and high‐linear energy transfer heavy‐ion irradiation demonstrated by whole‐genome resequencing of Arabidopsis mutants</title><author>Kazama, Yusuke ; Ishii, Kotaro ; Hirano, Tomonari ; Wakana, Taeko ; Yamada, Mieko ; Ohbu, Sumie ; Abe, Tomoko</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4548-304aa57a77befff7db5378cf7ba21980394746ebc1d105a96ffe02fa8fff3fc83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Arabidopsis</topic><topic>Arabidopsis - genetics</topic><topic>Arabidopsis - physiology</topic><topic>Arabidopsis - radiation effects</topic><topic>Arabidopsis thaliana</topic><topic>Beams (radiation)</topic><topic>chromosomal rearrangement</topic><topic>Chromosome Aberrations - radiation effects</topic><topic>Chromosome rearrangements</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Energy transfer</topic><topic>Gene Rearrangement</topic><topic>Gene sequencing</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Heavy Ions</topic><topic>heavy‐ion beam</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Ion irradiation</topic><topic>Ions</topic><topic>Irradiation</topic><topic>linear energy transfer</topic><topic>Linear energy transfer (LET)</topic><topic>Linear Energy Transfer - radiation effects</topic><topic>Mutagenesis</topic><topic>Mutants</topic><topic>Mutation</topic><topic>mutation spectrum</topic><topic>Next-generation sequencing</topic><topic>Radiation, Ionizing</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Deletion - radiation effects</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kazama, Yusuke</creatorcontrib><creatorcontrib>Ishii, Kotaro</creatorcontrib><creatorcontrib>Hirano, Tomonari</creatorcontrib><creatorcontrib>Wakana, Taeko</creatorcontrib><creatorcontrib>Yamada, Mieko</creatorcontrib><creatorcontrib>Ohbu, Sumie</creatorcontrib><creatorcontrib>Abe, Tomoko</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>The Plant journal : for cell and molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kazama, Yusuke</au><au>Ishii, Kotaro</au><au>Hirano, Tomonari</au><au>Wakana, Taeko</au><au>Yamada, Mieko</au><au>Ohbu, Sumie</au><au>Abe, Tomoko</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Different mutational function of low‐ and high‐linear energy transfer heavy‐ion irradiation demonstrated by whole‐genome resequencing of Arabidopsis mutants</atitle><jtitle>The Plant journal : for cell and molecular biology</jtitle><addtitle>Plant J</addtitle><date>2017-12</date><risdate>2017</risdate><volume>92</volume><issue>6</issue><spage>1020</spage><epage>1030</epage><pages>1020-1030</pages><issn>0960-7412</issn><eissn>1365-313X</eissn><abstract>Summary
Heavy‐ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double‐stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm−1) and C ions (LET: 30.0 keV μm−1), by whole‐genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Conversely, C ions induced more single‐base substitutions and small indels (<100 bp) than Ar ions, with 28.1 and 56.9 per mutant genome under Ar‐ and C‐ion irradiation, respectively. Moreover, the rearrangements induced by Ar‐ion irradiation were more complex than those induced by C‐ion irradiation, and tended to accompany single base substitutions or small indels located close by. In conjunction with the detection of causative genes through high‐throughput sequencing, selective irradiation by beams with different effects will be a powerful tool for forward genetics as well as studies on chromosomal rearrangements.
Significance Statement
In the heavy‐ion irradiation, the value of linear energy transfer (LET) can be manipulated by the selection of ion species and particle velocity. Here, we show that the type of induced mutations is affected by the value of LET. Our findings will allow researchers to select the mutation spectrum depending on the purpose of their research.</abstract><cop>England</cop><pub>Blackwell Publishing Ltd</pub><pmid>29024116</pmid><doi>10.1111/tpj.13738</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | The Plant journal : for cell and molecular biology, 2017-12, Vol.92 (6), p.1020-1030 |
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| subjects | Arabidopsis Arabidopsis - genetics Arabidopsis - physiology Arabidopsis - radiation effects Arabidopsis thaliana Beams (radiation) chromosomal rearrangement Chromosome Aberrations - radiation effects Chromosome rearrangements Deoxyribonucleic acid DNA Energy transfer Gene Rearrangement Gene sequencing Genetics Genomes Heavy Ions heavy‐ion beam High-Throughput Nucleotide Sequencing Ion irradiation Ions Irradiation linear energy transfer Linear energy transfer (LET) Linear Energy Transfer - radiation effects Mutagenesis Mutants Mutation mutation spectrum Next-generation sequencing Radiation, Ionizing Sequence Analysis, DNA Sequence Deletion - radiation effects |
| title | Different mutational function of low‐ and high‐linear energy transfer heavy‐ion irradiation demonstrated by whole‐genome resequencing of Arabidopsis mutants |
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