{"_buckets": {"deposit": "f07eb232-918e-432c-a0ea-c937ec97a901"}, "_deposit": {"created_by": 21, "id": "1508", "owners": [21], "pid": {"revision_id": 0, "type": "depid", "value": "1508"}, "status": "published"}, "_oai": {"id": "oai:ir.soken.ac.jp:00001508", "sets": ["21"]}, "author_link": ["0", "0", "0"], "item_1_biblio_info_21": {"attribute_name": "書誌情報（ソート用）", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2009-09-30", "bibliographicIssueDateType": "Issued"}, "bibliographic_titles": [{}]}]}, "item_1_creator_2": {"attribute_name": "著者名", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "島谷, 善平"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_creator_3": {"attribute_name": "フリガナ", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "シマタニ, ゼンペイ"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_1_date_granted_11": {"attribute_name": "学位授与年月日", "attribute_value_mlt": [{"subitem_dategranted": "2009-09-30"}]}, "item_1_degree_grantor_5": {"attribute_name": "学位授与機関", "attribute_value_mlt": [{"subitem_degreegrantor": [{"subitem_degreegrantor_name": "総合研究大学院大学"}]}]}, "item_1_degree_name_6": {"attribute_name": "学位名", "attribute_value_mlt": [{"subitem_degreename": "博士（学術）"}]}, "item_1_description_1": {"attribute_name": "ID", "attribute_value_mlt": [{"subitem_description": "2009528", "subitem_description_type": "Other"}]}, "item_1_description_12": {"attribute_name": "要旨", "attribute_value_mlt": [{"subitem_description": "　　As a major provision for more than half of the world’s population, rice (\u003ci\u003eOryza sativa\u003c/i\u003e  L.) is one of the most important plant species and has great economic importance. Also, rice has been focused on as an excellent model plant for cereal genomics studies due to  its following features; 1) the smallest genome size (389 Mb) among the cereal grasses,  2) syntenic relation with other agronomically important \u003ci\u003ePoaceae\u003c/i\u003e species such as maize,  barley and wheat, 3) available varied resources including a large number of genetic markers, genomic libraries, many mutant lines and retrotransposon tagged lines, 4) there exists well developed technologies for rice genome manipulation such as  \u003ci\u003eAgrobacterium tumefaciens\u003c/i\u003e-mediated gene transformation and gene targeting with homologous recombination. Consequently, fine quality map-based genome sequencing of rice was completed in 2005.\u003cbr /\u003e　　One of the most challenging goals for the plant-research community going forward is to identify the function and regulation of rice genes. Thus, both forward and reverse genetic approaches have been developed to elucidate these functions. However, because the tissue culture process is a necessary step in most of the currently available procedures used in rice genome research, somaclonal variations, which refer to genetic and epigenetic mutations induced by tissue culture, can hamper these approaches. Therefore, a lot of attention has been given to recently identified endogenous DNA transposons that are active under natural growth conditions, a character that is quite useful to development of more efficient rice transposon tagging as a functional genomics tool free from somaclonal variation.\u003cbr /\u003e　　One such DNA transposon, \u003ci\u003enDart1-0 (\u003cu\u003en\u003c/u\u003eon-autonomous \u003cu\u003eD\u003c/u\u003eNA-based \u003cu\u003ea\u003c/u\u003ective \u003cu\u003er\u003c/u\u003eice  \u003cu\u003et\u003c/u\u003eransposon one-zero\u003c/i\u003e) in the \u003ci\u003ehAT\u003c/i\u003e superfamily, had been identified as a causative element of spontaneous leaf variegation shown in the mutant line pyl-v (\u003cu\u003ep\u003c/u\u003eale-\u003cu\u003ey\u003c/u\u003eellow-\u003cu\u003el\u003c/u\u003eeaf \u003cu\u003ev\u003c/u\u003eariegated). This mutable phenotype is caused by the disruption and restoration of the nuclear-coded essential chloroplast protease gene, \u003ci\u003eOsClpP5\u003c/i\u003e, due to the insertion and  subsequent excision of \u003ci\u003enDart1-0\u003c/i\u003e. As a typical non-autonomous transposon in the \u003ci\u003ehAT\u003c/i\u003e\u003cbr/\u003esuperfamily, \u003ci\u003enDart1-0\u003c/i\u003e can transpose only when the \u003ci\u003etrans\u003c/i\u003e-acting transposase is supplied from an autonomous element, \u003ci\u003eaDart (\u003cu\u003ea\u003c/u\u003ective autonomous \u003cu\u003eDart\u003c/u\u003e\u003c/i\u003e). On the other hand, an indicator line, pyl-stb (\u003cu\u003epyl\u003c/u\u003e-\u003cu\u003est\u003c/u\u003ea\u003cu\u003eb\u003c/u\u003ele) shows uniform pale-yellow leaves with no \u003ci\u003enDart1-0\u003c/i\u003e excision due to a lack of an \u003ci\u003eaDart\u003c/i\u003e. The result of test crosses between pyl-v and pyl-stb lines indicated that the pyl-v line carries an \u003ci\u003eaDart\u003c/i\u003e element in its genome.\u003cbr /\u003e　　In the published genomic sequence of the cultivar Nipponbare, there are 38 candidate autonomous \u003ci\u003eDart\u003c/i\u003e elements that have putative transposase genes with no apparent nonsense or frameshift mutations. However, from the result of test crosses with the pyl -stb line, it was shown that Nipponbare carries no \u003ci\u003eaDart\u003c/i\u003e elements in its genome. Meanwhile, the excision of some endogenous \u003ci\u003enDart1\u003c/i\u003e elements in Nipponbare and pyl- stb was induced by treatment with a DNA methylation inhibitor, 5-azacytidine. Hence, these lines were predicted to carry epigenetically silenced autonomous elements, \u003ci\u003eiDarts\u003c/i\u003e (\u003ci\u003einactive autonomous \u003cu\u003eDarts\u003c/u\u003e\u003c/i\u003e).\u003cbr /\u003e　　The first aims of this study were identifying the \u003ci\u003eaDart\u003c/i\u003e element in the pyl-v line and  demonstrating its molecular criteria as an autonomous element. To this end, I performed map-based cloning and revealed that the \u003ci\u003eaDart\u003c/i\u003e element in the pyl-v line coincides with one of the 38 candidate autonomous elements, \u003ci\u003eiDart1-27\u003c/i\u003e, residing on chromosome 6 in  Nipponbare. Also, I have found that all of the examined transcripts of the \u003ci\u003eDart\u003c/i\u003e  transposase gene were derived from \u003ci\u003eDart1-27\u003c/i\u003ein the pyl-v line. These results strongly suggested that \u003ci\u003eDart1-27\u003c/i\u003ein pyl-v acts on \u003ci\u003enDart1-0\u003c/i\u003e as an active \u003ci\u003eaDart\u003c/i\u003e element. Then, I demonstrated that \u003ci\u003eiDart1-27\u003c/i\u003e cloned from the Nipponbare genome can be converted to an active \u003ci\u003eaDart\u003c/i\u003e element in \u003ci\u003eArabidopsis thaliana\u003c/i\u003e plants when its methylation status was eliminated during the cloning process; \u003ci\u003eDart1-27\u003c/i\u003e excised \u003ci\u003enDart1-0\u003c/i\u003e as well as itself from the introduced vectors and integrated into various sites of the \u003ci\u003eA. thaliana\u003c/i\u003egenome. These results clearly indicated that \u003ci\u003eDart1-27\u003c/i\u003e is a functional autonomous element, and it is active as an \u003ci\u003eaDart\u003c/i\u003e element in the pyl-v line whereas epigenetically silenced as \u003ci\u003eiDart1- 27\u003c/i\u003e in Nipponbare. Furthermore, I showed other \u003ci\u003eDart\u003c/i\u003e elements, \u003ci\u003eDart1-1, Dart1-20, Dart1-28\u003c/i\u003e and \u003ci\u003eDart1-52\u003c/i\u003e are also functional autonomous elements, but they are  epigenetically silenced as \u003ci\u003eiDarts\u003c/i\u003e in Nipponbare.\u003cbr /\u003e 　Next, in order to study if there are any regulatory mechanisms that control the activity of the \u003ci\u003eDart/nDart\u003c/i\u003e system in the pyl-stb line, I introduced \u003ci\u003eDart1-27\u003c/i\u003e derivatives into the pyl-stb line and evaluated their activity. As a prerequisite for this transgenic approach, I carefully confirmed that during each step of the \u003ci\u003eA. tumefaciens\u003c/i\u003e-mediated transformation process the endogenous \u003ci\u003eiDart\u003c/i\u003e elements in the pyl-stb genome are almost never activated (0.1%). Based on this confirmation, I introduced \u003ci\u003eDart1-27\u003c/i\u003e derivatives into pyl-stb and demonstrated that they can mobilize \u003ci\u003enDart1-0\u003c/i\u003e elements from the \u003ci\u003eOsClpP5\u003c/i\u003e gene as well as from an introduced \u003ci\u003eGUSPlus\u003c/i\u003e gene at a high frequency in transgenic pyl-stb plants. This result reconfirmed that \u003ci\u003eDart1-27\u003c/i\u003e is a functional autonomous element able to act on \u003ci\u003enDart\u003c/i\u003e elements when its methylation status is eliminated, as shown in \u003ci\u003eA. thaliana\u003c/i\u003eplants. From the results of phenotypic analysis of transgenic pyl-stb plants, it was suggested that there is a development-dependent regulation of \u003ci\u003eDart\u003c/i\u003eactivity in regenerated pyl-stb plants; most of the transgenic pyl-stb plants introduced with \u003ci\u003eDart1-27\u003c/i\u003e derivatives were the pyl-stb phenotype at their 4-6 leaves stage, but almost all of them became the pyl-v phenotype at their 7-10 leaves stage.\u003cbr /\u003e　　In this manuscript, I have unambiguously demonstrated that the active autonomous element in the pyl-v line is \u003ci\u003eDart1-27\u003c/i\u003e on chromosome 6 and that the rice genome contains multiple potential autonomous \u003ci\u003eDart\u003c/i\u003e elements silenced epigenetically. From analysis of transgenic pyl-stb plants, I have also indicated a development-dependent regulation that could be a key to further elucidating \u003ci\u003eDart/nDart\u003c/i\u003e regulation mechanisms in the rice genome. I believe these results will facilitate an effective gene tagging system using the \u003ci\u003eDart/nDart\u003c/i\u003e elements in rice.", "subitem_description_type": "Other"}]}, "item_1_description_7": {"attribute_name": "学位記番号", "attribute_value_mlt": [{"subitem_description": "総研大甲第1293号", "subitem_description_type": "Other"}]}, "item_1_select_14": {"attribute_name": "所蔵", "attribute_value_mlt": [{"subitem_select_item": "有"}]}, "item_1_select_16": {"attribute_name": "複写", "attribute_value_mlt": [{"subitem_select_item": "印刷物から複写可"}]}, "item_1_select_17": {"attribute_name": "公開状況", "attribute_value_mlt": [{"subitem_select_item": "要旨のみ公開"}]}, "item_1_select_8": {"attribute_name": "研究科", "attribute_value_mlt": [{"subitem_select_item": "生命科学研究科"}]}, "item_1_select_9": {"attribute_name": "専攻", "attribute_value_mlt": [{"subitem_select_item": "19 基礎生物学専攻"}]}, "item_1_text_10": {"attribute_name": "学位授与年度", "attribute_value_mlt": [{"subitem_text_value": "2009"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "SHIMATANI, Zenpei", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "0", "nameIdentifierScheme": "WEKO"}]}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2016-02-17"}], "displaytype": "simple", "download_preview_message": "", "file_order": 0, "filename": "甲1293_要旨.pdf", "filesize": [{"value": "344.0 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_11", "mimetype": "application/pdf", "size": 344000.0, "url": {"label": "要旨・審査要旨", "url": "https://ir.soken.ac.jp/record/1508/files/甲1293_要旨.pdf"}, "version_id": "b13718b7-05c3-4b55-bcdb-d8b7dc535449"}]}, "item_language": {"attribute_name": "言語", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"resourcetype": "thesis", "resourceuri": "http://purl.org/coar/resource_type/c_46ec"}]}, "item_title": "Characterization of autonomous Dart1　transposons belonging to the hAT superfamily in rice", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Characterization of autonomous Dart1　transposons belonging to the hAT superfamily in rice"}, {"subitem_title": "Characterization of autonomous Dart1　transposons belonging to the hAT superfamily in rice", "subitem_title_language": "en"}]}, "item_type_id": "1", "owner": "21", "path": ["21"], "permalink_uri": "https://ir.soken.ac.jp/records/1508", "pubdate": {"attribute_name": "公開日", "attribute_value": "2010-06-09"}, "publish_date": "2010-06-09", "publish_status": "0", "recid": "1508", "relation": {}, "relation_version_is_last": true, "title": ["Characterization of autonomous Dart1　transposons belonging to the hAT superfamily in rice"], "weko_shared_id": -1}