WEKO3
アイテム
{"_buckets": {"deposit": "87a92436-f07d-4525-a8fc-ebe078febd8f"}, "_deposit": {"created_by": 27, "id": "769", "owners": [27], "pid": {"revision_id": 0, "type": "depid", "value": "769"}, "status": "published"}, "_oai": {"id": "oai:oist.repo.nii.ac.jp:00000769", "sets": ["40"]}, "author_link": ["3954", "3953", "3955"], "item_10001_biblio_info_7": {"attribute_name": "Bibliographic Information", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2018-04-04", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "5", "bibliographicPageEnd": "688", "bibliographicPageStart": "676", "bibliographicVolumeNumber": "28", "bibliographic_titles": [{}, {"bibliographic_title": "Genome Research", "bibliographic_titleLang": "en"}]}]}, "item_10001_creator_3": {"attribute_name": "Author", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Li, Cai"}], "nameIdentifiers": [{"nameIdentifier": "3953", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Lenhard, Boris"}], "nameIdentifiers": [{"nameIdentifier": "3954", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Luscombe, Nicholas M."}], "nameIdentifiers": [{"nameIdentifier": "3955", "nameIdentifierScheme": "WEKO"}]}]}, "item_10001_description_5": {"attribute_name": "Abstract", "attribute_value_mlt": [{"subitem_description": "Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed approximately 200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage. TSSs were grouped according to their evolutionary age using sequence alignment information as a proxy. Comparisons of young and old TSSs revealed that (1) new TSSs emerge through a combination of intrinsic factors, like the sequence properties of transposable elements and tandem repeats, and extrinsic factors such as their proximity to existing regulatory modules; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the genomic robustness and evolvability in these processes.", "subitem_description_type": "Other"}]}, "item_10001_publisher_8": {"attribute_name": "Publisher", "attribute_value_mlt": [{"subitem_publisher": "Cold Spring Harbor Laboratory Press"}]}, "item_10001_relation_13": {"attribute_name": "PubMedNo.", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:pmid/29618487", "subitem_relation_type_select": "PMID"}}]}, "item_10001_relation_14": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:doi/10.1101/gr.231449.117", "subitem_relation_type_select": "DOI"}}]}, "item_10001_relation_17": {"attribute_name": "Related site", "attribute_value_mlt": [{"subitem_relation_type_id": {"subitem_relation_type_id_text": "https://genome.cshlp.org/content/28/5/676.long", "subitem_relation_type_select": "URI"}}]}, "item_10001_rights_15": {"attribute_name": "Rights", "attribute_value_mlt": [{"subitem_rights": "© 2018 Li et al."}]}, "item_10001_source_id_9": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "1549-5469", "subitem_source_identifier_type": "ISSN"}, {"subitem_source_identifier": "1088-9051", "subitem_source_identifier_type": "ISSN"}]}, "item_10001_version_type_20": {"attribute_name": "Author\u0027s flag", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_970fb48d4fbd8a85", "subitem_version_type": "VoR"}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2019-03-14"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "Li-2018-Integrated analysis sheds light on evo.pdf", "filesize": [{"value": "1.8 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensefree": "Creative Commons \nAttribution 4.0 International\n(https://creativecommons.org/licenses/by/4.0/)", "licensetype": "license_free", "mimetype": "application/pdf", "size": 1800000.0, "url": {"label": "Li-2018-Integrated analysis sheds light on evo", "url": "https://oist.repo.nii.ac.jp/record/769/files/Li-2018-Integrated analysis sheds light on evo.pdf"}, "version_id": "64c71463-d63e-4277-88d4-f21d83ff2aff"}]}, "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": "journal article", "resourceuri": "http://purl.org/coar/resource_type/c_6501"}]}, "item_title": "Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome", "subitem_title_language": "en"}]}, "item_type_id": "10001", "owner": "27", "path": ["40"], "permalink_uri": "https://oist.repo.nii.ac.jp/records/769", "pubdate": {"attribute_name": "公開日", "attribute_value": "2018-12-07"}, "publish_date": "2018-12-07", "publish_status": "0", "recid": "769", "relation": {}, "relation_version_is_last": true, "title": ["Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome"], "weko_shared_id": 27}
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
https://oist.repo.nii.ac.jp/records/769
https://oist.repo.nii.ac.jp/records/76960635f6c-973f-4af2-b8ac-29e1e8cba227
名前 / ファイル | ライセンス | アクション |
---|---|---|
Li-2018-Integrated analysis sheds light on evo (1.8 MB)
|
Creative Commons
Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/) |
Item type | 学術雑誌論文 / Journal Article(1) | |||||
---|---|---|---|---|---|---|
公開日 | 2018-12-07 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Li, Cai
× Li, Cai× Lenhard, Boris× Luscombe, Nicholas M. |
|||||
書誌情報 |
en : Genome Research 巻 28, 号 5, p. 676-688, 発行日 2018-04-04 |
|||||
抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed approximately 200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage. TSSs were grouped according to their evolutionary age using sequence alignment information as a proxy. Comparisons of young and old TSSs revealed that (1) new TSSs emerge through a combination of intrinsic factors, like the sequence properties of transposable elements and tandem repeats, and extrinsic factors such as their proximity to existing regulatory modules; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the genomic robustness and evolvability in these processes. | |||||
出版者 | ||||||
出版者 | Cold Spring Harbor Laboratory Press | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1549-5469 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1088-9051 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/29618487 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1101/gr.231449.117 | |||||
権利 | ||||||
権利情報 | © 2018 Li et al. | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://genome.cshlp.org/content/28/5/676.long | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |