ログイン
言語:

WEKO3

  • トップ
  • ランキング
To
lat lon distance
To

Field does not validate



インデックスリンク

インデックスツリー

メールアドレスを入力してください。

WEKO

One fine body…

WEKO

One fine body…

アイテム

{"_buckets": {"deposit": "0fc6c6cb-c00d-4b86-9903-4634f954ef44"}, "_deposit": {"id": "24639", "owners": [], "pid": {"revision_id": 0, "type": "depid", "value": "24639"}, "status": "published"}, "_oai": {"id": "oai:nagoya.repo.nii.ac.jp:00024639", "sets": ["501"]}, "author_link": ["72958", "72959", "72960"], "item_10_biblio_info_6": {"attribute_name": "書誌情報", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2017-06-30", "bibliographicIssueDateType": "Issued"}, "bibliographicPageEnd": "64", "bibliographicPageStart": "57", "bibliographicVolumeNumber": "618", "bibliographic_titles": [{"bibliographic_title": "Gene", "bibliographic_titleLang": "en"}]}]}, "item_10_description_4": {"attribute_name": "抄録", "attribute_value_mlt": [{"subitem_description": "FUS, an RNA-binding protein (RBP), is mutated or abnormally regulated in neurodegenerative disorders. FUS regulates various aspects of RNA metabolisms. FUS binding sites are rich in GU contents and are highly degenerative. FUS-binding motifs of GGU, GGUG, GUGGU and CGCGC have been previously reported. These motifs, however, are applicable to a small fraction of FUS-binding sites. As CLIP-seq tags are enriched in genes that are highly expressed, we normalized CLIP-seq tags by Nascent-seq tags or RNA-seq tags of mouse N2a cells.Nascent-seq identifies nascent transcripts before being processed for splicing and polyadenylation. We extracted frequently observed 4-nt motifs from Nascent-seq normalized CLIP regions, RNA-seq-normalized CLIP regions,and native CLIP regions. Specific GU-rich motifs were best detected in Nascent-seq-normalized CLIP regions. Analysis of structural motifs using Nascent-seq-normalized CLIP regions also predicted GU-rich sequence forming a stem structure. Sensitivity and specificity were calculated by examining whether the extracted motifs were present at the cross-linking-induced mutation sites (CIMS), where FUS was directly bound. We found that a combination of six motifs (UGUG, CUGG, UGGU, GCUG, GUGG, and UUGG), which were extracted from Nascent-seq-normalized CLIP-regions, had a better discriminative power than (i) motifs extracted from RNA-seqnormalized CLIP regions, (ii) motifs extracted from native CLIP regions, (iii) previously reported individual motifs, or (iv) 15 motifs in SpliceAid 2. Validation of the 6 GU-rich (6GUR) motifs using CLIP-seq of the cerebrum and the whole brain showed that the 6GUR motifs were specifically enriched in CIMS. The number of the 6GUR motifs in an uninterrupted region was counted and multiplied by four to calculate the area, which was defined as the 6GUR-Score. The 6GUR-Score of 8 or more best discriminated CIMS from CIMS-flanking regions. We propose that the 6GUR motifs predict FUS-binding sites more efficiently than previously reported individual motifs or 15 motifs in SpliceAid 2.", "subitem_description_language": "en", "subitem_description_type": "Abstract"}]}, "item_10_identifier_60": {"attribute_name": "URI", "attribute_value_mlt": [{"subitem_identifier_type": "DOI", "subitem_identifier_uri": "https://doi.org/10.1016/j.gene.2017.04.008"}, {"subitem_identifier_type": "HDL", "subitem_identifier_uri": "http://hdl.handle.net/2237/26860"}]}, "item_10_publisher_32": {"attribute_name": "出版者", "attribute_value_mlt": [{"subitem_publisher": "Elsevier", "subitem_publisher_language": "en"}]}, "item_10_relation_11": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type": "isVersionOf", "subitem_relation_type_id": {"subitem_relation_type_id_text": "https://doi.org/10.1016/j.gene.2017.04.008", "subitem_relation_type_select": "DOI"}}]}, "item_10_rights_12": {"attribute_name": "権利", "attribute_value_mlt": [{"subitem_rights": "© 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/", "subitem_rights_language": "en"}]}, "item_10_select_15": {"attribute_name": "著者版フラグ", "attribute_value_mlt": [{"subitem_select_item": "author"}]}, "item_10_source_id_7": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "0378-1119", "subitem_source_identifier_type": "PISSN"}]}, "item_1615787544753": {"attribute_name": "出版タイプ", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_ab4af688f83e57aa", "subitem_version_type": "AM"}]}, "item_access_right": {"attribute_name": "アクセス権", "attribute_value_mlt": [{"subitem_access_right": "open access", "subitem_access_right_uri": "http://purl.org/coar/access_right/c_abf2"}]}, "item_creator": {"attribute_name": "著者", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Takeda, Jun-ichi", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "72958", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Masuda, Akio", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "72959", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Ohno, Kinji", "creatorNameLang": "en"}], "nameIdentifiers": [{"nameIdentifier": "72960", "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": "2018-06-30"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "Preprint_1st_draft.pdf", "filesize": [{"value": "807.9 kB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensetype": "license_note", "mimetype": "application/pdf", "size": 807900.0, "url": {"label": "Preprint_1st_draft.pdf ファイル公開:2018/06/30", "objectType": "fulltext", "url": "https://nagoya.repo.nii.ac.jp/record/24639/files/Preprint_1st_draft.pdf"}, "version_id": "f39bab3b-3b85-4d94-9b6c-17dd0e4d429c"}]}, "item_keyword": {"attribute_name": "キーワード", "attribute_value_mlt": [{"subitem_subject": "FUS", "subitem_subject_scheme": "Other"}, {"subitem_subject": "RNA-binding protein", "subitem_subject_scheme": "Other"}, {"subitem_subject": "RNA-binding motif", "subitem_subject_scheme": "Other"}, {"subitem_subject": "CLIP-seq", "subitem_subject_scheme": "Other"}, {"subitem_subject": "Nascent-seq", "subitem_subject_scheme": "Other"}]}, "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": "Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq", "subitem_title_language": "en"}]}, "item_type_id": "10", "owner": "1", "path": ["501"], "permalink_uri": "http://hdl.handle.net/2237/26860", "pubdate": {"attribute_name": "PubDate", "attribute_value": "2017-08-02"}, "publish_date": "2017-08-02", "publish_status": "0", "recid": "24639", "relation": {}, "relation_version_is_last": true, "title": ["Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq"], "weko_shared_id": -1}
  1. C100 医学部/医学系研究科
  2. C100a 雑誌掲載論文
  3. 学術雑誌

Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq

http://hdl.handle.net/2237/26860
http://hdl.handle.net/2237/26860
dc173024-4ec7-4d1f-9018-f7c6f8d95c46
名前 / ファイル ライセンス アクション
Preprint_1st_draft.pdf Preprint_1st_draft.pdf ファイル公開:2018/06/30 (807.9 kB)
Item type 学術雑誌論文 / Journal Article(1)
公開日 2017-08-02
タイトル
タイトル Six GU-rich (6GUR) FUS-binding motifs detected by normalization of CLIP-seq by Nascent-seq
言語 en
著者 Takeda, Jun-ichi

× Takeda, Jun-ichi

WEKO 72958

en Takeda, Jun-ichi

Search repository
Masuda, Akio

× Masuda, Akio

WEKO 72959

en Masuda, Akio

Search repository
Ohno, Kinji

× Ohno, Kinji

WEKO 72960

en Ohno, Kinji

Search repository
アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利
言語 en
権利情報 © 2017. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
キーワード
主題Scheme Other
主題 FUS
キーワード
主題Scheme Other
主題 RNA-binding protein
キーワード
主題Scheme Other
主題 RNA-binding motif
キーワード
主題Scheme Other
主題 CLIP-seq
キーワード
主題Scheme Other
主題 Nascent-seq
抄録
内容記述 FUS, an RNA-binding protein (RBP), is mutated or abnormally regulated in neurodegenerative disorders. FUS regulates various aspects of RNA metabolisms. FUS binding sites are rich in GU contents and are highly degenerative. FUS-binding motifs of GGU, GGUG, GUGGU and CGCGC have been previously reported. These motifs, however, are applicable to a small fraction of FUS-binding sites. As CLIP-seq tags are enriched in genes that are highly expressed, we normalized CLIP-seq tags by Nascent-seq tags or RNA-seq tags of mouse N2a cells.Nascent-seq identifies nascent transcripts before being processed for splicing and polyadenylation. We extracted frequently observed 4-nt motifs from Nascent-seq normalized CLIP regions, RNA-seq-normalized CLIP regions,and native CLIP regions. Specific GU-rich motifs were best detected in Nascent-seq-normalized CLIP regions. Analysis of structural motifs using Nascent-seq-normalized CLIP regions also predicted GU-rich sequence forming a stem structure. Sensitivity and specificity were calculated by examining whether the extracted motifs were present at the cross-linking-induced mutation sites (CIMS), where FUS was directly bound. We found that a combination of six motifs (UGUG, CUGG, UGGU, GCUG, GUGG, and UUGG), which were extracted from Nascent-seq-normalized CLIP-regions, had a better discriminative power than (i) motifs extracted from RNA-seqnormalized CLIP regions, (ii) motifs extracted from native CLIP regions, (iii) previously reported individual motifs, or (iv) 15 motifs in SpliceAid 2. Validation of the 6 GU-rich (6GUR) motifs using CLIP-seq of the cerebrum and the whole brain showed that the 6GUR motifs were specifically enriched in CIMS. The number of the 6GUR motifs in an uninterrupted region was counted and multiplied by four to calculate the area, which was defined as the 6GUR-Score. The 6GUR-Score of 8 or more best discriminated CIMS from CIMS-flanking regions. We propose that the 6GUR motifs predict FUS-binding sites more efficiently than previously reported individual motifs or 15 motifs in SpliceAid 2.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 Elsevier
言語
言語 eng
資源タイプ
資源タイプresource http://purl.org/coar/resource_type/c_6501
タイプ journal article
出版タイプ
出版タイプ AM
出版タイプResource http://purl.org/coar/version/c_ab4af688f83e57aa
DOI
関連タイプ isVersionOf
識別子タイプ DOI
関連識別子 https://doi.org/10.1016/j.gene.2017.04.008
ISSN
収録物識別子タイプ PISSN
収録物識別子 0378-1119
書誌情報 en : Gene

巻 618, p. 57-64, 発行日 2017-06-30
著者版フラグ
値 author
URI
識別子 https://doi.org/10.1016/j.gene.2017.04.008
識別子タイプ DOI
URI
識別子 http://hdl.handle.net/2237/26860
識別子タイプ HDL
戻る
0
views
See details
Views

Versions

Ver.1 2021-03-01 13:57:43.625153
Show All versions

Share

Mendeley Twitter Facebook Print Addthis

Cite as

エクスポート

OAI-PMH
  • OAI-PMH JPCOAR
  • OAI-PMH DublinCore
  • OAI-PMH DDI
Other Formats
  • JSON
  • BIBTEX

Confirm


Powered by WEKO3


Powered by WEKO3