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Predicting conformational ensembles and genome-wide Transcription Factor binding sites from DNA sequences
https://repo.qst.go.jp/records/48751
https://repo.qst.go.jp/records/48751616fd7c5-605d-4260-8398-14c2b331a09f
| Item type | 学術雑誌論文 / Journal Article(1) | |||||
|---|---|---|---|---|---|---|
| 公開日 | 2018-04-19 | |||||
| タイトル | ||||||
| タイトル | Predicting conformational ensembles and genome-wide Transcription Factor binding sites from DNA sequences | |||||
| 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 | |||||
| アクセス権 | ||||||
| アクセス権 | metadata only access | |||||
| アクセス権URI | http://purl.org/coar/access_right/c_14cb | |||||
| 著者 |
M., Andrabi
× M., Andrabi× A.P., Hutchins× D., Miranda-Saavedra× H., Kono× R., Nussinov× K., Mizuguchi× S., Ahmad× 河野 秀俊 |
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| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | DNA shape is emerging as an important determinant of transcription factor binding beyond just the DNA sequence. The only tool for large scale DNA shape estimates, DNAshape was derived from Monte-Carlo simulations and predicts four broad and static DNA shape features, Propeller twist, Helical twist, Minor groove width and Roll. The contributions of other shape features e.g. Shift, Slide and Opening cannot be evaluated using DNAshape. Here, we report a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustive set of DNA shape features. We compared the DNAshape and DynaSeq predictions for the common features and applied both to predict the genome-wide binding sites of 1312 TFs available from protein interaction quantification (PIQ) data. The results indicate a good agreement between the two methods for the common shape features and point to advantages in using DynaSeq. Predictive models employing ensembles from individual conformational parameters revealed that base-pair opening - known to be important in strand separation - was the best predictor of transcription factor-binding sites (TFBS) followed by features employed by DNAshape. Of note, TFBS could be predicted not only from the features at the target motif sites, but also from those as far as 200 nucleotides away from the motif. | |||||
| 書誌情報 |
Scientific Reports 巻 7, p. 4071, 発行日 2017-06 |
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| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 2045-2322 | |||||
| DOI | ||||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | 10.1038/s41598-017-03199-6 | |||||
| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | https://www.ncbi.nlm.nih.gov/pubmed/28642456 | |||||
| 関連名称 | https://www.ncbi.nlm.nih.gov/pubmed/28642456 | |||||
