Academic Journal
Discovering sequence and structure landscapes in RNA interaction motifs
| العنوان: | Discovering sequence and structure landscapes in RNA interaction motifs |
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| المؤلفون: | Adinolfi M., Pietrosanto M., Parca L., Ausiello G., Ferre F., Helmer-Citterich M. |
| المساهمون: | Adinolfi, M, Pietrosanto, M, Parca, L, Ausiello, G, Ferre, F, Helmer-Citterich, M |
| سنة النشر: | 2019 |
| المجموعة: | Universitá degli Studi di Roma "Tor Vergata": ART - Archivio Istituzionale della Ricerca |
| مصطلحات موضوعية: | Settore BIO/11 - BIOLOGIA MOLECOLARE |
| الوصف: | RNA molecules are able to bind proteins, DNA and other small or long RNAs using information at primary, secondary or tertiary structure level. Recent techniques that use cross-linking and immunoprecipitation of RNAs can detect these interactions and, if followed by high-throughput sequencing, molecules can be analysed to find recurrent elements shared by interactors, such as sequence and/or structure motifs. Many tools are able to find sequence motifs from lists of target RNAs, while others focus on structure using different approaches to find specific interaction elements. In this work, we make a systematic analysis of RBP-RNA and RNA-RNA datasets to better characterize the interaction landscape with information about multi-motifs on the same RNAs. To achieve this goal, we updated our BEAM algorithm to combine both sequence and structure information to create pairs of patterns that model motifs of interaction. This algorithm was applied to several RNA binding proteins and ncRNAs interactors, confirming already known motifs and discovering new ones. This landscape analysis on interaction variability reflects the diversity of target recognition and underlines that often both primary and secondary structure are involved in molecular recognition. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| Relation: | info:eu-repo/semantics/altIdentifier/pmid/31162604; info:eu-repo/semantics/altIdentifier/wos/WOS:000471248400011; volume:47; issue:10; firstpage:4958; lastpage:4969; numberofpages:12; journal:NUCLEIC ACIDS RESEARCH; http://hdl.handle.net/2108/214829; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85067196016; https://academic.oup.com/nar/article/47/10/4958/5436775 |
| DOI: | 10.1093/nar/gkz250 |
| الاتاحة: | http://hdl.handle.net/2108/214829 https://doi.org/10.1093/nar/gkz250 https://academic.oup.com/nar/article/47/10/4958/5436775 |
| Rights: | info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.430CD5C6 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1093/nar/gkz250 |
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