رسالة جامعية
Function prediction of transcription start site associated RNAs (TSSaRNAs) in Halobacterium salinarum NRC-1 ; Predição de função para TSSaRNAs (transcritos associados a sitios de início de transcrição) em Halobacterium salinarum NRC-1
| العنوان: | Function prediction of transcription start site associated RNAs (TSSaRNAs) in Halobacterium salinarum NRC-1 ; Predição de função para TSSaRNAs (transcritos associados a sitios de início de transcrição) em Halobacterium salinarum NRC-1 |
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| المؤلفون: | Adam, Yagoub Ali Ibrahim |
| المساهمون: | Vencio, Ricardo Zorzetto Nicoliello |
| بيانات النشر: | Biblioteca Digital de Teses e Dissertações da USP Universidade de São Paulo Bioinformática |
| سنة النشر: | 2019 |
| المجموعة: | University of São Paulo: Digital Library of Theses and Dissertations / Biblioteca Digital de Teses e Dissertações da USP |
| مصطلحات موضوعية: | Anotação estrutural, Regulação baseada em RNA, Predição de ncRNAs, RNA não codificante, Interações de TSSaRNAs-LSm, Interações de RNA, Rfam, Halobacterium salinarum NRC-1, Estruturas de ncRNAs de ordem superior, TSSaRNAs, Funções de ncRNAs, Estruturas RNA, Anotação funcional, Docagem de RNA, RNA docking, RNA interactions, RNA structures, Structural annotation, RNA based regulation, Non-coding RNA, ncRNAs prediction, ncRNAs functions, Higher-order ncRNAs structures, Functional annotation, TSSaRNAs-LSm interactions |
| الوصف: | The Transcription Start Site Associated non-coding RNAs (TSSaRNAs) have been predicted across the three domain of life. However, still, there are no reliable annotation efforts to identify their biological functions and their underline molecular machinery. Therefore, this project addresses the question of what are the potential functions of TSSaRNAs regarding their roles in addressing the cellular functions. To answer this question, we aimed to accurately identify TSSaRNAs in the model organism Halobacterium salinarum NRC-1 (an Archean microorganism) that incubated at the standard growth condition. Consequently, we aimed to investigate TSSaRNAs structural stability in the term of the thermodynamic energies. Moreover, we attempted to functionally annotate TSSaRNAs based on Rfam functional classification of non-coding RNAs. Based on the statistical approach we developed an algorithm to predict TSSaRNA using next-generation RNA sequencing data (RNA-Seq). To perform structural annotation of TSSaRNAs, we investigated the structural stability of TSSaRNAs by modeling the secondary structures by minimizing the thermodynamic free energy. We simulated TSSaRNAs tertiary structures based on the secondary structures constrain using the Rosetta-Common RNA tool. The structures of the minimum free energy supposed to be biophysically stable structures. To investigate the higher order structures of TSSaRNAs, we studied the hybridization between TSSaRNAs and their cognate genes as part of RNA based regulation system. Also, based on our hypothesis that TSSaRNAs may bind to protein to trigger their function, we have investigated the interaction between TSSaRNAs and Lsm protein which known as a chaperone protein that mediates RNA function and involved in RNA processing. Our pipeline to perform the functional annotation of TSSaRNAs aimed to classify TSSaRNAs into their corresponding Rfam families based on two steps: either through querying TSSaRNAs sequences against the co-variance models of Rfam families or by querying the Rfam ... |
| نوع الوثيقة: | doctoral or postdoctoral thesis |
| وصف الملف: | application/pdf |
| اللغة: | English |
| العلاقة: | http://www.teses.usp.br/teses/disponiveis/95/95131/tde-02042019-201857Test/ |
| DOI: | 10.11606/T.95.2019.tde-02042019-201857 |
| الإتاحة: | https://doi.org/10.11606/T.95.2019.tde-02042019-201857Test http://www.teses.usp.br/teses/disponiveis/95/95131/tde-02042019-201857Test/ |
| حقوق: | Liberar o conteúdo para acesso público. |
| رقم الانضمام: | edsbas.1B08FAE5 |
| قاعدة البيانات: | BASE |
| DOI: | 10.11606/T.95.2019.tde-02042019-201857 |
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