Understanding the transcriptional landscape of non-coding genome in mammals
Widespread transcription in mammals revealed unexpected discovery of non-coding elements like long noncoding RNAs (lncRNAs) and repetitive elements. First, lncRNAs were previously identified in limited number of tissues or cell lines in mouse and the discovery of lncRNAs was still pending in many ot...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2017 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/572043 |
| Acceso en línea: | http://hdl.handle.net/10803/572043 |
| Access Level: | acceso abierto |
| Palabra clave: | lncRNAs (Long noncoding RNAs) TEs (Transposable elements) 575 |
| Sumario: | Widespread transcription in mammals revealed unexpected discovery of non-coding elements like long noncoding RNAs (lncRNAs) and repetitive elements. First, lncRNAs were previously identified in limited number of tissues or cell lines in mouse and the discovery of lncRNAs was still pending in many other tissues in mouse. To address this, we applied a computational pipeline that discovered 2,803 highconfidence novel lncRNAs by mapping and de novo assembling billions of RNA-Seq reads in eight tissues and a primary cell line in mouse. Further, we integrated this catalog of lncRNAs with chromatin state maps and found many regulatory lncRNAs (promoter-associated and enhancer-associated lncRNAs). Second, more than half of the human genome contains repetitive elements. However, it is not clear how they are expressed across all mammalian tissues. To address this, as a part of Genotype- Tissue Expression (GTEx) project, we profiled repetitive elements using 8,551 poly-A RNA-Seq datasets from 53 tissues across 550 individuals and found various repeat families transcribed across multiple human tissues in a tissue-specific manner. In summary, to understand the transcriptional landscape of non-coding genome, we mainly analyzed RNA-Seq datasets across many tissues in mammals and show that the non-coding elements like lncRNA and repetitive elements are not only transcribed but also tissue-specific. Together, this thesis work defines a unique collection of non-coding elements that are transcribed and tissue-specific in mammalian tissues. |
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