Yu, Ken Hung-On and Shi, Christina Huan and Wang, Bo and Chow, Savio Ho-Chit and Chung, Grace Tin-Yun and Lung, Raymond Wai-Ming and Tan, Ke-En and Lim, Yat-Yuen and Tsang, Anna Chi-Man and Lo, Kwok-Wai and Yip, Kevin Y. (2021) Quantifying full-length circular RNAs in cancer. Genome Research, 31 (12). pp. 2340-2353. ISSN 1088-9051, DOI https://doi.org/10.1101/gr.275348.121.
Full text not available from this repository.Abstract
Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.
| Item Type: | Article |
|---|---|
| Funders: | Hong Kong Research Grants Council (T12-401/13-R), Fundamental Research Grant Scheme (FRGS/1/2017/SKK08/UM/02/11), Hong Kong Research Grants Council (AoE/M-401/20), Collaborative Research Fund (C4001-18GF), General Research Fund (14113620, 14107420, 14170217, 14203119), Hong Kong Research Grants Council (C4045-18WF, C4054-16G , C4057-18EF, C7044-19GF), Hong Kong Epigenomics Project (EpiHK), Chinese University of Hong Kong |
| Subjects: | Q Science > Q Science (General) |
| Divisions: | Faculty of Science |
| Depositing User: | Ms. Juhaida Abd Rahim |
| Date Deposited: | 22 Feb 2022 03:16 |
| Last Modified: | 22 Feb 2022 03:16 |
| URI: | http://eprints.um.edu.my/id/eprint/26229 |
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