The landscape of chimeric RNAs in non-diseased tissues and cells
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Title |
The landscape of chimeric RNAs in non-diseased tissues and cells
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Creator |
Singh, Sandeep
Qin, Fujun Kumar, Shailesh Elfman, Justin Lin, Emily Pham, Lam-Phong Yang, Amy Li, Hui |
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Subject |
chimeric RNAs
non-diseased tissues and cells |
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Description |
Accepted date: January 20, 2020
Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras. NCI Grant [CA190713]; NIGMS Grant [GM132138]; St. Baldrick’s V Scholarship (to H.L.). Funding for open access charge: NIGMS [GM132138]. High-performance computing systems and services were provided by the Data Science Institute and the other Computation and Data Resource Exchange (CADRE) partner organizations at the University of Virginia. We thank the Biorepository and Tissue Research Facility (BTRF) at the University of Virginia for providing the clinical samples. We thank Dr Roger Abounader for providing the immortalized astrocyte cell line. |
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Date |
2020-01-24T09:34:34Z
2020-01-24T09:34:34Z 2020 |
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Type |
Article
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Identifier |
Nucleic Acids Research, 48(4): 1764-1778
1362-4962 https://doi.org/10.1093/nar/gkz1223 https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz1223/5713453 http://223.31.159.10:8080/jspui/handle/123456789/1034 |
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Language |
en_US
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Format |
application/pdf
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Publisher |
Oxford University Press
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