Landscape of Chimeric RNAs in Non-Cancerous Cells
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splici...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-03-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/4/466 |
| _version_ | 1797540198624526336 |
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| author | Chen Chen Samuel Haddox Yue Tang Fujun Qin Hui Li |
| author_facet | Chen Chen Samuel Haddox Yue Tang Fujun Qin Hui Li |
| author_sort | Chen Chen |
| collection | DOAJ |
| description | Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern. |
| first_indexed | 2024-03-10T12:56:40Z |
| format | Article |
| id | doaj.art-fd432e6861f8465c85afc126b3f7017a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T12:56:40Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-fd432e6861f8465c85afc126b3f7017a2023-11-21T11:52:49ZengMDPI AGGenes2073-44252021-03-0112446610.3390/genes12040466Landscape of Chimeric RNAs in Non-Cancerous CellsChen Chen0Samuel Haddox1Yue Tang2Fujun Qin3Hui Li4School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, ChinaDepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USASchool of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, Henan Province, ChinaDepartment of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USADepartment of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USAGene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.https://www.mdpi.com/2073-4425/12/4/466chimeric RNAfusion transcriptgene fusion |
| spellingShingle | Chen Chen Samuel Haddox Yue Tang Fujun Qin Hui Li Landscape of Chimeric RNAs in Non-Cancerous Cells Genes chimeric RNA fusion transcript gene fusion |
| title | Landscape of Chimeric RNAs in Non-Cancerous Cells |
| title_full | Landscape of Chimeric RNAs in Non-Cancerous Cells |
| title_fullStr | Landscape of Chimeric RNAs in Non-Cancerous Cells |
| title_full_unstemmed | Landscape of Chimeric RNAs in Non-Cancerous Cells |
| title_short | Landscape of Chimeric RNAs in Non-Cancerous Cells |
| title_sort | landscape of chimeric rnas in non cancerous cells |
| topic | chimeric RNA fusion transcript gene fusion |
| url | https://www.mdpi.com/2073-4425/12/4/466 |
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