Genome-wide identification of cancer-specific alternative splicing in circRNA
Abstract Circular RNA (circRNA) is a group of RNA families generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and introns. Furthermore,...
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doaj-a32953c416774fd18648cdd0b3de53b42020-11-25T01:31:23ZengBMCMolecular Cancer1476-45982019-03-011811510.1186/s12943-019-0996-0Genome-wide identification of cancer-specific alternative splicing in circRNAJing Feng0Ke Chen1Xin Dong2Xiaolong Xu3Yuxuan Jin4Xinyang Zhang5Wenbo Chen6Yujing Han7Lin Shao8Yang Gao9Chunjiang He10School of Computer Science, Wuhan UniversityDepartment of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversitySchool of Basic Medical Sciences, Wuhan UniversityAbstract Circular RNA (circRNA) is a group of RNA families generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and introns. Furthermore, cancer-specific alternative splicing of circRNA is less likely to be identified. Here, we proposed a de novo algorithm, CircSplice, that could identify internal alternative splicing in circRNA and compare differential circRNA splicing events between different conditions (http://gb.whu.edu.cn/CircSplice or https://github.com/GeneFeng/CircSplice). By applying CircSplice in clear cell renal cell carcinoma and bladder cancer, we detected 4498 and 2977 circRNA alternative splicing (circ-AS) events in the two datasets respectively and confirmed the expression of circ-AS events by RT-PCR. We further inspected the distributions and patterns of circ-AS in cancer and adjacent normal tissues. To further understand the potential functions of cancer-specific circ-AS, we classified those events into tumor suppressors and oncogenes and performed pathway enrichment analysis. This study is the first comprehensive view of cancer-specific circRNA alternative splicing, which could contribute significantly to regulation and functional research of circRNAs in cancers.http://link.springer.com/article/10.1186/s12943-019-0996-0Circular RNAscircRNAsAlternative splicingCancer-specificccRCC |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jing Feng Ke Chen Xin Dong Xiaolong Xu Yuxuan Jin Xinyang Zhang Wenbo Chen Yujing Han Lin Shao Yang Gao Chunjiang He |
spellingShingle |
Jing Feng Ke Chen Xin Dong Xiaolong Xu Yuxuan Jin Xinyang Zhang Wenbo Chen Yujing Han Lin Shao Yang Gao Chunjiang He Genome-wide identification of cancer-specific alternative splicing in circRNA Molecular Cancer Circular RNAs circRNAs Alternative splicing Cancer-specific ccRCC |
author_facet |
Jing Feng Ke Chen Xin Dong Xiaolong Xu Yuxuan Jin Xinyang Zhang Wenbo Chen Yujing Han Lin Shao Yang Gao Chunjiang He |
author_sort |
Jing Feng |
title |
Genome-wide identification of cancer-specific alternative splicing in circRNA |
title_short |
Genome-wide identification of cancer-specific alternative splicing in circRNA |
title_full |
Genome-wide identification of cancer-specific alternative splicing in circRNA |
title_fullStr |
Genome-wide identification of cancer-specific alternative splicing in circRNA |
title_full_unstemmed |
Genome-wide identification of cancer-specific alternative splicing in circRNA |
title_sort |
genome-wide identification of cancer-specific alternative splicing in circrna |
publisher |
BMC |
series |
Molecular Cancer |
issn |
1476-4598 |
publishDate |
2019-03-01 |
description |
Abstract Circular RNA (circRNA) is a group of RNA families generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and introns. Furthermore, cancer-specific alternative splicing of circRNA is less likely to be identified. Here, we proposed a de novo algorithm, CircSplice, that could identify internal alternative splicing in circRNA and compare differential circRNA splicing events between different conditions (http://gb.whu.edu.cn/CircSplice or https://github.com/GeneFeng/CircSplice). By applying CircSplice in clear cell renal cell carcinoma and bladder cancer, we detected 4498 and 2977 circRNA alternative splicing (circ-AS) events in the two datasets respectively and confirmed the expression of circ-AS events by RT-PCR. We further inspected the distributions and patterns of circ-AS in cancer and adjacent normal tissues. To further understand the potential functions of cancer-specific circ-AS, we classified those events into tumor suppressors and oncogenes and performed pathway enrichment analysis. This study is the first comprehensive view of cancer-specific circRNA alternative splicing, which could contribute significantly to regulation and functional research of circRNAs in cancers. |
topic |
Circular RNAs circRNAs Alternative splicing Cancer-specific ccRCC |
url |
http://link.springer.com/article/10.1186/s12943-019-0996-0 |
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