CASH: a constructing comprehensive splice site method for detecting alternative splicing events
文献类型：期刊论文
| 作者 | Wu, Wenwu1; Zong, Jie2; Chen, Dai2; Guo, Qinghua2; Zhang, Bo2; Wei, Ning3; Cheng, Yuanming3; Feng, Ying3; Cheng, Jian4; Zhou, Xuexia5 |
| 刊名 | BRIEFINGS IN BIOINFORMATICS
 |
| 出版日期 | 2018 |
| 卷号 | 19期号:5页码:905-917 |
| ISSN号 | 1467-5463 |
| 关键词 | alternative splicing RNA-seq SRSF10 splicing model evolution |
| DOI | 10.1093/bib/bbx034 |
| 文献子类 | Article |
| 英文摘要 | RNA-sequencing (RNA-seq) can generate millions of reads to provide clues for analyzing novel or abnormal alternative splicing (AS) events in cells. However, current methods for exploring AS events are still far from being satisfactory. Here, we present Comprehensive AS Hunting (CASH), which constructs comprehensive splice sites including known and novel AS sites in cells, and identifies differentially AS events between cells. We illuminated the versatility of CASH on RNA-seq data from a wide range of species and also on simulated in silico data, validated the advantages of CASH over other AS predictors and exhibited novel differentially AS events. Moreover, we used CASH to identify SRSF10-regulated AS events and investigated the evolution of SRSF10-regulated splicing. The results showed that SRSF10-regulated splicing events are highly evolvable from chickens, mice to humans. However, SRSF10-regulated splicing model was observed to be immutable, in which SRSF10 binding to cassette exon promotes exon inclusion while binding to downstream exon induces exon skipping. Altogether, CASH can significantly improve the detection of AS events and facilitate the study of AS regulation and function in cells; the SRSF10 data first demonstrate a flexibility of SRSF10 with their regulated splicing events but an immutability of SRSF10-regulated splicing model to produce opposite AS outcomes in vertebrates. |
| 学科主题 | Biochemistry & Molecular Biology ; Mathematical & Computational Biology |
| WOS关键词 | RNA-SEQ DATA ; SR PROTEINS ; TRANSCRIPTOME ; GENE ; RECONSTRUCTION ; ANNOTATION ; EXPRESSION ; REPRESSION ; EVOLUTION ; ENHANCERS |
| 语种 | 英语 |
| 出版者 | OXFORD UNIV PRESS |
| WOS记录号 | WOS:000453743200016 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1163]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Zhejiang A&F Univ, Hangzhou, Zhejiang, Peoples R China; 2.Novel Bioinformat Co Ltd, Shanghai, Peoples R China; 3.Chinese Acad Sci, Inst Nutr Sci, Beijing, Peoples R China; 4.Chinese Acad Sci, Tianjin Inst Ind Biotechnol, Beijing, Peoples R China; 5.Tianjin Med Univ, Gen Hosp, Tianjin, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Wu, Wenwu,Zong, Jie,Chen, Dai,et al. CASH: a constructing comprehensive splice site method for detecting alternative splicing events[J]. BRIEFINGS IN BIOINFORMATICS,2018,19(5):905-917. |
| APA | Wu, Wenwu.,Zong, Jie.,Chen, Dai.,Guo, Qinghua.,Zhang, Bo.,...&,.(2018).CASH: a constructing comprehensive splice site method for detecting alternative splicing events.BRIEFINGS IN BIOINFORMATICS,19(5),905-917. |
| MLA | Wu, Wenwu,et al."CASH: a constructing comprehensive splice site method for detecting alternative splicing events".BRIEFINGS IN BIOINFORMATICS 19.5(2018):905-917. |
入库方式： OAI收割
来源：上海营养与健康研究所
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