Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
| العنوان: | Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data |
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| المؤلفون: | Gang Wei, Yu Yang, Yue-Qing Hu, Jun Yao, Zhaozhao Zhao, Weixu Wang, Dong Ding, Qiushi Xu, Ran Wei, Ting Ni, Liye Zhang |
| المصدر: | Genome Res |
| بيانات النشر: | Cold Spring Harbor Laboratory, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Messenger RNA, Polyadenylation, Method, Cancer, RNA-Seq, Computational biology, Biology, bacterial infections and mycoses, medicine.disease, Introns, respiratory tract diseases, medicine.anatomical_structure, Neoplasms, RNA splicing, Genetics, medicine, Humans, Coding region, RNA, Messenger, TSC1, skin and connective tissue diseases, Gene, Genetics (clinical) |
| الوصف: | Intronic polyadenylation (IpA) usually leads to changes in the coding region of an mRNA, and its implication in diseases has been recognized, although at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2. Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m6A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes. |
| تدمد: | 1549-5469 1088-9051 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::17460b94a60b1af96da0eccb40907cb0 https://doi.org/10.1101/gr.271627.120 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....17460b94a60b1af96da0eccb40907cb0 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15495469 10889051 |
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