TY  - JOUR
A1  - Zhao, Zhaozhao
A1  - Xu, Qiushi
A1  - Wei, Ran
A1  - Wang, Weixu
A1  - Ding, Dong
A1  - Yang, Yu
A1  - Yao, Jun
A1  - Zhang, Liye
A1  - Hu, Yue-Qing
A1  - Wei, Gang
A1  - Ni, Ting
T1  - Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
Y1  - 2021/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2095 
EP  - 2106 
DO  - 10.1101/gr.271627.120 
VL  - 31 
IS  - 11 
UR  - http://genome.cshlp.org/content/31/11/2095.abstract 
N2  - 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. 
ER  -