RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2021 
FD November 01 
VO 31 
IS 11 
SP 2095 
OP 2106 
DO 10.1101/gr.271627.120 
UL http://genome.cshlp.org/content/31/11/2095.abstract 
AB 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.