RT Journal
A1 Yu, Ken Hung-On
A1 Shi, Christina Huan
A1 Wang, Bo
A1 Chow, Savio Ho-Chit
A1 Chung, 
Grace Tin-Yun
A1 Lung, Raymond Wai-Ming
A1 Tan, Ke-En
A1 Lim, Yat-Yuen
A1 Tsang, 
Anna Chi-Man
A1 Lo, Kwok-Wai
A1 Yip, Kevin Y.
T1 Quantifying full-length circular RNAs in cancer
JF Genome Research 
JO Genome Research 
YR 2021 
FD December 01 
VO 31 
IS 12 
SP 2340 
OP 2353 
DO 10.1101/gr.275348.121 
UL http://genome.cshlp.org/content/31/12/2340.abstract 
AB Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.