title: Circular RNA profile in gliomas revealed by identification tool UROBORUS.
abstract: Recent evidence suggests that many endogenous circular RNAs (circRNAs) may play roles in biological processes. However, the expression patterns and functions of circRNAs in human diseases are not well understood. Computationally identifying circRNAs from total RNA-seq data is a primary step in studying their expression pattern and biological roles. In this work, we have developed a computational pipeline named UROBORUS to detect circRNAs in total RNA-seq data. By applying UROBORUS to RNA-seq data from 46 gliomas and normal brain samples, we detected thousands of circRNAs supported by at least two read counts, followed by successful experimental validation on 24 circRNAs from the randomly selected 27 circRNAs. UROBORUS is an efficient tool that can detect circRNAs with low expression levels in total RNA-seq without RNase R treatment. The circRNAs expression profiling revealed more than 476 circular RNAs differentially expressed in control brain tissues and gliomas. Together with parental gene expression, we found that circRNA and its parental gene have diversified expression patterns in gliomas and control brain tissues. This study establishes an efficient and sensitive approach for predicting circRNAs using total RNA-seq data. The UROBORUS pipeline can be accessed freely for non-commercial purposes at http://uroborus.openbioinformatics.org/.
authors.affiliation: Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Song
authors.affiliation: Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Naibo
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Department of Gynecology and Obstetrics, The First Affiliated Hospital with Nanjing Medical University, Nanjing 210029, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Han
authors.affiliation: Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Byoung-San
authors.initials: BS
authors.lastname: Moon
authors.affiliation: USC Norris Comprehensive Cancer Center, Department of Neurology and Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA roselai@usc.edu.
authors.forename: Rose K
authors.initials: RK
authors.lastname: Lai
authors.affiliation: Zilkha Neurogenetic Institute, Department of Psychiatry and Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA kaiwang@usc.edu.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA 90089, USA wangelu@usc.edu.
authors.forename: Wange
authors.initials: W
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D001921:Brain / Q000166:cytology; D019295:Computational Biology / Q000379:methods*; D015723:Gene Library; D005910:Glioma / Q000235:genetics*; D006801:Humans; D012313:RNA / Q000235:genetics*; D000079962:RNA, Circular; D017423:Sequence Analysis, RNA
chemical_list: D000079962:RNA, Circular; D012313:RNA