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CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs

Jing Wu, Yan Li, Cheng Wang, Yiqiang Cui, Tianyi Xu, Chang Wang, Xiao Wang, Jiahao Sha, Bin Jiang, Kai Wang, Zhibin Hu, Xuejiang Guo (+1 others)
2020 Genomics, Proteomics & Bioinformatics  
However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved.  ...  Circular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms  ...  Therefore, to address the problem of full-length assembly and quantification of circRNA, in this work, we developed CircAST.  ... 
doi:10.1016/j.gpb.2019.03.004 pmid:32007626 pmcid:PMC7056934 fatcat:jnm34xu4qnanbbuixj7t5rsqvm

Quantifying full-length circular RNAs in cancer

Ken Hung-On Yu, Christina Huan Shi, Bo Wang, Savio Ho-Chit Chow, Grace Tin-Yun Chung, Raymond Wai-Ming Lung, Ke-En Tan, Yat-Yuen Lim, Anna Chi-Man Tsang, Kwok-Wai Lo, Kevin Y. Yip
2021 Genome Research  
Compared to 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  ...  Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data.  ...  splice site selection-namely, cassette exon, intron retention, alternative 5 ′ splice site, and alternative 3 ′ splice site-can all be found in circRNAs (Zhang et al. 2016) .  ... 
doi:10.1101/gr.275348.121 pmid:34663689 pmcid:PMC8647826 fatcat:ieuhn75cvfauzaqd33ptw33lhm

RNA-seq data science: From raw data to effective interpretation [article]

Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin (+4 others)
2021 arXiv   pre-print
, and studying alternative splicing structure.  ...  involved in RNA sequencing, analysis, and software development.  ...  Patro for his valuable comments and suggestions on the manuscript. Competing Interests The authors declare no competing interests. References  ... 
arXiv:2010.02391v3 fatcat:krgm7uzmibdlfh2ylgqxmnh2qu

Viruses join the circular RNA world

Ke‐En Tan, Yat‐Yuen Lim
2020 The FEBS Journal  
Circular RNAs (circRNAs) are a recently discovered class of non-coding RNAs found in many species across the eukaryotic kingdom.  ...  These intriguing RNA species are formed through a unique mechanism that is known as back splicing in which the 5' and 3' termini are covalently joined.  ...  Ea Chee Kwee (University of Texas Southwestern Medical Center) and Dr. Jennifer Ann Harikrishna (Universiti Malaya) for critical review of the manuscript.  ... 
doi:10.1111/febs.15639 pmid:33236482 fatcat:43bs5kgn6nag7fy35swsj4dnaq