Screening and validation of lncRNAs and circRNAs as miRNA sponges

• Published in: Briefings in bioinformatics Vol. 18; no. 5; pp. 780 - 788
• Main Authors: Militello, Giuseppe, Weirick, Tyler, John, David, Döring, Claudia, Dimmeler, Stefanie, Uchida, Shizuka
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.09.2017; Oxford Publishing Limited (England)
• Subjects: Bioinformatics; BTG2 protein; Cell survival; Computational Biology; MicroRNAs; miRNA; Regulators; RNA, Long Noncoding - genetics; Sequestering; Sponges; Transcription; microRNA; lncRNA; circular RNA; transcriptome
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbw053

Abstract Intensive research in past two decades has uncovered the presence and importance of noncoding RNAs (ncRNAs), which includes microRNAs (miRs) and long ncRNAs (lncRNAs). These two classes of ncRNAs interact to a certain extent, as some lncRNAs bind to miRs to sequester them. Such lncRNAs are collectively called 'competing endogenous RNAs' or 'miRNA sponges'. In this study, we screened for lncRNAs that may act as miRNA sponges using the publicly available data sets and databases. To uncover the roles of miRNA sponges, loss-of-function experiments were conducted, which revealed the biological roles as miRNA sponges. LINC00324 is important for the cell survival by binding to miR-615-5p leading to the de-repression of its target BTG2. LOC400043 controls several biological functions via sequestering miR-28-3p and miR-96-5p, thereby changing the expressions of transcriptional regulators. Finally, we also screened for circular RNAs (circRNAs) that may function as miRNA sponges. The results were negative at least for the selected circRNAs in this study. In conclusion, miRNA sponges can be identified by applying a series of bioinformatics techniques and validated with biological experiments.