Monday, 18 July 2016

CircNet: a database of circular RNAs derived from transcriptome sequencing data.

Yu-Chen Liu and colleagues at the Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan has created a unique web resource CircNet.

Creation of this resource systematically utilized transcriptome sequencing data sets to  identify the expression of circRNAs in 464 RNA-seq samples

The CircNet database is available at

Liu, Yu-Chen, et al. "CircNet: a database of circular RNAs derived from transcriptome sequencing data." Nucleic acids research (2015): gkv940.

Sunday, 17 July 2016

The biogenesis and emerging roles of circular RNAs

Ling-Ling Chen from the State Key Laboratory of Molecular Biology, Shanghai Institutes for Biological Sciences reviews the field of circular RNAs

Abstract: Circular RNAs (circRNAs) are produced from precursor mRNA (pre-mRNA) back-splicing of thousands of genes in eukaryotes. Although circRNAs are generally expressed at low levels, recent findings have shed new light on their cell type-specific and tissue-specific expression and on the regulation of their biogenesis. Furthermore, the data indicate that circRNAs shape gene expression by titrating microRNAs, regulating transcription and interfering with splicing, thus effectively expanding the diversity and complexity of eukaryotic transcriptomes.

Chen, Ling-Ling. "The biogenesis and emerging roles of circular RNAs."Nature Reviews Molecular Cell Biology (2016).

Saturday, 16 July 2016

UROBORUS - New pipeline for Circular RNA detection from RNAseq data

Song and and colleagues from the University of Southern California published a new circular RNA prediction algorithm

UROBORUS. The major advantage of the pipeline is that it can identify circular RNAs from total RNAseq data without RNAaseR treatment. The pipeline is freely available online at for non-commercial purposes at

Song et al,
Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw075
First published online: February 11, 2016

Comparison of circular RNA prediction tools

Hansen and colleagues at the Aarhus University in Denmark compares five popular algorithms for the prediction of circular RNA candidates. The authors compare circRNA_finder, find_circ, CIRCexplorer, CIRI, and MapSplice and evaluate the false positive rate. Analysis concludes the utility of using multiple tools to reduce the false positivity.

Hansen et al,
Nucl. Acids Res. (07 April 2016) 44(6): e58.doi: 10.1093/nar/gkv1458
First published online: December 10, 2015

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

Fan and colleagues at the Peking University in Beijing, China developed a single cell poly-A independent RNA sequencing to elucidate the circular RNA transcriptome of mouse preimplantation embryos. The analysis discovered a total of over 2800 novel circular RNA transcripts in the embryos. This discovery apart from adding a significant number of circular RNAs to the compendium, is also the starting point to understanding the role of circRNAs in early embryogenesis and potential implications in development of diseases, including birth defects.

Fan et al
Genome Biol. 2015; 16(1): 148. Published online 2015 Jul 23. doi:  10.1186/s13059-015-0706-1