Luminal subtype-specific circRNAs in breast cancer cells by a novel tool for external data analysis.

Circular RNAs are molecules present in all eukaryotes that are generated from a large number of genes by a particular processing of transcripts. We have exploited poly(A-) RNA-Seq data generated in our lab in MCF-7 breast cancer cells to define a compilation of exonic circRNAs more comprehensive than previously existing lists. Development of novel computational algorithms allowed us to quantitatively evaluate expression of these circRNA also in publicly available data. We report here novel findings with important implications both for circRNA biogenesis and as specific markers for breast cancer. We observed and confirmed by ChIP analysis that exons involved in circularization events display significantly higher levels of the histone post-transcriptional modification H3K36me3 than non-circularizing exons. This suggests a clear link with a published alternative splicing mechanism in the circRNA biogenesis mechanism. We also found that circRNAs contain an unexpectedly elevated number of Ago binding sites, revamping the hypothesis of circRNAs acting as miRNA sponges in some cases. Finally, we report that a subset of MCF-7 circRNAs are specific to tumor versus normal tissue, while others can differentiate the Luminal tumor subtype, thus suggesting that circRNAs can be exploited as novel biomarkers and drug targets for breast cancer. Overall design: The RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material RNA depleted of both poly(A+) and ribosomal RNAs fractions. Pool of 12 libraries (pooled at equimolar concentration) was generated, quantified and run on the HiSeq2000 (Illumina) sequencer in 50 nts paired-end sequencing mode following manufacturer instruction. A total of 12 datasets, with an average depth from 30.7 to 116.1 million paired-end reads, were obtained, composed of triplicates of four MCF-7 culture conditions: i) hormone-deprived (HD) media ii) HD+ 17b-estradiol (6h) iii) medium added of FSC 5% iv) double-stranded RNA complementary to ESR1 mRNA (siRNA) (48h).