Identification of circular RNAs expressed in pluripotent cells and iPSC-derived cardiomyocytes

ALEJANDRO DAMIÁN LA GRECA; CAROLINA COLLI; MARIA AGUSTINA SCARAFIA; ALAN MIQUEAS MÖBBS; NATALIA LUCÍA SANTÍN VELAZQUE; ARIEL WAISMAN; LUCIA NATALIA MORO; GUSTAVO EMILIO SEVLEVER; CARLOS DANIEL LUZZANI; SANTIAGO GABRIEL MIRIUKA

Buenos Aires

Congreso; Latin American Society for Developmental Biology Meeting 2019; 2019

Latin American Society for Developmental Biology (LASDB)

Decades have passed since circular RNA (circRNA) molecules were first discovered, though only recently this non-coding RNA has come into attention. They are characterized by covalently-linked back-spliced junction events in which a splice donor site downstream joins a splice acceptor site upstream. circRNA expression was found in a wide diversity of cell types and physiopathological conditions. However, little is known about these processed transcripts during cell differentiation. In this work, we identified circRNAs in RNAseq samples from three stages of stem cell differentiation into cardiomyocytes, consisting of pluripotency (PSC, day0), mesoderm progenitors (MPC, day3.5) and immature cardiomyocytes (CPC, day21). To achieve this, we initially aligned good quality reads from three biological replicates of each stage to the human reference genome (hg38), instructing the aligner to save chimeric reads (out of order junctions) separately for identification of back-spliced isoforms. Robust expression of putative circRNAs was detected in the three cell populations (PSC: 5649, MPC: 4486, CPC: 2538), among which circular isoforms of FAT1, SMARCA5, HIPK3, ALPK2, FIRRE and SLC8A1 genes were validated by PCR after treatment with RNase R. In conclusion, our data revealed a stage-specific repertoire of circRNAs which could potentially be involved in fine-tuning the complex regulatory networks governing gene expression profiles during differentiation.