Identification of piRNAs expressed during cardiac differentiation

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

Bernal, Quilmes

Encuentro; II Reunión Argentina de Biología de ARNs no codificantes; 2018

Universidad Nacional de Quilmes

Over a decade has passed since piRNAs (PIWI interacting RNAs) were first discovered, though only recently this member of the ever-growing non-coding RNA (ncRNA) family has come into attention. This class of ncRNA is 24-32nt long and exhibits strong bias for uridine (U) residues at 5? ends, unlike its better known and more abundantly expressed shorter relatives, the miRNAs and siRNAs (~22nt long).Originally thought to be restricted almost exclusively to germline cells, piRNA expression was detected in somatic cells as well as in cancer cells. Although numerous studies showed that their role in germline cells is related to maintenance of chromatin architecture and stability by transcriptionally and epigenetically regulating transposable elements, accumulating evidence in somatic and cancer cells point to a wider spectrum of functions. In this work, we set to identify piRNAs expression profiles in small RNAseq samples from three stages of stem cell differentiation to cardiomyocyte cells, consisting of pluripotency (PSC, day 0), mesoderm progenitor (MPC, day 3.5) and immature cardiomyocyte (CPC, day 21). To achieve this, we initially aligned good quality reads from three biological replicates of each stage to the human reference genome (hg19) and filtered mapped reads to include only those between 24 and 32nt in length (25-35% of total mapped reads). Remaining reads showed remarkable coverage over piRNA loci (piRbase data), indicating strong presence of piRNAs, and the majority of these reads(~40%) evinced 5´ U residues. Conversely, the frequency of adenosine (A) residues in the 10th position of selected reads resulted low for all samples (less than 5%), suggesting that piRNA expression in these cells depends mainly on the primary mechanism of biogenesis and not on the "ping-pong" mechanism (secondary pathway), which is consistent with previous reports on other somatic cells. Further analysis revealed that 85 piRNAs are expressed in PSC, 104 in MPC and 71 in CPC and that 87% of the latter (62 piRNAs) are shared by the three populations. None of the expressed piRNAs overlap with transposable elements, while nearly half intersected with known genes for the three stages. Biological processes associated to these genes mostly involved epigenetic regulation and DNA/chromatin/nucleosome assembly. Cardiomyocytes cells exhibited 38 differentially expressed (DE) piRNAs compared to PSC (p