mRNA profiling after knockdown of lncRNA Cyrano

Pluripotency is tightly regulated via versatile pathways and is crucial for the maintenance of stem cells and their implementation for regenerative medicine. Cyrano, a well conserved lncRNA, is highly expressed in stem cells suggesting an important role of Cyrano in pluripotency. Cyrano was previously described to be essential for the maintenance of mouse ESC pluripotency. In contrast, using different genetic models, we here found Cyrano to be dispensable in murine and human iPSCs and in human ESCs. RNAseq in human iPSC revealed only a moderate influence of Cyrano on the global transcriptome, pluripotency-related pathways remaining unaffected. Overall design: Human iPSCs (monoclonal population with a guide RNA for Cyrano) were treated with 2µM doxycycline to induce the knockdown. The treatment for three days resulted in 98% knockdown of Cyrano. Total RNA was harvested, sequencing was performed in triplicates.