Cell-Type Specific Features of Circular RNA Expression
HeLa RNA was treated with RNase R or a mock treatment, and then subjected to qPCR with isoform-specific primers. The fraction of linear and circular isoforms was normalized to the value measured in the mock treatment. All tested circular isoforms resisted RNase R, including CYP24A1 (1106 nt), FAT1 (3283 nt), HIPK3 (1099 nt), RNF220 (742 nt), PVT1 (410 nt) and ABTB1 (130 nt). The depletion of the FAT1 circle (the largest circle tested) by RNase R may be due to occasional nicking by contaminating endonuclease activity. We hypothesize that the apparent increase in abundance of some upon RNase R treatment is due to more efficient priming in the RT after linear and ribosomal RNA depletion.