PANDORA-seq: expanding the small RNA repertoire by overcoming RNA modifications

Small non-coding RNAs (sncRNAs) are key molecules regulating gene expression. High-throughput RNA-seq greatly advanced sncRNA discovery; however, traditional cDNA library construction protocols generate biased sequencing results, in part due to RNA modifications that interfere with adapter ligation and reverse transcription processes, preventing the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (Panoramic RNA Display by Overcoming RNA modification Aborted Sequencing), employing a combination of enzymatic treatments to remove key RNA modifications that block adapter ligation and reverse transcription during cDNA library construction. PANDORA-Seq enables the discovery of thousands of modified sncRNAs previously undetected, mostly tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), which are tissue/cell-specifically detected across mouse brain, liver, spleen, sperm, mouse and human embryonic stem cells, and HeLa cells. Moreover, PANDORA-Seq reveals dynamic changes of tsRNAs and rsRNAs during reprogramming of induced pluripotent stem cells (iPSCs), pointing to future investigations on their potential regulatory functions. Overall design: Small RNA sequencing results of mouse/human tissues and cells under traditional, T4PNK treatment, AlkB treatment, or PANDORA-seq treatment. We performed mESC RNA transfection of 7 types of tsRNA/rsRNA (i.e., rsRNA-28S-1, tsRNA-Ala, tsRNA-Arg, tsRNA-Glu, tsRNA-His, tsRNA-Lys, and a pool of the abovementioned five tsRNAs (tsRNA-pool)) followed by embryoid body (EB) formation and transcriptomic RNA-seq of EBs at Day1, Day3 and Day6 after transfection.