Identification of an aberrant RNA associated with the initiation of transgene silencing [nanopore]

The reason why certain transgenes are targeted by silencing pathways, while others remain highly expressed and durable, has remained a major question for decades, in part due to the lack of technologies to study the initiation of transgene silencing.

We aimed to develop two technologies to identify the trigger that leads to transgene silencing: one to visualize the precise developmental time point of transgene silencing in a model plant and crop, and the second to identify all transcripts produced from a transgene in high depth without RNA fragmentation. By combining these two new methods, and Random Forest machine learning, we identified a cleaved aberrant RNA that accumulates to high levels in a small interfering RNA deficient mutant and in wild-type closely correlates with the onset of RNA interference, ultimately initiating transgene silencing.