Long-read RNA sequencing identifies isoform switching of a novel long non-coding RNA that promotes somatic cell reprogramming

The recent development of long-read RNA sequencing (lrRNAseq) technologies has paved the way to the exploration of RNA isoform diversity and its relevance in regulating cell fate and plasticity. However, drawing conclusions regarding the functionality of these newly identified isoforms is still very difficult. Here, we developed a very efficient system to reprogram mouse cells towards induced pluripotent cells and leveraged the strengths of lrRNAseq to study isoform diversity throughout reprogramming. We identified several isoforms derived from novel splice junctions occurring during this process. We demonstrate selective pressure on non-coding isoforms to be tightly regulated. We also show that isoform switching (IS) and diversification play a previously overlooked role in gene regulation to promote functional outcomes for reprogramming. Through IS analysis, we uncovered a novel long non-coding RNA (lncRNA) that undergoes IS during reprogramming to enhance the conversion of cells towards pluripotency. Knock-down of this lncRNA in mouse and human embryonic stem cells decreases the level of expression of pluripotency genes, suggesting that it is required for pluripotent stem cell maintenance. Together, our study provides a comprehensive resource to study full-length isoform usage and switching during reprogramming, but more importantly it demonstrates the power of lrRNAseq to identify functionally relevant gene isoforms in the context of pluripotency.