Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms

Chenchen Zhu

Chenchen Zhu, Stanford University, USA


Alternative splicing generates various RNA isoforms that form the complexity of eukaryotic transcriptomes, and mis-splicing of RNA isoforms are involved in numerous diseases including cardiovascular disease. Here, using Oxford Nanopore sequencing, we developed high-throughput experimental and computational methods that accurately quantify and compare genome-wide full-length isoform expression with 97.6% accuracy estimated by synthetic RNA isoform controls. We identified 24.1% of the known protein coding isoforms in GENCODE comprehensive annotation. An average of 3.14 isoforms per gene was observed and 15.6% of total spliced isoforms are novel. We conducted, for the first time, differential expression tests of full-length isoforms iPSC-CMs containing RBM20 WT and mutations known to be associated with dilated cardiomyopathy, and pinpointed the full-length isoforms which are mis-spliced in RBM20 mutant. Our discovery that for the mis-spliced genes, only specific but not all isoforms are differentially expressed suggests that splicing is precisely regulated at the isoform level.


Chenchen’s current work focuses on understanding the transcriptional landscape of the human heart using nanopore sequencing technology. His major pursuits include identifying novel transcript isoforms and assessing splicing changes in dilated cardiomyopathy. Previously, as a computational biologist, Chenchen’s research focused on integrating multi-omics datasets to identify causal mediators between genotype and complex phenotype.