Detection of differential isoform expression and usage during cellular differentiation using long-read RNA sequencing
About Wilfried Haerty
Wilfried Haerty completed his Ph.D. in 2004 at the University Paris VI, followed by postdocs at McMaster University and University of Oxford in 2011, investigating splicing regulation and the evolution of coding and non-coding genes. Since joining the Earlham Institute in late 2015, his group has been investigating splicing diversity at different scales, single cells, cell cultures, and tissues. We analyse long-read data to annotate novel features and transcripts, assess their regulation during differentiation and development, aiming to identify potential therapeutic targets.
We applied long-read and short-read RNA sequencing to identify full-length transcripts and quantify their expression during lineage commitment of human neuroblastoma cells. We compared the output of the technologies and confirmed the sensitivity of Oxford Nanopore long reads in quantifying gene and transcript expression and its power for identifying differential expression. Not only did we identify 5,656 differentially expressed transcripts, but we also report differential transcript expression for loci not differentially expressed at the gene level, highlighting the importance of investigating transcripts instead of genes. We also identified cases of isoform switching within the same gene during cell differentiation. We highlight the importance of using long-read sequencing to call expression and usage at the transcript level in order to understand the mechanisms enacting cellular differentiation.