The circadian isoform landscape of mouse livers.

Abstract

The mammalian circadian clock is an autoregulatory feedback process that is responsible for homeostasis in mouse livers. These circadian processes are well understood at the gene level; however, they are not well understood at the isoform level. To investigate circadian oscillations at the isoform level, we used the nanopore-based R2C2 method to create over 78 million highly accurate, full-length complementary DNA reads for 12 RNA samples extracted from mouse livers collected at 2 h intervals. To generate a circadian mouse liver isoform-level transcriptome, we processed these reads using the Mandalorion tool, which identified and quantified 58 612 isoforms, 1806 of which showed circadian oscillations. We performed detailed analysis on the circadian oscillation of these isoforms, their coding sequences, and transcription start sites and compiled easy-to-access resources for other researchers. This study and its results add a new layer of detail to the quantitative analysis of transcriptomes.