Investigation of diurnal polyadenylation site usage reveals differential regulation in the transcription of gene isoforms
Gene isoforms are mRNAs produced from the same locus, but that differ in their transcription start sites, protein coding DNA sequences, and/or untranslated regions. Consequently, different isoforms of the same gene can have altered gene function or even serve different biological functions. Conventional RNA-Seq strategies cannot accurately distinguish expression levels between distinct isoforms, and differences in gene expression studies almost always report total gene expression. However, increasing evidence indicates that differences in isoform usage may be important for the regulation of biological functions and for development of diseases such as cancer. Here, we aimed to define whether gene isoforms are subjected to differential regulation and expression by characterizing 24-hour rhythms in polyadenylation site (PAS) usage over the course of the day in the mouse liver. Conventional RNA-Seq experiments have shown that 15-30% of genes in the mouse liver are rhythmically expressed, and it is assumed that the comprising isoforms are expressed in a similar pattern. By performing 3?-end mRNA-Seq and using stringent criteria for defining differential rhythmic expression, we show that 15% of the genes with more than one PAS exhibit differential rhythmic expression. In particular, many genes known to be rhythmic in the mouse liver harbor at least one constitutively expressed isoform, while several hundred genes characterized as arrhythmically expressed also exhibit a rhythmic isoform. Analysis of PAS usage in nuclear mRNA and single-cell data reveals that the vast majority of isoform-specific regulation does not involve post-transcriptional regulation (e.g., miRNA targeting, RNA half-life) or cell subtype-specific differences in expression. Finally, characterization of PAS usage in Bmal1-/- mice revealed that co-transcriptional regulation plays a large role in the expression of specific gene isoforms. Taken together, our results indicate that gene isoforms can be differentially regulated, and imply that gene isoforms can behave as distinct transcriptional units. Furthermore, our data suggest that conventional RNA-Seq strategies are not the most appropriate choice for detecting changes in gene isoform expression. Overall design: 3' mRNA sequencing on WT total, nuclear, and polysomal RNA and Bmal1-/- total RNA from ad libitum-fed mice livers at 6 timepoints in sextuplicate