Long-read transcriptomics reveals viral load-dependent isoform switching in MERS-CoV-infected human lung cells
Coronaviruses extensively reprogram host gene expression, yet isoform-level regulation remains poorly defined. Here we combine time-resolved long-read RNA sequencing with proteomics to characterise host transcriptome dynamics during MERS-CoV infection. Notably, isoform switching is detectable at early timepoints in the absence of significant differential gene expression, indicating that post-transcriptional regulation precedes transcriptional responses. We identify widespread isoform switching that increases with viral load, indicating that transcriptome rewiring scales with infection severity. Isoform switching follows temporal trajectories linked to early translational and late stress and apoptotic pathways. Mechanistically, switching arises from balanced contributions of alternative splicing and transcriptional initiation and termination variation, with enrichment of previously unannotated isoforms in MERS-CoV infection. Despite extensive transcript-level changes, RNA-protein concordance remains weak, and isoform switching magnitude does not predict protein abundance, demonstrating decoupling between regulatory layers. Collectively, these findings establish isoform regulation as a temporally structured, viral load-dependent, and largely independent layer of host response.
Coronaviruses extensively reprogram host gene expression, yet isoform-level regulation remains poorly defined. Here we combine time-resolved long-read RNA sequencing with proteomics to characterise host transcriptome dynamics during MERS-CoV infection. Notably, isoform switching is detectable at early timepoints in the absence of significant differential gene expression, indicating that post-transcriptional regulation precedes transcriptional responses. We identify widespread isoform switching that increases with viral load, indicating that transcriptome rewiring scales with infection severity. Isoform switching follows temporal trajectories linked to early translational and late stress and apoptotic pathways. Mechanistically, switching arises from balanced contributions of alternative splicing and transcriptional initiation and termination variation, with enrichment of previously unannotated isoforms in MERS-CoV infection. Despite extensive transcript-level changes, RNA-protein concordance remains weak, and isoform switching magnitude does not predict protein abundance, demonstrating decoupling between regulatory layers. Collectively, these findings establish isoform regulation as a temporally structured, viral load-dependent, and largely independent layer of host response.