Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

Plant photomorphogenesis is a light-induced developmental switch that combines massive reprogramming of gene expression and a general enhancement in RNA Polymerase II activity. Yet, transcriptome analyses have failed to demonstrate a clear tendency toward gene upregulation. To solve this conundrum, we optimized a spike-in RNA-seq experimental and analysis pipeline and reconciled transcriptome dynamics with epigenomic and cytogenetic observations. We found that light induces a two-fold expansion of the transcriptome during Arabidopsis thaliana cotyledon photomorphogenesis, with 94% of the 9,128 differentially expressed genes being upregulated within the first six hours. Transcriptome augmentation was further detected at a similar strength in spike-free RNA-seq datasets from independent laboratories renormalized using stable genes that mimic the spike-in information. On this new basis, reinterpretation of light-mediated gene regulatory pathways revealed a quasi-exclusive positive effect of HY5 and other key light-induced transcription factors at target genes. This new standpoint unveiled the unilateral impact of light on the transcriptome of Arabidopsis cotyledons at the genome scale and opens new avenues for investigating global genome regulation during plant developmental and environmental responses.