Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis

Plant photomorphogenesis is a light-induced developmental switch combining rapid enrichment in RNA Polymerase II activity and massive gene expression reprogramming. Yet, all former transcriptome analyses of this transition detected no average tendency toward gene upregulation. By applying a spike-in RNA-seq approach, we solved this conundrum and reconciled transcriptome dynamics with epigenomic and cytogenetic data. This further unveiled that Arabidopsis cotyledon photomorphogenesis involves a ~2-fold expansion of the transcriptome, a trend that we reproducibly observed in datasets from independent laboratories upon normalization using a set of stable genes defined ad hoc. This new standpoint enabled us to reinterpret light-mediated gene regulatory paths and unveil a quasi-exclusive positive effect of light-induced transcription factors on target genes. Collectively, this study reveals how environmentally controlled variations of the transcriptional regime can functionally impact plant genome expression. It further establishes a framework for investigating the mechanisms of global genome regulation in these organisms. Overall design: ChIP-seq of RNA pol II and H2Bub of dissected cotyledons from 5-day-old Arabidopsis thaliana light and dark-grown seedlings. 3 Replicates are available for RNA Pol II, 2 for H2Bub. A spike-in was included (Drosophila S2 cells chromatin).