The first perception of light upon germination triggers photomorphogenesis (de-etiolation), a critical step in a plant’s life impacting agricultural yield and ecological success in natural contexts. This transition requires rapid and large-scale reprogramming of gene expression to induce the biogenesis of photosynthetic chloroplasts and photo-autotrophy, implicating reciprocal signaling between the nucleus and the other organelles. 

We formerly established that light sensing by nuclear photoreceptors regulates heterochromatin establishment during Arabidopsis cotyledon development. This developmental switch is further accompanied by a general increase in transcriptional activity (Bourbousse, Mestiri, et al., PNAS, 2015). These two massive changes are likely linked to the switch from a “quiescent” to an “active” metabolic state but the plastid or metabolic pathways involved are currently unknown. 

Combining large-scale and synchronized chromatin dynamics with the biogenesis of photosynthetic chloroplasts in a homogeneous population of cells, cotyledon photomorphogenesis constitutes an ideal system for investigating the coupling between cell metabolic status, genome conformation, and global regulation of mRNA synthesis.