All in the timing: epigenetic control of greening
During germination, the emerging seedling relies on a limited supply of energy and nutrients stored within itself and the seed. This often occurs underground in darkness where seedlings undergo skotomorphogenesis, characterized by hypocotyl elongation, reduced root growth, and small closed cotyledons forming an apical hook to protect the shoot apical meristem as the seedling grows though the soil towards sunlight. Such long and pale dark-grown seedlings are commonly referred to as etiolated (from the French étiolier (to make pale)). However, a seedling must eventually find sunlight and make an irreversible shift to photoautotrophic growth (photomorphogenesis or de-etiolation). This leads to a dramatic change in physiology, including reduced hypocotyl elongation, increased root growth, expansion and unfolding of the cotyledons, and the biogenesis of photosynthetic plastids (i.e. chloroplasts). Furthermore, this shift is accompanied by a massive change in gene expression, with about one-third of genes being reprogrammed. A large amount of the transcriptional response is regulated by the plant photoreceptors (phytochromes and cryptochromes) that activate transcriptional networks. Furthermore, this involves the rapid degradation of PHYTOCHROME INTERACTING FACTORS (PIFs), which are basic helix-loop-helix domain-containing transcription factors that repress photomorphogenesis in the dark.