Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors

Abstract

Significance Seedlings of terrestrial flowering plants such as Arabidopsis display dramatically different morphologies depending on growing in the dark or light. Dark-grown seedlings exhibit long hypocotyls, apical hook formation, and closed small cotyledons with etioplast. In contrast, light represses hypocotyl elongation, unfolds apical hook, and promotes cotyledon development. How light-controlled seedling morphogenesis is regulated at the transcriptional level remains elusive. To date, three families of transcription factors—PIFs, EIN3/EIL1, and HY5/HYH—have been shown to mediate light responses in seedlings. This study systemically investigates their roles in regulating specific morphological aspects and provides both transcriptomic and genetic evidence that PIFs, EIN3/EIL1, and HY5 are master transcription factors for the proper establishment of seedling skotomorphogenesis and photomorphogenesis.