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

Abstract

Three families of transcription factors have been reported to play key roles in light control of <i>Arabidopsis</i> seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated <i>HY5</i>ox/<i>pifQein3eil1</i>, which contained mutations of <i>EIN3/EIL1</i> and four <i>PIF</i> genes (<i>pifQein3eil1</i>) and overexpression of <i>HY5</i> Our results show that dark-grown <i>HY5</i>ox/<i>pifQein3eil1</i> seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the <i>pifQ</i> mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as <i>HLS1</i> to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.