Genome-wide identification of LEAFY target genes reveals novel insights into reproductive development in Arabidopsis thaliana

The transition from vegetative growth to flower formation is critical for the survival of flowering plants. The plant-specific transcription factor LEAFY (LFY) has central, evolutionarily conserved roles in this process, both in the formation of the first flower during the onset of reproduction and later in flower patterning. The genome-wide binding and expression studies presented here uncover largely distinct functions for direct LFY target genes at these two stages. LFY regulates a larger set of genes during flower development than previously anticipated, including upstream regulators of flowering time and genes in the auxin and gibberellin pathways that promote floral primordium outgrowth. We additionally show that LFY likely plays a role in the timing of floral homeotic gene expression through direct regulation of SEPALLATA3 . At the onset of reproduction, LFY directly represses the expression of genes regulating the plant\u27s response to external stimuli, which may facilitate resource allocation to flower development. Additionally, the computational pipeline for de novo cis motif analysis that we describe here uncovered stage-specific LFY consensus and cofactor motifs that likely contribute to differential LFY activity at both stages