LEAFY Target Genes Reveal Floral Regulatory Logic, cis Motifs, and a Link to Biotic Stimulus Response

Abstract

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 and later in floral patterning. We performed genome-wide binding and expression studies to elucidate the molecular mechanisms by which LFY executes these roles. Our study reveals that LFY directs an elaborate regulatory network in control of floral homeotic gene expression. LFY also controls the expression of genes that regulate the response to external stimuli in Arabidopsis. Thus, our findings support a key role for LFY in the coordination of reproductive stage development and disease response programs in plants that may ensure optimal allocation of plant resources for reproductive fitness. Finally, motif analyses reveal a possible mechanism for stage-specific LFY recruitment and suggest a role for LFY in overcoming polycomb repression.

Regulatory modules controlling maize inflorescence architecture

“…Recently, regulatory networks underlying important developmental processes such as flowering time and floral patterning have been elucidated in Arabidopsis (Kaufmann et al 2009(Kaufmann et al , 2010Pastore et al 2011;Winter et al 2011). Although these programs are largely conserved across eudicots, we know little about how such mechanisms extend to grasses and/or to what extent novel factors have been recruited to pattern grass-specific inflorescence morphology.…”

“…3J; Supplemental Table S11; Kaufmann et al 2009). Recent work from Arabidopsis showed that bZIPs and MADS-box TFs are likely co-factors of LFY in promoting floral differentiation (Winter et al 2011;Wu et al 2012) and thus may play qualitatively similar roles in maize in promoting branch determinacy.…”

CHD3 chromatin-remodeling factor PICKLE regulates floral transition partially via modulating LEAFY expression at the chromatin level in Arabidopsis

“…LFY is considered to be one of the key floral meristem iden- tity genes, and regulates many other downstream floral meristem identity genes (Weigel et al, 1992;Winter et al, 2011). In addition to its role in determining floral meristem identity, LFY has also been shown to regulate flowering time in Arabidopsis (Blazquez et …”

“…The expression of genes functioning in meristem identity transition was mis-regulated in the pkl-1 mutant, including LFY and many other floral homeotic genes. LFY is considered to be a key regulator of meristem identity transition, and also functions to activate the expression of its downstream floral homeotic genes via its binding to the specific regulatory elements close to transcription starting sites of its downstream genes, thereby to direct floral organ patterning (Weigel et al, 1992;Weigel and Nilsson, 1995;Winter et al, 2011). Our RNA-seq data showed that LFY and 14 LFY-regulated downstream genes were differentially regulated in the pkl-1 mutant ( Figure 5A, Table S3 in Supporting Information), and these genes can be mainly sorted into flowering time and floral homeotic groups (Winter et al, 2011).…”

“…In addition, a group of floral meristem identity genes were identified as the key factors for floral morphogenesis in the developmental biology of plants. As one of the key floral meristem identity genes, LEAFY (LFY) encodes a MADS box transcriptional factor, and regulates many other downstream floral meristem identity genes (Weigel et al, 1992;Winter et al, 2011). LFY is expressed in floral primordia, and its expression increases upon floral induction (Wagner et al, 1999).…”