Prediction of Regulatory Interactions from Genome Sequences Using a Biophysical Model for theArabidopsisLEAFY Transcription Factor  

Abstract

Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the ciselement fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.

Redefining C and D in the Petunia ABC

“…The presence or absence of LEAFY binding sites identified by this approach appears to be helpful in predicting to what extent a C-clade gene acts as a true C-function gene. The PMADS3 second intron has already been shown to harbor LEAFY binding sites (Moyroud et al, 2011), in line with its role as C-function gene. We resequenced the PMADS3 second intron and newly sequenced the second intron of FBP6 and could identify putative LEAFY binding sites in both genes (Figures 1B and 1C), which, in the case of PMADS3, corresponds to the initial analysis (Moyroud et al, 2011).…”

“…The PMADS3 second intron has already been shown to harbor LEAFY binding sites (Moyroud et al, 2011), in line with its role as C-function gene. We resequenced the PMADS3 second intron and newly sequenced the second intron of FBP6 and could identify putative LEAFY binding sites in both genes (Figures 1B and 1C), which, in the case of PMADS3, corresponds to the initial analysis (Moyroud et al, 2011). In addition, we identified conserved CCAAT-boxes ( Figure 1D), which are a hallmark of AG genes playing a role in early flower development and are required (U) and (X) Scanning electron micrographs of the stigmatic surface of wild-type (U) and fbp6-1 (X) flowers.…”

“…Bars indicate SE. Recently, a new model has been developed to predict LEAFY binding sites based on a position-specific scoring matrix (Moyroud et al, 2011). The presence or absence of LEAFY binding sites identified by this approach appears to be helpful in predicting to what extent a C-clade gene acts as a true C-function gene.…”

PIFs: Systems Integrators in Plant Development

“…In addition to the described binding by BZR1 , BRs might also target PIF5 through direct binding by BES1 . Intriguingly, several transcription factors involved in the regulation of flowering (AP1, SVP, LFY, AG, and SEP3) have also been identified to bind PIFs (Kaufmann et al, 2009(Kaufmann et al, , 2010Moyroud et al, 2011;Tao et al, 2012;Gregis et al, 2013;ÓMaoiléidigh et al, 2013), suggesting a direct link to the reported flowering phenotype of pif mutants (Brock et al, 2010;Nozue et al, 2011;Kumar et al, 2012). Finally, binding by REV and AGL15 (Zheng et al, 2009;Brandt et al, 2012) suggests that some of the PIFs might be involved in leaf patterning or embryogenesis, a possibility that needs to be explored.…”

Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth

“…As a control, we compared these data with the binding sites of LEAFY (LFY) (Moyroud et al, 2011), a transcription factor not known to be required for this morphogenetic response. We found that many shade upregulated genes were bound by PIF5, PIF4, ARF6, and BZR1 (Figures 3A and 3B).…”