Abstract
BackgroundDevelopment of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. In plants, MADS-domain transcription factors act as master regulators of developmental switches and organ specification. However, the mechanisms by which these factors dynamically regulate the expression of their target genes at different developmental stages are still poorly understood.ResultsWe characterized the relationship of chromatin accessibility, gene expression, and DNA binding of two MADS-domain proteins at different stages of Arabidopsis flower development. Dynamic changes in APETALA1 and SEPALLATA3 DNA binding correlated with changes in gene expression, and many of the target genes could be associated with the developmental stage in which they are transcriptionally controlled. We also observe dynamic changes in chromatin accessibility during flower development. Remarkably, DNA binding of APETALA1 and SEPALLATA3 is largely independent of the accessibility status of their binding regions and it can precede increases in DNA accessibility. These results suggest that APETALA1 and SEPALLATA3 may modulate chromatin accessibility, thereby facilitating access of other transcriptional regulators to their target genes.ConclusionsOur findings indicate that different homeotic factors regulate partly overlapping, yet also distinctive sets of target genes in a partly stage-specific fashion. By combining the information from DNA-binding and gene expression data, we are able to propose models of stage-specific regulatory interactions, thereby addressing dynamics of regulatory networks throughout flower development. Furthermore, MADS-domain TFs may regulate gene expression by alternative strategies, one of which is modulation of chromatin accessibility.
Highlights
Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs
The expression of floral homeotic MADS-box genes is regulated at the level of chromatin structure: outside the flower and at the earliest stages of floral meristem development, these genes are repressed by Polycomb group (PcG) protein complexes that act in concert with earlier acting MADSdomain Transcription factor (TF) and other transcriptional regulators [12]
Developmental dynamics of floral gene regulation We studied global changes in chromatin accessibility, gene expression, and DNA binding of two MADSdomain TFs at different stages of flower development (Figure 1)
Summary
Development of eukaryotic organisms is controlled by transcription factors that trigger specific and global changes in gene expression programs. The identities of different types of floral organs (sepals, petals, stamens, and carpels) are established by homeotic MADS-domain transcription factors (TFs) via [1,6,7]. These proteins have an important role in the specification of floral organ identities. The physical and genetic interactions between MADS-domain proteins and chromatin regulatory factors suggest an important role of these TFs in controlling chromatin dynamics during plant development. To gain a genome-wide perspective on the developmental dynamics of gene regulation in plants, we studied MADS-domain TF occupancy, chromatin accessibility, and gene expression changes at different stages of Arabidopsis flower development. By combining DNA-binding data and expression data, we established stage-specific gene regulatory interactions in floral morphogenesis
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