Molecular mechanisms of floral organ specification by MADS domain proteins

•Floral organ identities are specified by master-regulatory homeotic MADS proteins.•MADS proteins coordinate development via partially overlapping sets of target genes.•MADS proteins have specific target genes and antagonistically regulate common targets.•MADS proteins may regulate chromatin structure. Flower development is a model system to understand organ specification in plants. The identities of different types of floral organs are specified by homeotic MADS transcription factors that interact in a combinatorial fashion. Systematic identification of DNA-binding sites and target genes of these key regulators show that they have shared and unique sets of target genes. DNA binding by MADS proteins is not based on ‘simple’ recognition of a specific DNA sequence, but depends on DNA structure and combinatorial interactions. Homeotic MADS proteins regulate gene expression via alternative mechanisms, one of which may be to modulate chromatin structure and accessibility in their target gene promoters.