Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation

Large-scale studies are revealing many cross-family transcription factor (TF) interactions, supporting the idea that they play important roles in plant gene regulatory networks. Novel in vitro and in vivo approaches in combination with next-generation sequencing methods accelerate studies on TF functioning. Increasing numbers of TFs that play important roles as hubs connecting different genetic networks are being discovered. Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein–protein interactions between members of a particular plant TF family has long been recognised; however, a significant number of interfamily TF interactions has recently been reported. The biological implications and the molecular mechanisms involved in cross-family interactions have now started to be elucidated and the examples illustrate potential roles in the bridging of biological processes. Hence, cross-family TF interactions expand the molecular toolbox for plants with additional mechanisms to control and fine-tune robust gene expression patterns and to adapt to their continuously changing environment. Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein–protein interactions between members of a particular plant TF family has long been recognised; however, a significant number of interfamily TF interactions has recently been reported. The biological implications and the molecular mechanisms involved in cross-family interactions have now started to be elucidated and the examples illustrate potential roles in the bridging of biological processes. Hence, cross-family TF interactions expand the molecular toolbox for plants with additional mechanisms to control and fine-tune robust gene expression patterns and to adapt to their continuously changing environment. TFs bind independently to cis elements and each binding event adds another feature to the regulatory region of a gene. The final transcriptional output is variable and depends on the combination of TFs bound to the regulatory region. cooperative DNA-binding model describing the assembly of TFs and binding to a promoter. In this model TFs bind both cooperatively and additively and the composition of bound TFs is variable. short DNA sequence in a regulatory region of a gene (e.g., promoter, intron) that is recognised by and physically interacts with a DNA-binding TF. occurs when the binding affinity of two or more TFs is more than the sum of the individual affinities. a protein binding to a TF or TF complex that is essential for transcriptional repression of the gene bound by the TF. chromatin is digested with a nuclease and DNA occupied by TFs or other DNA-binding proteins is protected from degradation. a higher-order protein complex of TFs assembled at multiple cis-regulatory elements that cooperatively regulates the expression of a target gene. The DNA sequence acts as a scaffold to recruit all TFs that bind to a strictly ordered cis-element composition present in an enhanceosome. a highly connected node (protein) in a protein–protein interaction network. A hub in a genetic network has many connections with other genes and is therefore able to connect different pathways. novel DNA recognition properties that are revealed as a consequence of protein–protein interactions. a special class of TFs that can access their DNA target sites in compact chromatin and establish competence for the binding of other factors. computational modelling of the structure of complexes and interfaces formed by two or more interacting proteins.