Finding the Balance: Repression of Plant Gene Expression

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All life critically depends on the ability of organisms to set the expression levels of each of their genes. Textbook models claim that gene regulation is controlled by transcription factors (TFs); proteins that bind specific regions of the genome to 'turn on' or 'turn off' expression of target genes. The TFs provide specificity, identifying the correct genes to regulate, but they recruit other proteins to actually set the levels of gene expression. Many TFs turn off gene expression by recruiting proteins known as corepressors. Corepressors cannot bind DNA, but, once brought to a target by a specific TF, they can shut down expression of that target gene. More recent studies reject this simplistic model, in favour of a more nuanced model involving a regulated balance between activation and repression, to deliver the appropriate expression levels. Paradoxically then, in animals, repressive factors have been found to be part of complexes required to both repress and activate. An important class of animal and plant corepressors is the GRO/TUP1 family. The major group of these corepressors in plants is called TPL/TPR. TPL/TPRs are involved in multiple diverse plant processes and are absolutely fundamental to normal growth and development. Despite the fact that these regulators are so critical, their mode of action is poorly understood, with many open questions.There is accumulating evidence that plant TPL/TPR proteins inactivate gene expression as part of a larger complex containing histone deacetylase (HDAC) proteins. HDACs modify the chromatin structure of the target gene, rendering it inactive. In animals, HDACs are also associated with repression complexes, the most abundant of which is the nucleosome remodelling and deacetylase complex (NuRD). Currently, no such complex is known in plants. Some, but not all, of the core components of animal NuRDs are present in plant genomes and we recently identified homologues of animal NuRD components as TPL/TPR interaction partners. This raises the intriguing possibility that TPL/TPRs, which are so essential for normal plant function, repress transcription as part of a currently unknown plant NuRD-like complex. Such a complex would necessarily differ from those found in animals, because plants lack homologues of some of the core animal regulatory complex components. One aim of this proposal is therefore to isolate and characterise the first plant TPL/TPR-HDAC complex, both to understand how it controls gene expression and to compare it with the distinct, but analogous animal complexes. Using either newly identified components of the plant TPL/TPR-HDAC complex, or previously identified candidate components, we will then go on to use molecular genetics to investigate their role in gene expression.The balance model of transcriptional regulation is supported by the association of the animal NuRD-complex with both repressed and active genes. This model also provides a potential explanation for some perplexing results in plants. Our final aim is therefore to investigate whether these complexes are involved in both activation and repression in plants. By taking a global view of DNA-binding and gene expression, we will be able to identify the genomic regions that are associated with TPL/TPR corepressors and/or HDAC and to compare this to a genome-wide map of transcriptional activity. This powerful approach will allow us to quantify the genome association with TPL/TPR alone, HDAC alone and both together. We can then assign DNA association to a transcriptional status (activated or repressed) and, in some cases, compare this to the histone acetylation status of the gene.This project will provide a mechanistic framework for establishing a balance between repression and activation in plants that could be manipulated to alter plant development and responses. It will also reveal whether the novel plant regulatory complexes are involved in both repression and activation of gene expression.