Identification of key tissue-specific, biological processes through integration of enhancer information in maize gene regulatory networks

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Fagny, Maud | Kuijjer, Marieke | Stam, Maike | Joets, Johann | Turc, Olivier | Rozière, Julien | Pateyron, Stéphanie | Venon, Anthony | Vitte, Clémentine

Edité par CCSD -

International audience. Enhancers are important regulators of gene expression during tissue differentiation and development. In plants, their recent molecular characterization has revealed that they can activate the expression of several target genes through the fixation of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genome, where enhancers and target genes can be separated by hundreds of kilobases on the genome. I will present results of a recent study in which we investigated the enhancer-driven regulatory network of two maize tissues at different developmental stages: seedling leaves and husk. Using a systems biology approach, we integrated genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors binding to enhancers, and their potential target genes. We identified tissue-specific regulatory modules, composed of genes involved in the same biological processes and regulated by the same transcription factors, and show that two distinct transcription factor families drive the tissue-specificity of gene expression in husk and seedling leaves in maize. Identification of the enhancer-gene pairs involved in these tissue-specific regulatory modules and subsequent genomic analysis of these enhancers reveals that transposable elements are an important source of enhancers in maize.

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