Identifying key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

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

Edité par CCSD -

International audience. Enhancers are key regulators of the spatio-temporal coordination of gene expression, in particular during development. Their regulatory effect is mediated by the binding of transcription factors (TFs), which interact with target gene promoters through 3D-loops over long distances (2kb-1Mb). While enhancers have been identified as key players in the wiring of developmental gene regulatory networks in mammals, this question remains largely unexplored in plants. Transposable Elements (TEs) of various superfamilies have been proposed as a source of new cis-regulatory elements in plants and animals, but whether they contribute to the emergence of tissue-specific gene regulatory networks in plants remains to be fully elucidated.Here, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage (V2-IST) and husks (bracts) at flowering. By integrating enhancer, transcription factors binding sites (TFBSs) annotation and mRNA-seq data using a systems biology approach, we model the regulatory relationships between TFs and their potential target genes, and identify regulatory modules specific to husk and V2-IST. This allows us to tackle two main questions: What functions are regulated in a tissue-specific manner between husk and V2-IST, and what are the molecular players (genes, TFs, enhancers) involved? Do transposable elements contribute to enhancers and which biological function do they regulate?

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