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Enhancers are key regulators of the spatio-temporal expression of genes in eukaryotes, in particular during development. Their regulatory effect is mediated by the binding of transcription factors, which interact with target gene promoters through 3D-loops over distances reaching several dozens of megabases in some species. Groups of enhancers characterized by similar transcription factor binding sites (TFBSs) have been shown to shape complex regulatory networks, which control tissue-specific expression of genes involved in particular biological functions. Moreover, Transposable Elements (TEs) of various superfamilies have been proposed as a source of new regulatory elements in plants and animals. While enhancers have been identified as key players in the wiring of tissue-specific gene regulatory networks in mammals, and TEs have been shown to contribute to the emergence of these networks, this question remains largely unexplored in plants.  In this talk, I will discuss how integrating TFBS annotations of enhancers with gene co-expression data allows to infer tissue-specific enhancer-based regulatory network. I will present our results on the characterization of enhancers in two maize tissues at different stages: leaves at seedling stage (V2-IST) and husks (bracts) at flowering. In this work, we identified regulatory modules specific to each tissue, and, by analyzing enhancer sequences, we furthermore showed that two different TE families have shaped part of the regulatory network in the two tissues.