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 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 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. 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 regulatory elements in plants and animals, but whether TEs 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 combining TFBS annotation of enhancers previously detected in these two tissues (Oka et al., 2017) with 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. We show that V2-IST leaves are characterized by the response to hormones and macromolecule biogenesis and assembly, while husks are characterized by cell wall modification and response to abiotic stresses. Analysis of enhancers sequence reveals that two different TE superfamilies have shaped part of the regulatory network in the two tissues, TIR transposon Mutator in V2-IST, and MITE Pif/Harbinger in husk, and that MITEs have provided potential new TFBSs involved in husk tissue-specificity.

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