Transposable elements contribution to maize tissue differentiation

Maize, like many other crops, has a large genome size, and a large portion of its genome is filled with transposable elements. Recent analysis of distal cis-regulatory regions (dCREs) has revealed that the dCRE-gene distance peaks at 60kb in this species. Moreover, 3D chromatin folding analyses showed that about 25%-40% of dCREs are not targeting their closest gene, and that 34% of dCREs potentially regulate several genes. This highlights the difficulty to identify the regulatory relationships between dCREs and their target genes in maize. I will present recent results showing the power of systems biology to connect dCREs and corresponding transcription factors to their target genes in maize, and to decipher the regulatory modules underlying leaf tissue-specificity, together with their biological functions. How dCREs arise and rewire the gene regulatory network in plants is unclear. 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. I will show that TEs participate in shaping tissue-specific networks in maize, and that some have provided potential new transcription factor binding sites involved in leaf tissue-specificity.