Our research investigates the interactions between transposable elements (TEs) and their plant hosts. We study the evolution of TE sequences themselves, and how such changes feed into the cycle of escape and suppression that TEs and epigenetic defenses are interlocked into. These changes expand beyond the DNA sequence to the secondary structures of TE mRNAs. Using computational and experimental approaches, we study the complexity and evolutionary conservation of these structures, their importance for cis TE regulation, their use as recognition signals for silencing, and their contribution to the evolution of gene regulatory networks. Recently, we have uncovered evidence of an intragenomic conflict when TEs, possibly as a means to escape suppression, capture fragments of genes. Silencing the TE will come with the cost of silencing the gene, but, intriguingly, some genes do get silenced and lose their function. This may have implications to fundamental processes such as fractionation and pseudogenization. Through new collaborations, we are also exploring how the three-dimensional organization of chromosomes affects TE integration patterns, and how TEs drive the diversification and evolution of plant centromeres.

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