<i>Cis</i>-regulatory effects of carrot miniature inverted-repeat transposable elements on the expression of genes controlled by LHY/RVE transcription factors

Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed by MITEs on the expression of associated genes through redistributing <i>cis</i>-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors (TFs). Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the <i>DcTourist_15</i> family likely play a key role in redistributing these TF binding sites. We showed that insertional polymorphisms of <i>DcTourist_15</i> correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE TFs, <i>DcTourist_15</i> copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the <i>DcTourist_15</i> family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for TFs from the LHY/RVE family.