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

Background 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 MITE on the expression of associated genes through redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. Results We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors. Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs, but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these transcription factor binding sites. We showed that insertional polymorphisms of DcTourist_15 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 transcription factors, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests that phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Conclusions Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for transcription factors from the LHY/RVE family.