Plant genomes are dynamic landscapes shaped by transposable elements (TEs), mobile DNA sequences that can move or multiply within chromosomes. MITEs are particularly intriguing because they are small, abundant, and often located close to genes, where they can influence expression. Previous studies have suggested that MITEs may contribute cis-regulatory elements, but how this process works and whether it affects stress-related regulation remain insufficiently understood. Carrot provides a useful system because its genome contains many diverse and polymorphic MITEs. Due to these challenges, it is necessary to conduct in-depth research on how MITEs redistribute transcription factor binding sites and reshape gene-expression networks in plants.
Researchers from the Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, Poland, and the Department of Biological, Ecological, and Earth Sciences, University of South Carolina Aiken, United States, reported (DOI: 10.1093/hr/uhaf360) these findings in Horticulture Research on January 2, 2026. The open-access article examines how carrot miniature inverted-repeat transposable elements (MITEs) influence genes controlled by LATE ELONGATED HYPOCOTYL/REVEILLE (LHY/RVE) transcription factors and identifies DcTourist_15 as a likely driver of MITE-mediated regulatory rewiring in the carrot genome.
The study combined genome-wide computational screening, DNA affinity purification sequencing (DAP-seq), stress-response transcriptome analysis, comparative analysis with rice, and yeast one-hybrid validation. The researchers first searched the carrot genome for short DNA motifs enriched within MITEs and found many sequences resembling LHY/RVE binding sites. DAP-seq then identified 11,779 DcLHY binding sites, including 2,346 located in promoters of protein-coding genes. Among these sites, 1,429 overlapped with carrot MITEs, a much higher frequency than expected from random MITE-like genomic segments. The strongest signal came from DcTourist_15: 592 copies overlapped with DcLHY DAP-seq peaks, compared with only five copies from the related DcTourist_13.2 family. Yeast one-hybrid assays further supported the ability of DcLHY to bind the DcTourist_15 sequence. The team also found that carrot LHY/RVE genes responded mainly to cold and heat stress, and that DcTourist_15 insertion polymorphisms were associated with altered expression of nearby genes under both control and heat-stress conditions.
The authors said the findings show how mobile DNA can act as a source of regulatory innovation rather than simply as repetitive sequence. They said DcTourist_15 appears to carry regulatory signals into new genomic neighborhoods, sometimes placing nearby genes under the influence of circadian-clock and stress-response factors. Not every insertion is expected to be useful, they said, and many may be neutral or removed by selection. Still, the work illustrates how genome mobility can create expression differences that plants may later retain, refine, or discard as they adapt.
The findings may help researchers better understand how crops generate natural variation in stress responses. Because DcTourist_15 insertions can correspond with changes in nearby gene expression, such elements could become useful markers for studying carrot adaptation, heat response, and metabolic regulation. The study also found enrichment of LHY binding sites in rice MITEs, suggesting that MITE-driven regulatory rewiring may extend beyond carrot. Future research could test whether specific MITE–gene associations improve plant performance under field stresses such as heat, cold, or drought. More broadly, the work highlights noncoding mobile DNA as a potentially important resource for crop genetics and breeding.
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References
DOI
10.1093/hr/uhaf360
Original Source URL
https://doi.org/10.1093/hr/uhaf360
Funding information
The research was primarily financed by Polish National Science Center (NCN) project Opus17 no. 2019/33/B/NZ9/00757. The research performed at the University of South Carolina Aiken was supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number P20GM103499.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.