Spatial organization of the genome is hierarchically ordered, ranging from chromosome territories and A/B compartments to more local structures including topologically associated domains (TADs) and chromatin loops. A growing body of evidence suggests that the 3D architecture may affect gene transcription, DNA repair, and replication. In contrast to animal genomes, mechanisms underlying the structural organization of plant genomes remain relatively unexplored. 

In this study, we investigated the structure of submegabase-scale domains – TADs in carrot (Daucus carota L.) using publicly available high-throughput chromosome conformation capture (Hi-C) data. Hi-C sequencing reads were processed using HiCExplorer. We identified 239, 477, and 1108 TADs at resolutions of 100 kb, 50 kb, and 10 kb, respectively. In the TAD boundaries we searched for carrot miniature inverted-repeat transposable elements (MITE) copies. We revealed that MITEs were largely enriched at each mapping resolution, on average by 26% as compared to randomly selected genome segments of identical size. Among the MITE superfamilies, namely Stowaways, Tourists, Mutators, and hATs, all groups but Stowaways were significantly enriched. However, the most enriched sequence motif in the TAD boundaries at each resolution, as identified by the XSTREME tool, was precisely the canonical terminal inverted repeat (TIR) of carrot Stowaways. Our findings shed light on structure of TADs in carrot and suggest that MITEs are preferably inserted or maintained within TAD boundaries. Possibly, Stowaways could provide motifs which are important for the TAD formation. 

The research was financed by the Polish National Science Center (NCN) (projects Preludium-Bis 2022/47/O/NZ9/00290 and Opus 2019/33/B/NZ9/ 00757)