Transposon Elements Shape the Landscape of Enhancer-Promoter Interactions in Cotton Genome Regulation (PRJCA024429)
Here, we used RIC-seq to capture the global enhancer-promoter(E-P) interactions in tetraploid cotton, and compared E-P interactions between wild type and fuzzless/lintless (fl) cotton (Gossypium hirsutum).  We found that the genes corresponding to the specific E-P interactions in WT were enriched in pathways related to trichome development, indicating that the selective interaction of enhancer and promoter can be used to regulate fiber development in cotton.  Further analysis revealed that RNA-class transposon sequences were enriched in the E-P interaction region and formed complementary paired duplexes.  Finally, the GWAS data related to cotton traits were collected and mapped to the global E-P interactions map, which provided some interpretability for the trait differences caused by SNPs.