Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes

In this study, we explore the widespread contribution of TEs to mammalian 3D genomes by quantifying the extent to which they give rise to loops and domain border differences across various cell types and species using several 3D genome mapping technologies. The included code can be used to identify chromatin loops that connect ChromHMM defined regulatory elements, and calculate the proportion of reads within a defined region, compared to an enriched region of Hi-C reads generated through capture Hi-C.