Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying TEs function are still not clear. Here, we combined Hi-C, ATAC-seq, and ChIP-seq assays revealing the existence of multi-megabase super-sized loop (SSL) clusters in the X. tropicalis sperm genome. We show SSL anchors are inaccessible and devoid of architectural protein CTCF, RNA polymerase II, and histone modifications. Unexpectedly, we find SSL anchors are enriched exclusively with Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. Moreover, most SSL anchor-associated genes are not expressed during early embryo development, suggesting chromatin at SSL anchors maintains a repressive environment to limit transcription during embryogenesis. In sum, our work reveals that Helitrons demarcate an evolutionarily distinct and sperm-specific genome structure that may mediate transposition inhibition during spermatogenesis and transcriptional repression in embryogenesis.

 

3D genome structure; super chromatin loop cluster; sperm; embryogenesis; transcription