Super-sized clustered loops anchored at transposon Helitrons in Xenopus tropicalis sperm associate with late gene expression during embryogenesis [ChIP-Seq]

Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. SSCL anchors are inaccessible and absent of active histone modifications, implying that SSCLs are repressive in nature. Moreover, genes associated with SSCL anchors express late during development, suggesting 3D structure in sperm may associate with gene expression control during embryo development. The absence of CTCF and RNAPII at SSCL anchors argues against CTCF-mediated or transcription-related looping for the SSCLs establishment. Furthermore, our molecular simulation excludes looping and supports a phase separation model through which SSCLs may form. Taken together, our work reveals a previously undiscovered, repressive 3D structure in sperm that may mediate intergenerational gene regulation. Overall design: Xenopus tropicalis sperm and Xenopus tropicalis x Xenopus laevis hybrid staged embryos were obtained. Hi-C, ChIP-seq, ATAC-seq and RNA-seq were performed in these cells.