Divergent 3D genome architecture of male germ cells across vertebrates [Hi-C]

Yet, the mechanisms regulating these processes remain poorly characterized across lineages. Here, we integrate fluorescence-activated cell sorting, in situ Hi-C, and single-cell RNA sequencing to investigate germ line genome architecture in eutherians, marsupials, and reptiles, —lineages that last shared a common ancestor ~320 million years ago.

We uncover lineage-specific chromatin folding patterns in germ cells, shaped by chromosome morphology and genome size, which constrain DNA loop formation and inter-chromosomal interactions during meiosis. We also explore the relationship between 3D genome remodeling and gene regulation in the context of meiotic sex chromosome inactivation. In the tammar wallaby, we identify regions of the X that escape MSCI, suggesting incomplete silencing in marsupials.