Since the inception of my laboratory, we have focused our efforts on understanding the fundamentals of how two meters of DNA are packaged into the sperm nucleus to achieve a structure that is 13-times more compact than its oocyte complement. We developed the first humanized mouse model that faithfully recapitulates the expression of the entire suite of genes contained within the domain (1,2,3). This model system presented a pathway toward epigenetic analysis from a structural perspective. Our early clinical and mechanistic analyses showed that deletion of nuclear matrix attachment sites inhibited the expression of the protamine locus. In humans, this hampered histone replacement (4). Functional rescue of the human protamine locus was achieved with the insertion of nuclear matrix attachment sites in our humanized mouse model (5).
In sperm, these sites, and those surrounding promoters, remain histone bound even in this protamine compacted crystal-like structure. This observation led to the question: is this an exception to a rule or a fundamental property of the protamine packaged sperm nuclear genome? Resolution came with publishing the first genome-wide positioning of histones retained in both mouse and human sperm (6,7). This work revealed an additional layer of well-positioned nucleosomal bound CTCF sites segmenting the genome. Their frequency and distribution bore a marked resemblance to Topological Associated Domains observed in somatic cells (8), suggesting a preserved fundamental structure in the male somatic and gamete nucleus. This, along with our early clinical and structural studies (9), highlighted the significance of 4D structure (10) in the formation of healthy sperm.