By establishing that protamine lacunae—not retained nucleosomes—carry paternal epigenetic information, and that CENP-A mononucleosomes transmit centromere identity, this work overturns prevailing dogma and reframes the molecular logic of paternal epigenetic inheritance at single-molecule resolution.
We're looking at chromatin in sperm. A big question has always been: in mammalian sperm, most of the genome is packaged into these highly compacted protamine compartments, with only a few nucleosomes left over. There's always been this big question about how much epigenetic information is held in those nucleosomes.
What we found is that there's actually a lot of information, probably, in the gaps between the protamines. So it's not really about whether or not a nucleosome is there — it's whether there's a continuous protein coat or a gap between them. It's almost like it's the absence rather than the presence of the protein that matters.
Single-molecule chromatin fiber sequencing reveals that paternal epigenetic information in sperm is predominantly transmitted through protamine lacunae—accessible discontinuities in protamine coating that mark transcriptionally active regulatory elements—while centromere identity is specifically preserved through focal retention of CENP-A mono-nucleosomes, and excessive protamine replacement without appropriate nucleosome retention is associated with male infertility.
The transmission of the paternal genome requires extensive chromatin reorganization, in which nucleosomes are largely replaced by protamines that drive extreme condensation of the genome in the sperm head. Using Fiber-seq, we resolve patterns of paternal chromatin repackaging in sperm at single-molecule resolution, revealing the interplay between protamination and nucleosome retention. We find that nucleosome retention is probabilistic, with no locus universally occupied. Although promoters of spermatogenic genes preferentially harbor retained nucleosomes, the predominant carrier of paternal epigenetic information is protamine lacunae, accessible discontinuities in the protamine coat that preferentially mark critical regulatory elements. By contrast, centromere kinetochore binding regions robustly retain CENP-A mono-nucleosomes, providing a mechanism for the focal transmission of paternal centromeres. Finally, we find that paternal chromatin repackaging is altered in low-motility sperm. Together, these findings reveal distinct modes of paternal chromatin epigenetic inheritance with broad implications for development and infertility.