Tandem single-cell epigenetic and transcriptomic analysis reveals spatiotemporally distinct genomic features among testis cell lineages

The mammalian testis develops through coordinated differentiation of germline and somatic lineages. How chromatin maturation and epigenetic states guide testis development is not well understood. To address this, we generated paired single-nucleus chromatin and transcriptomic data from mouse testis cells from embryonic day 14.5 through postnatal day 4. Across lineages, epigenetic maturation differed temporally during development, spatially within the genome, and organizationally with bifurcating or linear trajectories. For instance, germ cell chromatin accessibility specifically at distal intergenic regions linked to genes implicated in spermatogonial stem cell function. Sertoli cells within seminiferous tubules or the rete displayed region-specific chromatin profiles. Among interstitial cells, epigenetic maturation marked canonical lineage drivers and modulated diverging cell fates. Finally, motif enrichment demonstrated cell-type specific activity among transcription factors, and cell-to-cell communication inferences illuminated interconnected networks among lineages. These findings highlight distinct maturations guiding testis development and identify candidate regulators with potential relevance to infertility.