Integrated single-cell chromatin profiling of testicular cell types from the cynomolgus macaque reveals functional gene regulatory networks during spermatogenesis
While the concerted activity of evolutionarily conserved transcription factor (TF) sub-networks are able to define cell states, the relationship of TF sub-network activity to spermatogonial stem cell (SSC) self- renewal vs. differentiation dynamics has not been explored in detail. Here we describe an integrated approach combining single-cell ATAC- and RNA-seq technologies to examine gene regulatory networks in testicular cell populations from the cynomolgus macaque. Germ cell subtypes can be efficiently identified and sub-classified by their distinct transcriptomic and epigenetic signatures. Concordantly we observe distinct motif enrichment in peaks specific to each cell state. We detect key TFs whose activity is only seen either in SSCs or in differentiating spermatogonia. This dichotomy in TF-activity may form the functional basis of SSCs regulation versus differentiation. Consistent with theories of positive spermatogonial selection and paternal age effects, we highlight that TFs associated with the SSC state correspond with an autosomal dominant inheritance pattern. With the X chromosome being uniquely regulated and utilized in male germ cells in contrast to the autosomes, we demonstrate roles for X-linked positive TF regulators that have functional roles in the SSC state.