Evolution of Chromatin and Transcriptome Dynamics During Primate Gonadogenesis

Sexual reproduction is the only way for mammals to create offspring – and it is the primary way for many other animals. It creates diversity in a population by combining gametes and thereby genetic information of both parents. Gonadogenesis creates ovaries or testes, sexually dimorphic organs that produce the female or male gametes and involves the processes of sex determination and differentiation. Given their essential role in the survival of the species, the large observed diversity of these processes is surprising. Spermatogenesis in the adult testis was shown to evolve rapidly and its unique transcriptional landscape promotes the emergence of new genes. This was formulated in the “out of the testis” hypothesis. However, the evolutionary dynamics of oogenesis remain less understood. Furthermore, many insights on gonadogenesis have come from mouse models. Considering the fast evolution of gonads, the applicability of these findings to the human process is imperfect – especially in regard to disorders/differences of sex development (DSD). In my dissertation work, I set out to improve our understanding of primate gonadogenesis and its evolutionary dynamics. For this, I analysed at the single cell level the chromatin accessibility and transcriptome of human and marmoset female and male prenatal gonadogenesis, including a sample from a developing testis of a foetus with Klinefelter syndrome (XXY). First, I confirmed the presence of X chromosome reactivation (XCR) and the following removal of X chromosome upregulation in the human germline – a model which was challenged by a recent study. I also showed the presence of XCR for the first time in marmoset and in a human prenatal XXY testis. Moreover, I highlighted the female-like expression of X chromosome inactivation-escaping genes in the XXY testis. Second, I identified sex-specific and shared nucleosome depleted regions (NDRs). I found that female-specific NDRs are predominantly acquired early during gonadogenesis and maintained, while male-specific NDRs are gained throughout development. I furthermore observed that the sequences of female-specific dynamic NDRs evolve slower than those of male-specific ones, suggesting that the female pathway has evolutionarily been the default. Notably, the X chromosome has accumulated male-specific NDRs throughout eutherian evolution, extending previous findings of enrichment of testis specific genes to the regulatory level. Third, I identified dynamically regulated genes during the differentiation of somatic and germ cells. Comparing the human and marmoset datasets to published mouse data of corresponding stages, I found genes with conserved or species-specific gene expression trajectories. I observed that genes with conserved trajectories are enriched in DSD genes, show higher connectivity in their gene regulatory networks and are assigned to more conserved regulatory sequences compared to genes with species-specific trajectories. These genes are promising candidates for further studies, as their conserved regulation suggest important functions in gonadogenesis. Under the genes that showed different expression trajectories between human and mouse, I found several DSD genes, suggesting that, for these genes, findings from mouse models are not directly transferrable to humans. In the last part, I found that the coding and non-coding regions of female somatic cells evolve slower than their male counter parts and that earlier cell types are more conserved than more differentiated ones. I observed that female germ cells are the fastest evolving cell type of the developing gonad, with a peak meiotic oogonia and primary oocytes, paralleling the previous findings of rapid evolution of spermatogenic cell types. I showed that this is accompanied by a highly permissive chromatin landscape and promiscuous transcription and propose that the “out of the testis” hypothesis can be extended to the prenatal ovary. My thesis work advances the understanding of primate gonadogenesis and its disorders, by characterizing regulatory and expression changes during prenatal development. My evolutionary analyses provide insights into the evolution of gonadal cell types and present oogenesis as a birthplace of new genes.