Oo-site: A dashboard to visualize gene expression during Drosophila oogenesis suggests meiotic entry is regulated post-transcriptionally

Determining how stem cell differentiation is controlled has important implications for understanding the etiology of degenerative disease and designing regenerative therapies. In vivo analyses of stem cell model systems have revealed regulatory paradigms for stem cell self-renewal and differentiation. The germarium of the female Drosophila gonad, which houses both germline and somatic stem cells, is one such model system. Bulk mRNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), and bulk translation efficiency (polysomeseq) of mRNAs are available for stem cells and their differentiating progeny within the Drosophila germanium. However, visualizing those data is hampered by the lack of a tool to spatially map gene expression and translational data in the germarium. Here, we have developed Oo-site (https://www.ranganlab.com/Oo-site), a tool for visualizing bulk RNA-seq, scRNA-seq, and translational efficiency data during different stages of germline differentiation, which makes these data accessible to non-bioinformaticians. Using this tool, we recapitulated previously reported expression patterns of developmentally regulated genes and discovered that meiotic genes, such as those that regulate the synaptonemal complex, are regulated at the level of translation.

Automated summary

Understanding how stem cell differentiation is regulated is crucial for degenerative disease research and regenerative therapy design. In this study, researchers developed a tool called Oo-site to visualize bulk RNA-seq, single-cell RNA-seq, and translational efficiency data during different stages of germline differentiation in Drosophila ovary. They successfully recapitulated known expression patterns of developmentally regulated genes and discovered translational regulation of meiotic genes.