Stem cell niche ageing involves coordinated changes in transcription and alternative splicing

Gene expression (GE) determines the functionality and properties of cell types. Alternative splicing (AS) enhances the complexity of the transcriptome, expanding the protein interactome. As GE and AS jointly contribute to the formation of new interaction networks with potentially significant cellular functions, they could serve as the foundation for fundamental biological processes like ageing. Here, we investigate ageing in the Drosophila female germline stem cell (GSC) niche and describe functional changes in both GE and AS in aged flies. The GSC niche comprises escort cells, terminal filament cells and cap cells. Comparison of their transcriptomes reveals that, while all these cell types share genes exhibiting differential GE and AS variations related to cell adhesion, cytoskeleton and neural signalling during ageing, each population also experiences distinctive changes. This demonstrates unique ageing signatures within niche cell types. In addition and depending on the niche cell population, sets of genes display changes in both GE and AS, revealing a coordinated effort in the regulation of transcription and splicing during niche ageing. One such gene is Fasciclin 2, a neural adhesion molecule which we report to be essential for niche functioning. Furthermore, some genes involved in AS undergo changes in GE and/or AS themselves, providing a mechanistic explanation for the coordination of these two processes in the regulation of stem cell niche ageing. This is the case of the splicing factor Smu1, described here as a key element necessary for ovarian niche homeostasis. Overall design: To investigate the changes in gene expression and alternative splicing during ageing in different populations of support cells in the ovarian niche of the Drosophila female. We compared niche cells isolated from 1 week (1w)-old and 4w-old ovaries. We generated 2 replicates of each age per cell type group (group 1: terminal filament cells + cup cells; group 2: escort cells) We also studied the differentially expressed genes and alternative splicing in niche cells with reduced levels of the splicing factor Smu1. Generated 2 replicates of control cells and 2 of experimental cells.