van Nierop Y Sanchez, P., Sekhar, P.S., Yildirim, K., Lange, T., Kreplin, L.Z., Boopathy, V.M., Rosswag de Souza, S., Dammer, K., Ibberson, D., Wang, Q., Domsch, K., Stokkermans, A., Pandey, S., Kaspar, P., Martinez-Gallegos, R., Gao, X., Singh, A., Engel, N., Port, F., Boutros, M., Bageritz, J., Lohmann, I. (2025). Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis.  Nat. Commun. 16(1): 6766.

FBrf0262957

Research paper

Cellular decision-making and tissue homeostasis are governed by transcriptional networks shaped by chromatin accessibility. Using single-nucleus multi-omics, we jointly profile gene expression and chromatin accessibility in 10,335 cells from the Drosophila testis apical tip. This enables inference of 147 cell type-specific enhancer-gene regulons using SCENIC + . We functionally validate key transcription factors, including ovo and klumpfuss, known from other stem cell systems but not previously linked to spermatogenesis. CRISPR-mediated knockout reveals their essential roles in germline stem cell regulation, and we provide evidence that they co-regulate shared targets through overlapping enhancer elements. We further uncover a critical role for canonical Wnt signaling, with Pangolin/Tcf activating lineage-specific targets in the germline, soma, and niche. The Pan eRegulon links Wnt activity to cell adhesion, intercellular signaling and germline stem cell maintenance. Together, our study defines the enhancer-driven regulatory landscape of early spermatogenesis and reveals conserved, combinatorial mechanisms of niche-dependent stem cell control.

PMC12284225 (PMC) (EuropePMC)