van Nierop Y Sanchez Patrick, Sekhar Pallavi Santhi, Yildirim Kerem, Lange Tim, Kreplin Laura Zoe, Boopathy Vigneshwarr Muruga, Rosswag de Souza Stephanie, Dammer Kim, Ibberson David, Wang Qian, Domsch Katrin, Stokkermans Anniek, Pandey Shubhanshu, Kaspar Petra, Martinez-Gallegos Rafael, Gao Xuefan, Singh Aakriti, Engel Natalja, Port Fillip, Boutros Michael, Bageritz Josephine, Lohmann Ingrid
Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology and Cell Networks-Cluster of Excellence, Heidelberg, Germany.
Deep Sequencing Core Facility, BioQuant, Heidelberg University, Heidelberg, Germany.
Nat Commun. 2025 Jul 23;16(1):6766. doi: 10.1038/s41467-025-62046-9.
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.
细胞决策和组织稳态受染色质可及性塑造的转录网络调控。利用单核多组学技术，我们对果蝇睾丸顶端的10335个细胞中的基因表达和染色质可及性进行了联合分析。这使得我们能够使用SCENIC+推断出147个细胞类型特异性增强子-基因调控子。我们在功能上验证了关键转录因子，包括ovo和klumpfuss，它们在其他干细胞系统中已知，但之前未与精子发生相关联。CRISPR介导的基因敲除揭示了它们在生殖系干细胞调控中的重要作用，并且我们提供证据表明它们通过重叠的增强子元件共同调控共享靶点。我们进一步发现经典Wnt信号传导的关键作用，其中Pangolin/Tcf激活生殖系、体细胞和微环境中的谱系特异性靶点。泛增强子调控子将Wnt活性与细胞粘附、细胞间信号传导和生殖系干细胞维持联系起来。总之，我们的研究定义了早期精子发生的增强子驱动的调控格局，并揭示了微环境依赖性干细胞控制的保守、组合机制。
