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<p>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 <i>Drosophila</i> testis apical tip. This enables inference of 147 cell type-specific enhancer-gene regulons using SCENIC + . We functionally validate key transcription factors, including <i>ovo</i> and <i>klumpfuss</i>, 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.</p>

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Dissecting the enhancer gene regulatory network in early Drosophila spermatogenesis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月23日

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  • Patrick van Nierop y Sanchez,
  • Pallavi Santhi Sekhar,
  • Kerem Yildirim,
  • Tim Lange,
  • Laura Zoe Kreplin,
  • Vigneshwarr Muruga Boopathy,
  • Stephanie Rosswag de Souza,
  • Kim Dammer,
  • David Ibberson,
  • Qian Wang,
  • Katrin Domsch,
  • Anniek Stokkermans,
  • Shubhanshu Pandey,
  • Petra Kaspar,
  • Rafael Martinez-Gallegos,
  • Xuefan Gao,
  • Aakriti Singh,
  • Natalja Engel,
  • Fillip Port,
  • Michael Boutros,
  • Josephine Bageritz,
  • Ingrid Lohmann

摘要

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.