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<p>Single-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational framework for identifying chromatin loops from single-cell contact data by integrating intra-cellular and neighboring inter-cellular contacts through a density-based voting strategy. Applied to Dip-C data from the mouse brain, CellLoop achieves improved loop detection consistent with spatial distances and compartmentalization signals, revealing single cell-specific chromatin loops associated with transcriptional regulation and cell identity. In HiRES embryogenesis data, CellLoop enables finer cell subtype delineation by reducing confounding cell cycle effects. Integration with GAGE-seq and MERFISH data redefines spatial domain functions through chromatin loop dynamics. Together, CellLoop provides a scalable and accurate approach for characterizing chromatin loop variability at single-cell resolution and highlights the utility of 3D genome features in interpreting transcriptional and spatial heterogeneity.</p>

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CellLoop: Identifying single-cell 3D genome chromatin loops

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月6日

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  • Yusen Ye,
  • Yiheng Wang,
  • Shiji Liu,
  • Yuxuan Hu,
  • Liang Yu,
  • Weibing Wang,
  • Shihua Zhang,
  • Hebing Chen,
  • Lin Gao

摘要

Single-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a computational framework for identifying chromatin loops from single-cell contact data by integrating intra-cellular and neighboring inter-cellular contacts through a density-based voting strategy. Applied to Dip-C data from the mouse brain, CellLoop achieves improved loop detection consistent with spatial distances and compartmentalization signals, revealing single cell-specific chromatin loops associated with transcriptional regulation and cell identity. In HiRES embryogenesis data, CellLoop enables finer cell subtype delineation by reducing confounding cell cycle effects. Integration with GAGE-seq and MERFISH data redefines spatial domain functions through chromatin loop dynamics. Together, CellLoop provides a scalable and accurate approach for characterizing chromatin loop variability at single-cell resolution and highlights the utility of 3D genome features in interpreting transcriptional and spatial heterogeneity.