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<p>We present HiChew, a novel chromatin conformation capture method combining efficient sticky-end ligation with post-PCR methylation-based enrichment. HiChew achieves approximately 50% valid pair ratios compared to 8% for unenriched methods, while maintaining high sensitivity. Its single-cell implementation, snHiChew, achieves 45–50% valid pair ratios, and enables 5–10&#xa0;kb resolution mapping with 70–80% bin coverage. Comparative analyses show strong concordance with conventional Hi-C for chromatin compartments, TADs, and loops. By combining scalability, cost-effectiveness and data quality, HiChew provides a powerful platform for advancing studies of 3D genome architecture analysis.</p>

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Highly efficient chromatin conformation capture with post-enrichment in single cells by HiChew

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月27日

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  • Zhichao Chen,
  • Yeming Xie,
  • Chen Zhang,
  • Chen Tan,
  • Fengying Ruan,
  • Wenfang Chen,
  • Meng Luo,
  • Mei Guo,
  • Zhe Xie,
  • Huimin Cao,
  • Meifang Tang,
  • Xiuqing Zhang,
  • Ying Zhang,
  • Chong Tang

摘要

We present HiChew, a novel chromatin conformation capture method combining efficient sticky-end ligation with post-PCR methylation-based enrichment. HiChew achieves approximately 50% valid pair ratios compared to 8% for unenriched methods, while maintaining high sensitivity. Its single-cell implementation, snHiChew, achieves 45–50% valid pair ratios, and enables 5–10 kb resolution mapping with 70–80% bin coverage. Comparative analyses show strong concordance with conventional Hi-C for chromatin compartments, TADs, and loops. By combining scalability, cost-effectiveness and data quality, HiChew provides a powerful platform for advancing studies of 3D genome architecture analysis.