What question did this study set out to answer?

The aim is to introduce HiChew, an innovative method for chromatin conformation capture that enhances data quality and efficiency.

April 28, 2026Genome biology0 citationsOpen Access

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

ZCZhichao ChenBGI Group (China)YXYeming XieBGI Group (China)CZChen ZhangBGI Group (China)

Key Points

The aim is to introduce HiChew, an innovative method for chromatin conformation capture that enhances data quality and efficiency.
Developed HiChew, combining sticky-end ligation and post-PCR enrichment.
Implemented snHiChew for single-cell applications.
Evaluated validity ratios and resolution mapping compared to conventional methods.
HiChew achieves approximately 50% valid pair ratios compared to 8% for unenriched methods.
snHiChew reaches 45–50% valid pair ratios with 70–80% bin coverage.
Strong concordance with conventional Hi-C observed for chromatins compartments and TADs.

Abstract

Abstract 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.

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