High efficient chromatin conformation capture with post-enrichment (HiChew) in single cells

We present HiChew (High efficient chromatin conformation capture with post-enrichment), a novel method for analyzing three-dimensional chromatin organization in single cells and low-input samples. HiChew combines efficient sticky-end ligation with post-PCR enrichment using methylation-based selection, addressing key limitations of existing chromatin conformation capture methods. The method achieves significantly higher valid pair ratios (approximately 50%) compared to unenriched methods (8%) while maintaining high capture sensitivity. For single-cell applications, snHiChew demonstrates superior performance with 45-50% valid pair ratios and the ability to generate up to 7.3 million unique valid contacts per cell. This enhanced efficiency enables high-resolution mapping of chromatin interactions at 5-10 kb resolution with 70-80% bin coverage. We validate HiChew's accuracy through comparative analyses with conventional Hi-C data, showing high correlations in compartment scores, topologically associating domains (TADs), and loop detection. The method's scalability and cost-effectiveness make it particularly suitable for large-scale single-cell chromatin conformation studies. HiChew represents a significant advancement in chromatin architecture analysis, offering improved efficiency without compromising data quality or sensitivity.