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High-resolution Hi-C profiling of human breast tissues using an optimized protocol for clinical samples.
Lavanya Choppavarapu1, Kun Fang1, Stephen Eacker2
1Divison of Biostatistics, Data Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
STAR Protocols
|January 13, 2026
Summary
We optimized a high-resolution Hi-C protocol for analyzing 3D genome structure in human breast tissue. This method enhances chromatin interaction analysis for advanced genomic studies.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Understanding the three-dimensional (3D) genome organization is crucial for deciphering gene regulation and cellular function.
- Existing Hi-C protocols may require optimization for specific tissue types like human breast tissue to achieve high resolution.
Purpose of the Study:
- To present an optimized high-resolution Hi-C protocol specifically for human breast tissues.
- To enable detailed genome-wide 3D chromatin analysis in this important tissue type.
Main Methods:
- Utilized the Phase Genomics Proximo Hi-C Kit for optimized protocol development.
- Incorporated liquid nitrogen tissue processing, controlled chromatin fragmentation, and proximity ligation.
- Employed streptavidin bead enrichment, library preparation on beads, and size selection for Illumina sequencing.
Main Results:
- Successfully generated high-quality material suitable for high-resolution, genome-wide 3D chromatin analysis.
- The protocol is detailed and reproducible for researchers working with human breast tissue samples.
Conclusions:
- The optimized Hi-C protocol provides a robust method for investigating 3D genome architecture in human breast tissues.
- This advancement facilitates deeper insights into the genomic landscape of breast tissue, potentially impacting cancer research and diagnostics.
