Related Experiment Video
Updated: Sep 29, 2025
09:20
Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
Published on: February 1, 2022
2.8K
HiCuT: An efficient and low input method to identify protein-directed chromatin interactions
Satish Sati1, Parker Jones1, Hali S Kim1
1Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Plos Genetics
|March 23, 2022
Summary
Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT) is a novel method for studying 3D genome organization. This technique requires less starting material and sequencing data, making it ideal for analyzing primary cells and rare cell populations.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- 3D genome organization is crucial for gene regulation, and its disruption can lead to disease.
- Existing chromosome conformation capture methods (e.g., HiChIP, ChIA-PET) require substantial cell numbers and sequencing data, limiting their application in primary cells.
- Analyzing long-range DNA-protein interactions is essential for understanding gene regulation and disease mechanisms.
Purpose of the Study:
- To introduce Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT), a novel method for high-resolution, protein-directed chromatin interaction analysis.
- To demonstrate HiCuT's efficiency and reduced input requirements compared to existing methods.
- To showcase HiCuT's utility in primary cells for linking genetic variations to candidate genes and identifying transcription factors.
Main Methods:
- Hi-C Coupled chromatin cleavage and Tagmentation (HiCuT): A transposase-assisted tagmentation method for capturing long-range chromatin interactions.
- Utilized significantly reduced cell input (100,000 cells) and sequencing reads (12 million) compared to conventional methods.
- Applied HiCuT to human primary skin cells for genomic profiling.
Main Results:
- HiCuT generates high-resolution, protein-directed chromatin interaction libraries with low background noise.
- Achieved comparable efficiency to HiChIP and ChIA-PET with 5-fold less starting material and 8-fold fewer sequencing reads.
- Successfully linked single nucleotide polymorphisms (SNPs) associated with skin disease to candidate genes in primary skin cells.
- Enabled unbiased identification of functionally relevant transcription factors.
Conclusions:
- HiCuT offers a more accessible and efficient approach for studying 3D genome organization, particularly in primary cells.
- This method expands the scope of genomic profiling to previously inaccessible systems like primary cells, tissue samples, and rare cell populations.
- HiCuT holds promise as a valuable tool for human genetics research and personalized epigenomics.
