In situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing.
Ping Wang1, Yuliang Feng1,2, Kun Zhu1,3,4
1The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut.
Current Protocols
|August 5, 2021
Summary
We developed an improved in situ Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) protocol. This method requires significantly fewer cells, making chromatin interaction mapping more accessible for rare samples.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) is crucial for mapping protein-mediated interactions.
- Current ChIA-PET methods demand large cell numbers (100 million), limiting applications with rare samples.
Purpose of the Study:
- To develop a streamlined in situ ChIA-PET protocol requiring fewer cells.
- To enable high-resolution chromatin contact map generation from limited cell populations.
Main Methods:
- Detailed step-by-step procedures for an in situ ChIA-PET protocol.
- Experimental protocol for sample preparation and data generation.
- Computational protocol for data processing and visualization using the ChIA-PIPE pipeline.
Main Results:
- The in situ ChIA-PET protocol requires as few as 1 million cells.
- The protocol simplifies experimental procedures and reduces ligation noise.
- Enables high-resolution chromatin contact map generation from diverse human and mouse primary cells.
Conclusions:
- The developed in situ ChIA-PET protocol significantly reduces input cell requirements.
- This advancement broadens the applicability of ChIA-PET in biomedical research, especially for rare samples.
- Facilitates high-resolution mapping of protein-mediated chromatin interactions across various cell types.
