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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Calculating the spatial density of regulatory chromatin interactions using multi-modal datasets from the same cell
Haiyan Gong1, Minghong Li1, Mengdie Ji2
1Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
STAR Protocols
|March 31, 2023
Summary
This study introduces a new protocol to calculate the spatial density of regulatory chromatin interactions (SD-RCI) using multiple genomic datasets. This method helps understand gene regulation and expression in human cell lines.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Understanding chromatin interactions is crucial for deciphering gene regulation.
- Existing methods may not fully capture the spatial dynamics of regulatory elements.
Purpose of the Study:
- To present a comprehensive protocol for calculating the spatial density of regulatory chromatin interactions (SD-RCI).
- To enable the analysis of regulatory interactions using integrated genomic data.
Main Methods:
- Utilized Hi-C, ATAC-seq, and ChIP-seq datasets from a human cell line.
- Developed a model for predicting regulatory chromatin interactions.
- Calculated SD-RCI and visualized its correlation with gene expression.
Main Results:
- A robust protocol for SD-RCI calculation was established.
- The protocol successfully integrates multiple high-throughput sequencing data types.
- Demonstrated the correlation between SD-RCI and gene expression patterns.
Conclusions:
- The presented protocol provides a novel approach to quantify regulatory chromatin interactions.
- This method is applicable to human cell line data and aids in understanding gene expression regulation.
- Facilitates further research into the spatial organization of the genome.
