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Related Experiment Video

Updated: Nov 9, 2025

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Published on: June 28, 2018

Identifying high-confidence capture Hi-C interactions using CHiCANE.

Erle M Holgersen¹, Andrea Gillespie¹, Olivia C Leavy^2,3

¹The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.

Nature Protocols

|April 10, 2021

Summary

This summary is machine-generated.

CHiCANE simplifies the analysis of Capture Hi-C (CHi-C) data, enabling researchers to identify gene regulatory interactions. This toolkit aids in understanding genome organization and gene expression by processing CHi-C profiles effectively.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Identifying regulatory interactions is crucial for understanding gene expression and genome organization.
Capture Hi-C (CHi-C) is a key technology for mapping these interactions.
Existing CHi-C analysis tools are fragmented and challenging to use.

Purpose of the Study:

To present CHiCANE, a specialized toolkit for the primary analysis and interpretation of CHi-C data.
To provide a standardized protocol for processing and analyzing CHi-C, rCHi-C, and pCHi-C libraries.
To facilitate the functional interpretation of regulatory interactions identified by CHi-C.

Main Methods:

Development of the CHiCANE toolkit for CHi-C data processing and interaction calling.
Demonstration of CHiCANE's application to region capture Hi-C (rCHi-C) and promoter capture Hi-C (pCHi-C) libraries.
Inclusion of quality assessment and downstream analysis modules for rCHi-C and pCHi-C data.

Main Results:

CHiCANE provides a unified approach for CHi-C data analysis.
The toolkit enables quality assessment and functional interpretation of interaction peaks.
The protocol is demonstrated for both rCHi-C and pCHi-C datasets.

Conclusions:

CHiCANE addresses the challenges in CHi-C data analysis, offering a comprehensive solution.
The toolkit supports meaningful interpretation of regulatory interactions, advancing genomic studies.
CHiCANE is available as an R package, promoting accessibility for researchers.