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Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
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Mapping 3D genome architecture through in situ DNase Hi-C
Vijay Ramani1, Darren A Cusanovich1, Ronald J Hause1
1Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Nature Protocols
|September 30, 2016
Summary
A new method, in situ DNase Hi-C, reveals the inactive murine X chromosome
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Chromosome conformation capture (3C) techniques are essential for studying genome-wide chromosomal architecture.
- Previous methods relied on restriction enzymes for chromatin digestion, limiting resolution.
Purpose of the Study:
- To introduce and validate a novel 3C protocol, in situ DNase Hi-C, for high-resolution 3D genome studies.
- To investigate the 3D structure of the inactive murine X chromosome.
Main Methods:
- Developed in situ DNase Hi-C, a restriction enzyme-free chromatin conformation capture method.
- Utilized DNase I for chromatin digestion, followed by proximity ligation and next-generation sequencing.
- Optimized the protocol for mammalian cells, adaptable to various cell/tissue types.
Main Results:
- Demonstrated that the inactive murine X chromosome adopts a bipartite structure.
- Generated libraries with higher effective resolution compared to traditional Hi-C.
- The protocol is efficient, requiring approximately 4 days of bench work.
Conclusions:
- In situ DNase Hi-C offers enhanced resolution for 3D genome studies, particularly with high sequencing depth or hybrid capture.
- This method provides a valuable tool for investigating chromosomal architecture in various biological contexts.
