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Updated: May 13, 2026
09:32
Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
Published on: October 14, 2022
Analysis of chromatin organization by deep sequencing technologies
James L Platt1, Nick A Kent, Adrian J Harwood
1Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Methods in Molecular Biology (Clifton, N.J.)
|March 16, 2013
Summary
Micrococcal nuclease (MNase) mapping combined with high-throughput sequencing enables genome-wide identification of DNA-protein interactions. This technique precisely maps nucleosomes and transcription factor binding sites across the entire genome.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Micrococcal nuclease (MNase) cleaves DNA but is blocked by DNA-protein interactions.
- Previous MNase applications were limited to single-gene analyses.
- Mapping DNA-protein interactions is crucial for understanding gene regulation.
Purpose of the Study:
- To detail protocols for genome-wide mapping of DNA-protein interactions using MNase and high-throughput sequencing.
- To enable precise mapping of nucleosomes and transcription factor binding sites across the genome.
Main Methods:
- MNase digestion of DNA.
- High-throughput, paired-end DNA sequencing.
- Bioinformatic analysis of sequencing data.
Main Results:
- Developed protocols for global mono-nucleosome positioning with ~160 bp resolution.
- Demonstrated applicability for mapping broader DNA-protein interactions or site-specific transcription factor binding at ~50 bp resolution.
Conclusions:
- MNase combined with high-throughput sequencing provides a powerful tool for genome-wide mapping of DNA-protein interactions.
- This approach significantly advances the study of chromatin structure and gene regulation.
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