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Updated: May 26, 2026
10:40
Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
Published on: September 10, 2013
Analysis of nucleosome positioning using a nucleosome-scanning assay
Juan Jose Infante1, G Lynn Law, Elton T Young
1Department of Microbiology, University of Washington, Seattle, WA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|December 21, 2011
Summary
The nucleosome-scanning assay (NuSA) maps nucleosome positions using micrococcal nuclease (MNase) and quantitative real-time PCR (qPCR). This method offers high-resolution chromatin analysis and protein-DNA interaction insights.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Understanding nucleosome positioning is crucial for gene regulation.
- Existing methods may lack resolution or throughput for detailed promoter analysis.
Purpose of the Study:
- To present the nucleosome-scanning assay (NuSA) as a method for high-resolution nucleosome mapping.
- To demonstrate NuSA's utility in analyzing DNA sequence protection by proteins and its application with ChIP for histone variant identification.
Main Methods:
- Coupling mononucleosomal DNA isolation (after MNase digestion) with quantitative real-time PCR (qPCR).
- Utilizing NuSA for detailed analysis of individual promoters.
- Integrating NuSA with chromatin immunoprecipitation (ChIP) for histone analysis.
Main Results:
- NuSA provides a high-resolution map of nucleosome location and occupancy.
- The assay quantifies DNA sequence protection by proteins and its variation under different conditions.
- Combined NuSA-ChIP identifies histone variants and modifications associated with specific nucleosomes.
Conclusions:
- NuSA is a simple, rapid, and high-resolution technique for mapping nucleosomes and analyzing protein-DNA interactions in chromatin.
- NuSA is valuable for detailed promoter analysis and identifying epigenetic marks on specific nucleosomes.
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