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Genome-scale mapping of DNase I hypersensitivity
Sam John1, Peter J Sabo, Theresa K Canfield
1Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
Current Protocols in Molecular Biology
|July 4, 2013
Summary
DNase I-seq maps genome-wide chromatin accessibility, identifying regulatory elements like promoters and enhancers. This high-resolution technique provides an unbiased view of genomic regulatory landscapes.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Chromatin accessibility is crucial for gene regulation.
- Identifying regulatory elements in complex genomes is challenging.
Purpose of the Study:
- To describe the DNase I-seq method for mapping chromatin accessibility.
- To detail the process of isolating nuclei, digesting with DNase I, and fractionating hypersensitive sites.
Main Methods:
- DNase I-seq utilizes the endonuclease DNase I to map accessible chromatin regions.
- Methods include nuclei isolation, controlled DNase I digestion, and biochemical fractionation.
- Preparation for high-throughput sequencing is a key component.
Main Results:
- DNase I hypersensitive sites (DHSs) are identified as regions of open chromatin.
- These DHSs correspond to known regulatory features such as promoters and enhancers.
- The method provides a global and high-resolution map of regulatory elements.
Conclusions:
- DNase I-seq is a robust and unbiased method for studying genome-wide chromatin accessibility.
- It effectively defines regulatory features without prior assumptions about genomic patterns.
- This technique is valuable for understanding complex genome regulation.
