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DNA Microarrays

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Updated: Jun 22, 2026

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

Published on: July 21, 2014

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

Yoichiro Shibata¹, Gregory E Crawford

¹Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA.

Methods in Molecular Biology (Clifton, N.J.)

|June 3, 2009

Summary

This summary is machine-generated.

DNaseI hypersensitive sites mark active gene regulatory elements. A new high-throughput DNase-chip method enables targeted or genome-wide identification of these crucial cis-acting elements.

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Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

DNaseI hypersensitive sites are reliable markers for active gene regulatory elements like promoters and enhancers.
Traditional methods using Southern blots were limited to analyzing small genomic regions.

Purpose of the Study:

To introduce DNase-chip, a high-throughput method for identifying cis-acting gene regulatory elements.
To enable both targeted and genome-wide analysis of regulatory elements.

Main Methods:

Enzymatic digestion of nuclear DNA using DNaseI to identify accessible chromatin regions.
Adaptation of DNase-chip protocol for high-throughput analysis.

Main Results:

DNase-chip allows for the identification of cis-acting regulatory elements.
The method supports both targeted and genome-wide analyses.

Conclusions:

DNase-chip offers a scalable and efficient approach to map gene regulatory elements.
This method advances the study of gene regulation at a genomic scale.