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Published on: April 2, 2018
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DNase I Chromatin Accessibility Analysis
Brook S Nepon-Sixt1, Mark G Alexandrow1
1Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA.
Bio-Protocol
|March 3, 2021
Summary
This study introduces a new assay to measure DNA accessibility in human cells using DNase I and qPCR. This method helps understand how chromatin structure impacts essential cellular functions.
Area of Science:
- Molecular Biology
- Genomics
- Cell Biology
Background:
- Chromatin organizes DNA and regulates key cellular processes like replication and transcription.
- Chromatin conformation (accessible or inaccessible) dictates genomic function.
- Assessing chromatin accessibility is crucial for understanding genome regulation.
Purpose of the Study:
- To develop and validate a novel assay for determining human genomic region accessibility.
- To utilize DNase I nuclease activity and quantitative PCR (qPCR) to measure accessibility.
- To investigate the molecular mechanisms governing chromatin accessibility and its impact on cellular functions.
Main Methods:
- Development of a DNase I-based assay to assess chromatin accessibility.
- Application of the assay to a specific human genomic region, the Lamin B2 origin of DNA replication.
- Quantification of nuclease activity effects on qPCR signals from target DNA sites.
Main Results:
- The assay successfully measures the accessibility of specific human genomic regions.
- Demonstrated the utility of the assay in interrogating chromatin conformation.
- Provided a method to link chromatin accessibility to cellular processes.
Conclusions:
- The developed assay is a powerful tool for studying chromatin accessibility.
- This method facilitates the investigation of molecular mechanisms regulating genome function.
- Understanding chromatin accessibility is vital for comprehending DNA replication, repair, and transcription.
