Related Experiment Video
Updated: Mar 21, 2026
11:42
Chromatin Immunoprecipitation Assay Using Micrococcal Nucleases in Mammalian Cells
Published on: May 10, 2019
15.6K
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility.
Jakub Mieczkowski1, April Cook1, Sarah K Bowman1
1Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Nature Communications
|May 7, 2016
Summary
We developed a new method, MNase accessibility (MACC), to measure chromatin accessibility and nucleosome positioning. MACC reveals that nucleosome occupancy does not always correlate with DNA accessibility in regulatory regions.
Area of Science:
- Molecular Biology
- Genomics
- Epigenetics
Background:
- Chromatin accessibility is crucial for gene regulation.
- Nucleosome placement influences DNA accessibility.
- Existing methods quantify nucleosome protection from enzymatic digestion.
Purpose of the Study:
- Introduce a novel metric, MNase accessibility (MACC), to measure chromatin accessibility.
- Quantify nucleosome location and accessibility within the same assay.
- Investigate the relationship between nucleosome occupancy and accessibility.
Main Methods:
- Utilized micrococcal nuclease (MNase) digestion in a novel manner.
- Combined information from multiple MNase digests of increasing depths.
- Developed the MACC metric to quantify chromatin accessibility and nucleosome heterogeneity.
- Performed MACC with and without histone immunoprecipitation to compare histone and non-histone protection.
Main Results:
- MACC quantifies the heterogeneity of nucleosome accessibility.
- Changes in accessibility at regulatory regions (enhancers, promoters) do not correlate with changes in nucleosome occupancy.
- High nucleosome occupancy does not necessarily prevent high DNA accessibility.
Conclusions:
- Novel principles of chromatin regulation are revealed.
- Nucleosome occupancy and accessibility are distinct regulatory features.
- MACC provides a comprehensive measure of chromatin accessibility and nucleosome positioning.
More Related Videos
Related Concept Videos
02:54Nucleosome Remodeling
11.6K
Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
11.6K
02:36Chromatin Immunoprecipitation- ChIP
12.8K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
12.8K
02:33The Nucleosome
19.6K
DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
19.6K
02:10The Nucleosome Core Particle
15.1K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
15.1K