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Related Concept Videos

Nucleosome Remodeling02:54

Nucleosome Remodeling

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...
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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 Nucleosome Core Particle01:12

The Nucleosome Core Particle

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.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
The Nucleosome02:33

The Nucleosome

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...
The Nucleosome02:33

The Nucleosome

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...
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can 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.
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Mapping Mammalian 3D Genome Interactions with Micro-C-XL
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Published on: November 3, 2023

Micrococcal nuclease does not substantially bias nucleosome mapping.

James Allan1, Ross M Fraser, Tom Owen-Hughes

  • 1Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK. J.Allan@ed.ac.uk

Journal of Molecular Biology
|February 8, 2012
PubMed
Summary

Comparing micrococcal nuclease (MNase) and caspase-activated DNase (CAD) for mapping nucleosome positioning, this study found both enzymes identify similar DNA binding sites. This suggests MNase bias in nucleosome mapping is not significant under these conditions.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Nucleosome positioning is crucial for DNA accessibility and gene regulation.
  • Micrococcal nuclease (MNase) is commonly used for mapping nucleosomes, but potential biases exist.
  • Understanding enzyme-specific cleavage mechanisms is key to accurate nucleosome mapping.

Purpose of the Study:

  • To compare nucleosome positioning data generated by MNase and caspase-activated DNase (CAD).
  • To assess sequence-directed nucleosome positioning on genomic DNA.
  • To evaluate potential biases introduced by MNase in nucleosome mapping.

Main Methods:

  • High-throughput sequencing was used to map sequence-directed nucleosome positioning.
  • Chromatins reconstituted with chicken or frog histones were digested to mononucleosomes using MNase or CAD.
  • Enzyme cleavage sites and histone octamer binding strengths were identified and quantified.

Main Results:

  • Both MNase and CAD showed distinct sequence specificities in their cleavage patterns.
  • CAD-produced nucleosomes were longer, with cleavage sites further from the dyad compared to MNase.
  • Despite mechanistic differences, both nucleases identified equivalent nucleosome positioning patterns.

Conclusions:

  • The study indicates that MNase does not introduce significant bias in nucleosome positioning data under the tested conditions.
  • Both MNase and CAD are effective tools for mapping sequence-directed nucleosome positioning.
  • Findings support the reliability of MNase for chromatin studies.