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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 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.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
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...
Position-effect Variegation02:32

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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...

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A Multilabel Single Molecule Localization Microscopy Protocol for Investigation of Chromatin in the Dense Nuclear Environment
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A Multilabel Single Molecule Localization Microscopy Protocol for Investigation of Chromatin in the Dense Nuclear Environment

Published on: June 5, 2026

Predicting nucleosome positioning using a duration Hidden Markov Model.

Liqun Xi1, Yvonne Fondufe-Mittendorf, Lei Xia

  • 1Department of Statistics, Northwestern University, Evanston, IL 60208, USA.

BMC Bioinformatics
|June 26, 2010
PubMed
Summary
This summary is machine-generated.

A new tool, NuPoP, predicts nucleosome positioning by modeling linker DNA length. This method improves accuracy in understanding genome organization and function.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nucleosomes are fundamental DNA packing units in eukaryotic cells.
  • Nucleosome positioning is crucial for genome function and is influenced by DNA sequence.
  • Predicting nucleosome positioning aids in understanding genome organization.

Purpose of the Study:

  • To develop a fast and accurate software tool for predicting nucleosome positioning.
  • To improve the understanding of how genome nucleosome organization facilitates genome function.

Main Methods:

  • A duration Hidden Markov model was developed to predict nucleosome positioning.
  • The model explicitly incorporates linker DNA length.
  • Models trained on yeast data were re-scaled for cross-species predictions based on base composition.

Main Results:

  • The developed software tool is named NuPoP and is available for free download.
  • Simulation studies confirmed improved prediction accuracy (sensitivity and false discovery rate) by modeling linker length and using base composition re-scaling.
  • NuPoP demonstrated improved sensitivity compared to two existing methods.

Conclusions:

  • Modeling linker DNA length and employing base composition re-scaling enhance nucleosome positioning prediction.
  • NuPoP offers a user-friendly tool for predicting nucleosome occupancy and positioning maps for genomic sequences.
  • The tool shows superior performance in sensitivity for nucleosome positioning prediction.