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Related Concept Videos

Nucleosome Remodeling02:54

Nucleosome Remodeling

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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.
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The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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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.
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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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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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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The Nucleosome02:33

The Nucleosome

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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.
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The Nucleosome01:19

The Nucleosome

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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...
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data.

Weizhong Chen1, Yi Liu2, Shanshan Zhu3

  • 11] Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China [2] Graduate University of Chinese Academy of Sciences, Beijing 100049, China.

Nature Communications
|September 19, 2014
PubMed
Summary
This summary is machine-generated.

We developed iNPS, an improved algorithm for genome-wide nucleosome positioning, detecting 60% more nucleosomes with higher accuracy. This advancement offers deeper insights into gene regulation and cellular processes like T-cell activation.

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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Accurate genome-wide nucleosome positioning is crucial for understanding gene regulation.
  • Existing algorithms like NPS have limitations in precision and nucleosome detection.

Purpose of the Study:

  • To develop and validate an improved nucleosome-positioning algorithm, iNPS.
  • To enhance the accuracy and scope of nucleosome detection compared to existing methods.

Main Methods:

  • Development of the iNPS algorithm, featuring precise boundary determination and MNase-seq signal integration.
  • Refinement of nucleosome detection by merging/separating shoulder peaks.
  • Validation against established methods and application to T-cell activation data.

Main Results:

  • iNPS detects 60% more nucleosomes with improved boundary precision.
  • Enhanced nucleosome width and center-to-center distance distributions result in sharper patterns.
  • Higher significance and lower false positive rates compared to previous methods.

Conclusions:

  • iNPS offers superior performance for genome-wide nucleosome positioning analysis.
  • The algorithm facilitates the detection of nucleosome repositioning during T-cell activation, revealing novel biological insights.