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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 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...

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Related Experiment Video

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

BINOCh: binding inference from nucleosome occupancy changes.

Clifford A Meyer1, Housheng H He, Myles Brown

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA. cliff@jimmy.harvard.edu

Bioinformatics (Oxford, England)
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces BINOCh, a software tool that analyzes nucleosome occupancy changes to identify transcription factors. BINOCh helps understand cellular responses and differentiation programs using ChIP-seq data.

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Last Updated: Jun 2, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Published on: December 12, 2017

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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcription factor binding alters nucleosome occupancy, with flanking regions increasing and nearby regions decreasing.
  • Enhancer-proximal nucleosome occupancy can be measured genome-wide using ChIP-seq for histone modifications like H3K4me2.

Purpose of the Study:

  • To present BINOCh, a software package for inferring transcription factor identities.
  • To enable biologists to utilize nucleosome occupancy data for understanding gene regulation.

Main Methods:

  • Utilizing ChIP-seq data targeting histone modifications (e.g., H3K4me2) to assess genome-wide nucleosome occupancy.
  • Developing and applying the BINOCh software package for data analysis.

Main Results:

  • The BINOCh package facilitates the inference of key transcription factors from nucleosome occupancy patterns.
  • Demonstrates a method to link nucleosome dynamics to specific transcription factor activities.

Conclusions:

  • BINOCh provides a valuable tool for dissecting regulatory mechanisms controlling cellular responses and differentiation.
  • The software aids in identifying transcription factors driving cellular state transitions using accessible genomic data.