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Related Concept Videos

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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Chromatin Immunoprecipitation- ChIP02:36

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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.
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Chromatin Packaging01:32

Chromatin Packaging

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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Chromatin Packaging02:21

Chromatin Packaging

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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
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Histone Modification02:32

Histone Modification

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Updated: May 4, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
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The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

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Chromatin modification mapping in nanochannels.

Shuang Fang Lim1, Alena Karpusenko1, Ansel L Blumers1

  • 1Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA.

Biomicrofluidics
|January 8, 2014
PubMed
Summary
This summary is machine-generated.

This study maps histone tail modifications on elongated chromatin within nanofluidic channels. Challenges remain in site-specific profiling due to antibody aggregation interfering with chromatin structure.

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High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo
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High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

Published on: August 14, 2020

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Nanotechnology

Background:

  • Histone modifications are crucial epigenetic markers regulating gene expression.
  • Analyzing these modifications at high resolution is essential for understanding chromatin dynamics.
  • Nanofluidic channels offer a unique environment for studying biological macromolecules.

Purpose of the Study:

  • To develop and validate a method for simultaneous mapping of multiple histone tail modifications.
  • To investigate chromatin structure and histone modification patterns in confined environments.
  • To assess the feasibility of site-specific profiling of histone modifications.

Main Methods:

  • Utilizing nanofluidic channels to elongate chromatin fibers.
  • Employing fluorescently tagged monoclonal antibodies for histone modification detection.
  • Analyzing reconstituted chromatin with distinct histone sources and specific modification probes (H3K4me3, H3K9ac).

Main Results:

  • Successfully mapped multiple histone tail modifications simultaneously on confined chromatin.
  • Distinguished between chromatin from different histone sources based on modification patterns.
  • Observed ratios of H3K4me3 and H3K9ac modifications consistent with histone mixture compositions.
  • Identified antibody aggregation as a significant challenge for site-specific profiling within single genomic molecules.

Conclusions:

  • Nanofluidic confinement enables enhanced detection of histone modifications.
  • The developed method allows for distinguishing chromatin origins and assessing modification ratios.
  • Further optimization is needed to overcome antibody-related challenges for single-molecule resolution.