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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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 is an enzyme that can...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...

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Related Experiment Video

Updated: Jun 15, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

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

Published on: April 11, 2014

Combinatorial profiling of chromatin binding modules reveals multisite discrimination.

Adam L Garske1, Samuel S Oliver, Elise K Wagner

  • 1[1] Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA. [2] These authors contributed equally to this work.

Nature Chemical Biology
|March 2, 2010
PubMed
Summary
This summary is machine-generated.

Histone modifications regulate gene expression via the histone code. New research reveals additional critical PTMs on histone H3, like Thr6 phosphorylation, impacting protein binding and chromatin regulation.

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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

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Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

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Related Experiment Videos

Last Updated: Jun 15, 2026

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

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

Published on: April 11, 2014

A Multilabel Single Molecule Localization Microscopy Protocol for Investigation of Chromatin in the Dense Nuclear Environment
08:49

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

Published on: June 5, 2026

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Chromatin Biology

Background:

  • Post-translational modifications (PTMs) on histone proteins are crucial for gene regulation, forming the basis of the 'histone code'.
  • Specific interactions between PTMs and chromatin-binding proteins dictate transcriptional outcomes.
  • Understanding the combinatorial effects of multiple PTMs on histone tails is essential for deciphering epigenetic regulation.

Purpose of the Study:

  • To investigate the role of additional PTMs on the histone H3 N-terminus in modulating the binding specificity of chromatin readers.
  • To identify novel PTMs that influence the recognition of histone H3 by chromatin-binding modules.
  • To elucidate the structural mechanisms underlying multisite PTM recognition.

Main Methods:

  • Utilized a large combinatorial peptide library (5,000 members) based on the histone H3 N-terminus, randomized for PTMs.
  • Interrogated the binding specificity of six chromatin-binding modules targeting Lys4 methylation.
  • Employed mass spectrometry, antibody-based detection, and Nuclear Magnetic Resonance (NMR) spectroscopy.

Main Results:

  • Identified Thr3 phosphorylation, Arg2 methylation, and Thr6 phosphorylation as critical PTMs modulating histone H3 recognition.
  • Demonstrated that Thr6 phosphorylation has the most diverse impact on protein binding, suggesting a significant regulatory role.
  • Confirmed the existence of Thr6 phosphorylation on native H3 and elucidated the structural basis for discrimination by the ING2 protein.

Conclusions:

  • Multisite PTM recognition on histone H3 exhibits a spectrum of binding affinities, incorporating both switch-like and rheostat-like properties.
  • These graded effects, influenced by reader specificity, provide a nuanced mechanism for epigenetic regulation.
  • The discovery of previously uncharacterized PTMs like Thr6 phosphorylation expands our understanding of the histone code and its regulatory potential.