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Related Concept Videos

Histone Modification02:32

Histone Modification

16.2K
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
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone...
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Histone Modification02:32

Histone Modification

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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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.
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...
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Histone Variants at the Centromere02:30

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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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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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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Related Experiment Video

Updated: Feb 7, 2026

Chromatin Immunoprecipitation ChIP of Histone Modifications from Saccharomyces cerevisiae
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Histone Native Chromatin Immunoprecipitation.

Alicia Alonso1, Emily Bernstein2,3, Dan Hasson4,5

  • 1Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medical College, New York, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 4, 2018
PubMed
Summary

This study details a native chromatin immunoprecipitation (ChIP) protocol for analyzing histone variants and posttranslational modifications (PTMs) genome-wide. The native ChIP method offers higher resolution and signal-to-noise ratio for PTM and histone variant occupancy patterns.

Keywords:
ChIP-seqHistone PTMsHistone variantsNative chromatin immunoprecipitationNext-generation sequencing

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Genomics

Background:

  • Chromatin immunoprecipitation (ChIP) is a key technique for studying genome-wide histone variant and posttranslational modification (PTM) distribution.
  • Traditional cross-linked ChIP methods can sometimes limit the resolution and signal quality of these analyses.
  • Understanding histone modifications is crucial for deciphering gene regulation and cellular processes.

Purpose of the Study:

  • To present a detailed protocol for native ChIP.
  • To describe downstream DNA library preparation for next-generation sequencing.
  • To adapt the native ChIP protocol for low cell input (down to 50,000 cells).

Main Methods:

  • Detailed native ChIP protocol development.
  • Optimization of downstream DNA library preparation for next-generation sequencing.
  • Adaptation of the protocol for reduced cell input.

Main Results:

  • Native ChIP provides higher resolution occupancy pattern data for histone PTMs and variants compared to cross-linked ChIP.
  • The protocol achieves a higher signal-to-noise ratio for analyzing histone modifications.
  • Successful adaptation allows native ChIP analysis from as few as 50,000 cells.

Conclusions:

  • Native ChIP is a powerful, high-resolution method for studying histone variants and PTMs genome-wide.
  • The described protocol is robust and adaptable, even for limited cell samples.
  • This method enhances the study of epigenetic regulation through improved ChIP analysis.