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Related Concept Videos

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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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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Euchromatin01:01

Euchromatin

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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Updated: Dec 29, 2025

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
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Measuring significant changes in chromatin conformation with ACCOST.

Kate B Cook1, Borislav H Hristov1, Karine G Le Roch2

  • 1Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065, USA.

Nucleic Acids Research
|February 9, 2020
PubMed
Summary

This study introduces ACCOST, a new statistical method to accurately compare 3D chromatin architecture across different cell types using Hi-C data. ACCOST effectively accounts for the genomic distance effect, improving differential contact identification.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Chromatin conformation capture techniques like Hi-C provide insights into the 3D organization of the genome.
  • Direct comparison of Hi-C data between samples is challenging due to inherent data properties, such as the genomic distance effect.
  • The genomic distance effect, where contact frequency decreases with genomic separation, varies between experiments, complicating differential analyses.

Purpose of the Study:

  • To develop a robust statistical method for identifying differential chromatin contacts from Hi-C data.
  • To address the confounding influence of the genomic distance effect in comparative Hi-C analyses.
  • To provide an unbiased statistical confidence measure for altered chromatin conformation.

Main Methods:

  • Developed ACCOST (Altered Chromatin COnformation STatistics), a novel statistical approach.
  • Extended the DEseq statistical model by repurposing 'size factors' to specifically model the genomic distance effect in Hi-C data.
  • Applied ACCOST to analyze simulated and real Hi-C datasets.

Main Results:

  • ACCOST provides unbiased statistical confidence estimates for differential Hi-C contacts.
  • The method effectively accounts for variations in the genomic distance effect across different Hi-C experiments.
  • Performance comparisons show ACCOST favorably compares with existing methods like diffHiC, FIND, and HiCcompare.

Conclusions:

  • ACCOST offers a reliable solution for comparing 3D genome architecture across diverse biological conditions using Hi-C data.
  • The method enhances the accuracy of differential contact identification by properly modeling the genomic distance effect.
  • ACCOST is a valuable tool for researchers studying chromatin organization and its role in cellular function and disease.