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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.
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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.
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Related Experiment Video

Updated: Jul 7, 2026

Capturing Chromosome Conformation Across Length Scales
10:15

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Mapping chromatin interactions by chromosome conformation capture.

Adriana Miele1, Nele Gheldof, Tomoko M Tabuchi

  • 1University of Massachusetts Medical School, Worcester, Massachusetts, USA.

Current Protocols in Molecular Biology
|February 12, 2008
PubMed
Summary

Chromosome conformation capture (3C) analyzes intermediate chromosome structures crucial for gene regulation by detecting physical interactions between DNA elements. This method, using formaldehyde cross-linking and PCR, is detailed for yeast and mammalian cells.

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Last Updated: Jul 7, 2026

Capturing Chromosome Conformation Across Length Scales
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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

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Published on: October 14, 2022

Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

Associated Chromosome Trap for Identifying Long-range DNA Interactions

Published on: April 23, 2011

Area of Science:

  • Molecular Biology
  • Genetics
  • Genomics

Background:

  • Chromosome conformation capture (3C) offers insights into 3D genome organization.
  • Understanding chromatin interactions is key to deciphering gene regulation.
  • Intermediate-level chromosome structures (kilobase range) are critical for regulatory processes.

Purpose of the Study:

  • To provide detailed protocols for performing the 3C assay.
  • To enable the detection of physical interactions between DNA sequence elements.
  • To facilitate the study of gene regulation mechanisms.

Main Methods:

  • The 3C technique utilizes formaldehyde cross-linking to stabilize chromatin interactions.
  • Post-crosslinking, chromatin segments are processed and analyzed.
  • Polymerase Chain Reaction (PCR) is employed for detecting specific DNA interactions.

Main Results:

  • The study details protocols applicable to both yeast (Saccharomyces cerevisiae) and mammalian cells.
  • The 3C assay successfully detects physical contacts between distant genomic regions, such as enhancers and genes.
  • The methodology allows for the quantification of these interactions.

Conclusions:

  • The 3C technique is a valuable tool for investigating the spatial organization of chromosomes.
  • Detailed protocols enhance the accessibility and reproducibility of 3C experiments.
  • This method aids in understanding the relationship between chromosome structure and gene regulation.