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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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Heterochromatin02:38

Heterochromatin

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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 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...
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Related Experiment Video

Updated: Aug 9, 2025

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis
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NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells.

Pierre-Olivier Estève1, Udayakumar S Vishnu1, Hang Gyeong Chin1

  • 1Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 22, 2023
PubMed
Summary

A new method visualizes and sequences accessible chromatin in mammalian cells. This technique enables detailed genomic analysis of epigenetic information, including promoter and enhancer activity.

Keywords:
BiotinDNA Polymerase IDNA labelingDNA libraryFluorescent dyeMicroscopyNEBNextNicking enzymeOpen chromatinSlidesdNTPs

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Understanding chromatin accessibility is crucial for studying gene regulation and cellular function.
  • Current methods for analyzing accessible chromatin can be complex and lack in situ visualization capabilities.

Purpose of the Study:

  • To develop a novel method for in situ visualization, quantitation, and sequencing of accessible chromatin.
  • To enable cellular-level analysis of epigenetic information within the mammalian cell.

Main Methods:

  • Cells are fixed with formaldehyde and processed using a modified nick translation method.
  • DNA polymerase incorporates labeled nucleotides (biotin, fluorescent dyes) into accessible chromatin.
  • On-bead next-generation sequencing (NGS) library preparation is performed for genomic analysis.

Main Results:

  • The method allows for simultaneous fluorescence visualization and sequencing of accessible chromatin.
  • It enables quantification of chromatin accessibility at the cellular level.
  • The technology facilitates genomic analysis of epigenetic marks, including promoter and enhancer regions, nucleosome positioning, and protein binding.

Conclusions:

  • This novel technique provides a powerful tool for studying chromatin accessibility and epigenetic regulation.
  • It offers a comprehensive approach for in situ analysis of genomic and epigenomic information in mammalian cells.