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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...

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Related Experiment Video

Updated: Jun 27, 2026

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
10:41

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.

Yong Zhang1, Hyunjin Shin, Jun S Song

  • 1Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, 44 Binney St, Boston, MA 02115, USA.

BMC Genomics
|November 19, 2008
PubMed
Summary

This study introduces a new computational method to map nucleosome positioning and histone modifications genome-wide. The findings reveal over 438,000 positioned nucleosomes crucial for epigenetic gene regulation in human T cells.

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Last Updated: Jun 27, 2026

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
10:41

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Published on: April 5, 2018

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
08:04

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Area of Science:

  • Genomics
  • Epigenetics
  • Computational Biology

Background:

  • Nucleosome positioning and covalent modifications are vital for epigenetic regulation.
  • Genome-wide studies of these features in humans are limited.

Purpose of the Study:

  • To develop a novel computational framework for identifying positioned nucleosomes and their histone modification profiles.
  • To analyze nucleosome positioning and modifications in human CD4+ T cells.

Main Methods:

  • Development of a computational framework for analyzing nucleosome-resolution histone modification ChIP-Seq data.
  • Application of the framework to histone methylation ChIP-Seq data in human CD4+ T cells.

Main Results:

  • Identification of over 438,000 positioned nucleosomes.
  • Positioned nucleosomes are predominantly located in functionally important regions like genes, promoters, and transcription factor binding sites.
  • Demonstration of the role of nucleosome positioning and modifications in epigenetic gene regulation.

Conclusions:

  • The developed method offers an effective framework for studying nucleosome positioning and epigenetic marks in mammalian genomes.
  • The algorithm is open-source and publicly available.