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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...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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 is an enzyme that can...

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Related Experiment Video

Updated: Jun 17, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
12:39

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

Published on: December 10, 2012

Bayesian network analysis of targeting interactions in chromatin.

Bas van Steensel1, Ulrich Braunschweig, Guillaume J Filion

  • 1Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands. b.v.steensel@nki.nl

Genome Research
|December 17, 2009
PubMed
Summary

This study models how chromatin proteins interact to control gene expression in Drosophila. The network reveals new targeting relationships, like HP1 proteins competitively targeting HP3 to specific genes.

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RNA-Associated Chromatin DNA-DNA Interaction Method
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RNA-Associated Chromatin DNA-DNA Interaction Method

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Last Updated: Jun 17, 2026

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
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Published on: December 10, 2012

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
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Published on: April 30, 2012

RNA-Associated Chromatin DNA-DNA Interaction Method
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RNA-Associated Chromatin DNA-DNA Interaction Method

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Area of Science:

  • Genetics
  • Molecular Biology
  • Systems Biology

Background:

  • Gene expression in eukaryotes is regulated by numerous chromatin proteins.
  • Chromatin proteins influence each other's genomic binding through recruitment or competition.
  • The complex network of these targeting interactions remains poorly understood.

Purpose of the Study:

  • To construct a Bayesian network model of targeting interactions among 43 chromatin components in Drosophila cells.
  • To predict novel functional relationships and understand the global interplay of chromatin targeting.

Main Methods:

  • Genome-wide binding maps were utilized to build the Bayesian network model.
  • The model analyzed targeting interactions among a broad set of 43 chromatin components.

Main Results:

  • The model predicted numerous novel functional relationships between chromatin proteins.
  • HP1 and HP1C were found to competitively target the heterochromatin protein HP3 to distinct gene sets.
  • The Brahma remodeling factor plays a central role in targeting several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7.

Conclusions:

  • The developed network model offers a global perspective on the targeting interplay among numerous chromatin components.
  • This research elucidates complex regulatory mechanisms governing gene expression through chromatin protein interactions.