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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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Immunoprecipitation

Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
Chromatin Immunoprecipitation
Chromatin immunoprecipitation, also known as ChIP, is used to study protein-DNA or...

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Related Experiment Video

Updated: Jul 3, 2026

Methylated DNA Immunoprecipitation
21:24

Methylated DNA Immunoprecipitation

Published on: January 2, 2009

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Thomas A Down1, Vardhman K Rakyan, Daniel J Turner

  • 1Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK. thomas.down@gurdon.cam.ac.uk

Nature Biotechnology
|July 10, 2008
PubMed
Summary
This summary is machine-generated.

A new Bayesian tool, Batman, analyzes DNA methylation data from MeDIP-chip and MeDIP-seq. This robust method quantifies DNA methylation levels, improving genome-wide analysis and understanding epigenetic regulation.

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

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Published on: December 10, 2012

Area of Science:

  • Epigenetics
  • Genomics
  • Bioinformatics

Background:

  • DNA methylation is a critical epigenetic mechanism regulating mammalian gene expression.
  • Current immunoprecipitation-based DNA methylome analysis faces challenges in data analysis, particularly in quantifying absolute methylation levels.
  • Existing analytical tools struggle with the increasing volume and complexity of DNA methylation data.

Purpose of the Study:

  • To develop a robust, cross-platform computational tool for analyzing DNA methylation profiles.
  • To address the limitation of absolute methylation level estimation in immunoprecipitation-based methods.
  • To enable high-resolution, quantitative whole-genome DNA methylation profiling.

Main Methods:

  • Development of a Bayesian algorithm named Bayesian tool for methylation analysis (Batman).
  • Application of Batman to analyze data from methylated DNA immunoprecipitation followed by oligonucleotide array (MeDIP-chip) and next-generation sequencing (MeDIP-seq).
  • Generation of high-resolution whole-genome DNA methylome profiles using MeDIP-seq.

Main Results:

  • Batman successfully analyzes MeDIP-chip and MeDIP-seq data.
  • The developed MeDIP-seq approach provides high-resolution whole-genome DNA methylome profiles.
  • Data generated using MeDIP-seq showed strong correlation with bisulfite sequencing results.

Conclusions:

  • Combining MeDIP-seq or MeDIP-chip with Batman offers a robust, quantitative, and cost-effective strategy for DNA methylation analysis.
  • This approach enhances the understanding of DNA methylation's role in functional genomics.
  • Batman improves the analytical capabilities for epigenetic research, overcoming previous limitations in absolute methylation quantification.