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Chromatin Immunoprecipitation- ChIP02:36

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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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Updated: Oct 24, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Measuring Chromatin Accessibility: ATAC-Seq.

Sanjeeb Kumar Sahu1, Amitava Basu2, Vijay K Tiwari3

  • 1Salk Institute for Biological Studies, La Jolla, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 12, 2021
PubMed
Summary

This chapter details the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) method for genome-wide chromatin accessibility studies. It provides a historical overview and a comprehensive protocol for performing the ATAC-Seq assay.

Keywords:
ATAC-seqChromatin accessibilityGene regulationNucleosomeTransposase

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Chromatin accessibility is crucial for understanding gene regulation.
  • Previous methods offered limited genome-wide insights.
  • The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) emerged as a powerful technique.

Purpose of the Study:

  • To provide a historical context of chromatin accessibility research.
  • To present a detailed, step-by-step protocol for the ATAC-Seq assay.
  • To enable researchers to effectively implement ATAC-Seq in their studies.

Main Methods:

  • The chapter focuses on the ATAC-Seq methodology.
  • Key steps involve enzymatic fragmentation of accessible chromatin.
  • Sequencing and bioinformatic analysis follow fragmentation.

Main Results:

  • The protocol aims to yield reliable data on open chromatin regions.
  • Successful implementation allows for genome-wide mapping of accessible DNA.
  • This provides insights into regulatory element activity.

Conclusions:

  • ATAC-Seq is an effective method for genome-wide chromatin accessibility profiling.
  • The provided protocol facilitates the application of ATAC-Seq.
  • Understanding chromatin accessibility is vital for deciphering gene regulation.