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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.
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Related Experiment Video

Updated: Jun 20, 2026

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Mapping accessible chromatin regions using Sono-Seq.

Raymond K Auerbach¹, Ghia Euskirchen, Joel Rozowsky

¹Program in Computational Biology, Yale University, New Haven, CT 06520, USA.

Proceedings of the National Academy of Sciences of the United States of America

|August 27, 2009

Summary

This summary is machine-generated.

Sono-Seq is a new method using sonication and sequencing to map accessible chromatin regions. This technique identifies active promoter regions and offers insights into chromatin structure and ChIP-Seq experiments.

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Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Local chromatin structure disruptions often signify biologically important regulatory regions.
Understanding chromatin accessibility is crucial for deciphering gene regulation.

Purpose of the Study:

To introduce and validate Sono-Seq, a novel method for mapping chromatin accessibility.
To compare Sono-Seq with existing methods like FAIRE and DNase I hypersensitive sites.

Main Methods:

Sono-Seq combines sonication of cross-linked chromatin with size selection and massively parallel short-read sequencing.
Analysis involved correlating Sono-Seq sites with known regulatory marks and transcription factors.

Main Results:

Sono-Seq effectively maps regions of high chromatin accessibility, particularly in promoter regions.
Sono-Seq sites strongly associate with actively transcribed promoters, RNA Polymerase II, transcription start sites, H3K4me3 marks, and CpG islands.
Sono-Seq breakage patterns are distinct from, yet overlap with, FAIRE and DNase I hypersensitive sites.

Conclusions:

Sono-Seq is a simple and effective method for mapping local chromatin structure alterations.
The technique provides valuable insights for ChIP-Seq experiments and the use of reference samples.