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Chromatin Immunoprecipitation- ChIP

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: Aug 9, 2025

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

Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq.

George Spracklin¹, Liyan Yang², Sriharsa Pradhan³

¹Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA. george.spracklin@umassmed.edu.

Methods in Molecular Biology (Clifton, N.J.)

|February 22, 2023

Summary

This summary is machine-generated.

Protect-seq identifies inaccessible chromatin at the nuclear periphery. This genomics technique reveals regions linked to transcriptional repression and heterochromatin, aiding genome regulation studies.

Keywords:

Chromatin Genomics Heterochromatin Nuclear periphery Protect-seq

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Last Updated: Aug 9, 2025

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

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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Published on: December 12, 2017

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

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Published on: April 2, 2018

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Chromatin accessibility is key to identifying genomic regulatory elements like enhancers.
Open chromatin regions are nucleosome-free, but inaccessible chromatin remains less understood.
Inaccessible chromatin is often associated with transcriptional repression and heterochromatin formation.

Purpose of the Study:

To introduce and detail the Protect-seq genomics technique.
To identify inaccessible chromatin regions localized at the nuclear periphery.
To correlate these regions with known markers of transcriptional repression and heterochromatin.

Main Methods:

The Protect-seq protocol involves specific biochemical and sequencing steps.
Detailed methodology for performing Protect-seq is discussed.
Best practices for optimizing and executing the technique are provided.

Main Results:

Protect-seq successfully identifies regions of inaccessible chromatin.
These regions are significantly enriched for repressive histone modifications.
Results correlate with heterochromatin markers and peripheral nuclear localization.

Conclusions:

Protect-seq is a valuable tool for studying inaccessible chromatin.
The technique provides insights into genome organization and regulation at the nuclear periphery.
Understanding inaccessible chromatin complements open chromatin studies for a comprehensive genomic view.