Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A RaPID Macrocyclic Peptide Inhibitor of ROR1/2 Strongly Reduces Proliferation of Diffuse Intrinsic Pontine Glioma Cells.

ACS chemical biology·2026

Same author

A tumor-associated photoreceptor signature unifies distinct central nervous system malignancies.

Cancer cell·2026

Same author

Childhood brain tumors instruct cranial hematopoiesis and immunotolerance.

Nature genetics·2026

Same author

Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models.

Nature genetics·2025

Same author

Identification of a small molecule targeting EPLIN as a novel strategy for the treatment of pediatric neuroblastoma and medulloblastoma.

Cell death & disease·2025

Same author

Rolling Ultrasharp Microneedle Spheres Enable Topical Delivery of Biologics Through the Skin.

Advanced healthcare materials·2025

Same journal

Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.

Genome research·2026

Same journal

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution.

Genome research·2026

Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026

Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026

Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026

Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 28, 2025

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

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

Published on: April 2, 2018

Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.

Hua Zhang¹, Vamsi Krishna Polavarapu¹, Pengwei Xing¹

¹Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden.

Genome Research

|July 15, 2021

Summary

This summary is machine-generated.

We developed FFPE-ATAC, a sensitive method for profiling chromatin accessibility in archival formalin-fixed paraffin-embedded (FFPE) tissues. This technique enables better understanding of epigenetic regulation in cancer and precision medicine.

More Related Videos

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

Published on: March 26, 2011

Related Experiment Videos

Last Updated: Oct 28, 2025

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

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

Published on: April 2, 2018

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Published on: August 21, 2016

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses

Published on: March 26, 2011

Area of Science:

Epigenetics
Molecular Biology
Cancer Research

Background:

Archived formalin-fixed paraffin-embedded (FFPE) samples are crucial for cancer research.
Profiling chromatin accessibility in FFPE tissues is vital for understanding gene regulation.
DNA damage in FFPE samples poses challenges for chromatin accessibility mapping.

Purpose of the Study:

To develop a sensitive method for chromatin accessibility profiling in FFPE tissues.
To overcome challenges associated with DNA damage in FFPE samples.
To enable the study of epigenetic regulation in archival cancer tissues.

Main Methods:

Standard ATAC-seq was applied to FFPE nuclei, revealing limitations.
FFPE-ATAC, combining Tn5 transposition and T7 in vitro transcription, was developed.
High-quality chromatin accessibility profiles were generated from minimal FFPE tissue (500 nuclei).

Main Results:

FFPE-ATAC successfully generated high-quality chromatin accessibility profiles.
The method enabled dissection of chromatin profiles from regions of interest using H&E staining.
Disease-associated chromatin regulation was identified in long-archived human colorectal cancer FFPE tissues.

Conclusions:

FFPE-ATAC decodes chromatin states regulating gene expression in archival FFPE tissues.
The approach facilitates a deeper understanding of epigenetic regulation in cancer.
This method supports advancements in precision medicine through analysis of archival samples.