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Related Experiment Video

Updated: Jun 25, 2025

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis

Published on: March 23, 2021

Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.

Vishnu Udayakumaran Nair Sunitha Kumary¹, Bryan J Venters¹, Karthikeyan Raman²

¹EpiCypher Inc., Durham, NC 27709, USA.

|May 28, 2024

Summary

Mapping open chromatin regions is crucial for understanding gene regulation and disease. This review details methods for analyzing FFPE tissues, overcoming fixation challenges for chromatin accessibility studies.

Keywords:

FFPE chromatin nucleosome nucleosome-depleted region nucleosome-free region

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Published on: March 26, 2011

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Last Updated: Jun 25, 2025

Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis

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Published on: March 23, 2021

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

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Published on: April 5, 2018

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:

Genomics
Epigenetics
Molecular Biology

Background:

Nucleosome distribution dictates gene activity, with open chromatin linked to active promoters and enhancers.
Chromatin accessibility patterns are vital for understanding normal development and disease progression.
High-throughput sequencing methods like DNase-seq and ATAC-seq identify open chromatin, but face challenges with FFPE tissues.

Purpose of the Study:

To review common methods for mapping open chromatin regions.
To highlight recent optimizations for analyzing FFPE tissues.
To provide an overview of data analysis pipelines for chromatin accessibility studies.

Main Methods:

Review of established high-throughput sequencing techniques (DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, NicE-seq).
Discussion of recent technical advancements addressing FFPE tissue limitations.
Outline of a typical bioinformatics pipeline for data analysis.

Main Results:

FFPE tissues present significant challenges for chromatin accessibility assays due to crosslinking and DNA damage.
Optimized protocols are emerging to enable reliable chromatin mapping in FFPE samples.
Standardized data analysis pipelines are essential for consistent interpretation.

Conclusions:

Mapping chromatin accessibility in FFPE tissues is becoming feasible with optimized methods.
Understanding these patterns in FFPE samples can unlock insights into disease mechanisms.
Further development and standardization of FFPE-based chromatin accessibility studies are warranted.